Starting phenix.real_space_refine on Thu Oct 29 19:54:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mw4_24062/10_2026/7mw4_24062.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mw4_24062/10_2026/7mw4_24062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7mw4_24062/10_2026/7mw4_24062.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mw4_24062/10_2026/7mw4_24062.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mw4_24062/10_2026/7mw4_24062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mw4_24062/10_2026/7mw4_24062.map" model { file = "/net/cci-nas-00/data/ceres_data/7mw4_24062/10_2026/7mw4_24062.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mw4_24062/10_2026/7mw4_24062.cif" } resolution = 3.42 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 21412 2.51 5 N 5510 2.21 5 O 6672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33741 Number of models: 1 Model: "" Number of chains: 35 Chain: "C" Number of atoms: 7739 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1001, 7722 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 49, 'TRANS': 951} Chain breaks: 8 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 5, 'ARG:plan': 3, 'GLN:plan1': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 68 Conformer: "B" Number of residues, atoms: 1001, 7722 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 49, 'TRANS': 951} Chain breaks: 8 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 5, 'ARG:plan': 3, 'GLN:plan1': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 68 bond proxies already assigned to first conformer: 7877 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: "A" Number of atoms: 7760 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1004, 7743 Classifications: {'peptide': 1004} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 50, 'TRANS': 953} Chain breaks: 8 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 3, 'ASP:plan': 5, 'ARG:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 78 Conformer: "B" Number of residues, atoms: 1004, 7743 Classifications: {'peptide': 1004} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 50, 'TRANS': 953} Chain breaks: 8 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 3, 'ASP:plan': 5, 'ARG:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 78 bond proxies already assigned to first conformer: 7899 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: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1570 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 7699 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1004, 7690 Classifications: {'peptide': 1004} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 50, 'TRANS': 953} Chain breaks: 8 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 198 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 8, 'GLN:plan1': 5, 'ASP:plan': 5, 'ARG:plan': 5, 'HIS:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 109 Conformer: "B" Number of residues, atoms: 1004, 7690 Classifications: {'peptide': 1004} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 50, 'TRANS': 953} Chain breaks: 8 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 198 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 8, 'GLN:plan1': 5, 'ASP:plan': 5, 'ARG:plan': 5, 'HIS:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 109 bond proxies already assigned to first conformer: 7855 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: "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: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 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: "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 Chain: "B" 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 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 A1010 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A1010 " occ=0.50 residue: pdb=" N AGLN B1010 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B1010 " occ=0.50 Time building chain proxies: 11.74, per 1000 atoms: 0.35 Number of scatterers: 33741 At special positions: 0 Unit cell: (173.016, 167.676, 240.3, 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 6672 8.00 N 5510 7.00 C 21412 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 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=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.04 Simple disulfide: pdb=" SG CYS H 164 " - pdb=" SG CYS H 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=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 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=2.04 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 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS F 164 " - pdb=" SG CYS F 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=0, symmetry=0 Links applied BETA1-3 " NAG I 1 " - " NAG I 2 " " NAG Q 1 " - " NAG Q 2 " " NAG f 1 " - " NAG f 2 " BETA1-4 " 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 R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " NAG-ASN " NAG A1301 " - " ASN A 657 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A 61 " " NAG A1306 " - " ASN A 282 " " NAG A1307 " - " ASN A 122 " " NAG A1308 " - " ASN A 331 " " NAG A1309 " - " ASN A1074 " " 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 B1074 " " NAG B1309 " - " ASN B1074 " " 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 122 " " NAG C1308 " - " ASN C1074 " " 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 A1134 " " NAG S 1 " - " ASN A1098 " " NAG T 1 " - " ASN A 801 " " NAG U 1 " - " ASN A 717 " " NAG V 1 " - " ASN A 709 " " NAG W 1 " - " ASN A 234 " " NAG X 1 " - " ASN A 343 " " NAG Y 1 " - " ASN B 331 " " NAG Z 1 " - " ASN B1134 " " NAG a 1 " - " ASN B1098 " " NAG b 1 " - " ASN B 801 " " NAG c 1 " - " ASN B 717 " " NAG d 1 " - " ASN B 709 " " NAG e 1 " - " ASN B 234 " " NAG f 1 " - " ASN B 343 " Time building additional restraints: 3.06 Conformation dependent library (CDL) restraints added in 2.2 seconds 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8020 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 78 sheets defined 20.3% alpha, 33.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 601 through 605 removed outlier: 3.778A pdb=" N SER C 605 " --> pdb=" O THR C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.520A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.580A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.650A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.735A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.042A 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: 3.664A 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: 4.439A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 107 removed outlier: 3.623A 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 212 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 216 removed outlier: 4.433A pdb=" N THR H 215 " --> pdb=" O SER H 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.785A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.634A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.426A 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 756 removed outlier: 