Starting phenix.real_space_refine on Fri Mar 6 06:21:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m5e_23674/03_2026/7m5e_23674.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m5e_23674/03_2026/7m5e_23674.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7m5e_23674/03_2026/7m5e_23674.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m5e_23674/03_2026/7m5e_23674.map" model { file = "/net/cci-nas-00/data/ceres_data/7m5e_23674/03_2026/7m5e_23674.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m5e_23674/03_2026/7m5e_23674.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.126 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 18048 2.51 5 N 4521 2.21 5 O 5850 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 148 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28566 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 8915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1159, 8915 Classifications: {'peptide': 1159} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 58, 'TRANS': 1100} Chain breaks: 4 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 8915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1159, 8915 Classifications: {'peptide': 1159} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 58, 'TRANS': 1100} Chain breaks: 4 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "E" Number of atoms: 8915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1159, 8915 Classifications: {'peptide': 1159} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 58, 'TRANS': 1100} Chain breaks: 4 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "f" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 151 Unusual residues: {'FOL': 1, 'NAG': 7, 'SIA': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 151 Unusual residues: {'FOL': 1, 'NAG': 7, 'SIA': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "E" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 151 Unusual residues: {'FOL': 1, 'NAG': 7, 'SIA': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 6.61, per 1000 atoms: 0.23 Number of scatterers: 28566 At special positions: 0 Unit cell: (150.15, 141.75, 160.65, 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 5850 8.00 N 4521 7.00 C 18048 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 195 " distance=2.19 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 237 " distance=2.06 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 349 " distance=2.01 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS A 478 " distance=2.17 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 585 " distance=2.13 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 526 " distance=2.02 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 654 " distance=2.03 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 650 " distance=2.03 Simple disulfide: pdb=" SG CYS A 679 " - pdb=" SG CYS A 713 " distance=2.09 Simple disulfide: pdb=" SG CYS A 727 " - pdb=" SG CYS A 736 " distance=2.03 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.13 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.19 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.09 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.02 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.19 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.06 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 349 " distance=2.01 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 407 " distance=2.03 Simple disulfide: pdb=" SG CYS C 425 " - pdb=" SG CYS C 478 " distance=2.17 Simple disulfide: pdb=" SG CYS C 437 " - pdb=" SG CYS C 585 " distance=2.13 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 526 " distance=2.02 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 654 " distance=2.03 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 650 " distance=2.03 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 713 " distance=2.09 Simple disulfide: pdb=" SG CYS C 727 " - pdb=" SG CYS C 736 " distance=2.03 Simple disulfide: pdb=" SG CYS C 806 " - pdb=" SG CYS C 828 " distance=2.13 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 817 " distance=2.19 Simple disulfide: pdb=" SG CYS C 912 " - pdb=" SG CYS C 925 " distance=2.09 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " distance=2.02 Simple disulfide: pdb=" SG CYS C1156 " - pdb=" SG CYS C1164 " distance=2.03 Simple disulfide: pdb=" SG CYS E 30 " - pdb=" SG CYS E 195 " distance=2.19 Simple disulfide: pdb=" SG CYS E 176 " - pdb=" SG CYS E 214 " distance=2.03 Simple disulfide: pdb=" SG CYS E 185 " - pdb=" SG CYS E 237 " distance=2.06 Simple disulfide: pdb=" SG CYS E 339 " - pdb=" SG CYS E 349 " distance=2.01 Simple disulfide: pdb=" SG CYS E 383 " - pdb=" SG CYS E 407 " distance=2.03 Simple disulfide: pdb=" SG CYS E 425 " - pdb=" SG CYS E 478 " distance=2.17 Simple disulfide: pdb=" SG CYS E 437 " - pdb=" SG CYS E 585 " distance=2.13 Simple disulfide: pdb=" SG CYS E 503 " - pdb=" SG CYS E 526 " distance=2.02 Simple disulfide: pdb=" SG CYS E 603 " - pdb=" SG CYS E 654 " distance=2.03 Simple disulfide: pdb=" SG CYS E 620 " - pdb=" SG CYS E 650 " distance=2.03 Simple disulfide: pdb=" SG CYS E 679 " - pdb=" SG CYS E 713 " distance=2.09 Simple disulfide: pdb=" SG CYS E 727 " - pdb=" SG CYS E 736 " distance=2.03 Simple disulfide: pdb=" SG CYS E 806 " - pdb=" SG CYS E 828 " distance=2.13 Simple disulfide: pdb=" SG CYS E 811 " - pdb=" SG CYS E 817 " distance=2.19 Simple disulfide: pdb=" SG CYS E 912 " - pdb=" SG CYS E 925 " distance=2.09 Simple disulfide: pdb=" SG CYS E1106 " - pdb=" SG CYS E1117 " distance=2.02 Simple disulfide: pdb=" SG CYS E1156 " - pdb=" SG CYS E1164 " 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 ALPHA1-2 " MAN F 4 " - " MAN F 5 " " MAN F 6 " - " MAN F 7 " " MAN P 4 " - " MAN P 5 " " MAN P 6 " - " MAN P 7 " " MAN Z 4 " - " MAN Z 5 " " MAN Z 6 " - " MAN Z 7 " ALPHA1-3 " BMA B 3 " - " MAN B 4 " " BMA F 3 " - " MAN F 4 " " BMA H 3 " - " MAN H 4 " " BMA K 3 " - " MAN K 4 " " BMA L 3 " - " MAN L 4 " " BMA N 3 " - " MAN N 4 " " BMA P 3 " - " MAN P 4 " " BMA R 3 " - " MAN R 4 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " BMA X 3 " - " MAN X 4 " " BMA Z 3 " - " MAN Z 4 " " BMA b 3 " - " MAN b 4 " " BMA e 3 " - " MAN e 4 " " BMA f 3 " - " MAN f 4 " ALPHA1-6 " BMA F 3 " - " MAN F 6 " " BMA K 3 " - " MAN K 5 " " BMA L 3 " - " MAN L 5 " " BMA P 3 " - " MAN P 6 " " BMA U 3 " - " MAN U 5 " " BMA V 3 " - " MAN V 5 " " BMA Z 3 " - " MAN Z 6 " " BMA e 3 " - " MAN e 5 " " BMA f 3 " - " MAN f 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG D 1 " - " NAG D 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " NAG-ASN " NAG A1402 " - " ASN A 487 " " NAG A1403 " - " ASN A 592 " " NAG A1404 " - " ASN A 619 " " NAG A1405 " - " ASN A 719 " " NAG A1406 " - " ASN A 774 " " NAG A1407 " - " ASN A 785 " " NAG A1408 " - " ASN A 155 " " NAG B 1 " - " ASN A 222 " " NAG C1402 " - " ASN C 487 " " NAG C1403 " - " ASN C 592 " " NAG C1404 " - " ASN C 619 " " NAG C1405 " - " ASN C 719 " " NAG C1406 " - " ASN C 774 " " NAG C1407 " - " ASN C 785 " " NAG C1408 " - " ASN C 155 " " NAG D 1 " - " ASN A 236 " " NAG E1402 " - " ASN E 487 " " NAG E1403 " - " ASN E 592 " " NAG E1404 " - " ASN E 619 " " NAG E1405 " - " ASN E 719 " " NAG E1406 " - " ASN E 774 " " NAG E1407 " - " ASN E 785 " " NAG E1408 " - " ASN E 155 " " NAG F 1 " - " ASN A 410 " " NAG G 1 " - " ASN A 870 " " NAG H 1 " - " ASN A1213 " " NAG I 1 " - " ASN A 66 " " NAG J 1 " - " ASN A 104 " " NAG K 1 " - " ASN A 125 " " NAG L 1 " - " ASN A 166 " " NAG M 1 " - " ASN A 244 " " NAG N 1 " - " ASN C 222 " " NAG O 1 " - " ASN C 236 " " NAG P 1 " - " ASN C 410 " " NAG Q 1 " - " ASN C 870 " " NAG R 1 " - " ASN C1213 " " NAG S 1 " - " ASN C 66 " " NAG T 1 " - " ASN C 104 " " NAG U 1 " - " ASN C 125 " " NAG V 1 " - " ASN C 166 " " NAG W 1 " - " ASN C 244 " " NAG X 1 " - " ASN E 222 " " NAG Y 1 " - " ASN E 236 " " NAG Z 1 " - " ASN E 410 " " NAG a 1 " - " ASN E 870 " " NAG b 1 " - " ASN E1213 " " NAG c 1 " - " ASN E 66 " " NAG d 1 " - " ASN E 104 " " NAG e 1 " - " ASN E 125 " " NAG f 1 " - " ASN E 166 " " NAG g 1 " - " ASN E 244 " Time building additional restraints: 3.03 Conformation dependent library (CDL) restraints added in 1.2 seconds 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue is complicated and confusing pdb=" CB FOL A1401 " pdb=" CB FOL C1401 " pdb=" CB FOL E1401 " Number of C-beta restraints generated: 6456 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 57 sheets defined 27.8% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 37 through 41 Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 209 through 214 Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.907A pdb=" N TYR A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 removed outlier: 4.208A pdb=" N ARG A 307 " --> pdb=" O GLN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 351 Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 395 through 399 removed outlier: 3.759A pdb=" N PHE A 399 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 429 through 434 removed outlier: 4.122A pdb=" N ALA A 434 " --> pdb=" O PRO A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 457 removed outlier: 5.366A pdb=" N SER A 454 " --> pdb=" O SER A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 524 through 529 removed outlier: 3.893A pdb=" N SER A 528 " --> pdb=" O PRO A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 550 Processing helix chain 'A' and resid 596 through 600 removed outlier: 3.896A pdb=" N LEU A 600 " --> pdb=" O ALA A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 628 Processing helix chain 'A' and resid 678 through 682 Processing helix chain 'A' and resid 805 through 812 Processing helix chain 'A' and resid 814 through 822 Processing helix chain 'A' and resid 823 through 825 No H-bonds generated for 'chain 'A' and resid 823 through 825' Processing helix chain 'A' and resid 826 through 854 Processing helix chain 'A' and resid 888 through 897 Processing helix chain 'A' and resid 907 through 915 removed outlier: 3.720A pdb=" N MET A 913 " --> pdb=" O TYR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 931 Processing helix chain 'A' and resid 940 through 953 Processing helix chain 'A' and resid 954 through 959 Processing helix chain 'A' and resid 971 through 982 Processing helix chain 'A' and resid 986 through 993 Processing helix chain 'A' and resid 993 through 1007 Processing helix chain 'A' and resid 1016 through 1040 removed outlier: 3.843A pdb=" N LEU A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1058 Processing helix chain 'A' and resid 1059 through 1107 removed outlier: 4.572A pdb=" N ALA A1065 " --> pdb=" O PRO A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1223 Processing helix chain 'C' and resid 37 through 41 Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 209 through 214 Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.907A pdb=" N TYR C 231 " --> pdb=" O SER C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 307 removed outlier: 4.207A pdb=" N ARG C 307 " --> pdb=" O GLN