Starting phenix.real_space_refine on Mon Jul 6 07:43:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mw3_24061/07_2026/7mw3_24061.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mw3_24061/07_2026/7mw3_24061.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7mw3_24061/07_2026/7mw3_24061.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mw3_24061/07_2026/7mw3_24061.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mw3_24061/07_2026/7mw3_24061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mw3_24061/07_2026/7mw3_24061.map" model { file = "/net/cci-nas-00/data/ceres_data/7mw3_24061/07_2026/7mw3_24061.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mw3_24061/07_2026/7mw3_24061.cif" } resolution = 3.15 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= 0.003 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 147 5.16 5 C 21463 2.51 5 N 5539 2.21 5 O 6676 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33825 Number of models: 1 Model: "" Number of chains: 33 Chain: "L" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1595 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "H" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1576 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 7760 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1004, 7743 Classifications: {'peptide': 1004} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 50, 'TRANS': 953} Chain breaks: 8 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 2, 'ASP:plan': 5, 'ARG:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 72 Conformer: "B" Number of residues, atoms: 1004, 7743 Classifications: {'peptide': 1004} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 50, 'TRANS': 953} Chain breaks: 8 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 2, 'ASP:plan': 5, 'ARG:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 72 bond proxies already assigned to first conformer: 7900 Chain: "B" Number of atoms: 7788 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1006, 7771 Classifications: {'peptide': 1006} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 49, 'TRANS': 956} Chain breaks: 8 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 4, 'ARG:plan': 2, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 55 Conformer: "B" Number of residues, atoms: 1006, 7771 Classifications: {'peptide': 1006} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 49, 'TRANS': 956} Chain breaks: 8 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 4, 'ARG:plan': 2, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 55 bond proxies already assigned to first conformer: 7927 Chain: "G" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1595 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "F" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1576 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 7756 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1004, 7739 Classifications: {'peptide': 1004} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 50, 'TRANS': 953} Chain breaks: 8 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 3, 'ASP:plan': 5, 'ARG:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 72 Conformer: "B" Number of residues, atoms: 1004, 7739 Classifications: {'peptide': 1004} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 50, 'TRANS': 953} Chain breaks: 8 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 3, 'ASP:plan': 5, 'ARG:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 72 bond proxies already assigned to first conformer: 7896 Chain: "E" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1595 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1576 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 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 chiralities: 11 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AGLN C1010 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN C1010 " occ=0.50 residue: pdb=" N AGLN B1010 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B1010 " occ=0.50 residue: pdb=" N AGLN A1010 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A1010 " occ=0.50 Time building chain proxies: 10.21, per 1000 atoms: 0.30 Number of scatterers: 33825 At special positions: 0 Unit cell: (131.364, 167.676, 242.436, 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 147 16.00 O 6676 8.00 N 5539 7.00 C 21463 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 112 " distance=2.03 Simple disulfide: pdb=" SG CYS L 158 " - pdb=" SG CYS L 218 " distance=2.04 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS H 164 " - pdb=" SG CYS H 220 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 112 " distance=2.03 Simple disulfide: pdb=" SG CYS G 158 " - pdb=" SG CYS G 218 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 115 " distance=2.03 Simple disulfide: pdb=" SG CYS F 164 " - pdb=" SG CYS F 220 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 112 " distance=2.03 Simple disulfide: pdb=" SG CYS E 158 " - pdb=" SG CYS E 218 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 115 " distance=2.03 Simple disulfide: pdb=" SG CYS D 164 " - pdb=" SG CYS D 220 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-3 " NAG W 1 " - " NAG W 2 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 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 U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 657 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 165 " " NAG A1306 " - " ASN A 61 " " NAG A1307 " - " ASN A 122 " " NAG A1308 " - " ASN A 331 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 657 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 165 " " NAG B1305 " - " ASN B 61 " " NAG B1306 " - " ASN B 282 " " NAG B1307 " - " ASN B 125 " " NAG B1308 " - " ASN B 331 " " NAG B1309 " - " ASN B1074 " " NAG B1311 " - " ASN B 234 " " NAG C1301 " - " ASN C 657 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 165 " " NAG C1305 " - " ASN C 61 " " NAG C1306 " - " ASN C 282 " " NAG C1307 " - " ASN C 125 " " NAG C1309 " - " ASN C1074 " " NAG I 1 " - " ASN C 331 " " NAG J 1 " - " ASN C1134 " " NAG K 1 " - " ASN C1098 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C 717 " " NAG O 1 " - " ASN C 709 " " NAG P 1 " - " ASN C 234 " " NAG Q 1 " - " ASN C 343 " " NAG R 1 " - " ASN B1134 " " NAG S 1 " - " ASN B1098 " " NAG T 1 " - " ASN B 801 " " NAG U 1 " - " ASN B 717 " " NAG V 1 " - " ASN B 709 " " NAG W 1 " - " ASN B 343 " " NAG X 1 " - " ASN A1134 " " NAG Y 1 " - " ASN A1098 " " NAG Z 1 " - " ASN A 801 " " NAG a 1 " - " ASN A 717 " " NAG b 1 " - " ASN A 709 " " NAG c 1 " - " ASN A 234 " " NAG d 1 " - " ASN A 343 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 2.2 seconds 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8030 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 76 sheets defined 20.7% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'L' and resid 103 through 107 removed outlier: 3.530A pdb=" N THR L 107 " --> pdb=" O GLU L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 151 Processing helix chain 'L' and resid 207 through 211 Processing helix chain 'H' and resid 106 through 110 Processing helix chain 'H' and resid 180 through 182 No H-bonds generated for 'chain 'H' and resid 180 through 182' Processing helix chain 'H' and resid 211 through 213 No H-bonds generated for 'chain 'H' and resid 211 through 213' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.665A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.554A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 384 through 390 removed outlier: 