3.848A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.609A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.503A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.594A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.641A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.289A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.515A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.523A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.168A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 4.106A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 107 removed outlier: 3.603A 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 211 through 213 No H-bonds generated for 'chain 'D' and resid 211 through 213' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.055A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.116A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 Processing helix chain 'B' and resid 405 through 410 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 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.793A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.534A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.543A 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: 4.038A 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 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.622A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 4.068A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 107 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 180 through 182 No H-bonds generated for 'chain 'F' and resid 180 through 182' Processing helix chain 'F' and resid 211 through 213 No H-bonds generated for 'chain 'F' and resid 211 through 213' Processing sheet with id=AA1, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.613A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG C 190 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.538A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.616A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 132 through 135 removed outlier: 6.623A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 312 through 319 removed outlier: 5.839A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 325 through 326 removed outlier: 3.928A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.253A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.490A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'C' and resid 712 through 718 removed outlier: 6.483A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 721 through 728 removed outlier: 6.981A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.246A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 788 through 789 removed outlier: 5.687A pdb=" N ILE C 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'L' and resid 24 through 27 Processing sheet with id=AC1, first strand: chain 'L' and resid 30 through 33 removed outlier: 6.407A pdb=" N LEU L 31 " --> pdb=" O GLU L 129 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N GLN L 61 " --> pdb=" O LEU L 70 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N LEU L 70 " --> pdb=" O GLN L 61 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 50 through 51 Processing sheet with id=AC3, first strand: chain 'L' and resid 138 through 142 removed outlier: 6.093A pdb=" N TYR L 197 " --> pdb=" O ASN L 162 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 177 through 178 Processing sheet with id=AC5, first strand: chain 'H' and resid 22 through 25 Processing sheet with id=AC6, first strand: chain 'H' and resid 30 through 31 removed outlier: 4.999A pdb=" N ALA H 125 " --> pdb=" O GLY H 119 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLY H 119 " --> pdb=" O ALA H 125 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N TRP H 127 " --> pdb=" O ARG H 117 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ARG H 117 " --> pdb=" O TRP H 127 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N GLN H 129 " --> pdb=" O CYS H 115 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N CYS H 115 " --> pdb=" O GLN H 129 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N MET H 53 " --> pdb=" O TYR H 69 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR H 69 " --> pdb=" O MET H 53 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TRP H 55 " --> pdb=" O ILE H 67 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 144 through 148 removed outlier: 5.970A pdb=" N TYR H 200 " --> pdb=" O ASP H 168 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 144 through 148 removed outlier: 5.970A pdb=" N TYR H 200 " --> pdb=" O ASP H 168 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER H 201 " --> pdb=" O VAL H 193 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 175 through 178 removed outlier: 4.417A pdb=" N TYR H 218 " --> pdb=" O VAL H 235 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.637A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 48 through 55 Processing sheet with id=AD3, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.024A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 132 through 135 removed outlier: 6.618A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.546A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AD7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AD8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AD9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AE2, first strand: chain 'A' and resid 565 through 567 Processing sheet with id=AE3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.057A 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: 6.653A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 703 through 704 removed outlier: 7.100A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.182A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.182A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.284A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'E' and resid 24 through 26 Processing sheet with id=AF1, first strand: chain 'E' and resid 30 through 33 removed outlier: 5.751A pdb=" N LEU E 31 " --> pdb=" O GLU E 129 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TRP E 59 " --> pdb=" O LEU E 71 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 138 through 142 removed outlier: 6.129A pdb=" N TYR E 197 " --> pdb=" O ASN E 162 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 178 through 179 removed outlier: 4.769A pdb=" N TRP E 172 " --> pdb=" O GLN E 179 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 22 through 25 Processing sheet with id=AF5, first strand: chain 'D' and resid 29 through 31 removed outlier: 5.044A pdb=" N ALA D 125 " --> pdb=" O GLY D 119 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLY D 119 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N TRP D 127 " --> pdb=" O ARG D 117 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ARG D 117 " --> pdb=" O TRP D 127 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N GLN D 129 " --> pdb=" O CYS D 115 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N CYS D 115 " --> pdb=" O GLN D 129 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N MET D 53 " --> pdb=" O TYR D 69 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N TYR D 69 " --> pdb=" O MET D 53 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N TRP D 55 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 144 through 148 removed outlier: 6.215A pdb=" N TYR D 200 " --> pdb=" O ASP D 168 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 