Starting phenix.real_space_refine on Sun Sep 13 11:53:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yeo_72857/09_2026/9yeo_72857.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yeo_72857/09_2026/9yeo_72857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9yeo_72857/09_2026/9yeo_72857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yeo_72857/09_2026/9yeo_72857.map" model { file = "/net/cci-nas-00/data/ceres_data/9yeo_72857/09_2026/9yeo_72857.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yeo_72857/09_2026/9yeo_72857.cif" } resolution = 3.64 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= 0.003 sd= 0.020 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 148 5.16 5 C 14003 2.51 5 N 3781 2.21 5 O 4620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22552 Number of models: 1 Model: "" Number of chains: 50 Chain: "A" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1009 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "C" Number of atoms: 3544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3544 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "K" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 953 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "L" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "M" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 953 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "N" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "B" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1009 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "D" Number of atoms: 3544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3544 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 953 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "F" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "G" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 953 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "H" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "I" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1009 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "J" Number of atoms: 3544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3544 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "h" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 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: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" 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: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "D" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "I" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "J" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.04, per 1000 atoms: 0.27 Number of scatterers: 22552 At special positions: 0 Unit cell: (193.857, 146.205, 151.62, 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 148 16.00 O 4620 8.00 N 3781 7.00 C 14003 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=50, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS C 501 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.04 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 98 " - pdb=" SG CYS K 100C" distance=2.03 Simple disulfide: pdb=" SG CYS K 100 " - pdb=" SG CYS M 100 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS M 98 " - pdb=" SG CYS M 100C" distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS D 501 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 201 " - pdb=" SG CYS D 433 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 98 " - pdb=" SG CYS E 100C" distance=2.03 Simple disulfide: pdb=" SG CYS E 100 " - pdb=" SG CYS G 100 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 98 " - pdb=" SG CYS G 100C" distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Simple disulfide: pdb=" SG CYS I 605 " - pdb=" SG CYS J 501 " distance=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 74 " distance=2.03 Simple disulfide: pdb=" SG CYS J 119 " - pdb=" SG CYS J 205 " distance=2.03 Simple disulfide: pdb=" SG CYS J 126 " - pdb=" SG CYS J 196 " distance=2.03 Simple disulfide: pdb=" SG CYS J 131 " - pdb=" SG CYS J 157 " distance=2.03 Simple disulfide: pdb=" SG CYS J 201 " - pdb=" SG CYS J 433 " distance=2.02 Simple disulfide: pdb=" SG CYS J 218 " - pdb=" SG CYS J 247 " distance=2.03 Simple disulfide: pdb=" SG CYS J 228 " - pdb=" SG CYS J 239 " distance=2.03 Simple disulfide: pdb=" SG CYS J 296 " - pdb=" SG CYS J 331 " distance=2.03 Simple disulfide: pdb=" SG CYS J 378 " - pdb=" SG CYS J 445 " distance=2.03 Simple disulfide: pdb=" SG CYS J 385 " - pdb=" SG CYS J 418 " 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 P 4 " - " MAN P 5 " " MAN U 5 " - " MAN U 6 " " MAN U 8 " - " MAN U 9 " " MAN X 5 " - " MAN X 6 " " MAN X 8 " - " MAN X 9 " " MAN Z 4 " - " MAN Z 5 " " MAN e 5 " - " MAN e 6 " " MAN e 8 " - " MAN e 9 " " MAN h 5 " - " MAN h 6 " " MAN h 8 " - " MAN h 9 " " MAN j 4 " - " MAN j 5 " ALPHA1-3 " BMA P 3 " - " MAN P 4 " " BMA U 3 " - " MAN U 8 " " MAN U 4 " - " MAN U 7 " " BMA X 3 " - " MAN X 8 " " MAN X 4 " - " MAN X 7 " " BMA Z 3 " - " MAN Z 4 " " BMA e 3 " - " MAN e 8 " " MAN e 4 " - " MAN e 7 " " BMA h 3 " - " MAN h 8 " " MAN h 4 " - " MAN h 7 " " BMA j 3 " - " MAN j 4 " ALPHA1-6 " BMA P 3 " - " MAN P 6 " " BMA U 3 " - " MAN U 4 " " MAN U 4 " - " MAN U 5 " " BMA X 3 " - " MAN X 4 " " MAN X 4 " - " MAN X 5 " " BMA Z 3 " - " MAN Z 6 " " BMA e 3 " - " MAN e 4 " " MAN e 4 " - " MAN e 5 " " BMA h 3 " - " MAN h 4 " " MAN h 4 " - " MAN h 5 " " BMA j 3 " - " MAN j 6 " BETA1-4 " 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 R 1 " - " NAG R 2 " " 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 b 1 " - " NAG b 2 " " 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 h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 637 " " NAG A 703 " - " ASN A 618 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG B 703 " - " ASN B 618 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 197 " " NAG C 604 " - " ASN C 234 " " NAG C 605 " - " ASN C 339 " " NAG C 606 " - " ASN C 355 " " NAG C 607 " - " ASN C 392 " " NAG C 608 " - " ASN C 137 " " NAG D 601 " - " ASN D 88 " " NAG D 602 " - " ASN D 133 " " NAG D 603 " - " ASN D 197 " " NAG D 604 " - " ASN D 234 " " NAG D 605 " - " ASN D 339 " " NAG D 606 " - " ASN D 355 " " NAG D 607 " - " ASN D 392 " " NAG D 608 " - " ASN D 137 " " NAG I 701 " - " ASN I 611 " " NAG I 702 " - " ASN I 637 " " NAG I 703 " - " ASN I 618 " " NAG J 601 " - " ASN J 88 " " NAG J 602 " - " ASN J 133 " " NAG J 603 " - " ASN J 197 " " NAG J 604 " - " ASN J 234 " " NAG J 605 " - " ASN J 339 " " NAG J 606 " - " ASN J 355 " " NAG