3.822A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.172A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.525A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.575A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.576A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.994A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.537A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.974A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 200 removed outlier: 4.109A pdb=" N GLY B 199 " --> pdb=" O ASN B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.571A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.283A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 542 through 546 removed outlier: 3.786A pdb=" N GLY B 545 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.527A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.730A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.688A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.980A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.682A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.509A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 3.829A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 107 removed outlier: 3.811A pdb=" N THR G 107 " --> pdb=" O GLU G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 151 Processing helix chain 'G' and resid 207 through 211 Processing helix chain 'F' and resid 106 through 110 Processing helix chain 'F' and resid 211 through 213 No H-bonds generated for 'chain 'F' and resid 211 through 213' Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.745A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.532A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.912A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.216A 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 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.792A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.702A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.670A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.658A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.591A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.322A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.526A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.753A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.829A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 4.109A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 107 removed outlier: 3.609A pdb=" N THR E 107 " --> pdb=" O GLU E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 151 Processing helix chain 'E' and resid 207 through 211 Processing helix chain 'D' and resid 106 through 110 removed outlier: 3.514A pdb=" N SER D 110 " --> pdb=" O SER D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 216 removed outlier: 4.461A pdb=" N THR D 215 " --> pdb=" O SER D 211 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 24 through 27 Processing sheet with id=AA2, first strand: chain 'L' and resid 30 through 33 removed outlier: 6.702A pdb=" N LEU L 31 " --> pdb=" O GLU L 129 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TRP L 59 " --> pdb=" O LEU L 71 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 138 through 142 removed outlier: 5.223A pdb=" N SER L 155 " --> pdb=" O LEU L 205 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU L 205 " --> pdb=" O SER L 155 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N VAL L 157 " --> pdb=" O LEU L 203 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU L 203 " --> pdb=" O VAL L 157 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N LEU L 159 " --> pdb=" O SER L 201 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER L 201 " --> pdb=" O LEU L 159 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ASN L 161 " --> pdb=" O LEU L 199 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LEU L 199 " --> pdb=" O ASN L 161 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 178 through 179 removed outlier: 4.650A pdb=" N TRP L 172 " --> pdb=" O GLN L 179 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 24 through 25 Processing sheet with id=AA6, first strand: chain 'H' and resid 29 through 31 removed outlier: 3.658A pdb=" N GLN H 58 " --> pdb=" O VAL H 112 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N MET H 53 " --> pdb=" O TYR H 69 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TYR H 69 " --> pdb=" O MET H 53 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TRP H 55 " --> pdb=" O ILE H 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.304A pdb=" N GLY H 119 " --> pdb=" O PRO H 124 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 144 through 148 removed outlier: 6.076A pdb=" N TYR H 200 " --> pdb=" O ASP H 168 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 144 through 148 removed outlier: 6.076A pdb=" N TYR H 200 " --> pdb=" O ASP H 168 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER H 201 " --> pdb=" O VAL H 193 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 175 through 178 removed outlier: 4.107A pdb=" N TYR H 218 " --> pdb=" O VAL H 235 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.667A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.286A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR A 572 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.542A pdb=" N VAL C 289 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.728A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 132 through 140 removed outlier: 6.495A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 310 through 319 removed outlier: 5.461A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AB9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.643A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AC3, first strand: chain 'C' and resid 565 through 566 removed outlier: 6.768A pdb=" N PHE C 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.038A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 702 through 704 removed outlier: 7.084A pdb=" N ASN C 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.169A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AC8, first strand: chain 'C' and resid 788 through 789 removed outlier: 5.636A pdb=" N ILE C 788 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AD1, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AD2, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.762A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.777A 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: 6.742A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.629A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.890A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.838A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 134 through 140 removed outlier: 8.606A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.629A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.397A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.869A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.541A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AD9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AE2, first strand: chain 'B' and resid 551 through 554 removed outlier: 5.219A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.015A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AE5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.607A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.432A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE8, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE9, first strand: chain 'G' and resid 24 through 27 Processing sheet with id=AF1, first strand: chain 'G' and resid 30 through 33 removed outlier: 6.244A pdb=" N LEU G 31 " --> pdb=" O GLU G 129 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TRP G 59 " --> pdb=" O LEU G 71 