C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 351 Processing helix chain 'C' and resid 385 through 390 Processing helix chain 'C' and resid 395 through 399 removed outlier: 3.759A pdb=" N PHE C 399 " --> pdb=" O VAL C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 416 Processing helix chain 'C' and resid 429 through 434 removed outlier: 4.122A pdb=" N ALA C 434 " --> pdb=" O PRO C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 457 removed outlier: 5.366A pdb=" N SER C 454 " --> pdb=" O SER C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 524 through 529 removed outlier: 3.894A pdb=" N SER C 528 " --> pdb=" O PRO C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 550 Processing helix chain 'C' and resid 596 through 600 removed outlier: 3.896A pdb=" N LEU C 600 " --> pdb=" O ALA C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 628 Processing helix chain 'C' and resid 678 through 682 Processing helix chain 'C' and resid 805 through 812 Processing helix chain 'C' and resid 814 through 822 Processing helix chain 'C' and resid 823 through 825 No H-bonds generated for 'chain 'C' and resid 823 through 825' Processing helix chain 'C' and resid 826 through 854 Processing helix chain 'C' and resid 888 through 897 Processing helix chain 'C' and resid 907 through 915 removed outlier: 3.720A pdb=" N MET C 913 " --> pdb=" O TYR C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 926 through 931 Processing helix chain 'C' and resid 940 through 953 Processing helix chain 'C' and resid 954 through 959 Processing helix chain 'C' and resid 971 through 982 Processing helix chain 'C' and resid 986 through 993 Processing helix chain 'C' and resid 993 through 1007 Processing helix chain 'C' and resid 1016 through 1040 removed outlier: 3.843A pdb=" N LEU C1036 " --> pdb=" O ALA C1032 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU C1040 " --> pdb=" O LEU C1036 " (cutoff:3.500A) Processing helix chain 'C' and resid 1050 through 1058 Processing helix chain 'C' and resid 1059 through 1107 removed outlier: 4.572A pdb=" N ALA C1065 " --> pdb=" O PRO C1061 " (cutoff:3.500A) Processing helix chain 'C' and resid 1219 through 1223 Processing helix chain 'E' and resid 37 through 41 Processing helix chain 'E' and resid 49 through 53 Processing helix chain 'E' and resid 209 through 214 Processing helix chain 'E' and resid 222 through 231 removed outlier: 3.907A pdb=" N TYR E 231 " --> pdb=" O SER E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 307 removed outlier: 4.208A pdb=" N ARG E 307 " --> pdb=" O GLN E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 351 Processing helix chain 'E' and resid 385 through 390 Processing helix chain 'E' and resid 395 through 399 removed outlier: 3.759A pdb=" N PHE E 399 " --> pdb=" O VAL E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 411 through 416 Processing helix chain 'E' and resid 429 through 434 removed outlier: 4.123A pdb=" N ALA E 434 " --> pdb=" O PRO E 430 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 457 removed outlier: 5.366A pdb=" N SER E 454 " --> pdb=" O SER E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 468 Processing helix chain 'E' and resid 524 through 529 removed outlier: 3.893A pdb=" N SER E 528 " --> pdb=" O PRO E 525 " (cutoff:3.500A) Processing helix chain 'E' and resid 546 through 550 Processing helix chain 'E' and resid 596 through 600 removed outlier: 3.896A pdb=" N LEU E 600 " --> pdb=" O ALA E 597 " (cutoff:3.500A) Processing helix chain 'E' and resid 625 through 628 Processing helix chain 'E' and resid 678 through 682 Processing helix chain 'E' and resid 805 through 812 Processing helix chain 'E' and resid 814 through 822 Processing helix chain 'E' and resid 823 through 825 No H-bonds generated for 'chain 'E' and resid 823 through 825' Processing helix chain 'E' and resid 826 through 854 Processing helix chain 'E' and resid 888 through 897 Processing helix chain 'E' and resid 907 through 915 removed outlier: 3.720A pdb=" N MET E 913 " --> pdb=" O TYR E 909 " (cutoff:3.500A) Processing helix chain 'E' and resid 926 through 931 Processing helix chain 'E' and resid 940 through 953 Processing helix chain 'E' and resid 954 through 959 Processing helix chain 'E' and resid 971 through 982 Processing helix chain 'E' and resid 986 through 993 Processing helix chain 'E' and resid 993 through 1007 Processing helix chain 'E' and resid 1016 through 1040 removed outlier: 3.843A pdb=" N LEU E1036 " --> pdb=" O ALA E1032 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU E1040 " --> pdb=" O LEU E1036 " (cutoff:3.500A) Processing helix chain 'E' and resid 1050 through 1058 Processing helix chain 'E' and resid 1059 through 1107 removed outlier: 4.572A pdb=" N ALA E1065 " --> pdb=" O PRO E1061 " (cutoff:3.500A) Processing helix chain 'E' and resid 1219 through 1223 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 35 Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 64 removed outlier: 6.630A pdb=" N THR A 63 " --> pdb=" O TYR C 632 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL C 631 " --> pdb=" O VAL C 639 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL C 639 " --> pdb=" O LEU C 651 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 75 removed outlier: 4.185A pdb=" N ARG A 335 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.092A pdb=" N SER A 267 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N GLN A 280 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 88 through 89 removed outlier: 7.107A pdb=" N SER A 88 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR A 206 " --> pdb=" O SER A 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 92 through 93 Processing sheet with id=AA7, first strand: chain 'A' and resid 110 through 111 removed outlier: 4.564A pdb=" N ALA A 146 " --> pdb=" O ILE A 296 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU A 180 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N TYR A 241 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ALA A 182 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N PHE A 239 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N TYR A 184 " --> pdb=" O CYS A 237 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N CYS A 237 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 127 through 129 removed outlier: 3.789A pdb=" N ALA A 309 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 153 through 155 Processing sheet with id=AB1, first strand: chain 'A' and resid 359 through 366 removed outlier: 4.714A pdb=" N VAL A 659 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N SER A 365 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N VAL A 657 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY A 675 " --> pdb=" O PRO A 658 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 373 through 376 removed outlier: 4.710A pdb=" N VAL A 639 " --> pdb=" O LEU A 651 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL A 631 " --> pdb=" O VAL A 639 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 400 through 404 removed outlier: 3.603A pdb=" N SER A 440 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR A 483 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N VAL A 420 " --> pdb=" O THR A 483 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 407 through 409 Processing sheet with id=AB5, first strand: chain 'A' and resid 513 through 515 removed outlier: 5.416A pdb=" N SER A 498 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL A 561 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ILE A 500 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N SER A 559 " --> pdb=" O ILE A 500 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 717 through 724 removed outlier: 6.480A pdb=" N VAL A 718 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N SER A 761 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 9.600A pdb=" N SER A 720 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY A 732 " --> pdb=" O LEU A 735 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ALA A 737 " --> pdb=" O PRO A 730 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 768 through 769 removed outlier: 5.659A pdb=" N ILE A 768 " --> pdb=" O SER E 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1121 through 1130 removed outlier: 5.815A pdb=" N HIS A1122 " --> pdb=" O TYR A1141 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N TYR A1141 " --> pdb=" O HIS A1122 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N PHE A1172 " --> pdb=" O ALA A1152 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N GLY A1188 " --> pdb=" O ALA A1193 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ALA A1193 " --> pdb=" O GLY A1188 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1121 through 1130 removed outlier: 5.815A pdb=" N HIS A1122 " --> pdb=" O TYR A1141 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N TYR A1141 " --> pdb=" O HIS A1122 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N HIS A1146 " --> pdb=" O PRO A 783 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLU A1148 " --> pdb=" O SER A 781 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N SER A 781 " --> pdb=" O GLU A1148 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL A1150 " --> pdb=" O LYS A 779 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LYS A 779 " --> pdb=" O VAL A1150 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS A 779 " --> pdb=" O ALA E 969 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 801 through 804 removed outlier: 4.548A pdb=" N LYS A 801 " --> pdb=" O LEU A 935 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 857 through 858 Processing sheet with id=AC3, first strand: chain 'A' and resid 967 through 969 removed outlier: 3.985A pdb=" N LYS C 779 " --> pdb=" O ALA A 969 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LYS C 779 " --> pdb=" O VAL C1150 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL C1150 " --> pdb=" O LYS C 779 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N SER C 781 " --> pdb=" O GLU C1148 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLU C1148 " --> pdb=" O SER C 781 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N HIS C1146 " --> pdb=" O PRO C 783 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N TYR C1141 " --> pdb=" O HIS C1122 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N HIS C1122 " --> pdb=" O TYR C1141 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 967 through 969 removed outlier: 3.985A pdb=" N LYS C 779 " --> pdb=" O ALA A 969 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LYS C 779 " --> pdb=" O VAL C1150 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL C1150 " --> pdb=" O LYS C 779 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N SER C 781 " --> pdb=" O GLU C1148 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLU C1148 " --> pdb=" O SER C 781 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N HIS C1146 " --> pdb=" O PRO C 783 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N PHE C1172 " --> pdb=" O ALA C1152 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N GLY C1188 " --> pdb=" O ALA C1193 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ALA C1193 " --> pdb=" O GLY C1188 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1202 through 1205 removed outlier: 4.131A pdb=" N CYS A1164 " --> pdb=" O VAL A1205 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N ASN A1163 " --> pdb=" O ASP A1157 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AC7, first strand: chain 'C' and resid 63 through 64 removed outlier: 6.630A pdb=" N THR C 63 " --> pdb=" O TYR E 632 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL E 631 " --> pdb=" O VAL E 639 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 639 " --> pdb=" O LEU E 651 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 68 through 75 removed outlier: 4.185A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.092A pdb=" N SER C 267 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N GLN C 280 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 88 through 89 removed outlier: 7.107A pdb=" N SER C 88 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR C 206 " --> pdb=" O SER C 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 92 through 93 Processing sheet with id=AD3, first strand: chain 'C' and resid 110 through 111 removed outlier: 4.565A pdb=" N ALA C 146 " --> pdb=" O ILE C 296 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU C 180 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N TYR C 241 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA C 182 " --> pdb=" O PHE C 239 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N PHE C 239 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N TYR C 184 " --> pdb=" O CYS C 237 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N CYS C 237 " --> pdb=" O TYR C 184 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 127 through 129 removed outlier: 3.789A pdb=" N ALA C 309 " --> pdb=" O THR C 139 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 153 through 155 Processing sheet with id=AD6, first strand: chain 'C' and resid 359 through 366 removed outlier: 4.713A pdb=" N VAL C 659 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N SER C 365 " --> pdb=" O VAL C 657 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N VAL C 657 " --> pdb=" O SER C 365 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY C 675 " --> pdb=" O PRO C 658 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 400 through 404 removed outlier: 3.603A pdb=" N SER C 440 " --> pdb=" O GLN C 576 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR C 483 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N VAL C 420 " --> pdb=" O THR C 483 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 407 through 409 Processing sheet with id=AD9, first strand: chain 'C' and resid 513 through 515 removed outlier: 5.416A pdb=" N SER C 498 " --> pdb=" O VAL C 561 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL C 561 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ILE C 500 " --> pdb=" O SER C 559 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N SER C 559 " --> pdb=" O ILE C 500 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 717 through 724 removed outlier: 6.479A pdb=" N VAL C 718 " --> pdb=" O LEU C 759 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N SER C 761 " --> pdb=" O VAL C 718 " (cutoff:3.500A) removed outlier: 9.600A pdb=" N SER C 720 " --> pdb=" O SER C 761 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY C 732 " --> pdb=" O LEU C 735 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ALA C 737 " --> pdb=" O PRO C 730 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 801 through 804 removed outlier: 4.547A pdb=" N LYS C 801 " --> pdb=" O LEU C 935 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 857 through 858 Processing sheet with id=AE4, first strand: chain 'C' and resid 967 through 969 removed outlier: 3.984A pdb=" N LYS E 779 " --> pdb=" O ALA C 969 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LYS E 779 " --> pdb=" O VAL E1150 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL E1150 " --> pdb=" O LYS E 779 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N SER E 781 " --> pdb=" O GLU E1148 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLU E1148 " --> pdb=" O SER E 781 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N HIS E1146 " --> pdb=" O PRO E 783 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N TYR E1141 " --> pdb=" O HIS E1122 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N HIS E1122 " --> pdb=" O TYR E1141 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 967 through 969 removed outlier: 3.984A pdb=" N LYS E 779 " --> pdb=" O ALA C 969 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LYS E 779 " --> pdb=" O VAL E1150 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL E1150 " --> pdb=" O LYS E 779 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N SER E 781 " --> pdb=" O GLU E1148 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLU E1148 " --> pdb=" O SER E 781 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N HIS E1146 " --> pdb=" O PRO E 783 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N PHE E1172 " --> pdb=" O ALA E1152 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N GLY E1188 " --> pdb=" O ALA E1193 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ALA E1193 " --> pdb=" O GLY E1188 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1202 through 1205 removed outlier: 4.131A pdb=" N CYS C1164 " --> pdb=" O VAL C1205 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N ASN C1163 " --> pdb=" O ASP C1157 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 33 through 35 Processing sheet with id=AE8, first strand: chain 'E' and resid 68 through 75 removed outlier: 4.185A pdb=" N ARG E 335 " --> pdb=" O ASP E 326 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 83 through 85 removed outlier: 6.093A pdb=" N SER E 267 " --> pdb=" O GLN E 280 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N GLN E 280 " --> pdb=" O SER E 267 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 88 through 89 removed outlier: 7.107A pdb=" N SER E 88 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR E 206 " --> pdb=" O SER E 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'E' and resid 92 through 93 Processing sheet with id=AF3, first strand: chain 'E' and resid 110 through 111 removed outlier: 4.564A pdb=" N ALA E 146 " --> pdb=" O ILE E 296 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU E 180 " --> pdb=" O TYR E 241 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N TYR E 241 " --> pdb=" O LEU E 180 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA E 182 " --> pdb=" O PHE E 239 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N PHE E 239 " --> pdb=" O ALA E 182 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N TYR E 184 " --> pdb=" O CYS E 237 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N CYS E 237 " --> pdb=" O TYR E 184 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 127 through 129 removed outlier: 3.790A pdb=" N ALA E 309 " --> pdb=" O THR E 139 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 153 through 155 Processing sheet with id=AF6, first strand: chain 'E' and resid 359 through 366 removed outlier: 4.713A pdb=" N VAL E 659 " --> pdb=" O VAL E 363 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N SER E 365 " --> pdb=" O VAL E 657 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N VAL E 657 " --> pdb=" O SER E 365 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY E 675 " --> pdb=" O PRO E 658 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 400 through 404 removed outlier: 3.604A pdb=" N SER E 440 " --> pdb=" O GLN E 576 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR E 483 " --> pdb=" O VAL E 420 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL E 420 " --> pdb=" O THR E 483 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 407 through 409 Processing sheet with id=AF9, first strand: chain 'E' and resid 513 through 515 removed outlier: 5.416A pdb=" N SER E 498 " --> pdb=" O VAL E 561 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL E 561 " --> pdb=" O SER E 498 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ILE E 500 " --> pdb=" O SER E 559 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N SER E 559 " --> pdb=" O ILE E 500 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 717 through 724 removed outlier: 6.481A pdb=" N VAL E 718 " --> pdb=" O LEU E 759 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N SER E 761 " --> pdb=" O VAL E 718 " (cutoff:3.500A) removed outlier: 9.600A pdb=" N SER E 720 " --> pdb=" O SER E 761 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY E 732 " --> pdb=" O LEU E 735 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ALA E 737 " --> pdb=" O PRO E 730 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 801 through 804 removed outlier: 4.547A pdb=" N LYS E 801 " --> pdb=" O LEU E 935 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 1202 through 1205 removed outlier: 4.131A pdb=" N CYS E1164 " --> pdb=" O VAL E1205 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ASN E1163 " --> pdb=" O ASP E1157 " (cutoff:3.500A) 1182 hydrogen bonds defined for protein. 3111 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: 7.87 Time building geometry restraints manager: 3.