144 through 148 removed outlier: 6.215A pdb=" N TYR D 200 " --> pdb=" O ASP D 168 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 175 through 178 removed outlier: 4.341A pdb=" N TYR D 218 " --> pdb=" O VAL D 235 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 28 through 31 removed outlier: 4.032A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.895A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.538A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 135 through 140 removed outlier: 10.058A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.787A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AG6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.737A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AG8, first strand: chain 'B' and resid 551 through 554 removed outlier: 5.426A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N THR B 573 " --> pdb=" O ASP B 568 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ASP B 568 " --> pdb=" O THR B 573 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.387A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.036A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.036A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.423A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.727A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 24 through 27 Processing sheet with id=AH6, first strand: chain 'G' and resid 30 through 33 removed outlier: 3.746A pdb=" N LEU G 31 " --> pdb=" O LYS G 127 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TRP G 59 " --> pdb=" O LEU G 71 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 30 through 33 removed outlier: 3.746A pdb=" N LEU G 31 " --> pdb=" O LYS G 127 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR G 121 " --> pdb=" O GLN G 114 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 50 through 51 Processing sheet with id=AH9, first strand: chain 'G' and resid 138 through 142 removed outlier: 5.874A pdb=" N TYR G 197 " --> pdb=" O ASN G 162 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 169 through 174 Processing sheet with id=AI2, first strand: chain 'F' and resid 22 through 25 Processing sheet with id=AI3, first strand: chain 'F' and resid 29 through 31 removed outlier: 5.025A pdb=" N ALA F 125 " --> pdb=" O GLY F 119 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLY F 119 " --> pdb=" O ALA F 125 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N TRP F 127 " --> pdb=" O ARG F 117 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ARG F 117 " --> pdb=" O TRP F 127 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N GLN F 129 " --> pdb=" O CYS F 115 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N CYS F 115 " --> pdb=" O GLN F 129 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N MET F 53 " --> pdb=" O TYR F 69 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TYR F 69 " --> pdb=" O MET F 53 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TRP F 55 " --> pdb=" O ILE F 67 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'F' and resid 144 through 148 removed outlier: 6.193A pdb=" N TYR F 200 " --> pdb=" O ASP F 168 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'F' and resid 144 through 148 removed outlier: 6.193A pdb=" N TYR F 200 " --> pdb=" O ASP F 168 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'F' and resid 175 through 178 removed outlier: 4.454A pdb=" N TYR F 218 " --> pdb=" O VAL F 235 " (cutoff:3.500A) 1459 hydrogen bonds defined for protein. 3963 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: 8.57 Time building geometry restraints manager: 4.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10461 1.34 - 1.46: 8289 1.46 - 1.58: 15559 1.58 - 1.71: 0 1.71 - 1.83: 189 Bond restraints: 34498 Sorted by residual: bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.500 -0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" CA ALA A 706 " pdb=" C ALA A 706 " ideal model delta sigma weight residual 1.530 1.480 0.050 1.10e-02 8.26e+03 2.03e+01 bond pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.406 1.496 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " 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 C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.488 -0.082 2.00e-02 2.50e+03 1.68e+01 ... (remaining 34493 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 46057 2.17 - 4.35: 871 4.35 - 6.52: 89 6.52 - 8.70: 18 8.70 - 10.87: 1 Bond angle restraints: 47036 Sorted by residual: angle pdb=" N GLN A 498 " pdb=" CA GLN A 498 " pdb=" C GLN A 498 " ideal model delta sigma weight residual 109.58 102.98 6.60 1.63e+00 3.76e-01 1.64e+01 angle pdb=" C GLN C 506 " pdb=" CA GLN C 506 " pdb=" CB GLN C 506 " ideal model delta sigma weight residual 108.61 114.42 -5.81 1.53e+00 4.27e-01 1.44e+01 angle pdb=" N THR A1076 " pdb=" CA THR A1076 " pdb=" C THR A1076 " ideal model delta sigma weight residual 110.48 104.93 5.55 1.48e+00 4.57e-01 1.41e+01 angle pdb=" N VAL A 729 " pdb=" CA VAL A 729 " pdb=" C VAL A 729 " ideal model delta sigma weight residual 113.53 109.99 3.54 9.80e-01 1.04e+00 1.30e+01 angle pdb=" N THR B1076 " pdb=" CA THR B1076 " pdb=" C THR B1076 " ideal model delta sigma weight residual 110.53 105.79 4.74 1.32e+00 5.74e-01 1.29e+01 ... (remaining 47031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 18469 17.62 - 35.24: 1187 35.24 - 52.86: 172 52.86 - 70.49: 33 70.49 - 88.11: 28 Dihedral angle restraints: 19889 sinusoidal: 7414 harmonic: 12475 Sorted by residual: 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 -109.52 -70.48 0 5.00e+00 4.00e-02 1.99e+02 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 -111.35 -68.65 0 5.00e+00 4.00e-02 1.89e+02 dihedral pdb=" CB CYS L 43 " pdb=" SG CYS L 43 " pdb=" SG CYS L 112 " pdb=" CB CYS L 112 " ideal model delta sinusoidal sigma weight residual 93.00 163.63 -70.63 1 1.00e+01 1.00e-02 6.42e+01 ... (remaining 19886 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.551: 5595 0.551 - 1.102: 2 1.102 - 1.654: 0 1.654 - 2.205: 1 2.205 - 2.756: 5 Chirality restraints: 5603 Sorted by residual: 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 0.36 -2.76 2.00e-01 2.50e+01 1.90e+02 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 0.30 -2.70 2.00e-01 2.50e+01 1.82e+02 chirality pdb=" C1 NAG A1309 " pdb=" ND2 ASN A1074 " pdb=" C2 NAG A1309 " pdb=" O5 NAG A1309 " both_signs ideal model delta sigma weight residual False -2.40 0.12 -2.52 2.00e-01 2.50e+01 1.59e+02 ... (remaining 5600 not shown) Planarity restraints: 6040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1308 " -0.289 2.00e-02 2.50e+03 2.48e-01 7.66e+02 pdb=" C7 NAG B1308 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG B1308 " -0.173 2.00e-02 2.50e+03 pdb=" N2 NAG B1308 " 0.432 2.00e-02 2.50e+03 pdb=" O7 NAG B1308 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1309 " -0.213 2.00e-02 2.50e+03 1.78e-01 3.97e+02 pdb=" C7 NAG C1309 " 0.057 2.00e-02 2.50e+03 pdb=" C8 NAG C1309 " -0.151 2.00e-02 2.50e+03 pdb=" N2 NAG C1309 " 0.295 2.00e-02 2.50e+03 pdb=" O7 NAG C1309 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1310 " 0.197 2.00e-02 2.50e+03 1.63e-01 3.33e+02 pdb=" C7 NAG A1310 " -0.056 2.00e-02 2.50e+03 pdb=" C8 NAG A1310 " 0.144 2.00e-02 2.50e+03 pdb=" N2 NAG A1310 " -0.265 2.00e-02 2.50e+03 pdb=" O7 NAG A1310 " -0.020 2.00e-02 