J 607 " - " ASN J 392 " " NAG J 608 " - " ASN J 137 " " NAG O 1 " - " ASN C 160 " " NAG P 1 " - " ASN C 262 " " NAG Q 1 " - " ASN C 276 " " NAG R 1 " - " ASN C 363 " " NAG S 1 " - " ASN C 386 " " NAG T 1 " - " ASN C 448 " " NAG U 1 " - " ASN C 332 " " NAG V 1 " - " ASN C 156 " " NAG W 1 " - " ASN C 301 " " NAG X 1 " - " ASN C 295 " " NAG Y 1 " - " ASN D 160 " " NAG Z 1 " - " ASN D 262 " " NAG a 1 " - " ASN D 276 " " NAG b 1 " - " ASN D 363 " " NAG c 1 " - " ASN D 386 " " NAG d 1 " - " ASN D 448 " " NAG e 1 " - " ASN D 332 " " NAG f 1 " - " ASN D 156 " " NAG g 1 " - " ASN D 301 " " NAG h 1 " - " ASN D 295 " " NAG i 1 " - " ASN J 160 " " NAG j 1 " - " ASN J 262 " " NAG k 1 " - " ASN J 276 " " NAG l 1 " - " ASN J 363 " " NAG m 1 " - " ASN J 386 " " NAG n 1 " - " ASN J 448 " " NAG o 1 " - " ASN J 332 " " NAG p 1 " - " ASN J 156 " " NAG q 1 " - " ASN J 301 " " NAG r 1 " - " ASN J 295 " Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.3 seconds 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4902 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 38 sheets defined 20.7% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 544 removed outlier: 4.532A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU A 544 " --> pdb=" O GLN A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 596 removed outlier: 4.273A pdb=" N LYS A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 592 " --> pdb=" O ARG A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 627 through 636 removed outlier: 4.050A pdb=" N LYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLU A 634 " --> pdb=" O GLN A 630 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE A 635 " --> pdb=" O TRP A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 662 removed outlier: 3.807A pdb=" N ILE A 642 " --> pdb=" O TYR A 638 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR A 643 " --> pdb=" O THR A 639 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 63 removed outlier: 3.610A pdb=" N TYR C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.451A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 353 removed outlier: 3.868A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 391 removed outlier: 3.775A pdb=" N PHE C 391 " --> pdb=" O SER C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.574A pdb=" N ARG C 429 " --> pdb=" O MET C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 484 removed outlier: 4.129A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 30 No H-bonds generated for 'chain 'K' and resid 28 through 30' Processing helix chain 'K' and resid 61 through 67 removed outlier: 3.915A pdb=" N LYS K 64 " --> pdb=" O VAL K 61 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N GLY K 65 " --> pdb=" O SER K 62 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE K 67 " --> pdb=" O LYS K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 86 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 84 removed outlier: 3.584A pdb=" N ALA N 84 " --> pdb=" O GLU N 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 543 Processing helix chain 'B' and resid 569 through 595 removed outlier: 4.180A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 636 removed outlier: 4.116A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE B 635 " --> pdb=" O TRP B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 663 removed outlier: 3.800A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR B 643 " --> pdb=" O THR B 639 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 63 removed outlier: 3.670A pdb=" N TYR D 61 " --> pdb=" O ASP D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 117 removed outlier: 4.424A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 335 through 353 removed outlier: 3.842A pdb=" N LYS D 351 " --> pdb=" O LYS D 347 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N HIS D 352 " --> pdb=" O GLN D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 removed outlier: 3.555A pdb=" N THR D 373 " --> pdb=" O LEU D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 391 removed outlier: 3.856A pdb=" N PHE D 391 " --> pdb=" O SER D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 429 removed outlier: 3.554A pdb=" N ARG D 429 " --> pdb=" O MET D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 483 removed outlier: 4.176A pdb=" N TRP D 479 " --> pdb=" O MET D 475 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 30 No H-bonds generated for 'chain 'E' and resid 28 through 30' Processing helix chain 'E' and resid 61 through 64 removed outlier: 4.050A pdb=" N LYS E 64 " --> pdb=" O VAL E 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 61 through 64' Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.596A pdb=" N SER F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 30 No H-bonds generated for 'chain 'G' and resid 28 through 30' Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.665A pdb=" N SER H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 536 through 543 removed outlier: 4.453A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) Processing helix chain 'I' and resid 571 through 595 Processing helix chain 'I' and resid 618 through 625 Processing helix chain 'I' and resid 627 through 663 removed outlier: 4.016A pdb=" N LYS I 633 " --> pdb=" O LEU I 629 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ASN I 637 " --> pdb=" O LYS I 633 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N TYR I 638 " --> pdb=" O GLU I 634 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLN I 640 " --> pdb=" O SER I 636 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ILE I 641 " --> pdb=" O ASN I 637 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE I 642 " --> pdb=" O TYR I 638 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR I 643 " --> pdb=" O THR I 639 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY I 644 " --> pdb=" O GLN I 640 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 63 removed outlier: 3.589A pdb=" N TYR J 61 " --> pdb=" O ASP J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 117 removed outlier: 4.465A pdb=" N GLU J 102 " --> pdb=" O ASN J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 127 removed outlier: 3.516A pdb=" N CYS J 126 " --> pdb=" O THR J 123 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL J 127 " --> pdb=" O PRO J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 335 through 353 removed outlier: 3.831A pdb=" N LYS J 351 " --> pdb=" O LYS J 347 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N HIS J 352 " --> pdb=" O GLN J 348 " (cutoff:3.500A) Processing