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4691 1.30 - 1.44: 8240 1.44 - 1.57: 16009 1.57 - 1.71: 70 1.71 - 1.84: 192 Bond restraints: 29202 Sorted by residual: bond pdb=" C GLN C1097 " pdb=" O GLN C1097 " ideal model delta sigma weight residual 1.237 1.174 0.063 1.17e-02 7.31e+03 2.90e+01 bond pdb=" C GLN A1097 " pdb=" O GLN A1097 " ideal model delta sigma weight residual 1.237 1.174 0.063 1.17e-02 7.31e+03 2.90e+01 bond pdb=" C GLN E1097 " pdb=" O GLN E1097 " ideal model delta sigma weight residual 1.237 1.174 0.063 1.17e-02 7.31e+03 2.89e+01 bond pdb=" C SER E1095 " pdb=" O SER E1095 " ideal model delta sigma weight residual 1.236 1.170 0.066 1.26e-02 6.30e+03 2.73e+01 bond pdb=" C SER A1095 " pdb=" O SER A1095 " ideal model delta sigma weight residual 1.236 1.171 0.066 1.26e-02 6.30e+03 2.73e+01 ... (remaining 29197 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.21: 39015 4.21 - 8.42: 726 8.42 - 12.63: 15 12.63 - 16.84: 3 16.84 - 21.05: 3 Bond angle restraints: 39762 Sorted by residual: angle pdb=" N TRP E 960 " pdb=" CA TRP E 960 " pdb=" C TRP E 960 " ideal model delta sigma weight residual 111.14 132.19 -21.05 1.08e+00 8.57e-01 3.80e+02 angle pdb=" N TRP A 960 " pdb=" CA TRP A 960 " pdb=" C TRP A 960 " ideal model delta sigma weight residual 111.14 132.14 -21.00 1.08e+00 8.57e-01 3.78e+02 angle pdb=" N TRP C 960 " pdb=" CA TRP C 960 " pdb=" C TRP C 960 " ideal model delta sigma weight residual 111.14 132.12 -20.98 1.08e+00 8.57e-01 3.78e+02 angle pdb=" N TRP E 960 " pdb=" CA TRP E 960 " pdb=" CB TRP E 960 " ideal model delta sigma weight residual 110.07 95.92 14.15 1.45e+00 4.76e-01 9.52e+01 angle pdb=" N TRP A 960 " pdb=" CA TRP A 960 " pdb=" CB TRP A 960 " ideal model delta sigma weight residual 110.07 95.94 14.13 1.45e+00 4.76e-01 9.49e+01 ... (remaining 39757 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.84: 18444 26.84 - 53.67: 327 53.67 - 80.51: 132 80.51 - 107.35: 153 107.35 - 134.18: 18 Dihedral angle restraints: 19074 sinusoidal: 8958 harmonic: 10116 Sorted by residual: dihedral pdb=" N FOL C1401 " pdb=" C FOL C1401 " pdb=" C11 FOL C1401 " pdb=" C16 FOL C1401 " ideal model delta sinusoidal sigma weight residual -0.09 -134.27 134.18 1 2.00e+01 2.50e-03 4.07e+01 dihedral pdb=" N FOL A1401 " pdb=" C FOL A1401 " pdb=" C11 FOL A1401 " pdb=" C16 FOL A1401 " ideal model delta sinusoidal sigma weight residual -0.09 -134.22 134.13 1 2.00e+01 2.50e-03 4.07e+01 dihedral pdb=" N FOL E1401 " pdb=" C FOL E1401 " pdb=" C11 FOL E1401 " pdb=" C16 FOL E1401 " ideal model delta sinusoidal sigma weight residual -0.09 -134.18 134.09 1 2.00e+01 2.50e-03 4.07e+01 ... (remaining 19071 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 3281 0.086 - 0.173: 1081 0.173 - 0.259: 284 0.259 - 0.346: 134 0.346 - 0.432: 68 Chirality restraints: 4848 Sorted by residual: chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 4.62e+01 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 4.59e+01 chirality pdb=" C1 NAG g 2 " pdb=" O4 NAG g 1 " pdb=" C2 NAG g 2 " pdb=" O5 NAG g 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 4.58e+01 ... (remaining 4845 not shown) Planarity restraints: 4995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 166 " 0.067 2.00e-02 2.50e+03 6.82e-02 5.81e+01 pdb=" CG ASN E 166 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN E 166 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN E 166 " -0.103 2.00e-02 2.50e+03 pdb=" C1 NAG f 1 " 0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 166 " -0.067 2.00e-02 2.50e+03 6.81e-02 5.80e+01 pdb=" CG ASN A 166 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN A 166 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN A 166 " 0.103 2.00e-02 2.50e+03 pdb=" C1 NAG L 1 " -0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 166 " -0.067 2.00e-02 2.50e+03 6.80e-02 5.77e+01 pdb=" CG ASN C 166 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN C 166 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN C 166 " 0.102 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " -0.082 2.00e-02 2.50e+03 ... (remaining 4992 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 12880 2.93 - 3.42: 26224 3.42 - 3.91: 50843 3.91 - 4.41: 59031 4.41 - 4.90: 93363 Nonbonded interactions: 242341 Sorted by model distance: nonbonded pdb=" N ASP E 343 " pdb=" OD1 ASP E 343 " model vdw 2.433 3.120 nonbonded pdb=" N ASP A 343 " pdb=" OD1 ASP A 343 " model vdw 2.433 3.120 nonbonded pdb=" N ASP C 343 " pdb=" OD1 ASP C 343 " model vdw 2.434 3.120 nonbonded pdb=" OH TYR C 219 " pdb=" OE2 GLU C 247 " model vdw 2.490 3.040 nonbonded pdb=" OH TYR A 219 " pdb=" OE2 GLU A 247 " model vdw 2.490 3.040 ... (remaining 242336 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'H' selection = chain 'N' selection = chain 'R' selection = chain 'X' selection = chain 'b' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'O' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'Y' selection = chain 'c' selection = chain 'd' selection = chain 'g' } ncs_group { reference = chain 'F' selection = chain 'P' selection = chain 'Z' } ncs_group { reference = chain 'G' selection = chain 'Q' selection = chain 'a' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'U' selection = chain 'V' 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=1.00 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: 6.350 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 29.460 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.110 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:9.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 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 : 0.019 0.160 29382 Z= 1.006 Angle : 1.506 21.048 40251 Z= 0.969 Chirality : 0.109 0.432 4848 Planarity : 0.006 0.027 4944 Dihedral : 15.699 134.184 12465 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.83 % Favored : 98.09 % Rotamer: Outliers : 0.20 % Allowed : 0.81 % Favored : 98.98 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.13), residues: 3447 helix: -0.23 (0.17), residues: 702 sheet: 0.82 (0.18), residues: 750 loop : 0.62 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 334 TYR 0.050 0.006 TYR C 184 PHE 0.024 0.004 PHE A 473 TRP 0.016 0.004 TRP C1184 HIS 0.005 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.01816 (29202) covalent geometry : angle 1.46606 (39762) SS BOND : bond 0.07676 ( 51) SS BOND : angle 3.91319 ( 102) hydrogen bonds : bond 0.16508 ( 1144) hydrogen bonds : angle 7.75467 ( 3111) link_ALPHA1-2 : bond 0.06737 ( 6) link_ALPHA1-2 : angle 3.44573 ( 18) link_ALPHA1-3 : bond 0.07228 ( 15) link_ALPHA1-3 : angle 3.30445 ( 45) link_ALPHA1-6 : bond 0.05240 ( 9) link_ALPHA1-6 : angle 2.57418 ( 27) link_BETA1-4 : bond 0.06520 ( 48) link_BETA1-4 : angle 4.10400 ( 144) link_NAG-ASN : bond 0.06155 ( 51) link_NAG-ASN : angle 2.50696 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 445 time to evaluate : 0.963 Fit side-chains REVERT: A 71 TYR cc_start: 0.8475 (t80) cc_final: 0.8070 (t80) REVERT: C 161 MET cc_start: 0.6815 (mmm) cc_final: 0.6390 (mmm) REVERT: E 452 MET cc_start: 0.8852 (mtp) cc_final: 0.8592 (mtp) outliers start: 6 outliers final: 2 residues processed: 450 average time/residue: 0.6674 time to fit residues: 349.9096 Evaluate side-chains 252 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 250 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain C residue 199 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.1980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 HIS A 280 GLN A 521 ASN A1009 GLN A1169 ASN C 167 HIS C 280 GLN C 466 GLN C 521 ASN ** C 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 765 ASN C 812 ASN E 167 HIS E 280 GLN E 521 ASN E1009 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.128508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.094637 restraints weight = 31403.215| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.47 r_work: 0.2892 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 29382 Z= 0.190 Angle : 0.756 17.648 40251 Z= 0.373 Chirality : 0.050 0.347 4848 Planarity : 0.004 0.041 4944 Dihedral : 13.337 120.290 6511 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.83 % Allowed : 6.54 % Favored : 91.62 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.14), residues: 3447 helix: 0.86 (0.20), residues: 705 sheet: 0.60 (0.17), residues: 786 loop : 0.41 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1069 TYR 0.015 0.001 TYR E 909 PHE 0.015 0.002 PHE E 239 TRP 0.015 0.001 TRP A 960 HIS 0.007 0.001 HIS C 348 Details of bonding type rmsd covalent geometry : bond 0.00419 (29202) covalent geometry : angle 0.69834 (39762) SS BOND : bond 0.00804 ( 51) SS BOND : angle 1.97470 ( 102) hydrogen bonds : bond 0.05289 ( 1144) hydrogen bonds : angle 6.21981 ( 3111) link_ALPHA1-2 : bond 0.00491 ( 6) link_ALPHA1-2 : angle 1.76777 ( 18) link_ALPHA1-3 : bond 0.01121 ( 15) link_ALPHA1-3 : angle 2.22301 ( 45) link_ALPHA1-6 : bond 0.00842 ( 9) link_ALPHA1-6 : angle 1.91559 ( 27) link_BETA1-4 : bond 0.01195 ( 48) link_BETA1-4 : angle 3.19164 ( 144) link_NAG-ASN : bond 0.00917 ( 51) link_NAG-ASN : angle 2.98370 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 324 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: A 32 GLU cc_start: 0.8294 (tt0) cc_final: 0.7829 (tt0) REVERT: A 38 THR cc_start: 0.8048 (m) cc_final: 0.7770 (p) REVERT: A 49 ASP cc_start: 0.8155 (t0) cc_final: 0.7736 (t0) REVERT: A 50 VAL cc_start: 0.8261 (t) cc_final: 0.7956 (p) REVERT: A 56 ILE cc_start: 0.8616 (mt) cc_final: 0.8337 (mm) REVERT: A 71 TYR cc_start: 0.8563 (t80) cc_final: 0.7782 (t80) REVERT: A 261 GLN cc_start: 0.8600 (mt0) cc_final: 0.8235 (mt0) REVERT: A 306 ASP cc_start: 0.7559 (t0) cc_final: 0.6823 (t0) REVERT: A 352 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8268 (mt-10) REVERT: A 488 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7324 (tt) REVERT: A 740 ASP cc_start: 0.7343 (t0) cc_final: 0.6654 (m-30) REVERT: A 777 TYR cc_start: 0.8411 (m-80) cc_final: 0.8106 (m-80) REVERT: A 812 ASN cc_start: 0.8324 (t0) cc_final: 0.8095 (t160) REVERT: A 949 SER cc_start: 0.7980 (t) cc_final: 0.7777 (p) REVERT: A 994 GLN cc_start: 0.7493 (mt0) cc_final: 0.7263 (mt0) REVERT: A 1031 GLN cc_start: 0.7300 (mt0) cc_final: 0.6838 (tt0) REVERT: A 1068 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.8074 (t70) REVERT: A 1169 ASN cc_start: 0.8437 (m-40) cc_final: 0.7920 (t0) REVERT: C 32 GLU cc_start: 0.8291 (tt0) cc_final: 0.7862 (tt0) REVERT: C 38 THR cc_start: 0.8091 (m) cc_final: 0.7780 (p) REVERT: C 49 ASP cc_start: 0.8201 (t0) cc_final: 0.7677 (t70) REVERT: C 251 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8263 (tp) REVERT: C 815 GLN cc_start: 0.7266 (tm-30) cc_final: 0.6610 (mm110) REVERT: C 914 GLN cc_start: 0.7033 (OUTLIER) cc_final: 0.6784 (mp10) REVERT: C 987 GLN cc_start: 0.7172 (tp40) cc_final: 0.6926 (mm-40) REVERT: C 1031 GLN cc_start: 0.7354 (mt0) cc_final: 0.7017 (tt0) REVERT: C 1105 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7566 (tm-30) REVERT: C 1148 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8237 (mt-10) REVERT: E 32 GLU cc_start: 0.7896 (tt0) cc_final: 0.7441 (tt0) REVERT: E 452 MET cc_start: 0.8626 (mtp) cc_final: 0.8398 (mtp) REVERT: E 486 HIS cc_start: 0.8030 (m-70) cc_final: 0.7790 (m-70) REVERT: E 536 GLU cc_start: 0.7694 (mt-10) cc_final: 0.6862 (mm-30) REVERT: E 565 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7682 (tm-30) REVERT: E 722 LEU cc_start: 0.6671 (tt) cc_final: 0.6461 (tt) REVERT: E 815 GLN cc_start: 0.7340 (tm-30) cc_final: 0.6796 (mm110) REVERT: E 830 LYS cc_start: 0.7986 (mmtm) cc_final: 0.7237 (mtpm) REVERT: E 914 GLN cc_start: 0.6755 (mt0) cc_final: 0.6551 (mp10) REVERT: E 994 GLN cc_start: 0.7664 (mt0) cc_final: 0.7320 (mt0) REVERT: E 1039 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7990 (mm-30) REVERT: E 1069 ARG cc_start: 0.8175 (mtt-85) cc_final: 0.7894 (mtp180) REVERT: E 1105 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.6976 (tm-30) outliers start: 54 outliers final: 12 residues processed: 353 average time/residue: 0.6453 time to fit residues: 266.3073 Evaluate side-chains 277 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 258 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 1009 GLN Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 914 GLN Chi-restraints excluded: chain C residue 943 MET Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 1105 GLU Chi-restraints excluded: chain C residue 1148 GLU Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 943 MET Chi-restraints excluded: chain E residue 1105 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 103 optimal weight: 0.7980 chunk 298 optimal weight: 0.0270 chunk 289 optimal weight: 6.9990 chunk 154 optimal weight: 0.8980 chunk 150 optimal weight: 0.9990 chunk 267 optimal weight: 0.9990 chunk 317 optimal weight: 0.8980 chunk 342 optimal weight: 0.8980 chunk 222 optimal weight: 1.9990 chunk 173 optimal weight: 0.6980 chunk 255 optimal weight: 4.