2.50e+03 ... (remaining 6037 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2286 2.74 - 3.28: 33247 3.28 - 3.82: 55365 3.82 - 4.36: 66813 4.36 - 4.90: 114982 Nonbonded interactions: 272693 Sorted by model distance: nonbonded pdb=" O PHE H 83 " pdb=" OG1 THR H 87 " model vdw 2.196 3.040 nonbonded pdb=" NE2 GLN C 804 " pdb=" OE1 GLN C 935 " model vdw 2.211 3.120 nonbonded pdb=" OH TYR H 69 " pdb=" OE1 GLU H 78 " model vdw 2.218 3.040 nonbonded pdb=" OG1 THR D 52 " pdb=" O ILE D 70 " model vdw 2.228 3.040 nonbonded pdb=" NE2 GLN H 25 " pdb=" O GLY H 128 " model vdw 2.230 3.120 ... (remaining 272688 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 173 or resid 187 through 212 or (resid 213 thro \ ugh 215 and (name N or name CA or name C or name O or name CB )) or resid 216 th \ rough 318 or (resid 319 and (name N or name CA or name C or name O or name CB )) \ or resid 320 through 332 or (resid 333 and (name N or name CA or name C or name \ O or name CB )) or resid 334 through 407 or (resid 408 and (name N or name CA o \ r name C or name O or name CB )) or resid 409 through 448 or (resid 449 and (nam \ e N or name CA or name C or name O or name CB )) or resid 450 through 457 or (re \ sid 458 and (name N or name CA or name C or name O or name CB )) or resid 459 th \ rough 461 or (resid 462 and (name N or name CA or name C or name O or name CB )) \ or resid 463 through 464 or (resid 465 and (name N or name CA or name C or name \ O or name CB )) or resid 467 through 470 or (resid 471 and (name N or name CA o \ r name C or name O or name CB )) or resid 472 through 473 or (resid 474 through \ 475 and (name N or name CA or name C or name O or name CB )) or resid 476 throug \ h 497 or (resid 498 and (name N or name CA or name C or name O or name CB )) or \ resid 499 through 528 or (resid 529 and (name N or name CA or name C or name O o \ r name CB )) or resid 530 through 557 or (resid 558 and (name N or name CA or na \ me C or name O or name CB )) or resid 559 through 618 or (resid 619 and (name N \ or name CA or name C or name O or name CB )) or resid 620 through 1009 or resid \ 1011 through 1309)) selection = (chain 'B' and (resid 27 through 139 or (resid 140 and (name N or name CA or nam \ e C or name O or name CB )) or resid 141 through 173 or resid 187 through 465 or \ resid 467 through 1009 or resid 1011 through 1309)) selection = (chain 'C' and (resid 27 through 139 or (resid 140 and (name N or name CA or nam \ e C or name O or name CB )) or resid 141 through 172 or (resid 173 through 187 a \ nd (name N or name CA or name C or name O or name CB )) or resid 188 through 318 \ or (resid 319 and (name N or name CA or name C or name O or name CB )) or resid \ 320 through 407 or (resid 408 and (name N or name CA or name C or name O or nam \ e CB )) or resid 409 through 448 or (resid 449 and (name N or name CA or name C \ or name O or name CB )) or resid 450 through 457 or (resid 458 and (name N or na \ me CA or name C or name O or name CB )) or resid 459 through 461 or (resid 462 a \ nd (name N or name CA or name C or name O or name CB )) or resid 463 through 464 \ or (resid 465 and (name N or name CA or name C or name O or name CB )) or resid \ 467 through 470 or (resid 471 and (name N or name CA or name C or name O or nam \ e CB )) or resid 472 through 473 or (resid 474 through 475 and (name N or name C \ A or name C or name O or name CB )) or resid 476 through 497 or (resid 498 and ( \ name N or name CA or name C or name O or name CB )) or resid 499 through 557 or \ (resid 558 and (name N or name CA or name C or name O or name CB )) or resid 559 \ through 618 or (resid 619 and (name N or name CA or name C or name O or name CB \ )) or resid 620 through 1009 or resid 1011 through 1309)) } ncs_group { reference = chain 'D' selection = (chain 'F' and (resid 21 through 31 or (resid 32 and (name N or name CA or name \ C or name O or name CB )) or resid 33 through 237)) selection = (chain 'H' and (resid 21 through 31 or (resid 32 and (name N or name CA or name \ C or name O or name CB )) or resid 33 through 237)) } 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' selection = chain 'e' selection = chain 'f' } 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: 5.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.670 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 38.850 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.129 34623 Z= 0.238 Angle : 0.882 43.760 47360 Z= 0.423 Chirality : 0.098 2.756 5603 Planarity : 0.007 0.248 5989 Dihedral : 12.071 88.107 11716 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.15 % Favored : 95.64 % Rotamer: Outliers : 0.17 % Allowed : 0.14 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 0.89 % 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: -0.10 (0.13), residues: 4229 helix: 1.39 (0.19), residues: 722 sheet: 0.70 (0.14), residues: 1292 loop : -1.06 (0.12), residues: 2215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 765 TYR 0.022 0.001 TYR D 69 PHE 0.030 0.001 PHE F 146 TRP 0.020 0.001 TRP L 59 HIS 0.007 0.001 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.22 (34498) covalent geometry : angle 0.70679 / 0.39 (47036) SS BOND : bond 0.00226 / 0.13 ( 51) SS BOND : angle 0.77452 / 0.57 ( 102) hydrogen bonds : bond 0.14580 / 9.43 ( 1384) hydrogen bonds : angle 7.54094 / 5.24 ( 3963) link_BETA1-3 : bond 0.00628 / 0.29 ( 3) link_BETA1-3 : angle 4.91672 / 3.05 ( 9) link_BETA1-4 : bond 0.00733 / 0.49 ( 20) link_BETA1-4 : angle 2.62100 / 1.75 ( 60) link_NAG-ASN : bond 0.04190 / 1.73 ( 51) link_NAG-ASN : angle 9.10181 / 5.91 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 271 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 214 LYS cc_start: 0.6132 (mmmt) cc_final: 0.5482 (mttm) REVERT: E 109 MET cc_start: 0.7937 (tpp) cc_final: 0.7694 (tpp) REVERT: E 172 TRP cc_start: 0.6451 (m100) cc_final: 0.5869 (m100) REVERT: E 210 TYR cc_start: 0.7049 (t80) cc_final: 0.6611 (t80) REVERT: E 214 LYS cc_start: 0.4772 (tppt) cc_final: 0.4552 (tppt) REVERT: F 170 PHE cc_start: 0.7817 (t80) cc_final: 0.7307 (t80) outliers start: 3 outliers final: 1 residues processed: 274 average time/residue: 0.2028 time to fit residues: 94.2300 Evaluate side-chains 191 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: [197, 388, 215, 20, 132, 261, 248, 207, 401, 424, 155] chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 9.9990 chunk 424 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 450 ASN C1010 GLN A C1011 GLN L 100 HIS H 179 ASN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN A 580 GLN A 901 GLN A1002 GLN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 901 GLN ** F 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.091305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.063942 restraints weight = 196326.348| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.54 r_work: 0.2969 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 34623 Z= 0.250 Angle : 0.777 18.035 47360 Z= 0.367 Chirality : 0.056 0.634 5603 Planarity : 0.006 0.099 5989 Dihedral : 4.991 69.696 4573 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.60 % Favored : 95.16 % Rotamer: Outliers : 0.87 % Allowed : 4.63 % Favored : 94.