helix chain 'J' and resid 368 through 373 removed outlier: 3.652A pdb=" N THR J 373 " --> pdb=" O LEU J 369 " (cutoff:3.500A) Processing helix chain 'J' and resid 425 through 429 removed outlier: 3.507A pdb=" N ARG J 429 " --> pdb=" O MET J 426 " (cutoff:3.500A) Processing helix chain 'J' and resid 475 through 484 removed outlier: 4.024A pdb=" N TRP J 479 " --> pdb=" O MET J 475 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU J 482 " --> pdb=" O ASN J 478 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 603 through 609 removed outlier: 3.739A pdb=" N THR A 606 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N VAL C 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.921A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.778A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 92 through 94 Processing sheet with id=AA5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'C' and resid 256 through 257 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 256 through 257 current: chain 'C' and resid 284 through 308 removed outlier: 4.241A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR C 303 " --> pdb=" O ASP C 321A" (cutoff:3.500A) removed outlier: 5.225A pdb=" N ASP C 321A" --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 316 through 323 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 465 through 470 Processing sheet with id=AA7, first strand: chain 'K' and resid 3 through 8 removed outlier: 3.742A pdb=" N HIS K 3 " --> pdb=" O SER K 25 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER K 25 " --> pdb=" O HIS K 3 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 10 through 12 current: chain 'K' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 57 through 59 current: chain 'K' and resid 100C through 100D Processing sheet with id=AA9, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.679A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS L 45 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 4 through 6 removed outlier: 3.882A pdb=" N LEU M 20 " --> pdb=" O LEU M 80 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 11 through 12 current: chain 'M' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 57 through 59 current: chain 'M' and resid 100C through 100D Processing sheet with id=AB4, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.630A pdb=" N VAL N 19 " --> pdb=" O ILE N 75 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.594A pdb=" N ILE N 11 " --> pdb=" O GLN N 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'N' and resid 53 through 54 removed outlier: 6.377A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE N 87 " --> pdb=" O PHE N 36 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 603 through 609 removed outlier: 3.736A pdb=" N THR B 606 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N VAL D 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 45 through 47 removed outlier: 3.840A pdb=" N ILE D 225 " --> pdb=" O VAL D 245 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 75 through 76 removed outlier: 3.771A pdb=" N VAL D 75 " --> pdb=" O CYS D 54 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 92 through 94 removed outlier: 3.506A pdb=" N PHE D 93 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 170 through 177 Processing sheet with id=AC3, first strand: chain 'D' and resid 256 through 257 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 256 through 257 current: chain 'D' and resid 284 through 302 removed outlier: 7.322A pdb=" N GLN D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N SER D 334 " --> pdb=" O GLN D 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 330 through 334 current: chain 'D' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 381 through 385 current: chain 'D' and resid 465 through 470 Processing sheet with id=AC4, first strand: chain 'D' and resid 304 through 307 Processing sheet with id=AC5, first strand: chain 'D' and resid 423 through 424 Processing sheet with id=AC6, first strand: chain 'E' and resid 5 through 7 Processing sheet with id=AC7, first strand: chain 'E' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 10 through 12 current: chain 'E' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 57 through 59 current: chain 'E' and resid 100C through 100D Processing sheet with id=AC8, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AC9, first strand: chain 'F' and resid 10 through 11 Processing sheet with id=AD1, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.317A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 3 through 6 removed outlier: 4.089A pdb=" N LEU G 20 " --> pdb=" O LEU G 80 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 10 through 12 current: chain 'G' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 57 through 59 current: chain 'G' and resid 100C through 100D Processing sheet with id=AD4, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AD5, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.595A pdb=" N ILE H 11 " --> pdb=" O GLN H 105 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 603 through 609 removed outlier: 3.632A pdb=" N THR I 606 " --> pdb=" O VAL J 36 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N VAL J 36 " --> pdb=" O THR I 606 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 45 through 47 removed outlier: 3.927A pdb=" N ILE J 225 " --> pdb=" O VAL J 245 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 75 through 76 removed outlier: 3.734A pdb=" N VAL J 75 " --> pdb=" O CYS J 54 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 92 through 94 Processing sheet with id=AE1, first strand: chain 'J' and resid 169 through 177 Processing sheet with id=AE2, first strand: chain 'J' and resid 256 through 257 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 256 through 257 current: chain 'J' and resid 284 through 307 removed outlier: 6.643A pdb=" N ASN J 301 " --> pdb=" O ILE J 322 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ILE J 322 " --> pdb=" O ASN J 301 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N THR J 303 " --> pdb=" O GLY J 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 317 through 323 current: chain 'J' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 381 through 385 current: chain 'J' and resid 465 through 469 603 hydrogen bonds defined for protein. 1563 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: 4.20 Time building geometry restraints manager: 3.