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 HIS A 466 GLN A 842 GLN A 848 ASN A1020 GLN A1097 GLN C 167 HIS C 681 HIS C 994 GLN C1020 GLN ** E 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 987 GLN E1009 GLN E1020 GLN E1084 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.128303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.094357 restraints weight = 31528.928| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.47 r_work: 0.2889 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 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 : 0.004 0.089 29382 Z= 0.159 Angle : 0.690 18.368 40251 Z= 0.332 Chirality : 0.048 0.604 4848 Planarity : 0.004 0.039 4944 Dihedral : 11.079 102.122 6507 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.87 % Allowed : 8.71 % Favored : 89.42 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.14), residues: 3447 helix: 1.09 (0.20), residues: 705 sheet: 0.35 (0.17), residues: 909 loop : 0.22 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1069 TYR 0.017 0.001 TYR A 184 PHE 0.014 0.001 PHE A 239 TRP 0.007 0.001 TRP A 310 HIS 0.003 0.001 HIS C 167 Details of bonding type rmsd covalent geometry : bond 0.00353 (29202) covalent geometry : angle 0.62211 (39762) SS BOND : bond 0.00828 ( 51) SS BOND : angle 2.17090 ( 102) hydrogen bonds : bond 0.04622 ( 1144) hydrogen bonds : angle 5.84346 ( 3111) link_ALPHA1-2 : bond 0.00428 ( 6) link_ALPHA1-2 : angle 1.66099 ( 18) link_ALPHA1-3 : bond 0.01166 ( 15) link_ALPHA1-3 : angle 1.45784 ( 45) link_ALPHA1-6 : bond 0.00981 ( 9) link_ALPHA1-6 : angle 1.84073 ( 27) link_BETA1-4 : bond 0.01036 ( 48) link_BETA1-4 : angle 2.64115 ( 144) link_NAG-ASN : bond 0.01008 ( 51) link_NAG-ASN : angle 3.67785 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 289 time to evaluate : 1.087 Fit side-chains revert: symmetry clash REVERT: A 38 THR cc_start: 0.8044 (m) cc_final: 0.7818 (p) REVERT: A 49 ASP cc_start: 0.8264 (t0) cc_final: 0.7817 (t0) REVERT: A 50 VAL cc_start: 0.8412 (t) cc_final: 0.8110 (p) REVERT: A 56 ILE cc_start: 0.8643 (mt) cc_final: 0.8381 (mm) REVERT: A 71 TYR cc_start: 0.8560 (t80) cc_final: 0.7824 (t80) REVERT: A 161 MET cc_start: 0.7636 (mmt) cc_final: 0.7296 (tpt) REVERT: A 306 ASP cc_start: 0.7660 (t0) cc_final: 0.6854 (t0) REVERT: A 352 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8277 (mt-10) REVERT: A 473 PHE cc_start: 0.7503 (m-80) cc_final: 0.7177 (m-80) REVERT: A 740 ASP cc_start: 0.7511 (t0) cc_final: 0.6669 (m-30) REVERT: A 777 TYR cc_start: 0.8409 (m-80) cc_final: 0.8088 (m-80) REVERT: A 812 ASN cc_start: 0.8369 (t0) cc_final: 0.8058 (t160) REVERT: A 842 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.6597 (mp-120) REVERT: A 994 GLN cc_start: 0.7564 (mt0) cc_final: 0.7323 (mt0) REVERT: A 1009 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7813 (tt0) REVERT: A 1031 GLN cc_start: 0.7306 (mt0) cc_final: 0.6875 (tt0) REVERT: A 1151 SER cc_start: 0.9271 (m) cc_final: 0.9064 (t) REVERT: A 1169 ASN cc_start: 0.8491 (m-40) cc_final: 0.7968 (t0) REVERT: C 32 GLU cc_start: 0.8354 (tt0) cc_final: 0.7955 (tt0) REVERT: C 38 THR cc_start: 0.8052 (m) cc_final: 0.7788 (p) REVERT: C 49 ASP cc_start: 0.8370 (t0) cc_final: 0.7850 (t70) REVERT: C 200 SER cc_start: 0.8544 (m) cc_final: 0.8257 (p) REVERT: C 251 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8312 (tp) REVERT: C 565 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8190 (tm-30) REVERT: C 588 LEU cc_start: 0.7903 (tp) cc_final: 0.7694 (tp) REVERT: C 647 ASN cc_start: 0.8392 (m-40) cc_final: 0.8055 (m-40) REVERT: C 725 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: C 812 ASN cc_start: 0.8326 (t0) cc_final: 0.7934 (t160) REVERT: C 815 GLN cc_start: 0.7277 (tm-30) cc_final: 0.6709 (mm110) REVERT: C 943 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7821 (ttm) REVERT: C 987 GLN cc_start: 0.7101 (tp40) cc_final: 0.6873 (mm-40) REVERT: C 1010 THR cc_start: 0.8204 (p) cc_final: 0.7720 (t) REVERT: C 1031 GLN cc_start: 0.7331 (mt0) cc_final: 0.6998 (tt0) REVERT: C 1039 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7788 (mm-30) REVERT: C 1148 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8215 (mt-10) REVERT: E 536 GLU cc_start: 0.7702 (mt-10) cc_final: 0.6988 (mm-30) REVERT: E 565 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7756 (tm-30) REVERT: E 595 LYS cc_start: 0.7690 (mtpp) cc_final: 0.7452 (mtpp) REVERT: E 812 ASN cc_start: 0.8384 (t0) cc_final: 0.8042 (t160) REVERT: E 815 GLN cc_start: 0.7350 (tm-30) cc_final: 0.6856 (mm110) REVERT: E 914 GLN cc_start: 0.6919 (mt0) cc_final: 0.6710 (mp10) REVERT: E 994 GLN cc_start: 0.7677 (mt0) cc_final: 0.7450 (mt0) REVERT: E 1039 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8097 (mm-30) REVERT: E 1069 ARG cc_start: 0.8233 (mtt-85) cc_final: 0.7876 (mtp85) REVERT: E 1105 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.6897 (tm-30) outliers start: 55 outliers final: 19 residues processed: 319 average time/residue: 0.6172 time to fit residues: 232.2160 Evaluate side-chains 291 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 265 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 842 GLN Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 1009 GLN Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 943 MET Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 1148 GLU Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain E residue 943 MET Chi-restraints excluded: chain E residue 1062 GLU Chi-restraints excluded: chain E residue 1105 GLU Chi-restraints excluded: chain E residue 1112 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 84 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 193 optimal weight: 4.9990 chunk 270 optimal weight: 1.9990 chunk 246 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 GLN A 848 ASN A1132 ASN C 36 GLN ** C 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 HIS E 987 GLN E1009 GLN E1132 ASN E1169 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.122736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.089968 restraints weight = 31954.839| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.35 r_work: 0.2825 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 29382 Z= 0.327 Angle : 0.801 18.640 40251 Z= 0.389 Chirality : 0.053 0.510 4848 Planarity : 0.005 0.040 4944 Dihedral : 9.399 83.579 6507 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.61 % Allowed : 9.02 % Favored : 88.37 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.28 (0.14), residues: 3447 helix: 0.75 (0.20), residues: 705 sheet: 0.44 (0.17), residues: 858 loop : -0.06 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 841 TYR 0.018 0.002 TYR E 184 PHE 0.022 0.002 PHE A 850 TRP 0.011 0.002 TRP A 310 HIS 0.006 0.002 HIS C1138 Details of bonding type rmsd covalent geometry : bond 0.00782 (29202) covalent geometry : angle 0.73696 (39762) SS BOND : bond 0.01079 ( 51) SS BOND : angle 2.64965 ( 102) hydrogen bonds : bond 0.05512 ( 1144) hydrogen bonds : angle 5.95243 ( 3111) link_ALPHA1-2 : bond 0.00207 ( 6) link_ALPHA1-2 : angle 1.68298 ( 18) link_ALPHA1-3 : bond 0.01092 ( 15) link_ALPHA1-3 : angle 1.76628 ( 45) link_ALPHA1-6 : bond 0.01027 ( 9) link_ALPHA1-6 : angle 1.31433 ( 27) link_BETA1-4 : bond 0.00925 ( 48) link_BETA1-4 : angle 2.67970 ( 144) link_NAG-ASN : bond 0.01005 ( 51) link_NAG-ASN : angle 3.83268 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 253 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8524 (t0) cc_final: 0.8139 (t0) REVERT: A 50 VAL cc_start: 0.8524 (t) cc_final: 0.8207 (p) REVERT: A 71 TYR cc_start: 0.8781 (t80) cc_final: 0.8083 (t80) REVERT: A 306 ASP cc_start: 0.8098 (t0) cc_final: 0.7730 (t0) REVERT: A 488 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7647 (tt) REVERT: A 565 GLU cc_start: 0.8209 (tm-30) cc_final: 0.8001 (tm-30) REVERT: A 777 TYR cc_start: 0.8844 (m-80) cc_final: 0.8569 (m-80) REVERT: A 842 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7173 (mp10) REVERT: A 914 GLN cc_start: 0.7004 (OUTLIER) cc_final: 0.6607 (mt0) REVERT: A 1010 THR cc_start: 0.8431 (p) cc_final: 0.7941 (t) REVERT: A 1031 GLN cc_start: 0.7722 (mt0) cc_final: 0.7282 (tt0) REVERT: A 1105 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7967 (tm-30) REVERT: A 1169 ASN cc_start: 0.8576 (m-40) cc_final: 0.8128 (t0) REVERT: C 49 ASP cc_start: 0.8573 (t0) cc_final: 0.8153 (t70) REVERT: C 141 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7528 (mtm110) REVERT: C 291 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8617 (mtpt) REVERT: C 422 ASP cc_start: 0.7387 (t70) cc_final: 0.6839 (m-30) REVERT: C 812 ASN cc_start: 0.8647 (t0) cc_final: 0.8261 (t160) REVERT: C 1031 GLN cc_start: 0.7816 (mt0) cc_final: 0.7492 (tt0) REVERT: C 1039 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8207 (mm-30) REVERT: C 1105 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8055 (tm-30) REVERT: E 261 GLN cc_start: 0.8876 (mt0) cc_final: 0.8672 (mt0) REVERT: E 355 ASP cc_start: 0.7263 (OUTLIER) cc_final: 0.7010 (m-30) REVERT: E 536 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7215 (mm-30) REVERT: E 565 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7859 (tm-30) REVERT: E 815 GLN cc_start: 0.7736 (tm-30) cc_final: 0.7330 (mm110) REVERT: E 841 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.6559 (mpp-170) REVERT: E 914 GLN cc_start: 0.7137 (mt0) cc_final: 0.6904 (mp10) REVERT: E 1039 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8352 (mm-30) REVERT: E 1069 ARG cc_start: 0.8506 (mtt-85) cc_final: 0.8147 (mtp85) REVERT: E 1105 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7230 (tm-30) outliers start: 77 outliers final: 33 residues processed: 307 average time/residue: 0.6244 time to fit residues: 225.9498 Evaluate side-chains 279 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 236 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 842 GLN Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 914 GLN Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 1105 GLU Chi-restraints excluded: chain A residue 1131 PRO Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 291 LYS Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 400 LYS Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 853 VAL Chi-restraints excluded: chain C residue 943 MET Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 1105 GLU Chi-restraints excluded: chain C residue 1131 PRO Chi-restraints excluded: chain C residue 1151 SER Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 355 ASP Chi-restraints excluded: chain E residue 386 SER Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 841 ARG Chi-restraints excluded: chain E residue 853 VAL Chi-restraints excluded: chain E