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 0.89 % 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: 4229 helix: 1.53 (0.19), residues: 716 sheet: 0.57 (0.14), residues: 1319 loop : -1.08 (0.13), residues: 2194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 765 TYR 0.027 0.002 TYR A 170 PHE 0.033 0.002 PHE A 906 TRP 0.024 0.002 TRP L 59 HIS 0.013 0.002 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.25 (34498) covalent geometry : angle 0.70539 / 0.35 (47036) SS BOND : bond 0.00339 / 0.20 ( 51) SS BOND : angle 0.94075 / 0.67 ( 102) hydrogen bonds : bond 0.04560 / 2.99 ( 1384) hydrogen bonds : angle 6.12803 / 4.24 ( 3963) link_BETA1-3 : bond 0.00646 / 0.32 ( 3) link_BETA1-3 : angle 3.92692 / 2.42 ( 9) link_BETA1-4 : bond 0.00606 / 0.40 ( 20) link_BETA1-4 : angle 2.16083 / 1.50 ( 60) link_NAG-ASN : bond 0.01567 / 0.83 ( 51) link_NAG-ASN : angle 5.53150 / 3.69 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 222 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 86 PHE cc_start: 0.7379 (m-80) cc_final: 0.7126 (m-80) REVERT: L 214 LYS cc_start: 0.5696 (mmmt) cc_final: 0.5401 (mttt) REVERT: H 39 MET cc_start: 0.1874 (tmm) cc_final: 0.1649 (tmm) REVERT: A 104 TRP cc_start: 0.7866 (m-90) cc_final: 0.6993 (m-10) REVERT: E 50 ASP cc_start: 0.8284 (m-30) cc_final: 0.7851 (p0) REVERT: E 114 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.8138 (pp30) REVERT: E 210 TYR cc_start: 0.6931 (t80) cc_final: 0.6709 (t80) REVERT: G 57 MET cc_start: 0.8153 (tpp) cc_final: 0.7819 (ttm) REVERT: F 170 PHE cc_start: 0.8402 (t80) cc_final: 0.7790 (t80) outliers start: 28 outliers final: 18 residues processed: 241 average time/residue: 0.2007 time to fit residues: 82.3247 Evaluate side-chains 215 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 196 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain L residue 60 PHE Chi-restraints excluded: chain L residue 100 HIS Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain E residue 52 TYR Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain G residue 127 LYS Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain F residue 208 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: [131, 44, 382, 304, 1, 72, 2, 211, 187, 202, 134] chunk 131 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 382 optimal weight: 0.9990 chunk 304 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 211 optimal weight: 0.4980 chunk 187 optimal weight: 8.9990 chunk 202 optimal weight: 0.5980 chunk 134 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1106 GLN L 100 HIS L 161 ASN H 188 HIS ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN A 501 ASN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 137 ASN ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.092689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.065283 restraints weight = 203589.095| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.66 r_work: 0.3015 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 34623 Z= 0.128 Angle : 0.676 15.391 47360 Z= 0.316 Chirality : 0.052 0.531 5603 Planarity : 0.005 0.099 5989 Dihedral : 4.734 68.820 4573 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.75 % Favored : 96.02 % Rotamer: Outliers : 0.81 % Allowed : 6.37 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 0.89 % 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: 0.02 (0.13), residues: 4229 helix: 1.78 (0.20), residues: 723 sheet: 0.64 (0.14), residues: 1274 loop : -0.99 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 765 TYR 0.028 0.001 TYR E 73 PHE 0.025 0.001 PHE G 140 TRP 0.032 0.002 TRP C 353 HIS 0.009 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (34498) covalent geometry : angle 0.60520 / 0.30 (47036) SS BOND : bond 0.00211 / 0.12 ( 51) SS BOND : angle 0.75137 / 0.55 ( 102) hydrogen bonds : bond 0.03916 / 2.58 ( 1384) hydrogen bonds : angle 5.78839 / 4.00 ( 3963) link_BETA1-3 : bond 0.00826 / 0.40 ( 3) link_BETA1-3 : angle 3.59943 / 2.24 ( 9) link_BETA1-4 : bond 0.00613 / 0.42 ( 20) link_BETA1-4 : angle 1.94926 / 1.32 ( 60) link_NAG-ASN : bond 0.01668 / 0.90 ( 51) link_NAG-ASN : angle 5.10854 / 3.34 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 208 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 456 PHE cc_start: 0.6562 (m-80) cc_final: 0.6293 (m-80) REVERT: L 110 TYR cc_start: 0.6130 (m-80) cc_final: 0.5660 (m-80) REVERT: L 131 LYS cc_start: 0.1386 (ttpt) cc_final: 0.1080 (tptt) REVERT: L 214 LYS cc_start: 0.5642 (mmmt) cc_final: 0.5418 (mttt) REVERT: H 121 ARG cc_start: 0.7762 (mmp80) cc_final: 0.6852 (mpt-90) REVERT: H 200 TYR cc_start: 0.4921 (m-80) cc_final: 0.4721 (m-80) REVERT: A 104 TRP cc_start: 0.7805 (m-90) cc_final: 0.6948 (m-10) REVERT: A 780 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8321 (mp0) REVERT: E 50 ASP cc_start: 0.8301 (m-30) cc_final: 0.7794 (p0) REVERT: G 57 MET cc_start: 0.8114 (tpp) cc_final: 0.7735 (ttm) REVERT: G 197 TYR cc_start: 0.8362 (OUTLIER) cc_final: 0.8112 (m-10) REVERT: F 170 PHE cc_start: 0.8428 (t80) cc_final: 0.7758 (t80) outliers start: 26 outliers final: 20 residues processed: 226 average time/residue: 0.1932 time to fit residues: 74.6995 Evaluate side-chains 207 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 186 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain L residue 60 PHE Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain G residue 127 LYS Chi-restraints excluded: chain G residue 197 TYR Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 219 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: [245, 59, 163, 78, 134, 341, 317, 61, 323, 30, 254] chunk 245 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 163 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 134 optimal weight: 7.9990 chunk 341 optimal weight: 0.9980 chunk 317 optimal weight: 0.0470 chunk 61 optimal weight: 5.9990 chunk 323 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 254 optimal weight: 3.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 188 HIS ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN A 501 ASN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 580 GLN ** F 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.092543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.064991 restraints weight = 215791.047| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.77 r_work: 0.3009 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 34623 Z= 0.136 Angle : 0.662 15.444 47360 Z= 0.309 Chirality : 0.051 0.499 5603 Planarity : 0.005 0.099 5989 Dihedral : 4.628 67.708 4573 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.05 % Favored : 95.69 % Rotamer: Outliers : 0.87 % Allowed : 6.81 % Favored : 92.