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7011 1.34 - 1.47: 5930 1.47 - 1.59: 9836 1.59 - 1.71: 0 1.71 - 1.84: 196 Bond restraints: 22973 Sorted by residual: bond pdb=" N VAL I 518 " pdb=" CA VAL I 518 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.90e-02 2.77e+03 4.12e+00 bond pdb=" N ASP H 1 " pdb=" CA ASP H 1 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.36e+00 bond pdb=" N ASP N 1 " pdb=" CA ASP N 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N GLU D 32 " pdb=" CA GLU D 32 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 ... (remaining 22968 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 30298 1.57 - 3.15: 733 3.15 - 4.72: 132 4.72 - 6.29: 15 6.29 - 7.87: 1 Bond angle restraints: 31179 Sorted by residual: angle pdb=" CA CYS J 433 " pdb=" CB CYS J 433 " pdb=" SG CYS J 433 " ideal model delta sigma weight residual 114.40 122.27 -7.87 2.30e+00 1.89e-01 1.17e+01 angle pdb=" N CYS J 433 " pdb=" CA CYS J 433 " pdb=" CB CYS J 433 " ideal model delta sigma weight residual 110.25 114.74 -4.49 1.36e+00 5.41e-01 1.09e+01 angle pdb=" CB GLU A 654 " pdb=" CG GLU A 654 " pdb=" CD GLU A 654 " ideal model delta sigma weight residual 112.60 117.87 -5.27 1.70e+00 3.46e-01 9.61e+00 angle pdb=" C GLN G 81 " pdb=" N MET G 82 " pdb=" CA MET G 82 " ideal model delta sigma weight residual 121.54 127.29 -5.75 1.91e+00 2.74e-01 9.08e+00 angle pdb=" C THR C 461 " pdb=" N ASN C 462 " pdb=" CA ASN C 462 " ideal model delta sigma weight residual 121.54 127.03 -5.49 1.91e+00 2.74e-01 8.25e+00 ... (remaining 31174 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 13955 17.91 - 35.81: 1173 35.81 - 53.72: 336 53.72 - 71.63: 54 71.63 - 89.54: 29 Dihedral angle restraints: 15547 sinusoidal: 7940 harmonic: 7607 Sorted by residual: dihedral pdb=" CA CYS J 433 " pdb=" C CYS J 433 " pdb=" N MET J 434 " pdb=" CA MET J 434 " ideal model delta harmonic sigma weight residual 180.00 140.19 39.81 0 5.00e+00 4.00e-02 6.34e+01 dihedral pdb=" CB CYS D 201 " pdb=" SG CYS D 201 " pdb=" SG CYS D 433 " pdb=" CB CYS D 433 " ideal model delta sinusoidal sigma weight residual 93.00 28.95 64.05 1 1.00e+01 1.00e-02 5.40e+01 dihedral pdb=" CB CYS K 100 " pdb=" SG CYS K 100 " pdb=" SG CYS M 100 " pdb=" CB CYS M 100 " ideal model delta sinusoidal sigma weight residual -86.00 -30.70 -55.30 1 1.00e+01 1.00e-02 4.13e+01 ... (remaining 15544 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3144 0.045 - 0.090: 479 0.090 - 0.134: 274 0.134 - 0.179: 21 0.179 - 0.224: 3 Chirality restraints: 3921 Sorted by residual: chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN C 160 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" C1 NAG Y 1 " pdb=" ND2 ASN D 160 " pdb=" C2 NAG Y 1 " pdb=" O5 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" C3 MAN X 4 " pdb=" C2 MAN X 4 " pdb=" C4 MAN X 4 " pdb=" O3 MAN X 4 " both_signs ideal model delta sigma weight residual False 2.47 2.28 0.19 2.00e-01 2.50e+01 9.07e-01 ... (remaining 3918 not shown) Planarity restraints: 3867 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE I 519 " -0.020 2.00e-02 2.50e+03 1.80e-02 5.68e+00 pdb=" CG PHE I 519 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE I 519 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE I 519 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE I 519 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE I 519 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE I 519 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR L 94 " -0.032 5.00e-02 4.00e+02 4.81e-02 3.69e+00 pdb=" N PRO L 95 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR N 94 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.68e+00 pdb=" N PRO N 95 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO N 95 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO N 95 " 0.027 5.00e-02 4.00e+02 ... (remaining 3864 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5023 2.79 - 3.32: 23000 3.32 - 3.84: 35620 3.84 - 4.37: 41256 4.37 - 4.90: 69924 Nonbonded interactions: 174823 Sorted by model distance: nonbonded pdb=" O ASN M 82B" pdb=" OD1 ASN M 82B" model vdw 2.260 3.040 nonbonded pdb=" O ASN E 82B" pdb=" OD1 ASN E 82B" model vdw 2.286 3.040 nonbonded pdb=" O THR L 97 " pdb=" OG1 THR L 97 " model vdw 2.407 3.040 nonbonded pdb=" OG SER E 68 " pdb=" O GLN E 81 " model vdw 2.433 3.040 nonbonded pdb=" OD1 ASN J 339 " pdb=" O5 NAG J 605 " model vdw 2.437 3.040 ... (remaining 174818 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'g' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'q' } ncs_group { reference = chain 'P' selection = chain 'Z' selection = chain 'j' } ncs_group { reference = chain 'U' selection = chain 'X' selection = chain 'e' selection = chain 'h' } ncs_group { reference = chain 'V' selection = chain 'f' selection = chain 'o' selection = chain 'p' selection = chain 'r' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.560 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: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.520 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 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 : 0.003 0.039 23161 Z= 0.137 Angle : 0.660 8.514 31693 Z= 0.325 Chirality : 0.043 0.224 3921 Planarity : 0.004 0.048 3804 Dihedral : 13.995 89.535 10495 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.13 % Favored : 93.68 % Rotamer: Outliers : 1.21 % Allowed : 15.22 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.16), residues: 2612 helix: 0.90 (0.27), residues: 402 sheet: -0.75 (0.19), residues: 756 loop : -1.23 (0.16), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 46 TYR 0.032 0.001 TYR F 94 PHE 0.041 0.001 PHE I 519 TRP 0.010 0.001 TRP G 103 HIS 0.008 0.001 HIS K 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (22973) covalent geometry : angle 0.59696 / 0.31 (31179) SS BOND : bond 0.00298 / 0.17 ( 50) SS BOND : angle 1.33377 / 0.95 ( 100) hydrogen bonds : bond 0.18479 / 12.53 ( 603) hydrogen bonds : angle 7.17221 / 5.15 ( 1563) link_ALPHA1-2 : bond 0.01166 / 0.68 ( 11) link_ALPHA1-2 : angle 3.13827 / 1.96 ( 33) link_ALPHA1-3 : bond 0.01204 / 0.72 ( 11) link_ALPHA1-3 : angle 2.41758 / 1.30 ( 33) link_ALPHA1-6 : bond 0.01132 / 0.70 ( 11) link_ALPHA1-6 : angle 2.48897 / 1.43 ( 33) link_BETA1-4 : bond 0.00542 / 0.32 ( 42) link_BETA1-4 : angle 2.16474 / 1.62 ( 126) link_NAG-ASN : bond 0.00438 / 0.29 ( 63) link_NAG-ASN : angle 2.53442 / 1.77 ( 189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 257 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 627 THR cc_start: 0.8296 (p) cc_final: 0.8089 (p) REVERT: A 657 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8327 (tm-30) REVERT: C 110 SER cc_start: 0.9242 (m) cc_final: 0.8937 (p) REVERT: C 125 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9285 (mt) REVERT: C 432 GLN cc_start: 0.7360 (tm-30) cc_final: 0.7082 (tm-30) REVERT: C 434 MET cc_start: 0.8675 (tmm) cc_final: 0.8414 (tpp) REVERT: K 90 TYR cc_start: 0.7263 (m-10) cc_final: 0.7057 (m-10) REVERT: M 101 ASP cc_start: 0.8845 (t0) cc_final: 0.8523 (t0) REVERT: N 36 PHE cc_start: 0.8045 (m-80) cc_final: 0.7840 (m-80) REVERT: N 47 LEU cc_start: 0.8684 (mp) cc_final: 0.7965 (mp) REVERT: N 48 ILE cc_start: 0.8599 (mm) cc_final: 0.8113 (tp) REVERT: N 93 ASN cc_start: 0.9192 (t0) cc_final: 0.8769 (t0) REVERT: B 589 ASP cc_start: 0.8696 (m-30) cc_final: 0.8422 (m-30) REVERT: D 112 TRP cc_start: 0.8853 (t-100) cc_final: 0.8627 (t-100) REVERT: D 271 MET cc_start: 0.7824 (mmm) cc_final: 0.7616 (mmm) REVERT: E 69 ILE cc_start: 0.7106 (tp) cc_final: 0.6858 (mt) REVERT: F 38 GLN cc_start: 0.7585 (pt0) cc_final: 0.7178 (pp30) REVERT: F 93 ASN cc_start: 0.6427 (t0) cc_final: 0.5691 (t0) REVERT: G 29 PHE cc_start: 0.8330 (t80) cc_final: 0.7911 (t80) REVERT: H 47 LEU cc_start: 0.8515 (mp) cc_final: 0.8135 (mm) REVERT: H 62 PHE cc_start: 0.7361 (m-80) cc_final: 0.6768 (m-80) REVERT: H 78 LEU cc_start: 0.7491 (mp) cc_final: 0.6666 (tt) REVERT: I 584 GLU cc_start: 0.8473 (pt0) cc_final: 0.8220 (pt0) REVERT: I 587 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9235 (mm) REVERT: J 378 CYS cc_start: 0.7498 (OUTLIER) cc_final: 0.7159 (t) REVERT: J 475 MET cc_start: 0.6804 (ptp) cc_final: 0.6560 (ptp) outliers start: 28 outliers final: 18 residues processed: 279 average time/residue: 0.1706 time to fit residues: 73.8888 Evaluate side-chains 216 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 195 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain M residue 77 SER Chi-restraints excluded: chain M residue 100 HIS Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 94 TYR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 100 CYS Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 103 TRP Chi-restraints excluded: chain I residue 587 LEU Chi-restraints excluded: chain I residue 660 LEU Chi-restraints excluded: chain J residue 339 ASN Chi-restraints excluded: chain J residue 378 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 258 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 72 HIS C 374 HIS C 411 ASN K 13 GLN L 37 GLN L 91 HIS N 37 GLN D 72 HIS D 114 GLN D 280 ASN D 374 HIS E 46 GLN F 3 GLN F 38 GLN G 76 ASN H 91 HIS I 625 ASN J 72 HIS J 280 ASN J 374 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.073146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.055323 restraints weight = 102992.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.057335 restraints weight = 51511.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.058614 restraints weight = 35169.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.059383 restraints weight = 28096.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.059866 restraints weight = 24549.117| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23161 Z= 0.148 Angle : 0.714 11.759 31693 Z= 0.337 Chirality : 0.047 0.313 3921 Planarity : 0.004 0.055 3804 Dihedral : 8.054 58.306 5696 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.94 % Favored : 94.91 % Rotamer: Outliers : 3.10 % Allowed : 14.96 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.16), residues: 2612 helix: 1.12 (0.27), residues: 405 sheet: -0.75 (0.18), residues: 840 loop : -1.15 (0.16), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 18 TYR 0.034 0.002 TYR F 94 PHE 0.021 0.002 PHE L 98 TRP 0.029 0.002 TRP H 35 HIS 0.004 0.001 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (22973) covalent geometry : angle 0.65823 / 0.32 (31179) SS BOND : bond 0.00404 / 0.20 ( 50) SS BOND : angle 1.43181 / 0.99 ( 100) hydrogen bonds : bond 0.04295 / 2.81 ( 603) hydrogen bonds : angle 5.48025 / 3.93 ( 1563) link_ALPHA1-2 : bond 0.00618 / 0.36 ( 11) link_ALPHA1-2 : angle 2.01571 / 1.19 ( 33) link_ALPHA1-3 : bond 0.01023 / 0.59 ( 11) link_ALPHA1-3 : angle 2.17068 / 1.24 ( 33) link_ALPHA1-6 : bond 0.00641 / 0.39 ( 11) link_ALPHA1-6 : angle 2.17428 / 1.26 ( 33) link_BETA1-4 : bond 0.00437 / 0.26 ( 42) link_BETA1-4 : angle 1.80190 / 1.35 ( 126) link_NAG-ASN : bond 0.00562 / 0.38 ( 63) link_NAG-ASN : angle 2.87985 / 2.08 ( 189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 217 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASN cc_start: 0.8862 (OUTLIER) cc_final: 0.8271 (t0) REVERT: A 625 ASN cc_start: 0.8075 (t0) cc_final: 0.7870 (t0) REVERT: A 657 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8471 (tm-30) REVERT: C 110 SER cc_start: 0.9215 (m) cc_final: 0.8867 (p) REVERT: C 432 GLN cc_start: 0.7460 (tm-30) cc_final: 0.7246 (tm-30) REVERT: C 479 TRP cc_start: 0.8488 (m-10) cc_final: 0.7969 (m-90) REVERT: K 90 TYR cc_start: 0.7321 (m-10) cc_final: 0.7062 (m-10) REVERT: K 102 LEU cc_start: 0.8999 (tp) cc_final: 0.8700 (tt) REVERT: L 37 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.8122 (tm-30) REVERT: L 73 LEU cc_start: 0.7525 (tp) cc_final: 0.7319 (tp) REVERT: L 93 ASN cc_start: 0.6410 (t0) cc_final: 0.6177 (t0) REVERT: M 101 ASP cc_start: 0.9023 (t0) cc_final: 0.8705 (t0) REVERT: N 4 MET cc_start: 0.6412 (tmm) cc_final: 0.5634 (tmm) REVERT: N 47 LEU cc_start: 0.8815 (mp) cc_final: 0.8248 (mp) REVERT: N 48 ILE cc_start: 0.8943 (mm) cc_final: 0.8584 (tp) REVERT: N 93 ASN cc_start: 0.9277 (t0) cc_final: 0.8817 (t0) REVERT: B 589 ASP cc_start: 0.8715 (m-30) cc_final: 0.8373 (m-30) REVERT: D 271 MET cc_start: 0.7964 (mmm) cc_final: 0.7699 (mmm) REVERT: D 340 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8559 (tm-30) REVERT: D 426 MET cc_start: 0.8391 (ptm) cc_final: 0.7921 (ptm) REVERT: E 13 GLN cc_start: 0.7186 (mm-40) cc_final: 0.6985 (mm-40) REVERT: E 69 ILE cc_start: 0.7538 (tp) cc_final: 0.7269 (mt) REVERT: F 38 GLN cc_start: 0.7456 (pt0) cc_final: 0.7223 (pp30) REVERT: F 93 ASN cc_start: 0.6788 (t0) cc_final: 0.6160 (t0) REVERT: G 29 PHE cc_start: 0.8128 (t80) cc_final: 0.7819 (t80) REVERT: G 34 MET cc_start: 0.7725 (mmm) cc_final: 0.7417 (mmp) REVERT: G 64 LYS cc_start: 0.9140 (mmmt) cc_final: 0.8569 (mmmm) REVERT: H 47 LEU cc_start: 0.8603 (mp) cc_final: 0.8163 (mm) REVERT: H 62 PHE cc_start: 0.7332 (m-80) cc_final: 0.6649 (m-80) REVERT: H 78 LEU cc_start: 0.7736 (mp) cc_final: 0.6894 (tt) REVERT: I 587 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9234 (mm) REVERT: I 625 ASN cc_start: 0.8377 (OUTLIER) cc_final: 0.7943 (p0) outliers start: 72 outliers final: 29 residues processed: 274 average