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 138 through 142 removed outlier: 6.194A pdb=" N TYR G 197 " --> pdb=" O ASN G 162 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 168 through 174 Processing sheet with id=AF4, first strand: chain 'F' and resid 29 through 31 removed outlier: 5.106A pdb=" N ALA F 125 " --> pdb=" O GLY F 119 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLY F 119 " --> pdb=" O ALA F 125 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N TRP F 127 " --> pdb=" O ARG F 117 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ARG F 117 " --> pdb=" O TRP F 127 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N GLN F 129 " --> pdb=" O CYS F 115 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N CYS F 115 " --> pdb=" O GLN F 129 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N MET F 53 " --> pdb=" O TYR F 69 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N TYR F 69 " --> pdb=" O MET F 53 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TRP F 55 " --> pdb=" O ILE F 67 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 37 through 42 Processing sheet with id=AF6, first strand: chain 'F' and resid 144 through 148 removed outlier: 6.110A pdb=" N TYR F 200 " --> pdb=" O ASP F 168 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 144 through 148 removed outlier: 6.110A pdb=" N TYR F 200 " --> pdb=" O ASP F 168 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER F 201 " --> pdb=" O VAL F 193 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 175 through 178 removed outlier: 4.133A pdb=" N TYR F 218 " --> pdb=" O VAL F 235 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.766A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.716A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.028A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'A' and resid 132 through 140 removed outlier: 3.875A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N CYS A 136 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N TYR A 160 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ASP A 138 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N ARG A 158 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'A' and resid 312 through 319 removed outlier: 5.833A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'A' and resid 354 through 358 removed outlier: 7.196A pdb=" N ASN A 437 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N PHE A 374 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AG7, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AG8, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.155A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'A' and resid 714 through 728 removed outlier: 6.200A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.291A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'A' and resid 1076 through 1077 removed outlier: 3.578A pdb=" N THR A1105 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.848A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 24 through 27 Processing sheet with id=AH5, first strand: chain 'E' and resid 30 through 33 removed outlier: 6.256A pdb=" N LEU E 31 " --> pdb=" O GLU E 129 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TRP E 59 " --> pdb=" O LEU E 71 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'E' and resid 50 through 51 Processing sheet with id=AH7, first strand: chain 'E' and resid 138 through 142 removed outlier: 5.839A pdb=" N TYR E 197 " --> pdb=" O ASN E 162 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'E' and resid 169 through 174 Processing sheet with id=AH9, first strand: chain 'D' and resid 22 through 25 Processing sheet with id=AI1, first strand: chain 'D' and resid 29 through 31 removed outlier: 5.083A pdb=" N ALA D 125 " --> pdb=" O GLY D 119 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLY D 119 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N TRP D 127 " --> pdb=" O ARG D 117 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ARG D 117 " --> pdb=" O TRP D 127 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N GLN D 129 " --> pdb=" O CYS D 115 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N CYS D 115 " --> pdb=" O GLN D 129 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N MET D 53 " --> pdb=" O TYR D 69 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TYR D 69 " --> pdb=" O MET D 53 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N TRP D 55 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'D' and resid 144 through 148 removed outlier: 6.089A pdb=" N TYR D 200 " --> pdb=" O ASP D 168 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'D' and resid 144 through 148 removed outlier: 6.089A pdb=" N TYR D 200 " --> pdb=" O ASP D 168 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'D' and resid 175 through 178 removed outlier: 4.383A pdb=" N TYR D 218 " --> pdb=" O VAL D 235 " (cutoff:3.500A) 1393 hydrogen bonds defined for protein. 3756 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.88 Time building geometry restraints manager: 4.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7653 1.33 - 1.46: 9701 1.46 - 1.58: 17043 1.58 - 1.71: 0 1.71 - 1.84: 189 Bond restraints: 34586 Sorted by residual: bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.504 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.498 -0.092 2.00e-02 2.50e+03 2.12e+01 bond pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.406 1.491 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C1 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.406 1.483 -0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.40e+01 ... (remaining 34581 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 46485 2.53 - 5.07: 600 5.07 - 7.60: 50 7.60 - 10.14: 7 10.14 - 12.67: 2 Bond angle restraints: 47144 Sorted by residual: angle pdb=" N VAL C 130 " pdb=" CA VAL C 130 " pdb=" C VAL C 130 " ideal model delta sigma weight residual 111.91 104.47 7.44 8.90e-01 1.26e+00 7.00e+01 angle pdb=" N ASN A1074 " pdb=" CA ASN A1074 " pdb=" C ASN A1074 " ideal model delta sigma weight residual 111.30 122.09 -10.79 1.43e+00 4.89e-01 5.69e+01 angle pdb=" N PHE C 559 " pdb=" CA PHE C 559 " pdb=" C PHE C 559 " ideal model delta sigma weight residual 112.92 121.77 -8.85 1.23e+00 6.61e-01 5.17e+01 angle pdb=" N PHE A1075 " pdb=" CA PHE A1075 " pdb=" C PHE A1075 " ideal model delta sigma weight residual 110.50 119.20 -8.70 1.41e+00 5.03e-01 3.81e+01 angle pdb=" N ILE A 233 " pdb=" CA ILE A 233 " pdb=" C ILE A 233 " ideal model delta sigma weight residual 109.12 118.13 -9.01 1.58e+00 4.01e-01 3.25e+01 ... (remaining 47139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 18529 17.84 - 35.67: 1171 35.67 - 53.51: 214 53.51 - 71.35: 39 71.35 - 89.19: 17 Dihedral angle restraints: 19970 sinusoidal: 7477 harmonic: 12493 Sorted by residual: dihedral pdb=" CA SER L 27 " pdb=" C SER L 27 " pdb=" N PRO L 28 " pdb=" CA PRO L 28 " ideal model delta harmonic sigma weight residual -180.00 -107.92 -72.08 0 5.00e+00 4.00e-02 2.08e+02 dihedral pdb=" CA SER G 27 " pdb=" C SER G 27 " pdb=" N PRO G 28 " pdb=" CA PRO G 28 " ideal model delta harmonic sigma weight residual -180.00 -107.98 -72.02 0 5.00e+00 4.00e-02 2.07e+02 dihedral pdb=" CA SER E 27 " pdb=" C SER E 27 " pdb=" N PRO E 28 " pdb=" CA PRO E 28 " ideal model delta harmonic sigma weight residual -180.00 -108.20 -71.80 0 5.00e+00 4.00e-02 2.06e+02 ... (remaining 19967 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.579: 5590 0.579 - 1.159: 3 1.159 - 1.738: 0 1.738 - 2.318: 1 2.318 - 2.897: 1 Chirality restraints: 5595 Sorted by residual: chirality pdb=" C1 NAG C1309 " pdb=" ND2 ASN C1074 " pdb=" C2 NAG C1309 " pdb=" O5 NAG C1309 " both_signs ideal model delta sigma weight