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 0.89 % 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: 0.06 (0.13), residues: 4229 helix: 1.85 (0.20), residues: 723 sheet: 0.62 (0.14), residues: 1298 loop : -0.95 (0.13), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 765 TYR 0.030 0.001 TYR E 73 PHE 0.025 0.001 PHE G 140 TRP 0.041 0.002 TRP L 59 HIS 0.008 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (34498) covalent geometry : angle 0.59304 / 0.29 (47036) SS BOND : bond 0.00207 / 0.11 ( 51) SS BOND : angle 0.73992 / 0.54 ( 102) hydrogen bonds : bond 0.03729 / 2.46 ( 1384) hydrogen bonds : angle 5.59953 / 3.87 ( 3963) link_BETA1-3 : bond 0.00757 / 0.38 ( 3) link_BETA1-3 : angle 3.56102 / 2.21 ( 9) link_BETA1-4 : bond 0.00592 / 0.41 ( 20) link_BETA1-4 : angle 1.89447 / 1.29 ( 60) link_NAG-ASN : bond 0.01580 / 0.85 ( 51) link_NAG-ASN : angle 4.98900 / 3.24 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 392 PHE cc_start: 0.6917 (m-80) cc_final: 0.6327 (m-80) REVERT: L 131 LYS cc_start: 0.1393 (ttpt) cc_final: 0.1095 (tptt) REVERT: H 121 ARG cc_start: 0.7652 (mmp80) cc_final: 0.7153 (mpt-90) REVERT: H 172 GLU cc_start: 0.4643 (pm20) cc_final: 0.3066 (mt-10) REVERT: A 740 MET cc_start: 0.8826 (ttp) cc_final: 0.8492 (ttp) REVERT: A 780 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8327 (mp0) REVERT: E 50 ASP cc_start: 0.8226 (m-30) cc_final: 0.7764 (p0) REVERT: G 57 MET cc_start: 0.8125 (tpp) cc_final: 0.7815 (ttm) REVERT: F 170 PHE cc_start: 0.8361 (t80) cc_final: 0.7881 (t80) outliers start: 28 outliers final: 20 residues processed: 217 average time/residue: 0.1962 time to fit residues: 72.1135 Evaluate side-chains 209 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain L residue 60 PHE Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain G residue 127 LYS Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 219 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: [375, 372, 343, 383, 216, 373, 134, 144, 43, 307, 130] chunk 375 optimal weight: 2.9990 chunk 372 optimal weight: 0.5980 chunk 343 optimal weight: 0.8980 chunk 383 optimal weight: 0.0070 chunk 216 optimal weight: 0.8980 chunk 373 optimal weight: 3.9990 chunk 134 optimal weight: 10.0000 chunk 144 optimal weight: 7.9990 chunk 43 optimal weight: 0.0980 chunk 307 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1071 GLN L 98 ASN L 161 ASN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN A 955 ASN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN ** F 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.093622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.067457 restraints weight = 263618.778| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 5.17 r_work: 0.2979 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 34623 Z= 0.114 Angle : 0.637 15.734 47360 Z= 0.297 Chirality : 0.050 0.487 5603 Planarity : 0.005 0.098 5989 Dihedral : 4.462 67.183 4573 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.72 % Favored : 95.99 % Rotamer: Outliers : 0.98 % Allowed : 7.48 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 0.89 % 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: 0.16 (0.13), residues: 4229 helix: 2.00 (0.20), residues: 723 sheet: 0.61 (0.14), residues: 1306 loop : -0.86 (0.13), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 765 TYR 0.031 0.001 TYR E 73 PHE 0.025 0.001 PHE G 140 TRP 0.038 0.001 TRP L 59 HIS 0.007 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (34498) covalent geometry : angle 0.57003 / 0.28 (47036) SS BOND : bond 0.00193 / 0.11 ( 51) SS BOND : angle 0.67661 / 0.51 ( 102) hydrogen bonds : bond 0.03446 / 2.28 ( 1384) hydrogen bonds : angle 5.38269 / 3.72 ( 3963) link_BETA1-3 : bond 0.00841 / 0.42 ( 3) link_BETA1-3 : angle 3.35676 / 2.09 ( 9) link_BETA1-4 : bond 0.00614 / 0.42 ( 20) link_BETA1-4 : angle 1.80026 / 1.21 ( 60) link_NAG-ASN : bond 0.01527 / 0.83 ( 51) link_NAG-ASN : angle 4.85597 / 3.15 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 204 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 131 LYS cc_start: 0.1391 (ttpt) cc_final: 0.1078 (tptt) REVERT: H 51 TYR cc_start: 0.6657 (m-80) cc_final: 0.6214 (m-80) REVERT: H 121 ARG cc_start: 0.7576 (mmp80) cc_final: 0.7188 (mpt-90) REVERT: H 172 GLU cc_start: 0.4668 (pm20) cc_final: 0.3269 (mt-10) REVERT: A 104 TRP cc_start: 0.7957 (m-90) cc_final: 0.7109 (m-10) REVERT: A 740 MET cc_start: 0.8923 (ttp) cc_final: 0.8620 (ttp) REVERT: A 780 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8419 (mp0) REVERT: E 50 ASP cc_start: 0.8438 (m-30) cc_final: 0.7804 (p0) REVERT: B 907 ASN cc_start: 0.9270 (OUTLIER) cc_final: 0.8856 (m110) REVERT: F 170 PHE cc_start: 0.8376 (t80) cc_final: 0.7697 (t80) outliers start: 32 outliers final: 25 residues processed: 229 average time/residue: 0.1921 time to fit residues: 74.9131 Evaluate side-chains 207 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 181 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain L residue 60 PHE Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain G residue 127 LYS Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 208 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: [153, 273, 353, 402, 260, 168, 388, 241, 19, 378, 37] chunk 153 optimal weight: 6.9990 chunk 273 optimal weight: 3.9990 chunk 353 optimal weight: 1.9990 chunk 402 optimal weight: 8.9990 chunk 260 optimal weight: 20.0000 chunk 168 optimal weight: 3.9990 chunk 388 optimal weight: 3.9990 chunk 241 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 chunk 378 optimal weight: 0.0980 chunk 37 optimal weight: 8.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 161 ASN A 388 ASN A 955 ASN A1011 GLN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS B 137 ASN ** F 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.091520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.064285 restraints weight = 199610.812| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.69 r_work: 0.2972 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 34623 Z= 0.222 Angle : 0.698 15.734 47360 Z= 0.329 Chirality : 0.052 0.509 5603 Planarity : 0.005 0.099 5989 Dihedral : 4.702 66.592 4573 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.84 % Favored : 94.97 % Rotamer: Outliers : 1.14 % Allowed : 7.76 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 0.89 % 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: 0.03 (0.13), residues: 4229 helix: 1.83 (0.20), residues: 713 sheet: 0.55 (0.14), residues: 1319 loop : -0.95 (0.13), residues: 2197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 237 TYR 0.027 0.002 TYR B 369 PHE 0.024 0.002 PHE G 140 TRP 0.027 0.002 TRP L 59 HIS 0.007 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.22 (34498) covalent geometry : angle 0.63460 / 0.31 (47036) SS BOND : bond 0.00432 / 0.18 ( 51) SS BOND : angle 0.86013 / 0.60 ( 102) hydrogen bonds : bond 0.04007 / 2.65 ( 1384) hydrogen bonds : angle 5.52883 / 3.82 ( 3963) link_BETA1-3 : bond 0.00567 / 0.28 ( 3) link_BETA1-3 : angle 3.56616 / 2.21 ( 9) link_BETA1-4 : bond 0.00544 / 0.38 ( 20) link_BETA1-4 : angle 1.94113 / 1.34 ( 60) link_NAG-ASN : bond 0.01505 / 0.79 ( 51) link_NAG-ASN : angle 4.92343 / 3.22 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 193 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 392 PHE cc_start: 0.7202 (m-80) cc_final: 0.7001 (m-80) REVERT: L 131 LYS cc_start: 0.1468 (ttpt) cc_final: 0.1158 (tptt) REVERT: H 51 TYR cc_start: 0.6530 (m-80) cc_final: 0.6142 (m-80) REVERT: H 80 ASN cc_start: 0.5051 (m-40) cc_final: 0.3962 (t0) REVERT: H 121 ARG cc_start: 0.7510 (mmp80) cc_final: 0.7267 (mpt-90) REVERT: E 50 ASP cc_start: 0.8328 (m-30) cc_final: 0.7783 (p0) REVERT: F 170 PHE cc_start: 0.8458 (t80) cc_final: 0.7875 (t80) outliers start: 38 outliers final: 31 residues processed: 223 average time/residue: 0.1891 time to fit residues: 71.4548 Evaluate side-chains 216 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 185 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 543 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain L residue 60 PHE Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain H residue 200 TYR Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 93 LYS Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain G residue 127 LYS Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 208 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: [403, 241, 290, 88, 188, 369, 24, 132, 299, 190, 276] chunk 403 optimal weight: 20.0000 chunk 241 optimal weight: 0.5980 chunk 290 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 188 optimal weight: 0.8980 chunk 369 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 chunk 299 optimal weight: 0.0170 chunk 190 optimal weight: 3.9990 chunk 276 optimal weight: 5.