residue 899 THR Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain E residue 943 MET Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 1105 GLU Chi-restraints excluded: chain E residue 1112 LYS Chi-restraints excluded: chain E residue 1131 PRO Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 144 optimal weight: 1.9990 chunk 307 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 294 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 321 optimal weight: 0.9990 chunk 210 optimal weight: 0.4980 chunk 256 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 GLN A 842 GLN A 848 ASN A1009 GLN ** C 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1009 GLN E1031 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.125637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.093698 restraints weight = 31847.407| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.32 r_work: 0.2945 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 29382 Z= 0.157 Angle : 0.681 24.958 40251 Z= 0.327 Chirality : 0.047 0.495 4848 Planarity : 0.004 0.037 4944 Dihedral : 8.005 71.379 6507 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.31 % Allowed : 9.83 % Favored : 87.86 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.31 (0.14), residues: 3447 helix: 1.01 (0.20), residues: 711 sheet: 0.27 (0.17), residues: 873 loop : -0.04 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1069 TYR 0.016 0.001 TYR A 184 PHE 0.015 0.001 PHE A 239 TRP 0.007 0.001 TRP A 310 HIS 0.003 0.001 HIS A 681 Details of bonding type rmsd covalent geometry : bond 0.00352 (29202) covalent geometry : angle 0.61548 (39762) SS BOND : bond 0.00720 ( 51) SS BOND : angle 2.41753 ( 102) hydrogen bonds : bond 0.04422 ( 1144) hydrogen bonds : angle 5.67188 ( 3111) link_ALPHA1-2 : bond 0.00276 ( 6) link_ALPHA1-2 : angle 1.64908 ( 18) link_ALPHA1-3 : bond 0.01095 ( 15) link_ALPHA1-3 : angle 1.56943 ( 45) link_ALPHA1-6 : bond 0.01011 ( 9) link_ALPHA1-6 : angle 1.29574 ( 27) link_BETA1-4 : bond 0.00878 ( 48) link_BETA1-4 : angle 2.40221 ( 144) link_NAG-ASN : bond 0.00851 ( 51) link_NAG-ASN : angle 3.56674 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 249 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8439 (t0) cc_final: 0.8027 (t0) REVERT: A 50 VAL cc_start: 0.8595 (t) cc_final: 0.8264 (p) REVERT: A 71 TYR cc_start: 0.8706 (t80) cc_final: 0.8076 (t80) REVERT: A 306 ASP cc_start: 0.7996 (t0) cc_final: 0.7626 (t0) REVERT: A 488 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7552 (tt) REVERT: A 652 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.6503 (mmt180) REVERT: A 777 TYR cc_start: 0.8745 (m-80) cc_final: 0.8421 (m-80) REVERT: A 842 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.6365 (mp-120) REVERT: A 914 GLN cc_start: 0.6916 (OUTLIER) cc_final: 0.6489 (mt0) REVERT: A 1031 GLN cc_start: 0.7594 (mt0) cc_final: 0.7180 (tt0) REVERT: A 1105 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7796 (tm-30) REVERT: A 1169 ASN cc_start: 0.8565 (m-40) cc_final: 0.8094 (t0) REVERT: C 38 THR cc_start: 0.8204 (m) cc_final: 0.7957 (p) REVERT: C 49 ASP cc_start: 0.8577 (t0) cc_final: 0.8097 (t70) REVERT: C 251 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8579 (tp) REVERT: C 422 ASP cc_start: 0.7475 (t70) cc_final: 0.6935 (m-30) REVERT: C 536 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7149 (mm-30) REVERT: C 812 ASN cc_start: 0.8606 (t0) cc_final: 0.8186 (t160) REVERT: C 1031 GLN cc_start: 0.7535 (mt0) cc_final: 0.7224 (tt0) REVERT: C 1039 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8069 (mm-30) REVERT: E 355 ASP cc_start: 0.7166 (OUTLIER) cc_final: 0.6890 (m-30) REVERT: E 536 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7211 (mm-30) REVERT: E 565 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7697 (tm-30) REVERT: E 815 GLN cc_start: 0.7615 (tm-30) cc_final: 0.7171 (mm110) REVERT: E 841 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7389 (mtm180) REVERT: E 914 GLN cc_start: 0.7090 (mt0) cc_final: 0.6866 (mp10) REVERT: E 1039 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8272 (mm-30) REVERT: E 1069 ARG cc_start: 0.8369 (mtt-85) cc_final: 0.8058 (mtp85) REVERT: E 1105 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.6958 (tm-30) outliers start: 68 outliers final: 30 residues processed: 294 average time/residue: 0.6488 time to fit residues: 224.5282 Evaluate side-chains 269 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 230 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 842 GLN Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 914 GLN Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 1105 GLU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 943 MET Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 1062 GLU Chi-restraints excluded: chain C residue 1068 ASP Chi-restraints excluded: chain C residue 1151 SER Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 355 ASP Chi-restraints excluded: chain E residue 386 SER Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 661 VAL Chi-restraints excluded: chain E residue 841 ARG Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain E residue 943 MET Chi-restraints excluded: chain E residue 964 LEU Chi-restraints excluded: chain E residue 1062 GLU Chi-restraints excluded: chain E residue 1105 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 317 optimal weight: 0.4980 chunk 232 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 150 optimal weight: 0.0030 chunk 250 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 chunk 216 optimal weight: 1.9990 chunk 209 optimal weight: 3.9990 overall best weight: 1.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 848 ASN C 427 GLN ** C 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 GLN C1132 ASN E 421 ASN E 647 ASN E1009 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.123557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.090943 restraints weight = 32014.996| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.35 r_work: 0.2911 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 29382 Z= 0.252 Angle : 0.740 26.824 40251 Z= 0.356 Chirality : 0.049 0.461 4848 Planarity : 0.004 0.050 4944 Dihedral : 7.803 60.446 6507 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.31 % Allowed : 10.21 % Favored : 87.49 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.14), residues: 3447 helix: 0.96 (0.20), residues: 705 sheet: 0.24 (0.17), residues: 873 loop : -0.16 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1069 TYR 0.018 0.002 TYR E 184 PHE 0.020 0.002 PHE A 239 TRP 0.008 0.001 TRP A 310 HIS 0.004 0.001 HIS C1138 Details of bonding type rmsd covalent geometry : bond 0.00594 (29202) covalent geometry : angle 0.67501 (39762) SS BOND : bond 0.01087 ( 51) SS BOND : angle 2.80642 ( 102) hydrogen bonds : bond 0.04921 ( 1144) hydrogen bonds : angle 5.73173 ( 3111) link_ALPHA1-2 : bond 0.00230 ( 6) link_ALPHA1-2 : angle 1.61672 ( 18) link_ALPHA1-3 : bond 0.01004 ( 15) link_ALPHA1-3 : angle 1.64591 ( 45) link_ALPHA1-6 : bond 0.00980 ( 9) link_ALPHA1-6 : angle 1.28350 ( 27) link_BETA1-4 : bond 0.00833 ( 48) link_BETA1-4 : angle 2.40282 ( 144) link_NAG-ASN : bond 0.00884 ( 51) link_NAG-ASN : angle 3.69694 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 226 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8448 (t0) cc_final: 0.8027 (t0) REVERT: A 50 VAL cc_start: 0.8475 (t) cc_final: 0.8146 (p) REVERT: A 71 TYR cc_start: 0.8812 (t80) cc_final: 0.8094 (t80) REVERT: A 306 ASP cc_start: 0.8107 (t0) cc_final: 0.7777 (t0) REVERT: A 488 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7648 (tt) REVERT: A 777 TYR cc_start: 0.8791 (m-80) cc_final: 0.8511 (m-80) REVERT: A 914 GLN cc_start: 0.7023 (OUTLIER) cc_final: 0.6603 (mt0) REVERT: A 1031 GLN cc_start: 0.7618 (mt0) cc_final: 0.7197 (tt0) REVERT: A 1105 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7813 (tm-30) REVERT: A 1169 ASN cc_start: 0.8557 (m-40) cc_final: 0.8087 (t0) REVERT: C 49 ASP cc_start: 0.8607 (t0) cc_final: 0.8126 (t0) REVERT: C 251 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8524 (tp) REVERT: C 291 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8558 (mtpt) REVERT: C 422 ASP cc_start: 0.7446 (t70) cc_final: 0.6892 (m-30) REVERT: C 536 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7171 (mm-30) REVERT: C 587 LYS cc_start: 0.8317 (tptt) cc_final: 0.7056 (ttmm) REVERT: C 725 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7207 (mp0) REVERT: C 812 ASN cc_start: 0.8610 (t0) cc_final: 0.8194 (t160) REVERT: C 1031 GLN cc_start: 0.7689 (mt0) cc_final: 0.7365 (tt0) REVERT: C 1039 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8095 (mm-30) REVERT: E 355 ASP cc_start: 0.7162 (OUTLIER) cc_final: 0.6887 (m-30) REVERT: E 536 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7213 (mm-30) REVERT: E 565 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7806 (tm-30) REVERT: E 815 GLN cc_start: 0.7662 (tm-30) cc_final: 0.7213 (mm110) REVERT: E 841 ARG cc_start: 0.7540 (OUTLIER) cc_final: 0.7236 (mtm180) REVERT: E 844 ASP cc_start: 0.7674 (m-30) cc_final: 0.7254 (m-30) REVERT: E 914 GLN cc_start: 0.7160 (mt0) cc_final: 0.6919 (mp10) REVERT: E 1039 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8161 (mm-30) REVERT: E 1069 ARG cc_start: 0.8386 (mtt-85) cc_final: 0.8057 (mtp85) REVERT: E 1105 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7107 (tm-30) outliers start: 68 outliers final: 35 residues processed: 273 average time/residue: 0.6485 time to fit residues: 207.4409 Evaluate side-chains 266 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 222 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 665 LYS Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 914 GLN Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 1105 GLU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 291 LYS Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 400 LYS Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 943 MET Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 1062 GLU Chi-restraints excluded: chain C residue 1151 SER Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 319 GLN Chi-restraints excluded: chain E residue 355 ASP Chi-restraints excluded: chain E residue 386 SER Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 661 VAL Chi-restraints excluded: chain E residue 841 ARG Chi-restraints excluded: chain E residue 899 THR Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain E residue 943 MET Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 964 LEU Chi-restraints excluded: chain E residue 1062 GLU Chi-restraints excluded: chain E residue 1105 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 132 optimal weight: 0.8980 chunk 165 optimal weight: 0.0010 chunk 137 optimal weight: 0.9990 chunk 148 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 313 optimal weight: 0.6980 chunk 217 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 848 ASN C 427 GLN ** C 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.127255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.095027 