residual False -2.40 0.50 -2.90 2.00e-01 2.50e+01 2.10e+02 chirality pdb=" C1 NAG B1309 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG B1309 " pdb=" O5 NAG B1309 " both_signs ideal model delta sigma weight residual False -2.40 -0.66 -1.74 2.00e-01 2.50e+01 7.61e+01 chirality pdb=" C1 NAG A1310 " pdb=" ND2 ASN A1074 " pdb=" C2 NAG A1310 " pdb=" O5 NAG A1310 " both_signs ideal model delta sigma weight residual False -2.40 -1.37 -1.03 2.00e-01 2.50e+01 2.65e+01 ... (remaining 5592 not shown) Planarity restraints: 6055 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1309 " 0.247 2.00e-02 2.50e+03 2.09e-01 5.48e+02 pdb=" C7 NAG B1309 " -0.060 2.00e-02 2.50e+03 pdb=" C8 NAG B1309 " 0.164 2.00e-02 2.50e+03 pdb=" N2 NAG B1309 " -0.357 2.00e-02 2.50e+03 pdb=" O7 NAG B1309 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1308 " 0.232 2.00e-02 2.50e+03 1.97e-01 4.87e+02 pdb=" C7 NAG C1308 " -0.057 2.00e-02 2.50e+03 pdb=" C8 NAG C1308 " 0.157 2.00e-02 2.50e+03 pdb=" N2 NAG C1308 " -0.336 2.00e-02 2.50e+03 pdb=" O7 NAG C1308 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1309 " 0.082 2.00e-02 2.50e+03 6.75e-02 5.69e+01 pdb=" C7 NAG A1309 " -0.022 2.00e-02 2.50e+03 pdb=" C8 NAG A1309 " 0.062 2.00e-02 2.50e+03 pdb=" N2 NAG A1309 " -0.107 2.00e-02 2.50e+03 pdb=" O7 NAG A1309 " -0.015 2.00e-02 2.50e+03 ... (remaining 6052 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 8 2.22 - 2.89: 13083 2.89 - 3.56: 45655 3.56 - 4.23: 79593 4.23 - 4.90: 135953 Nonbonded interactions: 274292 Sorted by model distance: nonbonded pdb=" ND2 ASN C1074 " pdb=" C1 NAG C1308 " model vdw 1.549 3.550 nonbonded pdb=" ND2 ASN A1074 " pdb=" C1 NAG A1309 " model vdw 1.559 3.550 nonbonded pdb=" ND2 ASN B1074 " pdb=" C1 NAG B1310 " model vdw 1.559 3.550 nonbonded pdb=" OE1 GLU G 129 " pdb=" OH TYR G 197 " model vdw 2.134 3.040 nonbonded pdb=" OG SER C 530 " pdb=" OE1 GLN C 580 " model vdw 2.153 3.040 ... (remaining 274287 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 172 or resid 187 through 339 or (resid 340 and \ (name N or name CA or name C or name O or name CB )) or resid 341 through 461 or \ (resid 462 and (name N or name CA or name C or name O or name CB )) or resid 46 \ 3 through 465 or resid 467 through 528 or (resid 529 and (name N or name CA or n \ ame C or name O or name CB )) or resid 530 through 1009 or resid 1011 through 13 \ 09)) selection = (chain 'B' and (resid 27 through 113 or (resid 114 and (name N or name CA or nam \ e C or name O or name CB )) or resid 115 through 128 or (resid 129 and (name N o \ r name CA or name C or name O or name CB )) or resid 130 through 212 or (resid 2 \ 13 through 215 and (name N or name CA or name C or name O or name CB )) or resid \ 216 through 238 or (resid 239 and (name N or name CA or name C or name O or nam \ e CB )) or resid 240 through 244 or (resid 245 and (name N or name CA or name C \ or name O or name CB )) or resid 263 through 465 or resid 467 through 528 or (re \ sid 529 and (name N or name CA or name C or name O or name CB )) or resid 530 th \ rough 557 or (resid 558 and (name N or name CA or name C or name O or name CB )) \ or resid 559 through 1009 or resid 1011 through 1309)) selection = (chain 'C' and (resid 27 through 113 or (resid 114 and (name N or name CA or nam \ e C or name O or name CB )) or resid 115 through 172 or resid 187 through 238 or \ (resid 239 and (name N or name CA or name C or name O or name CB )) or resid 24 \ 0 through 332 or (resid 333 and (name N or name CA or name C or name O or name C \ B )) or resid 334 through 461 or (resid 462 and (name N or name CA or name C or \ name O or name CB )) or resid 463 through 465 or resid 467 through 557 or (resid \ 558 and (name N or name CA or name C or name O or name CB )) or resid 559 throu \ gh 1009 or resid 1011 through 1309)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' 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 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 37.670 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.150 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 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 : 0.004 0.117 34707 Z= 0.231 Angle : 0.820 35.008 47453 Z= 0.421 Chirality : 0.071 2.897 5595 Planarity : 0.007 0.209 6007 Dihedral : 12.309 89.187 11787 Min Nonbonded Distance : 1.549 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.53 % Favored : 96.12 % Rotamer: Outliers : 0.33 % Allowed : 0.28 % Favored : 99.39 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 1.34 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.12), residues: 4235 helix: 1.24 (0.19), residues: 719 sheet: 0.27 (0.14), residues: 1236 loop : -1.04 (0.12), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 44 TYR 0.020 0.001 TYR B 369 PHE 0.026 0.001 PHE A 220 TRP 0.022 0.001 TRP H 178 HIS 0.004 0.001 HIS D 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.22 (34586) covalent geometry : angle 0.71206 / 0.40 (47144) SS BOND : bond 0.00292 / 0.20 ( 51) SS BOND : angle 1.21372 / 0.75 ( 102) hydrogen bonds : bond 0.13776 / 9.58 ( 1341) hydrogen bonds : angle 7.52630 / 5.24 ( 3756) Misc. bond : bond 0.00012 / 0.01 ( 1) link_BETA1-3 : bond 0.00571 / 0.30 ( 1) link_BETA1-3 : angle 1.18474 / 0.52 ( 3) link_BETA1-4 : bond 0.00445 / 0.27 ( 20) link_BETA1-4 : angle 1.60130 / 0.98 ( 60) link_NAG-ASN : bond 0.03131 / 1.67 ( 48) link_NAG-ASN : angle 7.31342 / 4.97 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 254 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 38 ARG cc_start: 0.7570 (ttm-80) cc_final: 0.7072 (ttm-80) REVERT: D 233 LYS cc_start: 0.5764 (mmmt) cc_final: 0.5321 (mmmt) outliers start: 9 outliers final: 5 residues processed: 262 average time/residue: 0.2067 time to fit residues: 90.6001 Evaluate side-chains 203 residues out of total 3719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 198 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 1074 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.0570 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 1.9990 chunk 424 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 overall best weight: 0.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN B 542 ASN A 901 GLN E 51 ASN E 100 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.086134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.066665 restraints weight = 174331.904| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 3.76 r_work: 0.2996 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.0777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34707 Z= 0.141 Angle : 0.636 14.640 47453 Z= 0.313 Chirality : 0.049 0.552 5595 Planarity : 0.005 0.115 6007 Dihedral : 5.048 71.380 4593 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.46 % Favored : 96.26 % Rotamer: Outliers : 0.75 % Allowed : 4.06 % Favored : 95.