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 161 ASN A 955 ASN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS F 25 GLN ** F 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.092827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.066762 restraints weight = 212524.621| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 4.60 r_work: 0.2986 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 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: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 34623 Z= 0.124 Angle : 0.648 15.933 47360 Z= 0.303 Chirality : 0.051 0.496 5603 Planarity : 0.005 0.098 5989 Dihedral : 4.535 65.950 4573 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.79 % Favored : 96.02 % Rotamer: Outliers : 0.98 % Allowed : 8.49 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 0.89 % 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: 0.15 (0.13), residues: 4229 helix: 1.96 (0.20), residues: 721 sheet: 0.65 (0.14), residues: 1287 loop : -0.88 (0.13), residues: 2221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 765 TYR 0.028 0.001 TYR B 369 PHE 0.027 0.001 PHE G 140 TRP 0.017 0.001 TRP C 353 HIS 0.006 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (34498) covalent geometry : angle 0.58310 / 0.29 (47036) SS BOND : bond 0.00218 / 0.11 ( 51) SS BOND : angle 0.79760 / 0.61 ( 102) hydrogen bonds : bond 0.03547 / 2.36 ( 1384) hydrogen bonds : angle 5.38665 / 3.72 ( 3963) link_BETA1-3 : bond 0.00789 / 0.39 ( 3) link_BETA1-3 : angle 3.34157 / 2.08 ( 9) link_BETA1-4 : bond 0.00586 / 0.40 ( 20) link_BETA1-4 : angle 1.78408 / 1.20 ( 60) link_NAG-ASN : bond 0.01491 / 0.81 ( 51) link_NAG-ASN : angle 4.80222 / 3.13 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 197 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 392 PHE cc_start: 0.7322 (m-80) cc_final: 0.7121 (m-80) REVERT: L 131 LYS cc_start: 0.1613 (ttpt) cc_final: 0.1284 (tptt) REVERT: H 51 TYR cc_start: 0.6502 (m-80) cc_final: 0.6055 (m-80) REVERT: H 80 ASN cc_start: 0.5072 (m-40) cc_final: 0.3903 (t0) REVERT: H 121 ARG cc_start: 0.7567 (mmp80) cc_final: 0.7182 (mpt-90) REVERT: E 50 ASP cc_start: 0.8399 (m-30) cc_final: 0.7778 (p0) REVERT: B 907 ASN cc_start: 0.9273 (OUTLIER) cc_final: 0.8852 (m110) REVERT: F 170 PHE cc_start: 0.8465 (t80) cc_final: 0.7847 (t80) outliers start: 32 outliers final: 29 residues processed: 219 average time/residue: 0.1992 time to fit residues: 74.3887 Evaluate side-chains 219 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain L residue 60 PHE Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain H residue 200 TYR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain G residue 127 LYS Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 208 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: [69, 359, 410, 310, 389, 379, 409, 49, 193, 104, 194] chunk 69 optimal weight: 3.9990 chunk 359 optimal weight: 0.9980 chunk 410 optimal weight: 0.8980 chunk 310 optimal weight: 0.9980 chunk 389 optimal weight: 3.9990 chunk 379 optimal weight: 2.9990 chunk 409 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 193 optimal weight: 0.9980 chunk 104 optimal weight: 0.0000 chunk 194 optimal weight: 4.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN ** F 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.092852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.067088 restraints weight = 222540.120| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 4.72 r_work: 0.2976 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 34623 Z= 0.126 Angle : 0.644 15.793 47360 Z= 0.301 Chirality : 0.050 0.491 5603 Planarity : 0.005 0.098 5989 Dihedral : 4.444 64.949 4573 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.31 % Favored : 95.50 % Rotamer: Outliers : 1.01 % Allowed : 8.77 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 0.89 % 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: 4229 helix: 2.06 (0.20), residues: 715 sheet: 0.68 (0.14), residues: 1299 loop : -0.87 (0.13), residues: 2215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 765 TYR 0.027 0.001 TYR B 369 PHE 0.024 0.001 PHE G 140 TRP 0.015 0.001 TRP C 353 HIS 0.006 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (34498) covalent geometry : angle 0.58094 / 0.29 (47036) SS BOND : bond 0.00196 / 0.10 ( 51) SS BOND : angle 0.70649 / 0.53 ( 102) hydrogen bonds : bond 0.03474 / 2.32 ( 1384) hydrogen bonds : angle 5.29252 / 3.65 ( 3963) link_BETA1-3 : bond 0.00749 / 0.37 ( 3) link_BETA1-3 : angle 3.34529 / 2.08 ( 9) link_BETA1-4 : bond 0.00579 / 0.40 ( 20) link_BETA1-4 : angle 1.76292 / 1.18 ( 60) link_NAG-ASN : bond 0.01459 / 0.79 ( 51) link_NAG-ASN : angle 4.73721 / 3.09 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 194 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 392 PHE cc_start: 0.7473 (m-80) cc_final: 0.7195 (m-80) REVERT: L 131 LYS cc_start: 0.1648 (ttpt) cc_final: 0.1295 (tptt) REVERT: H 51 TYR cc_start: 0.6461 (m-80) cc_final: 0.6071 (m-80) REVERT: H 80 ASN cc_start: 0.5145 (m-40) cc_final: 0.4017 (t0) REVERT: H 121 ARG cc_start: 0.7511 (mmp80) cc_final: 0.7204 (mpt-90) REVERT: E 50 ASP cc_start: 0.8516 (m-30) cc_final: 0.7803 (p0) REVERT: B 907 ASN cc_start: 0.9271 (OUTLIER) cc_final: 0.8859 (m110) REVERT: F 170 PHE cc_start: 0.8463 (t80) cc_final: 0.7824 (t80) outliers start: 33 outliers final: 32 residues processed: 217 average time/residue: 0.1929 time to fit residues: 72.0456 Evaluate side-chains 222 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 189 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain L residue 60 PHE Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain H residue 200 TYR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 127 LYS Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 208 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: [110, 409, 336, 337, 253, 122, 58, 81, 295, 157, 421] chunk 110 optimal weight: 0.5980 chunk 409 optimal weight: 4.9990 chunk 336 optimal weight: 2.9990 chunk 337 optimal weight: 0.9980 chunk 253 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 295 optimal weight: 3.9990 chunk 157 optimal weight: 10.0000 chunk 421 optimal weight: 10.0000 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 498 GLN L 161 ASN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN D 188 HIS G 148 GLN F 24 GLN ** F 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.091307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.064360 restraints weight = 183957.314| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 3.51 r_work: 0.2983 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 34623 Z= 0.198 Angle : 0.688 15.832 47360 Z= 0.325 Chirality : 0.052 0.516 5603 Planarity : 0.005 0.098 