restraints weight = 31752.124| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.35 r_work: 0.2905 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 29382 Z= 0.136 Angle : 0.654 22.766 40251 Z= 0.313 Chirality : 0.046 0.456 4848 Planarity : 0.004 0.040 4944 Dihedral : 6.773 49.806 6507 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.93 % Allowed : 10.75 % Favored : 87.32 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.23 (0.14), residues: 3447 helix: 0.97 (0.20), residues: 747 sheet: 0.08 (0.16), residues: 942 loop : -0.04 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1069 TYR 0.012 0.001 TYR C1141 PHE 0.015 0.001 PHE E 239 TRP 0.007 0.001 TRP A 310 HIS 0.002 0.001 HIS C1146 Details of bonding type rmsd covalent geometry : bond 0.00295 (29202) covalent geometry : angle 0.59005 (39762) SS BOND : bond 0.00992 ( 51) SS BOND : angle 2.54608 ( 102) hydrogen bonds : bond 0.04045 ( 1144) hydrogen bonds : angle 5.53830 ( 3111) link_ALPHA1-2 : bond 0.00311 ( 6) link_ALPHA1-2 : angle 1.59364 ( 18) link_ALPHA1-3 : bond 0.00978 ( 15) link_ALPHA1-3 : angle 1.50321 ( 45) link_ALPHA1-6 : bond 0.00987 ( 9) link_ALPHA1-6 : angle 1.31792 ( 27) link_BETA1-4 : bond 0.00848 ( 48) link_BETA1-4 : angle 2.22053 ( 144) link_NAG-ASN : bond 0.00734 ( 51) link_NAG-ASN : angle 3.42258 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 251 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8491 (t0) cc_final: 0.8073 (t0) REVERT: A 50 VAL cc_start: 0.8634 (t) cc_final: 0.8351 (p) REVERT: A 306 ASP cc_start: 0.8062 (t0) cc_final: 0.7677 (t0) REVERT: A 652 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.6571 (mmt180) REVERT: A 777 TYR cc_start: 0.8687 (m-80) cc_final: 0.8430 (m-80) REVERT: A 812 ASN cc_start: 0.8643 (t0) cc_final: 0.8279 (t160) REVERT: A 958 VAL cc_start: 0.7767 (p) cc_final: 0.7399 (m) REVERT: A 1008 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8370 (ptp) REVERT: A 1031 GLN cc_start: 0.7677 (mt0) cc_final: 0.7281 (tt0) REVERT: A 1039 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7656 (mm-30) REVERT: A 1068 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.8004 (t70) REVERT: A 1105 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7781 (tm-30) REVERT: A 1169 ASN cc_start: 0.8610 (m-40) cc_final: 0.8179 (t0) REVERT: C 49 ASP cc_start: 0.8620 (t0) cc_final: 0.8166 (t0) REVERT: C 251 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8561 (tp) REVERT: C 422 ASP cc_start: 0.7534 (t70) cc_final: 0.7037 (m-30) REVERT: C 536 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7230 (mm-30) REVERT: C 587 LYS cc_start: 0.8390 (tptt) cc_final: 0.7142 (ttmm) REVERT: C 812 ASN cc_start: 0.8611 (t0) cc_final: 0.8165 (t160) REVERT: C 1031 GLN cc_start: 0.7669 (mt0) cc_final: 0.7387 (tt0) REVERT: C 1039 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8133 (mm-30) REVERT: C 1105 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7966 (tt0) REVERT: E 355 ASP cc_start: 0.7159 (OUTLIER) cc_final: 0.6864 (m-30) REVERT: E 382 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.6987 (mm-30) REVERT: E 536 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7284 (mm-30) REVERT: E 565 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7796 (tm-30) REVERT: E 815 GLN cc_start: 0.7696 (tm-30) cc_final: 0.7243 (mm110) REVERT: E 841 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7363 (mtm180) REVERT: E 844 ASP cc_start: 0.7571 (m-30) cc_final: 0.7170 (m-30) REVERT: E 914 GLN cc_start: 0.7132 (mt0) cc_final: 0.6908 (mp10) REVERT: E 1039 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8167 (mm-30) REVERT: E 1069 ARG cc_start: 0.8459 (mtt-85) cc_final: 0.8209 (mtp85) outliers start: 57 outliers final: 23 residues processed: 286 average time/residue: 0.6026 time to fit residues: 204.1760 Evaluate side-chains 265 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 233 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 652 ARG Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1105 GLU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 1105 GLU Chi-restraints excluded: chain C residue 1151 SER Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 319 GLN Chi-restraints excluded: chain E residue 355 ASP Chi-restraints excluded: chain E residue 382 GLU Chi-restraints excluded: chain E residue 386 SER Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 661 VAL Chi-restraints excluded: chain E residue 841 ARG Chi-restraints excluded: chain E residue 943 MET Chi-restraints excluded: chain E residue 964 LEU Chi-restraints excluded: chain E residue 1062 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 159 optimal weight: 1.9990 chunk 329 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 172 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 260 optimal weight: 0.5980 chunk 338 optimal weight: 0.4980 chunk 311 optimal weight: 1.9990 chunk 249 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 GLN A 848 ASN A 987 GLN A1003 GLN A1072 ASN ** C 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 486 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.123931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.091220 restraints weight = 32090.896| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.36 r_work: 0.2913 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 29382 Z= 0.241 Angle : 0.717 21.568 40251 Z= 0.345 Chirality : 0.048 0.394 4848 Planarity : 0.004 0.039 4944 Dihedral : 7.102 48.129 6507 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.66 % Allowed : 11.09 % Favored : 87.25 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.14), residues: 3447 helix: 0.81 (0.19), residues: 747 sheet: 0.15 (0.17), residues: 894 loop : -0.27 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1069 TYR 0.015 0.002 TYR E 292 PHE 0.017 0.002 PHE A 183 TRP 0.008 0.001 TRP A 310 HIS 0.004 0.001 HIS C1138 Details of bonding type rmsd covalent geometry : bond 0.00570 (29202) covalent geometry : angle 0.65321 (39762) SS BOND : bond 0.00953 ( 51) SS BOND : angle 2.75472 ( 102) hydrogen bonds : bond 0.04802 ( 1144) hydrogen bonds : angle 5.66655 ( 3111) link_ALPHA1-2 : bond 0.00244 ( 6) link_ALPHA1-2 : angle 1.58832 ( 18) link_ALPHA1-3 : bond 0.00866 ( 15) link_ALPHA1-3 : angle 1.58494 ( 45) link_ALPHA1-6 : bond 0.00921 ( 9) link_ALPHA1-6 : angle 1.25480 ( 27) link_BETA1-4 : bond 0.00782 ( 48) link_BETA1-4 : angle 2.29503 ( 144) link_NAG-ASN : bond 0.00904 ( 51) link_NAG-ASN : angle 3.59723 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 235 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8496 (t0) cc_final: 0.8063 (t0) REVERT: A 50 VAL cc_start: 0.8456 (t) cc_final: 0.8144 (p) REVERT: A 306 ASP cc_start: 0.8169 (t0) cc_final: 0.7837 (t0) REVERT: A 777 TYR cc_start: 0.8795 (m-80) cc_final: 0.8505 (m-80) REVERT: A 1031 GLN cc_start: 0.7643 (mt0) cc_final: 0.7207 (tt0) REVERT: A 1039 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7743 (mm-30) REVERT: A 1068 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.8007 (t70) REVERT: A 1069 ARG cc_start: 0.8382 (mtp85) cc_final: 0.7984 (mtp180) REVERT: A 1105 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7771 (tm-30) REVERT: A 1169 ASN cc_start: 0.8555 (m-40) cc_final: 0.8080 (t0) REVERT: C 251 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8529 (tp) REVERT: C 382 GLU cc_start: 0.7749 (pt0) cc_final: 0.6937 (tt0) REVERT: C 422 ASP cc_start: 0.7508 (t70) cc_final: 0.6941 (m-30) REVERT: C 536 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7157 (mm-30) REVERT: C 812 ASN cc_start: 0.8620 (t0) cc_final: 0.8177 (t160) REVERT: C 943 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8146 (ttm) REVERT: C 1031 GLN cc_start: 0.7587 (mt0) cc_final: 0.7260 (tt0) REVERT: C 1039 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8193 (mm-30) REVERT: E 261 GLN cc_start: 0.8799 (mt0) cc_final: 0.8465 (mt0) REVERT: E 355 ASP cc_start: 0.7151 (OUTLIER) cc_final: 0.6850 (m-30) REVERT: E 417 LEU cc_start: 0.8402 (mt) cc_final: 0.8176 (mt) REVERT: E 536 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7201 (mm-30) REVERT: E 565 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7870 (tm-30) REVERT: E 815 GLN cc_start: 0.7698 (tm-30) cc_final: 0.7269 (mm110) REVERT: E 841 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7335 (mtm180) REVERT: E 844 ASP cc_start: 0.7613 (m-30) cc_final: 0.7211 (m-30) REVERT: E 914 GLN cc_start: 0.7088 (mt0) cc_final: 0.6873 (mp10) REVERT: E 1039 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8204 (mm-30) REVERT: E 1069 ARG cc_start: 0.8381 (mtt-85) cc_final: 0.8126 (mtp85) REVERT: E 1105 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7160 (tm-30) outliers start: 49 outliers final: 28 residues processed: 265 average time/residue: 0.6438 time to fit residues: 204.1373 Evaluate side-chains 266 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 231 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1105 GLU Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 943 MET Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain C residue 1151 SER Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 319 GLN Chi-restraints excluded: chain E residue 355 ASP Chi-restraints excluded: chain E residue 386 SER Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 661 VAL Chi-restraints excluded: chain E residue 662 ILE Chi-restraints excluded: chain E residue 841 ARG Chi-restraints excluded: chain E residue 943 MET Chi-restraints excluded: chain E residue 949 SER Chi-restraints excluded: chain E residue 964 LEU Chi-restraints excluded: chain E residue 1062 GLU Chi-restraints excluded: chain E residue 1105 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 316 optimal weight: 0.0770 chunk 14 optimal weight: 0.9980 chunk 198 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 219 optimal weight: 0.6980 chunk 127 optimal weight: 0.8980 chunk 194 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 chunk 154 optimal weight: 0.3980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 GLN E 486 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.126751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.093299 restraints weight = 31444.056| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.43 r_work: 0.2874 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 29382 Z= 0.133 Angle : 0.652 21.093 40251 Z= 0.311 Chirality : 0.045 0.417 4848 Planarity : 0.004 0.038 4944 Dihedral : 6.420 45.167 6507 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.22 % Allowed : 11.53 % Favored : 87.25 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.14), residues: 3447 helix: 0.98 (0.20), residues: 750 sheet: 0.08 (0.16), residues: 942 loop : -0.06 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1069 TYR 0.012 0.001 TYR C1141 PHE 0.013 0.001 PHE A 183 TRP 0.007 0.001 TRP A 310 HIS 0.003 0.001 HIS C 681 Details of bonding type rmsd covalent geometry : bond 0.00292 (29202) covalent geometry : angle 0.58787 (39762) SS BOND : bond 0.00914 ( 51) SS BOND : angle 2.51065 ( 102) hydrogen