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 1.34 % 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: -0.22 (0.13), residues: 4235 helix: 1.70 (0.20), residues: 728 sheet: 0.29 (0.14), residues: 1248 loop : -1.03 (0.12), residues: 2259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 85 TYR 0.025 0.001 TYR G 164 PHE 0.029 0.001 PHE A 92 TRP 0.013 0.001 TRP H 178 HIS 0.004 0.001 HIS E 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (34586) covalent geometry : angle 0.60089 / 0.31 (47144) SS BOND : bond 0.00255 / 0.18 ( 51) SS BOND : angle 1.03607 / 0.65 ( 102) hydrogen bonds : bond 0.04278 / 2.92 ( 1341) hydrogen bonds : angle 5.97336 / 4.14 ( 3756) Misc. bond : bond 0.00012 / 0.01 ( 1) link_BETA1-3 : bond 0.00630 / 0.33 ( 1) link_BETA1-3 : angle 1.59449 / 0.73 ( 3) link_BETA1-4 : bond 0.00414 / 0.24 ( 20) link_BETA1-4 : angle 1.20997 / 0.78 ( 60) link_NAG-ASN : bond 0.00710 / 0.52 ( 48) link_NAG-ASN : angle 3.71377 / 2.39 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 221 time to evaluate : 1.229 Fit side-chains revert: symmetry clash REVERT: L 106 ASP cc_start: 0.7607 (m-30) cc_final: 0.7213 (m-30) REVERT: L 214 LYS cc_start: 0.5273 (tptt) cc_final: 0.5038 (tptp) REVERT: H 83 PHE cc_start: 0.8541 (m-80) cc_final: 0.8339 (m-80) REVERT: C 559 PHE cc_start: 0.8285 (m-10) cc_final: 0.8054 (m-80) REVERT: B 474 GLN cc_start: 0.7986 (tt0) cc_final: 0.7654 (tt0) REVERT: B 740 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8421 (tpp) REVERT: A 131 CYS cc_start: 0.7027 (m) cc_final: 0.6045 (m) REVERT: D 109 ASP cc_start: 0.8502 (m-30) cc_final: 0.7934 (m-30) outliers start: 24 outliers final: 14 residues processed: 233 average time/residue: 0.2138 time to fit residues: 81.7191 Evaluate side-chains 208 residues out of total 3719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 193 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 117 GLU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 221 ASN Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain E residue 232 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 314 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 326 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 308 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 171 optimal weight: 4.9990 chunk 200 optimal weight: 4.9990 chunk 329 optimal weight: 1.9990 chunk 341 optimal weight: 6.9990 chunk 400 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 171 GLN H 25 GLN ** H 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN B 542 ASN B1010 GLN B A 188 ASN A 540 ASN E 51 ASN ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.081652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.062574 restraints weight = 166528.247| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.68 r_work: 0.2904 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 34707 Z= 0.328 Angle : 0.768 12.923 47453 Z= 0.382 Chirality : 0.054 0.550 5595 Planarity : 0.006 0.135 6007 Dihedral : 5.424 73.972 4587 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.78 % Favored : 94.96 % Rotamer: Outliers : 1.11 % Allowed : 6.39 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 1.34 % 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: -0.54 (0.13), residues: 4235 helix: 1.41 (0.19), residues: 721 sheet: -0.01 (0.14), residues: 1287 loop : -1.18 (0.12), residues: 2227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 319 TYR 0.026 0.002 TYR B1067 PHE 0.035 0.003 PHE C 906 TRP 0.023 0.002 TRP A1102 HIS 0.009 0.002 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00774 / 0.33 (34586) covalent geometry : angle 0.73642 / 0.38 (47144) SS BOND : bond 0.00395 / 0.27 ( 51) SS BOND : angle 1.40212 / 0.94 ( 102) hydrogen bonds : bond 0.05004 / 3.40 ( 1341) hydrogen bonds : angle 6.01731 / 4.18 ( 3756) Misc. bond : bond 0.00026 / 0.01 ( 1) link_BETA1-3 : bond 0.00372 / 0.20 ( 1) link_BETA1-3 : angle 1.84157 / 0.88 ( 3) link_BETA1-4 : bond 0.00334 / 0.20 ( 20) link_BETA1-4 : angle 1.72023 / 1.12 ( 60) link_NAG-ASN : bond 0.00829 / 0.61 ( 48) link_NAG-ASN : angle 3.77137 / 2.48 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 209 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: L 72 ILE cc_start: 0.8985 (mm) cc_final: 0.8749 (mm) REVERT: H 83 PHE cc_start: 0.8659 (m-80) cc_final: 0.8316 (m-80) REVERT: C 740 MET cc_start: 0.8820 (tmm) cc_final: 0.8416 (ttt) REVERT: B 740 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8381 (tpp) REVERT: G 179 GLN cc_start: 0.5605 (mm-40) cc_final: 0.5369 (mm-40) REVERT: F 131 THR cc_start: 0.9098 (OUTLIER) cc_final: 0.8843 (p) REVERT: A 131 CYS cc_start: 0.6985 (m) cc_final: 0.6120 (m) REVERT: A 699 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8926 (mt) REVERT: D 109 ASP cc_start: 0.8398 (m-30) cc_final: 0.8076 (m-30) outliers start: 37 outliers final: 22 residues processed: 229 average time/residue: 0.1963 time to fit residues: 75.0480 Evaluate side-chains 213 residues out of total 3719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 188 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 221 ASN Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 216 TYR Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 148 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 384 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 295 optimal weight: 0.7980 chunk 239 optimal weight: 0.9990 chunk 278 optimal weight: 9.9990 chunk 112 optimal weight: 0.6980 chunk 224 optimal weight: 0.7980 chunk 208 optimal weight: 0.9990 chunk 411 optimal weight: 0.9980 chunk 205 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN A C1011 GLN C1135 ASN B 542 ASN A 188 ASN D 25 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.084453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.064946 restraints weight = 188775.536| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.88 r_work: 0.2953 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34707 Z= 0.134 Angle : 0.613 13.227 47453 Z= 0.302 Chirality : 0.048 0.511 5595 Planarity : 0.005 0.115 6007 Dihedral : 4.929 72.363 4587 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.53 % Favored : 96.26 % Rotamer: Outliers : 1.11 % Allowed : 7.56 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 1.34 % 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: -0.32 (0.13), residues: 4235 helix: 1.77 (0.20), residues: 728 sheet: 0.12 (0.14), residues: 1264 loop : -1.08 (0.12), residues: 2243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 44 TYR 0.019 0.001 TYR B1067 PHE 0.023 0.001 PHE A 92 TRP 0.026 0.001 TRP H 178 HIS 0.004 0.001 HIS F 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (34586) covalent geometry : angle 0.58555 / 0.30 (47144) SS BOND : bond 0.00317 / 0.20 ( 51) SS BOND : angle 0.98671 / 0.65 ( 102) hydrogen bonds : bond 0.03917 / 2.66 ( 1341) hydrogen bonds : angle 5.67343 / 3.93 ( 3756) Misc. bond : bond 0.00015 / 0.01 ( 1) link_BETA1-3 : bond 0.00572 / 0.30 ( 1) link_BETA1-3 : angle 1.77843 / 0.82 ( 3) link_BETA1-4 : bond 0.00370 / 0.21 ( 20) link_BETA1-4 : angle 1.25378 / 0.82 ( 60) link_NAG-ASN : bond 0.00706 / 0.50 ( 48) link_NAG-ASN : angle 3.15948 / 2.03 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 216 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 82 ASN cc_start: 0.8453 (t0) cc_final: 0.8179 (t0) REVERT: H 83 PHE cc_start: 0.8668 (m-80) cc_final: 0.8160 (m-80) REVERT: C 740 MET cc_start: 0.8835 (tmm) cc_final: 0.8372 (ttt) REVERT: B 105 ILE cc_start: 0.8864 (mm) cc_final: 0.8424 (tt) REVERT: B 740 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8434 (tpp) REVERT: G 73 TYR cc_start: 0.8786 (p90) cc_final: 0.8223 (p90) REVERT: A 131 CYS cc_start: 0.6771 (m) cc_final: 0.5769 (m) REVERT: A 220 PHE cc_start: 0.7916 (OUTLIER) cc_final: 0.7652 (t80) REVERT: D 129 GLN cc_start: 0.8675 (pt0) cc_final: 0.8359 (pt0) outliers start: 37 outliers final: 17 residues processed: 238 average time/residue: 0.1903 time to fit residues: 75.9586 Evaluate side-chains 208 residues out of total 3719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 189 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain G residue 105 ASP Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain F residue 115 CYS Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain E residue 216 TYR Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain D residue 231 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 414 optimal weight: 5.9990 chunk 312 optimal weight: 0.7980 chunk 345 optimal weight: 0.9980 chunk 183 optimal weight: 0.1980 chunk 371 optimal weight: 1.9990 chunk 289 optimal weight: 5.9990 chunk 403 optimal weight: 0.8980 