time/residue: 0.1601 time to fit residues: 69.6333 Evaluate side-chains 217 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 183 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain M residue 100 HIS Chi-restraints excluded: chain N residue 94 TYR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 340 GLU Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 433 CYS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 103 TRP Chi-restraints excluded: chain I residue 587 LEU Chi-restraints excluded: chain I residue 625 ASN Chi-restraints excluded: chain J residue 33 ASN Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 339 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 228 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 244 optimal weight: 0.9980 chunk 189 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 133 optimal weight: 8.9990 chunk 207 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 211 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 195 ASN M 3 HIS D 302 ASN I 543 ASN I 625 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.072193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.054206 restraints weight = 103451.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.056123 restraints weight = 54279.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.057336 restraints weight = 38011.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.058066 restraints weight = 30827.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.058522 restraints weight = 27155.595| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23161 Z= 0.192 Angle : 0.723 11.998 31693 Z= 0.341 Chirality : 0.046 0.288 3921 Planarity : 0.004 0.061 3804 Dihedral : 7.929 58.536 5679 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.36 % Favored : 94.49 % Rotamer: Outliers : 3.32 % Allowed : 16.16 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.81 % 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: -0.98 (0.16), residues: 2612 helix: 1.10 (0.27), residues: 405 sheet: -0.60 (0.18), residues: 817 loop : -1.18 (0.16), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 19 TYR 0.027 0.001 TYR L 94 PHE 0.020 0.002 PHE F 98 TRP 0.012 0.001 TRP J 96 HIS 0.004 0.001 HIS J 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 (22973) covalent geometry : angle 0.66990 / 0.33 (31179) SS BOND : bond 0.00398 / 0.24 ( 50) SS BOND : angle 1.41175 / 0.98 ( 100) hydrogen bonds : bond 0.04236 / 2.76 ( 603) hydrogen bonds : angle 5.24352 / 3.76 ( 1563) link_ALPHA1-2 : bond 0.00496 / 0.30 ( 11) link_ALPHA1-2 : angle 2.09226 / 1.23 ( 33) link_ALPHA1-3 : bond 0.00891 / 0.52 ( 11) link_ALPHA1-3 : angle 2.24789 / 1.33 ( 33) link_ALPHA1-6 : bond 0.00591 / 0.35 ( 11) link_ALPHA1-6 : angle 2.27537 / 1.39 ( 33) link_BETA1-4 : bond 0.00362 / 0.21 ( 42) link_BETA1-4 : angle 1.71933 / 1.27 ( 126) link_NAG-ASN : bond 0.00519 / 0.36 ( 63) link_NAG-ASN : angle 2.81668 / 2.04 ( 189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 189 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASN cc_start: 0.8725 (OUTLIER) cc_final: 0.8263 (t0) REVERT: A 657 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8429 (tm-30) REVERT: C 432 GLN cc_start: 0.7434 (tm-30) cc_final: 0.7191 (tm-30) REVERT: C 479 TRP cc_start: 0.8490 (m-90) cc_final: 0.7980 (m-90) REVERT: K 75 ARG cc_start: 0.8590 (ptp90) cc_final: 0.8095 (ptp90) REVERT: K 90 TYR cc_start: 0.7439 (m-10) cc_final: 0.7109 (m-10) REVERT: L 37 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.8194 (tm-30) REVERT: L 45 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8174 (pttp) REVERT: L 93 ASN cc_start: 0.6663 (t0) cc_final: 0.6425 (t0) REVERT: M 101 ASP cc_start: 0.9027 (t0) cc_final: 0.8736 (t0) REVERT: N 4 MET cc_start: 0.6798 (tmm) cc_final: 0.6535 (tmm) REVERT: N 48 ILE cc_start: 0.8950 (mm) cc_final: 0.8623 (tp) REVERT: N 93 ASN cc_start: 0.9293 (t0) cc_final: 0.8823 (t0) REVERT: B 589 ASP cc_start: 0.8665 (m-30) cc_final: 0.8436 (m-30) REVERT: D 112 TRP cc_start: 0.8805 (t-100) cc_final: 0.8365 (t60) REVERT: D 137 ASN cc_start: 0.7035 (OUTLIER) cc_final: 0.6695 (m110) REVERT: D 426 MET cc_start: 0.8244 (ptm) cc_final: 0.7200 (ptm) REVERT: E 69 ILE cc_start: 0.7511 (tp) cc_final: 0.7192 (mt) REVERT: F 93 ASN cc_start: 0.6900 (t0) cc_final: 0.6380 (t0) REVERT: G 34 MET cc_start: 0.8012 (mmm) cc_final: 0.7597 (mmp) REVERT: G 64 LYS cc_start: 0.9171 (mmmt) cc_final: 0.8548 (mmmm) REVERT: H 47 LEU cc_start: 0.8949 (mp) cc_final: 0.8576 (mm) REVERT: H 78 LEU cc_start: 0.7725 (mp) cc_final: 0.6919 (tt) REVERT: I 587 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9326 (mm) REVERT: I 625 ASN cc_start: 0.8418 (OUTLIER) cc_final: 0.8064 (p0) REVERT: I 648 GLU cc_start: 0.8451 (pp20) cc_final: 0.8191 (pp20) outliers start: 77 outliers final: 43 residues processed: 249 average time/residue: 0.1530 time to fit residues: 60.9512 Evaluate side-chains 220 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 171 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 94 TYR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 302 ASN Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain G residue 83 ARG Chi-restraints excluded: chain G residue 103 TRP Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain I residue 570 VAL Chi-restraints excluded: chain I residue 583 VAL Chi-restraints excluded: chain I residue 587 LEU Chi-restraints excluded: chain I residue 625 ASN Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 339 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 13 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 210 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 chunk 235 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.072265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.054302 restraints weight = 103387.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.056238 restraints weight = 53999.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.057458 restraints weight = 37698.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.058212 restraints weight = 30556.