5989 Dihedral : 4.659 65.370 4573 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.74 % Favored : 95.05 % Rotamer: Outliers : 1.17 % Allowed : 8.91 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 0.89 % 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: 0.05 (0.13), residues: 4229 helix: 1.81 (0.20), residues: 723 sheet: 0.62 (0.14), residues: 1293 loop : -0.95 (0.13), residues: 2213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 765 TYR 0.026 0.002 TYR B 369 PHE 0.021 0.002 PHE F 146 TRP 0.015 0.002 TRP C 353 HIS 0.006 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 (34498) covalent geometry : angle 0.62718 / 0.31 (47036) SS BOND : bond 0.00239 / 0.13 ( 51) SS BOND : angle 0.78203 / 0.57 ( 102) hydrogen bonds : bond 0.03917 / 2.60 ( 1384) hydrogen bonds : angle 5.44859 / 3.76 ( 3963) link_BETA1-3 : bond 0.00571 / 0.28 ( 3) link_BETA1-3 : angle 3.43560 / 2.13 ( 9) link_BETA1-4 : bond 0.00557 / 0.38 ( 20) link_BETA1-4 : angle 1.88292 / 1.29 ( 60) link_NAG-ASN : bond 0.01468 / 0.77 ( 51) link_NAG-ASN : angle 4.79873 / 3.15 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 198 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 392 PHE cc_start: 0.7311 (m-80) cc_final: 0.7084 (m-80) REVERT: L 131 LYS cc_start: 0.1546 (ttpt) cc_final: 0.1223 (tmtt) REVERT: H 51 TYR cc_start: 0.6582 (m-80) cc_final: 0.6190 (m-80) REVERT: H 80 ASN cc_start: 0.4749 (m-40) cc_final: 0.3488 (t0) REVERT: H 121 ARG cc_start: 0.7659 (mmp80) cc_final: 0.7317 (mpt-90) REVERT: E 50 ASP cc_start: 0.8279 (m-30) cc_final: 0.7750 (p0) REVERT: D 202 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8286 (pt) REVERT: F 170 PHE cc_start: 0.8471 (t80) cc_final: 0.7937 (t80) outliers start: 39 outliers final: 32 residues processed: 226 average time/residue: 0.2014 time to fit residues: 77.0909 Evaluate side-chains 219 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain L residue 60 PHE Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain H residue 200 TYR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain D residue 93 LYS Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain G residue 127 LYS Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 208 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: [291, 123, 284, 217, 297, 1, 355, 63, 320, 369, 336] chunk 291 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 284 optimal weight: 5.9990 chunk 217 optimal weight: 0.5980 chunk 297 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 355 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 320 optimal weight: 0.0670 chunk 369 optimal weight: 0.9980 chunk 336 optimal weight: 0.0070 overall best weight: 1.1338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 955 ASN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS B 137 ASN ** F 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.091917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.065263 restraints weight = 162080.040| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 3.32 r_work: 0.3012 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 34623 Z= 0.148 Angle : 0.665 15.908 47360 Z= 0.313 Chirality : 0.051 0.509 5603 Planarity : 0.005 0.097 5989 Dihedral : 4.600 64.896 4573 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.34 % Favored : 95.45 % Rotamer: Outliers : 1.01 % Allowed : 9.16 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 0.89 % 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: 0.09 (0.13), residues: 4229 helix: 1.81 (0.19), residues: 732 sheet: 0.65 (0.14), residues: 1292 loop : -0.92 (0.13), residues: 2205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 765 TYR 0.028 0.001 TYR B 369 PHE 0.024 0.001 PHE F 146 TRP 0.016 0.001 TRP C 353 HIS 0.006 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (34498) covalent geometry : angle 0.60401 / 0.30 (47036) SS BOND : bond 0.00208 / 0.11 ( 51) SS BOND : angle 0.71965 / 0.53 ( 102) hydrogen bonds : bond 0.03691 / 2.45 ( 1384) hydrogen bonds : angle 5.37454 / 3.71 ( 3963) link_BETA1-3 : bond 0.00703 / 0.35 ( 3) link_BETA1-3 : angle 3.33828 / 2.07 ( 9) link_BETA1-4 : bond 0.00565 / 0.39 ( 20) link_BETA1-4 : angle 1.79345 / 1.22 ( 60) link_NAG-ASN : bond 0.01450 / 0.78 ( 51) link_NAG-ASN : angle 4.74132 / 3.10 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 392 PHE cc_start: 0.7242 (m-80) cc_final: 0.7013 (m-80) REVERT: L 131 LYS cc_start: 0.1662 (ttpt) cc_final: 0.1334 (tmtt) REVERT: H 51 TYR cc_start: 0.6612 (m-80) cc_final: 0.6179 (m-80) REVERT: H 80 ASN cc_start: 0.4749 (m-40) cc_final: 0.3447 (t0) REVERT: H 121 ARG cc_start: 0.7673 (mmp80) cc_final: 0.7426 (mpt-90) REVERT: D 202 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8302 (pt) REVERT: F 170 PHE cc_start: 0.8491 (t80) cc_final: 0.7902 (t80) outliers start: 33 outliers final: 32 residues processed: 217 average time/residue: 0.1959 time to fit residues: 72.7441 Evaluate side-chains 222 residues out of total 3718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 189 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain L residue 60 PHE Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain H residue 200 TYR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 93 LYS Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain G residue 127 LYS Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 208 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: [312, 130, 362, 386, 53, 190, 410, 276, 394, 265, 56] chunk 312 optimal weight: 0.9990 chunk 130 optimal weight: 8.9990 chunk 362 optimal weight: 2.9990 chunk 386 optimal weight: 0.0970 chunk 53 optimal weight: 4.9990 chunk 190 optimal weight: 1.9990 chunk 410 optimal weight: 0.9980 chunk 276 optimal weight: 2.9990 chunk 394 optimal weight: 1.9990 chunk 265 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 955 ASN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.092717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.067112 restraints weight = 204008.980| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 4.49 r_work: 0.2992 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 34623 Z= 0.124 Angle : 0.643 15.784 47360 Z= 0.301 Chirality : 0.050 0.492 5603 Planarity : 0.004 0.098 5989 Dihedral : 4.445 64.508 4573 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.15 % Favored : 95.64 % Rotamer: Outliers : 0.98 % Allowed : 9.35 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 0.89 % 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: 4229 helix: 2.01 (0.20), residues: 721 sheet: 0.73 (0.14), residues: 1268 loop : -0.85 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 765 TYR 0.027 0.001 TYR B 369 PHE 0.025 0.001 PHE F 146 TRP 0.016 0.001 TRP H 55 HIS 0.006 0.001 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (34498) covalent geometry : angle 0.58233 / 0.29 (47036) SS BOND : bond 0.00204 / 0.10 ( 51) SS BOND : angle 0.67393 / 0.50 ( 102) hydrogen bonds : bond 0.03427 / 2.28 ( 1384) hydrogen bonds : angle 5.22902 / 3.61 ( 3963) link_BETA1-3 : bond 0.00756 / 0.37 ( 3) link_BETA1-3 : angle 3.20192 / 1.99 ( 9) link_BETA1-4 : bond 0.00580 / 0.40 ( 20) link_BETA1-4 : angle 1.72012 / 1.15 ( 60) link_NAG-ASN : bond 0.01422 / 0.78 ( 51) link_NAG-ASN : angle 4.64010 / 3.03 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9273.52 seconds wall clock time: 159 minutes 11.40 seconds (9551.40 seconds total)