chunk 358 optimal weight: 1.9990 chunk 224 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 381 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN E 51 ASN D 221 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.084268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.064881 restraints weight = 181875.604| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 3.81 r_work: 0.2953 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 34707 Z= 0.140 Angle : 0.615 16.558 47453 Z= 0.300 Chirality : 0.048 0.502 5595 Planarity : 0.005 0.105 6007 Dihedral : 4.819 71.529 4585 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.86 % Favored : 95.90 % Rotamer: Outliers : 1.14 % Allowed : 8.33 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 1.34 % 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: -0.25 (0.13), residues: 4235 helix: 1.85 (0.20), residues: 732 sheet: 0.15 (0.14), residues: 1261 loop : -1.05 (0.13), residues: 2242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 44 TYR 0.020 0.001 TYR C 170 PHE 0.025 0.001 PHE C 168 TRP 0.020 0.001 TRP H 178 HIS 0.003 0.001 HIS F 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (34586) covalent geometry : angle 0.58851 / 0.29 (47144) SS BOND : bond 0.00224 / 0.16 ( 51) SS BOND : angle 1.16301 / 0.70 ( 102) hydrogen bonds : bond 0.03858 / 2.61 ( 1341) hydrogen bonds : angle 5.54553 / 3.84 ( 3756) Misc. bond : bond 0.00014 / 0.01 ( 1) link_BETA1-3 : bond 0.00530 / 0.28 ( 1) link_BETA1-3 : angle 1.67008 / 0.75 ( 3) link_BETA1-4 : bond 0.00316 / 0.19 ( 20) link_BETA1-4 : angle 1.28713 / 0.84 ( 60) link_NAG-ASN : bond 0.00674 / 0.49 ( 48) link_NAG-ASN : angle 3.07916 / 1.97 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 199 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 82 ASN cc_start: 0.8464 (t0) cc_final: 0.8181 (t0) REVERT: H 83 PHE cc_start: 0.8692 (m-80) cc_final: 0.8151 (m-80) REVERT: C 740 MET cc_start: 0.8832 (tmm) cc_final: 0.8390 (ttt) REVERT: B 277 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8481 (mt) REVERT: B 740 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8369 (tpp) REVERT: G 73 TYR cc_start: 0.8787 (p90) cc_final: 0.8336 (p90) REVERT: A 131 CYS cc_start: 0.6754 (m) cc_final: 0.5754 (m) REVERT: A 220 PHE cc_start: 0.7955 (OUTLIER) cc_final: 0.7734 (t80) REVERT: E 129 GLU cc_start: 0.8120 (pm20) cc_final: 0.7906 (pm20) REVERT: E 219 GLU cc_start: 0.7068 (mm-30) cc_final: 0.6725 (tp30) REVERT: D 39 MET cc_start: 0.8034 (mtm) cc_final: 0.7542 (mtp) REVERT: D 233 LYS cc_start: 0.5096 (mmmt) cc_final: 0.4822 (mmmt) outliers start: 38 outliers final: 25 residues processed: 224 average time/residue: 0.2133 time to fit residues: 79.7166 Evaluate side-chains 216 residues out of total 3719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 117 GLU Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 115 CYS Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain E residue 216 TYR Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain D residue 221 ASN Chi-restraints excluded: chain D residue 231 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 65 optimal weight: 4.9990 chunk 266 optimal weight: 2.9990 chunk 197 optimal weight: 0.6980 chunk 171 optimal weight: 4.9990 chunk 326 optimal weight: 0.0670 chunk 183 optimal weight: 0.0670 chunk 115 optimal weight: 3.9990 chunk 238 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 371 optimal weight: 0.7980 chunk 150 optimal weight: 0.6980 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN B 901 GLN D 129 GLN ** D 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.085211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.066117 restraints weight = 160597.475| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 3.58 r_work: 0.2990 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2991 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 34707 Z= 0.108 Angle : 0.586 13.115 47453 Z= 0.287 Chirality : 0.047 0.487 5595 Planarity : 0.005 0.100 6007 Dihedral : 4.659 70.616 4585 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.72 % Favored : 96.07 % Rotamer: Outliers : 1.33 % Allowed : 8.42 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 1.34 % 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: -0.13 (0.13), residues: 4235 helix: 1.99 (0.20), residues: 732 sheet: 0.21 (0.14), residues: 1299 loop : -1.00 (0.13), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 44 TYR 0.018 0.001 TYR B1067 PHE 0.023 0.001 PHE C 168 TRP 0.019 0.001 TRP H 178 HIS 0.002 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (34586) covalent geometry : angle 0.56192 / 0.28 (47144) SS BOND : bond 0.00213 / 0.15 ( 51) SS BOND : angle 0.94003 / 0.59 ( 102) hydrogen bonds : bond 0.03578 / 2.42 ( 1341) hydrogen bonds : angle 5.39054 / 3.73 ( 3756) Misc. bond : bond 0.00006 / 0.00 ( 1) link_BETA1-3 : bond 0.00536 / 0.28 ( 1) link_BETA1-3 : angle 1.53221 / 0.68 ( 3) link_BETA1-4 : bond 0.00379 / 0.22 ( 20) link_BETA1-4 : angle 1.23108 / 0.80 ( 60) link_NAG-ASN : bond 0.00690 / 0.49 ( 48) link_NAG-ASN : angle 2.94432 / 1.88 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 208 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 82 ASN cc_start: 0.8448 (t0) cc_final: 0.8209 (t0) REVERT: H 83 PHE cc_start: 0.8701 (m-80) cc_final: 0.8167 (m-80) REVERT: C 559 PHE cc_start: 0.8402 (m-10) cc_final: 0.8199 (m-80) REVERT: C 740 MET cc_start: 0.8770 (tmm) cc_final: 0.8354 (ttt) REVERT: B 105 ILE cc_start: 0.8843 (mm) cc_final: 0.8491 (tt) REVERT: B 277 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8515 (mt) REVERT: B 740 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8358 (tpp) REVERT: G 73 TYR cc_start: 0.8693 (p90) cc_final: 0.8269 (p90) REVERT: G 102 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.6587 (tmm) REVERT: F 173 PRO cc_start: 0.7676 (Cg_endo) cc_final: 0.7364 (Cg_exo) REVERT: A 131 CYS cc_start: 0.6786 (m) cc_final: 0.5814 (m) REVERT: A 220 PHE cc_start: 0.7926 (OUTLIER) cc_final: 0.7702 (t80) REVERT: D 39 MET cc_start: 0.8060 (mtm) cc_final: 0.7646 (mtp) outliers start: 45 outliers final: 29 residues processed: 237 average time/residue: 0.2161 time to fit residues: 85.1551 Evaluate side-chains 223 residues out of total 3719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 190 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 117 GLU Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain G residue 102 MET Chi-restraints excluded: chain G residue 105 ASP Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain E residue 216 TYR Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 231 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 312 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 354 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 235 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 219 optimal weight: 0.7980 chunk 378 optimal weight: 0.2980 chunk 398 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 371 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN E 51 ASN D 221 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.083851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.064579 restraints weight = 177366.663| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.73 r_work: 0.2947 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 34707 Z= 0.174 Angle : 0.618 12.785 47453 Z= 0.304 Chirality : 0.048 0.500 5595 Planarity : 0.005 0.101 6007 Dihedral : 4.743 71.020 4585 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.10 % Favored : 95.67 % Rotamer: Outliers : 1.22 % Allowed : 8.97 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 1.34 % 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 (0.13), residues: 4235 helix: 1.92 (0.20), residues: 726 sheet: 0.14 (0.14), residues: 1300 loop : -1.01 (0.13), residues: 2209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 44 TYR 0.021 0.001 TYR B1067 PHE 0.020 0.002 PHE C 168 TRP 0.024 0.001 TRP H 178 HIS 0.003 0.001 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (34586) covalent geometry : angle 0.59327 / 0.30 (47144) SS BOND : bond 0.00304 / 0.22 ( 51) SS BOND : angle 1.08177 / 0.70 ( 102) hydrogen bonds : bond 0.03882 / 2.63 ( 1341) hydrogen bonds : angle 5.42485 / 3.76 ( 3756) Misc. bond : bond 0.00017 / 0.01 ( 1) link_BETA1-3 : bond 0.00440 / 0.23 ( 1) link_BETA1-3 : angle 1.61044 / 0.73 ( 3) link_BETA1-4 : bond 0.00320 / 0.18 ( 20) link_BETA1-4 : angle 1.32730 / 0.87 ( 60) link_NAG-ASN : bond 0.00648 / 0.47 ( 48) link_NAG-ASN : angle 2.99381 / 1.93 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 197 time to evaluate : 1.256 Fit side-chains revert: symmetry clash REVERT: H 83 PHE cc_start: 0.8740 (m-80) cc_final: 0.8231 (m-80) REVERT: C 740 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8447 (ttt) REVERT: B 105 ILE cc_start: 0.8906 (mm) cc_final: 0.8481 (tt) REVERT: B 277 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8553 (mt) REVERT: B 740 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8397 (tpp) REVERT: G 73 TYR cc_start: 0.8688 (p90) cc_final: 0.8290 (p90) REVERT: G 102 MET cc_start: 0.7638 (OUTLIER) cc_final: 0.6557 (tmm) REVERT: G 117 GLU cc_start: 0.6916 (mt-10) cc_final: 0.6659 (mt-10) REVERT: G 150 LYS cc_start: 0.7520 (mppt) cc_final: 0.7067 (mtmm) REVERT: A 131 CYS cc_start: 0.6761 (m) cc_final: 0.5759 (m) REVERT: E 219 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6735 (tp30) REVERT: D 39 MET cc_start: 0.8169 (mtm) cc_final: 0.7801 (mtp) REVERT: D 65 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7857 (tt0) REVERT: D 233 LYS cc_start: 0.5047 (mmmt) cc_final: 0.4647 (mmmt) outliers start: 41 outliers final: 27 residues processed: 222 average time/residue: 0.2112 time to fit residues: 78.6839 Evaluate side-chains 220 residues out of total 3719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 188 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 117 GLU Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 102 MET Chi-restraints excluded: chain G residue 105 ASP Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain E residue 216 TYR Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 231 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 122 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 212 optimal weight: 2.9990 chunk 142 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 217 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 269 optimal weight: 0.8980 chunk 224 optimal weight: 2.9990 chunk 320 optimal weight: 8.9990 chunk 392 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 82 ASN ** H 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.083213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.064285 restraints weight = 183644.957| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.76 r_work: 0.2947 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 34707 Z= 0.180 Angle : 0.623 12.920 47453 Z= 0.307 Chirality : 0.049 0.503 5595 Planarity : 0.005 0.105 6007 Dihedral : 4.807 71.299 4585 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.03 % Favored : 95.76 % Rotamer: Outliers : 1.22 % Allowed : 9.17 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 1.34 % 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: -0.22 (0.13), residues: 4235 helix: 1.87 (0.20), residues: 726 sheet: 0.11 (0.14), residues: 1320 loop : -1.01 (0.13), residues: 2189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 44 TYR 0.020 0.001 TYR B1067 PHE 0.025 0.002 PHE C 168 TRP 0.028 0.001 TRP H 178 HIS 0.004 0.001 HIS F 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (34586) covalent geometry : angle 0.59837 / 0.30 (47144) SS BOND : bond 0.00294 / 0.21 ( 51) SS BOND : angle 1.05707 / 0.70 ( 102) hydrogen bonds : bond 0.03933 / 2.67 ( 1341) hydrogen bonds : angle 5.46023 / 3.78 ( 3756) Misc. bond : bond 0.00021 / 0.01 ( 1) link_BETA1-3 : bond 0.00493 / 0.26 ( 1) link_BETA1-3 : angle 1.72280 / 0.78 ( 3) link_BETA1-4 : bond 0.00317 / 0.18 ( 20) link_BETA1-4 : angle 1.34009 / 0.88 ( 60) link_NAG-ASN : bond 0.00645 / 0.47 ( 48) link_NAG-ASN : angle 2.99532 / 1.93 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 201 time to evaluate : 1.326 Fit side-chains revert: symmetry clash REVERT: L 103 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6149 (tm-30) REVERT: H 83 PHE cc_start: 0.8743 (m-80) cc_final: 0.8329 (m-80) REVERT: C 740 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8498 (ttt) REVERT: B 105 ILE cc_start: 0.8827 (mm) cc_final: 0.8463 (tt) REVERT: B 277 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8529 (mt) REVERT: B 740 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8393 (tpp) REVERT: G 73 TYR cc_start: 0.8628 (p90) cc_final: 0.8305 (p90) REVERT: G 102 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.6430 (tmm) REVERT: G 150 LYS cc_start: 0.7606 (mppt) cc_final: 0.7181 (mtmm) REVERT: F 100 MET cc_start: 0.7517 (OUTLIER) cc_final: 0.7300 (ttm) REVERT: A 131 CYS cc_start: 0.6843 (m) cc_final: 0.5984 (m) REVERT: E 52 TYR cc_start: 0.8427 (m-80) cc_final: 0.8193 (m-80) REVERT: E 219 GLU cc_start: 0.7083 (mm-30) cc_final: 0.6720 (tp30) REVERT: D 39 MET cc_start: 0.8184 (mtm) cc_final: 0.7728 (mtp) REVERT: D 65 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7836 (tt0) REVERT: D 233 LYS cc_start: 0.4979 (mmmt) cc_final: 0.4478 (mmmt) outliers start: 41 outliers final: 29 residues processed: 225 average time/residue: 0.2115 time to fit residues: 80.2654 Evaluate side-chains 226 residues out of total 3719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 117 GLU Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 102 MET Chi-restraints excluded: chain G residue 105 ASP Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain E residue 216 TYR Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 231 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 364 optimal weight: 0.1980 chunk 143 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 333 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 295 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 chunk 318 optimal weight: 5.9990 chunk 121 optimal weight: 0.8980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN B 542 ASN ** G 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.082228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.063372 restraints weight = 171948.867| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 3.66 r_work: 0.2930 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2935 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 34707 Z= 0.209 Angle : 0.648 12.894 47453 Z= 0.320 Chirality : 0.049 0.508 5595 Planarity : 0.005 0.109 6007 Dihedral : 4.927 71.952 4585 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.57 % Favored : 95.19 % Rotamer: Outliers : 1.19 % Allowed : 9.25 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 1.34 % 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: -0.33 (0.13), residues: 4235 helix: 1.81 (0.20), residues: 724 sheet: 0.02 (0.14), residues: 1318 loop : -1.07 (0.13), residues: 2193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 59 TYR 0.024 0.002 TYR B 369 PHE 0.023 0.002 PHE C 168 TRP 0.025 0.001 TRP H 178 HIS 0.005 0.001 HIS F 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 (34586) covalent geometry : angle 0.62305 / 0.31 (47144) SS BOND : bond 0.00279 / 0.19 ( 51) SS BOND : angle 1.13252 / 0.75 ( 102) hydrogen bonds : bond 0.04114 / 2.79 ( 1341) hydrogen bonds : angle 5.54133 / 3.84 ( 3756) Misc. bond : bond 0.00024 / 0.01 ( 