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.058620 restraints weight = 26840.536| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23161 Z= 0.156 Angle : 0.691 11.965 31693 Z= 0.325 Chirality : 0.046 0.287 3921 Planarity : 0.004 0.059 3804 Dihedral : 7.710 59.375 5676 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.21 % Favored : 94.68 % Rotamer: Outliers : 3.41 % Allowed : 16.59 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.81 % 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: -0.87 (0.16), residues: 2612 helix: 1.32 (0.28), residues: 393 sheet: -0.61 (0.18), residues: 870 loop : -1.09 (0.16), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 75 TYR 0.021 0.001 TYR F 94 PHE 0.017 0.002 PHE E 58 TRP 0.042 0.001 TRP H 35 HIS 0.003 0.001 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (22973) covalent geometry : angle 0.63966 / 0.31 (31179) SS BOND : bond 0.00348 / 0.22 ( 50) SS BOND : angle 1.37312 / 0.94 ( 100) hydrogen bonds : bond 0.03945 / 2.57 ( 603) hydrogen bonds : angle 5.11856 / 3.67 ( 1563) link_ALPHA1-2 : bond 0.00508 / 0.29 ( 11) link_ALPHA1-2 : angle 2.04341 / 1.20 ( 33) link_ALPHA1-3 : bond 0.00969 / 0.56 ( 11) link_ALPHA1-3 : angle 2.17600 / 1.28 ( 33) link_ALPHA1-6 : bond 0.00626 / 0.37 ( 11) link_ALPHA1-6 : angle 2.22840 / 1.33 ( 33) link_BETA1-4 : bond 0.00394 / 0.23 ( 42) link_BETA1-4 : angle 1.65730 / 1.22 ( 126) link_NAG-ASN : bond 0.00506 / 0.34 ( 63) link_NAG-ASN : angle 2.71689 / 1.97 ( 189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 180 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASN cc_start: 0.8717 (OUTLIER) cc_final: 0.8238 (t0) REVERT: A 584 GLU cc_start: 0.8151 (pt0) cc_final: 0.7933 (pt0) REVERT: C 479 TRP cc_start: 0.8428 (m-90) cc_final: 0.7948 (m-90) REVERT: K 90 TYR cc_start: 0.7436 (m-10) cc_final: 0.7103 (m-10) REVERT: L 93 ASN cc_start: 0.6737 (t0) cc_final: 0.6482 (t0) REVERT: M 101 ASP cc_start: 0.9009 (t0) cc_final: 0.8697 (t0) REVERT: M 103 TRP cc_start: 0.7648 (m100) cc_final: 0.7309 (m-90) REVERT: N 48 ILE cc_start: 0.8964 (mm) cc_final: 0.8657 (tp) REVERT: N 93 ASN cc_start: 0.9288 (t0) cc_final: 0.8553 (p0) REVERT: B 589 ASP cc_start: 0.8659 (m-30) cc_final: 0.8428 (m-30) REVERT: D 112 TRP cc_start: 0.8815 (t-100) cc_final: 0.8383 (t60) REVERT: D 137 ASN cc_start: 0.6919 (OUTLIER) cc_final: 0.6554 (m110) REVERT: E 69 ILE cc_start: 0.7483 (tp) cc_final: 0.7239 (mt) REVERT: F 93 ASN cc_start: 0.6851 (t0) cc_final: 0.6416 (t0) REVERT: G 64 LYS cc_start: 0.9201 (mmmt) cc_final: 0.8605 (mmmm) REVERT: H 4 MET cc_start: 0.8051 (tpp) cc_final: 0.7832 (tpp) REVERT: H 47 LEU cc_start: 0.8736 (mp) cc_final: 0.8401 (mt) REVERT: H 61 ARG cc_start: 0.6510 (OUTLIER) cc_final: 0.5866 (pmt-80) REVERT: H 78 LEU cc_start: 0.7697 (mp) cc_final: 0.6871 (tt) REVERT: I 587 LEU cc_start: 0.9557 (OUTLIER) cc_final: 0.9314 (mm) REVERT: I 625 ASN cc_start: 0.8376 (OUTLIER) cc_final: 0.8123 (p0) REVERT: I 648 GLU cc_start: 0.8455 (pp20) cc_final: 0.8176 (pp20) outliers start: 79 outliers final: 44 residues processed: 244 average time/residue: 0.1465 time to fit residues: 57.7571 Evaluate side-chains 218 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 169 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain M residue 3 HIS Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 94 TYR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 100 CYS Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 88 CYS Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 83 ARG Chi-restraints excluded: chain G residue 103 TRP Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain I residue 587 LEU Chi-restraints excluded: chain I residue 604 CYS Chi-restraints excluded: chain I residue 625 ASN Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 202 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 30 optimal weight: 0.5980 chunk 215 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 145 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 49 optimal weight: 0.2980 chunk 163 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.072233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.054398 restraints weight = 101371.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.056400 restraints weight = 50627.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.057680 restraints weight = 34546.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.058468 restraints weight = 27586.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.058954 restraints weight = 24051.236| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23161 Z= 0.127 Angle : 0.673 12.064 31693 Z= 0.316 Chirality : 0.045 0.282 3921 Planarity : 0.004 0.060 3804 Dihedral : 7.430 56.917 5674 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.02 % Favored : 94.91 % Rotamer: Outliers : 3.36 % Allowed : 16.77 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.81 % 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: -0.76 (0.16), residues: 2612 helix: 1.38 (0.28), residues: 393 sheet: -0.48 (0.18), residues: 881 loop : -1.06 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 46 TYR 0.025 0.001 TYR L 49 PHE 0.013 0.001 PHE F 71 TRP 0.019 0.001 TRP H 35 HIS 0.003 0.001 HIS K 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (22973) covalent geometry : angle 0.62434 / 0.31 (31179) SS BOND : bond 0.00298 / 0.18 ( 50) SS BOND : angle 1.11621 / 0.75 ( 100) hydrogen bonds : bond 0.03613 / 2.34 ( 603) hydrogen bonds : angle 4.94568 / 3.54 ( 1563) link_ALPHA1-2 : bond 0.00525 / 0.30 ( 11) link_ALPHA1-2 : angle 1.98387 / 1.17 ( 33) link_ALPHA1-3 : bond 0.00998 / 0.57 ( 11) link_ALPHA1-3 : angle 2.09671 / 1.21 ( 33) link_ALPHA1-6 : bond 0.00690 / 0.41 ( 11) link_ALPHA1-6 : angle 2.15512 / 1.27 ( 33) link_BETA1-4 : bond 0.00406 / 0.24 ( 42) link_BETA1-4 : angle 1.57939 / 1.16 ( 126) link_NAG-ASN : bond 0.00525 / 0.35 ( 63) link_NAG-ASN : angle 2.64017 / 1.94 ( 189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 185 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASN cc_start: 0.8875 (OUTLIER) cc_final: 0.8268 (t0) REVERT: A 584 GLU cc_start: 0.8205 (pt0) cc_final: 0.7989 (pt0) REVERT: C 479 TRP cc_start: 0.8481 (m-90) cc_final: 0.7822 (m-90) REVERT: K 75 ARG cc_start: 0.8766 (ptp90) cc_final: 0.8233 (ptp90) REVERT: K 82 MET cc_start: 0.4930 (ptm) cc_final: 0.4229 (ptm) REVERT: K 90 TYR cc_start: 0.7250 (m-10) cc_final: 0.6924 (m-10) REVERT: L 93 ASN cc_start: 0.6661 (t0) cc_final: 0.6294 (t0) REVERT: M 101 ASP cc_start: 0.9112 (t0) cc_final: 0.8809 (t0) REVERT: M 103 TRP cc_start: 0.7794 (m100) cc_final: 0.7328 (m-90) REVERT: N 48 ILE cc_start: 0.9023 (mm) cc_final: 0.8659 (tp) REVERT: N 92 LEU cc_start: 0.9249 (tt) cc_final: 0.9024 (mt) REVERT: N 93 ASN cc_start: 0.9308 (t0) cc_final: 0.8540 (p0) REVERT: D 112 TRP cc_start: 0.8874 (t-100) cc_final: 0.8440 (t60) REVERT: D 137 ASN cc_start: 0.6915 (OUTLIER) cc_final: 0.6541 (m110) REVERT: E 69 ILE cc_start: 0.7508 (tp) cc_final: 0.7287 (mt) REVERT: F 93 ASN cc_start: 0.6702 (t0) cc_final: 0.6220 (t0) REVERT: G 64 LYS cc_start: 0.9197 (mmmt) cc_final: 0.8578 (mmmm) REVERT: G 75 ARG cc_start: 