bonds : bond 0.04040 ( 1144) hydrogen bonds : angle 5.52350 ( 3111) link_ALPHA1-2 : bond 0.00323 ( 6) link_ALPHA1-2 : angle 1.56313 ( 18) link_ALPHA1-3 : bond 0.00872 ( 15) link_ALPHA1-3 : angle 1.47428 ( 45) link_ALPHA1-6 : bond 0.00925 ( 9) link_ALPHA1-6 : angle 1.32375 ( 27) link_BETA1-4 : bond 0.00787 ( 48) link_BETA1-4 : angle 2.14787 ( 144) link_NAG-ASN : bond 0.00791 ( 51) link_NAG-ASN : angle 3.48498 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 237 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8288 (t0) cc_final: 0.7788 (t0) REVERT: A 50 VAL cc_start: 0.8354 (t) cc_final: 0.8042 (p) REVERT: A 306 ASP cc_start: 0.8011 (t0) cc_final: 0.7707 (t0) REVERT: A 777 TYR cc_start: 0.8563 (m-80) cc_final: 0.8236 (m-80) REVERT: A 812 ASN cc_start: 0.8447 (t0) cc_final: 0.8084 (t160) REVERT: A 958 VAL cc_start: 0.7545 (p) cc_final: 0.7200 (m) REVERT: A 1008 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8285 (ptp) REVERT: A 1031 GLN cc_start: 0.7420 (mt0) cc_final: 0.7001 (tt0) REVERT: A 1039 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7569 (mm-30) REVERT: A 1068 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7844 (t70) REVERT: A 1069 ARG cc_start: 0.8271 (mtp85) cc_final: 0.7902 (mtp180) REVERT: A 1084 GLN cc_start: 0.8074 (mm110) cc_final: 0.7783 (tp-100) REVERT: A 1105 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7485 (tm-30) REVERT: A 1169 ASN cc_start: 0.8500 (m-40) cc_final: 0.7978 (t0) REVERT: C 49 ASP cc_start: 0.8543 (t0) cc_final: 0.7876 (t0) REVERT: C 251 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8401 (tp) REVERT: C 382 GLU cc_start: 0.7739 (pt0) cc_final: 0.6840 (tt0) REVERT: C 422 ASP cc_start: 0.7341 (t70) cc_final: 0.6741 (m-30) REVERT: C 536 GLU cc_start: 0.7447 (mm-30) cc_final: 0.6997 (mm-30) REVERT: C 587 LYS cc_start: 0.8238 (tptt) cc_final: 0.6951 (ttmm) REVERT: C 812 ASN cc_start: 0.8443 (t0) cc_final: 0.7993 (t160) REVERT: C 1031 GLN cc_start: 0.7333 (mt0) cc_final: 0.7001 (tt0) REVERT: C 1039 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8002 (mm-30) REVERT: E 261 GLN cc_start: 0.8613 (mt0) cc_final: 0.8287 (mt0) REVERT: E 417 LEU cc_start: 0.8212 (mt) cc_final: 0.7998 (mt) REVERT: E 536 GLU cc_start: 0.7788 (mt-10) cc_final: 0.6998 (mm-30) REVERT: E 565 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7780 (tm-30) REVERT: E 815 GLN cc_start: 0.7457 (tm-30) cc_final: 0.6943 (mm110) REVERT: E 841 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.7162 (mtm180) REVERT: E 844 ASP cc_start: 0.7340 (m-30) cc_final: 0.6928 (m-30) REVERT: E 914 GLN cc_start: 0.6969 (mt0) cc_final: 0.6736 (mp10) REVERT: E 1039 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8070 (mm-30) REVERT: E 1069 ARG cc_start: 0.8165 (mtt-85) cc_final: 0.7893 (mtp85) REVERT: E 1105 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.6914 (tm-30) outliers start: 36 outliers final: 26 residues processed: 260 average time/residue: 0.6266 time to fit residues: 192.2079 Evaluate side-chains 263 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 231 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 679 CYS Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1105 GLU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 319 GLN Chi-restraints excluded: chain E residue 386 SER Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 661 VAL Chi-restraints excluded: chain E residue 662 ILE Chi-restraints excluded: chain E residue 841 ARG Chi-restraints excluded: chain E residue 943 MET Chi-restraints excluded: chain E residue 964 LEU Chi-restraints excluded: chain E residue 1062 GLU Chi-restraints excluded: chain E residue 1105 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 146 optimal weight: 2.9990 chunk 187 optimal weight: 0.5980 chunk 184 optimal weight: 2.9990 chunk 280 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 234 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 240 optimal weight: 0.0970 chunk 105 optimal weight: 0.9990 chunk 185 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 987 GLN E 486 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.126410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.092963 restraints weight = 31307.246| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.42 r_work: 0.2872 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 29382 Z= 0.148 Angle : 0.691 25.609 40251 Z= 0.330 Chirality : 0.046 0.522 4848 Planarity : 0.004 0.038 4944 Dihedral : 6.337 45.842 6507 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.29 % Allowed : 11.46 % Favored : 87.25 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.14), residues: 3447 helix: 1.00 (0.20), residues: 750 sheet: 0.10 (0.16), residues: 942 loop : -0.04 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1069 TYR 0.013 0.001 TYR C1141 PHE 0.018 0.001 PHE E 239 TRP 0.006 0.001 TRP C 310 HIS 0.002 0.001 HIS E 486 Details of bonding type rmsd covalent geometry : bond 0.00334 (29202) covalent geometry : angle 0.62247 (39762) SS BOND : bond 0.00890 ( 51) SS BOND : angle 3.22273 ( 102) hydrogen bonds : bond 0.04174 ( 1144) hydrogen bonds : angle 5.47358 ( 3111) link_ALPHA1-2 : bond 0.00325 ( 6) link_ALPHA1-2 : angle 1.56255 ( 18) link_ALPHA1-3 : bond 0.00812 ( 15) link_ALPHA1-3 : angle 1.51767 ( 45) link_ALPHA1-6 : bond 0.00882 ( 9) link_ALPHA1-6 : angle 1.33284 ( 27) link_BETA1-4 : bond 0.00771 ( 48) link_BETA1-4 : angle 2.11653 ( 144) link_NAG-ASN : bond 0.00793 ( 51) link_NAG-ASN : angle 3.51011 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 235 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8285 (t0) cc_final: 0.7758 (t0) REVERT: A 50 VAL cc_start: 0.8371 (t) cc_final: 0.8059 (p) REVERT: A 306 ASP cc_start: 0.8018 (t0) cc_final: 0.7689 (t0) REVERT: A 777 TYR cc_start: 0.8610 (m-80) cc_final: 0.8279 (m-80) REVERT: A 812 ASN cc_start: 0.8447 (t0) cc_final: 0.8077 (t160) REVERT: A 958 VAL cc_start: 0.7571 (p) cc_final: 0.7227 (m) REVERT: A 1031 GLN cc_start: 0.7442 (mt0) cc_final: 0.7012 (tt0) REVERT: A 1039 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7589 (mm-30) REVERT: A 1068 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7786 (t70) REVERT: A 1069 ARG cc_start: 0.8227 (mtp85) cc_final: 0.7851 (mtp180) REVERT: A 1084 GLN cc_start: 0.8074 (mm110) cc_final: 0.7784 (tp-100) REVERT: A 1105 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7457 (tm-30) REVERT: A 1169 ASN cc_start: 0.8483 (m-40) cc_final: 0.7951 (t0) REVERT: C 49 ASP cc_start: 0.8536 (t0) cc_final: 0.8306 (t0) REVERT: C 155 ASN cc_start: 0.7943 (m-40) cc_final: 0.7688 (m110) REVERT: C 251 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8413 (tp) REVERT: C 382 GLU cc_start: 0.7750 (pt0) cc_final: 0.6819 (tt0) REVERT: C 422 ASP cc_start: 0.7306 (t70) cc_final: 0.6739 (m-30) REVERT: C 536 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7002 (mm-30) REVERT: C 587 LYS cc_start: 0.8309 (tptt) cc_final: 0.7025 (ttmm) REVERT: C 812 ASN cc_start: 0.8422 (t0) cc_final: 0.7970 (t160) REVERT: C 1031 GLN cc_start: 0.7314 (mt0) cc_final: 0.6956 (tt0) REVERT: C 1039 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8001 (mm-30) REVERT: E 261 GLN cc_start: 0.8596 (mt0) cc_final: 0.8261 (mt0) REVERT: E 355 ASP cc_start: 0.7041 (OUTLIER) cc_final: 0.6723 (m-30) REVERT: E 417 LEU cc_start: 0.8217 (mt) cc_final: 0.8004 (mt) REVERT: E 536 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7009 (mm-30) REVERT: E 565 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7712 (tm-30) REVERT: E 722 LEU cc_start: 0.6914 (tt) cc_final: 0.6182 (pp) REVERT: E 815 GLN cc_start: 0.7442 (tm-30) cc_final: 0.6948 (mm110) REVERT: E 841 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.7048 (mtm180) REVERT: E 844 ASP cc_start: 0.7382 (m-30) cc_final: 0.6962 (m-30) REVERT: E 914 GLN cc_start: 0.7008 (mt0) cc_final: 0.6760 (mp10) REVERT: E 1039 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8101 (mm-30) REVERT: E 1069 ARG cc_start: 0.8176 (mtt-85) cc_final: 0.7960 (mtp85) REVERT: E 1105 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.6949 (tm-30) outliers start: 38 outliers final: 25 residues processed: 260 average time/residue: 0.6126 time to fit residues: 187.7289 Evaluate side-chains 265 residues out of total 2976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 234 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 679 CYS Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 1068 ASP Chi-restraints excluded: chain A residue 1105 GLU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 958 VAL Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 319 GLN Chi-restraints excluded: chain E residue 355 ASP Chi-restraints excluded: chain E residue 386 SER Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 661 VAL Chi-restraints excluded: chain E residue 662 ILE Chi-restraints excluded: chain E residue 841 ARG Chi-restraints excluded: chain E residue 943 MET Chi-restraints excluded: chain E residue 964 LEU Chi-restraints excluded: chain E residue 1062 GLU Chi-restraints excluded: chain E residue 1105 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 39 optimal weight: 2.9990 chunk 206 optimal weight: 2.9990 chunk 240 optimal weight: 2.9990 chunk 231 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 304 optimal weight: 0.6980 chunk 228 optimal weight: 0.4980 chunk 343 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 239 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 733 GLN C 280 GLN ** C 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 486 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.124939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.091596 restraints weight = 31817.908| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.42 r_work: 0.2854 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 29382 Z= 0.190 Angle : 0.710 25.036 40251 Z= 0.342 Chirality : 0.047 0.446 4848 Planarity : 0.004 0.039 4944 Dihedral : 6.469 47.372 6507 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.25 % Allowed : 11.73 % Favored : 87.01 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.19 (0.14), residues: 3447 helix: 0.92 (0.19), residues: 750 sheet: 0.14 (0.16), residues: 948 loop : -0.12 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1069 TYR 0.013 0.001 TYR A 184 PHE 0.019 0.001 PHE A 239 TRP 0.007 0.001 TRP A 310 HIS 0.004 0.001 HIS C 681 Details of bonding type rmsd covalent geometry : bond 0.00439 (29202) covalent geometry : angle 0.64425 (39762) SS BOND : bond 0.00987 ( 51) SS BOND : angle 3.32056 ( 102) hydrogen bonds : bond 0.04430 ( 1144) hydrogen bonds : angle 5.53180 ( 3111) link_ALPHA1-2 : bond 0.00291 ( 6) link_ALPHA1-2 : angle 1.55467 ( 18) link_ALPHA1-3 : bond 0.00777 ( 15) link_ALPHA1-3 : angle 1.52024 ( 45) link_ALPHA1-6 : bond 0.00865 ( 9) link_ALPHA1-6 : angle 1.30948 ( 27) link_BETA1-4 : bond 0.00748 ( 48) link_BETA1-4 : angle 2.12017 ( 144) link_NAG-ASN : bond 0.00818 ( 51) link_NAG-ASN : angle 3.44624 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10582.53 seconds wall clock time: 180 minutes 48.58 seconds (10848.58 seconds total)