1) link_BETA1-3 : bond 0.00454 / 0.24 ( 1) link_BETA1-3 : angle 1.88520 / 0.87 ( 3) link_BETA1-4 : bond 0.00304 / 0.17 ( 20) link_BETA1-4 : angle 1.42865 / 0.93 ( 60) link_NAG-ASN : bond 0.00644 / 0.47 ( 48) link_NAG-ASN : angle 3.06818 / 1.98 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 194 time to evaluate : 1.297 Fit side-chains revert: symmetry clash REVERT: L 103 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6404 (tm-30) REVERT: L 149 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7369 (pp) REVERT: H 83 PHE cc_start: 0.8758 (m-80) cc_final: 0.8294 (m-80) REVERT: C 740 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8508 (ttt) REVERT: B 105 ILE cc_start: 0.8840 (mm) cc_final: 0.8489 (tt) REVERT: B 277 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8553 (mt) REVERT: B 740 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8404 (tpp) REVERT: G 73 TYR cc_start: 0.8624 (p90) cc_final: 0.8275 (p90) REVERT: G 102 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.6402 (tmm) REVERT: G 150 LYS cc_start: 0.7661 (mppt) cc_final: 0.7291 (mtmm) REVERT: A 131 CYS cc_start: 0.6872 (m) cc_final: 0.5985 (m) REVERT: E 52 TYR cc_start: 0.8476 (m-80) cc_final: 0.8233 (m-80) REVERT: D 39 MET cc_start: 0.8202 (mtm) cc_final: 0.7814 (mtp) REVERT: D 65 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7836 (tt0) REVERT: D 233 LYS cc_start: 0.5072 (mmmt) cc_final: 0.4572 (mmmt) outliers start: 40 outliers final: 30 residues processed: 218 average time/residue: 0.1932 time to fit residues: 70.2569 Evaluate side-chains 225 residues out of total 3719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 117 GLU Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 102 MET Chi-restraints excluded: chain G residue 105 ASP Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 221 ASN Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain E residue 216 TYR Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 231 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 161 optimal weight: 2.9990 chunk 372 optimal weight: 3.9990 chunk 289 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 420 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 310 optimal weight: 2.9990 chunk 274 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN G 148 GLN ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 HIS D 129 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.080834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.061977 restraints weight = 181368.818| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.75 r_work: 0.2896 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 34707 Z= 0.301 Angle : 0.729 13.030 47453 Z= 0.361 Chirality : 0.052 0.531 5595 Planarity : 0.005 0.108 6007 Dihedral : 5.280 73.713 4585 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.88 % Favored : 94.86 % Rotamer: Outliers : 1.19 % Allowed : 9.28 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 1.34 % 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: -0.59 (0.13), residues: 4235 helix: 1.65 (0.20), residues: 710 sheet: -0.18 (0.14), residues: 1344 loop : -1.23 (0.13), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 59 TYR 0.025 0.002 TYR B 369 PHE 0.024 0.002 PHE A 238 TRP 0.035 0.002 TRP H 178 HIS 0.008 0.001 HIS F 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00711 / 0.30 (34586) covalent geometry : angle 0.70382 / 0.36 (47144) SS BOND : bond 0.00369 / 0.25 ( 51) SS BOND : angle 1.33903 / 0.92 ( 102) hydrogen bonds : bond 0.04616 / 3.12 ( 1341) hydrogen bonds : angle 5.80200 / 4.02 ( 3756) Misc. bond : bond 0.00038 / 0.02 ( 1) link_BETA1-3 : bond 0.00398 / 0.21 ( 1) link_BETA1-3 : angle 2.18940 / 1.02 ( 3) link_BETA1-4 : bond 0.00313 / 0.18 ( 20) link_BETA1-4 : angle 1.66155 / 1.07 ( 60) link_NAG-ASN : bond 0.00667 / 0.48 ( 48) link_NAG-ASN : angle 3.24721 / 2.10 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 194 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 103 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6503 (tm-30) REVERT: H 83 PHE cc_start: 0.8785 (m-80) cc_final: 0.8279 (m-80) REVERT: C 740 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8452 (ttt) REVERT: B 277 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8506 (mt) REVERT: B 740 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8393 (tpp) REVERT: G 73 TYR cc_start: 0.8750 (p90) cc_final: 0.8406 (p90) REVERT: G 102 MET cc_start: 0.7634 (OUTLIER) cc_final: 0.6410 (tmm) REVERT: G 150 LYS cc_start: 0.7639 (mppt) cc_final: 0.7225 (mtmm) REVERT: F 131 THR cc_start: 0.9130 (OUTLIER) cc_final: 0.8916 (p) REVERT: A 131 CYS cc_start: 0.6833 (m) cc_final: 0.5877 (m) REVERT: A 1074 ASN cc_start: 0.7270 (p0) cc_final: 0.7045 (p0) REVERT: E 51 ASN cc_start: 0.8196 (OUTLIER) cc_final: 0.7952 (t0) REVERT: D 39 MET cc_start: 0.8252 (mtm) cc_final: 0.7909 (mtp) REVERT: D 65 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7899 (tt0) REVERT: D 108 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7701 (mm-30) REVERT: D 233 LYS cc_start: 0.5063 (mmmt) cc_final: 0.4486 (mmmt) outliers start: 40 outliers final: 30 residues processed: 219 average time/residue: 0.2138 time to fit residues: 78.0145 Evaluate side-chains 228 residues out of total 3719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 190 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 102 MET Chi-restraints excluded: chain G residue 105 ASP Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 115 CYS Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 221 ASN Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 216 TYR Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 231 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 251 optimal weight: 1.9990 chunk 225 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 253 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 221 optimal weight: 0.9980 chunk 331 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 418 optimal weight: 8.9990 chunk 3 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.080976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.062576 restraints weight = 148185.618| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.32 r_work: 0.2922 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2925 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2925 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.194 34707 Z= 0.277 Angle : 0.834 59.188 47453 Z= 0.441 Chirality : 0.051 0.531 5595 Planarity : 0.005 0.107 6007 Dihedral : 5.280 73.945 4585 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.93 % Favored : 94.81 % Rotamer: Outliers : 1.19 % Allowed : 9.58 % Favored : 89.22 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 1.34 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.13), residues: 4235 helix: 1.66 (0.20), residues: 710 sheet: -0.19 (0.14), residues: 1344 loop : -1.24 (0.13), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 59 TYR 0.024 0.002 TYR B 369 PHE 0.024 0.002 PHE A 238 TRP 0.031 0.002 TRP H 178 HIS 0.006 0.001 HIS F 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00642 / 0.28 (34586) covalent geometry : angle 0.81105 / 0.44 (47144) SS BOND : bond 0.00743 / 0.38 ( 51) SS BOND : angle 1.81483 / 1.04 ( 102) hydrogen bonds : bond 0.04536 / 3.07 ( 1341) hydrogen bonds : angle 5.80440 / 4.02 ( 3756) Misc. bond : bond 0.00018 / 0.01 ( 1) link_BETA1-3 : bond 0.00402 / 0.21 ( 1) link_BETA1-3 : angle 2.19201 / 1.02 ( 3) link_BETA1-4 : bond 0.00314 / 0.17 ( 20) link_BETA1-4 : angle 1.64860 / 1.06 ( 60) link_NAG-ASN : bond 0.00660 / 0.48 ( 48) link_NAG-ASN : angle 3.24769 / 2.10 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8718.04 seconds wall clock time: 150 minutes 11.82 seconds (9011.82 seconds total)