0.8513 (tpt90) cc_final: 0.8226 (tpt90) REVERT: H 47 LEU cc_start: 0.8896 (mp) cc_final: 0.8429 (mp) REVERT: H 61 ARG cc_start: 0.6469 (OUTLIER) cc_final: 0.6109 (pmt-80) REVERT: H 81 GLU cc_start: 0.9202 (pm20) cc_final: 0.8995 (pm20) REVERT: I 587 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9224 (mm) REVERT: I 625 ASN cc_start: 0.8689 (OUTLIER) cc_final: 0.8276 (p0) REVERT: I 648 GLU cc_start: 0.8601 (pp20) cc_final: 0.8145 (pp20) outliers start: 78 outliers final: 45 residues processed: 244 average time/residue: 0.1578 time to fit residues: 61.6846 Evaluate side-chains 218 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 168 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain M residue 3 HIS Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 94 TYR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 83 ARG Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain I residue 570 VAL Chi-restraints excluded: chain I residue 587 LEU Chi-restraints excluded: chain I residue 604 CYS Chi-restraints excluded: chain I residue 625 ASN Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 126 CYS Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 333 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 177 optimal weight: 0.3980 chunk 53 optimal weight: 0.8980 chunk 211 optimal weight: 0.9990 chunk 141 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 201 optimal weight: 5.9990 chunk 182 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 250 optimal weight: 0.7980 chunk 181 optimal weight: 30.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 13 GLN D 302 ASN E 99 ASN F 6 GLN J 33 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.072793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.054986 restraints weight = 102532.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.056935 restraints weight = 52883.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.058178 restraints weight = 36781.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.058937 restraints weight = 29622.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.059408 restraints weight = 26001.074| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 23161 Z= 0.124 Angle : 0.683 17.968 31693 Z= 0.320 Chirality : 0.045 0.275 3921 Planarity : 0.003 0.060 3804 Dihedral : 7.263 57.916 5669 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.17 % Favored : 94.75 % Rotamer: Outliers : 3.41 % Allowed : 17.33 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.81 % 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: -0.74 (0.16), residues: 2612 helix: 1.39 (0.28), residues: 393 sheet: -0.46 (0.17), residues: 918 loop : -1.06 (0.16), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 46 TYR 0.019 0.001 TYR G 97 PHE 0.024 0.001 PHE H 36 TRP 0.047 0.001 TRP H 35 HIS 0.007 0.001 HIS G 100A Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (22973) covalent geometry : angle 0.63593 / 0.31 (31179) SS BOND : bond 0.00364 / 0.19 ( 50) SS BOND : angle 1.34426 / 1.02 ( 100) hydrogen bonds : bond 0.03523 / 2.27 ( 603) hydrogen bonds : angle 4.86178 / 3.49 ( 1563) link_ALPHA1-2 : bond 0.00527 / 0.30 ( 11) link_ALPHA1-2 : angle 1.94324 / 1.15 ( 33) link_ALPHA1-3 : bond 0.00969 / 0.53 ( 11) link_ALPHA1-3 : angle 2.05702 / 1.19 ( 33) link_ALPHA1-6 : bond 0.00715 / 0.42 ( 11) link_ALPHA1-6 : angle 2.13525 / 1.26 ( 33) link_BETA1-4 : bond 0.00418 / 0.25 ( 42) link_BETA1-4 : angle 1.54032 / 1.13 ( 126) link_NAG-ASN : bond 0.00521 / 0.35 ( 63) link_NAG-ASN : angle 2.60517 / 1.91 ( 189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 180 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASN cc_start: 0.8801 (m-40) cc_final: 0.8235 (t0) REVERT: A 584 GLU cc_start: 0.8192 (pt0) cc_final: 0.7956 (pt0) REVERT: A 625 ASN cc_start: 0.8086 (t0) cc_final: 0.7787 (t0) REVERT: C 479 TRP cc_start: 0.8472 (m-90) cc_final: 0.7863 (m-90) REVERT: K 75 ARG cc_start: 0.8688 (ptp90) cc_final: 0.8207 (ptp90) REVERT: K 90 TYR cc_start: 0.7288 (m-10) cc_final: 0.6948 (m-10) REVERT: L 93 ASN cc_start: 0.6753 (t0) cc_final: 0.6384 (t0) REVERT: M 28 VAL cc_start: 0.8974 (p) cc_final: 0.8521 (p) REVERT: M 101 ASP cc_start: 0.9073 (t0) cc_final: 0.8796 (t0) REVERT: M 103 TRP cc_start: 0.7697 (m100) cc_final: 0.7240 (m-90) REVERT: N 48 ILE cc_start: 0.9038 (mm) cc_final: 0.8694 (tp) REVERT: N 93 ASN cc_start: 0.9299 (t0) cc_final: 0.8596 (p0) REVERT: D 112 TRP cc_start: 0.8894 (t-100) cc_final: 0.8490 (t60) REVERT: D 137 ASN cc_start: 0.6774 (OUTLIER) cc_final: 0.6404 (m110) REVERT: E 69 ILE cc_start: 0.7559 (tp) cc_final: 0.7239 (mt) REVERT: F 93 ASN cc_start: 0.6756 (t0) cc_final: 0.6280 (t0) REVERT: G 64 LYS cc_start: 0.9229 (mmmt) cc_final: 0.8646 (mmmm) REVERT: H 4 MET cc_start: 0.7873 (tpp) cc_final: 0.7378 (tpp) REVERT: H 33 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8564 (tp) REVERT: H 47 LEU cc_start: 0.8788 (mp) cc_final: 0.8360 (mt) REVERT: H 61 ARG cc_start: 0.6408 (OUTLIER) cc_final: 0.6074 (pmt-80) REVERT: H 78 LEU cc_start: 0.7790 (mp) cc_final: 0.6762 (tt) REVERT: I 589 ASP cc_start: 0.8854 (t0) cc_final: 0.8651 (t0) REVERT: I 625 ASN cc_start: 0.8626 (OUTLIER) cc_final: 0.8251 (p0) REVERT: I 647 GLU cc_start: 0.9043 (tt0) cc_final: 0.8525 (tm-30) REVERT: J 161 MET cc_start: 0.8401 (mmm) cc_final: 0.8197 (tpt) outliers start: 79 outliers final: 51 residues processed: 242 average time/residue: 0.1473 time to fit residues: 58.0832 Evaluate side-chains 220 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 165 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain M residue 3 HIS Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 94 TYR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 83 ARG Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain I residue 570 VAL Chi-restraints excluded: chain I residue 604 CYS Chi-restraints excluded: chain I residue 625 ASN Chi-restraints excluded: chain J residue 33 ASN Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 126 CYS Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 333 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 214 optimal weight: 1.9990 chunk 187 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 217 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 46 GLN F 55 GLN J 33 ASN J 66 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.070685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.052587 restraints weight = 102949.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.054469 restraints weight = 53947.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.055671 restraints weight = 37905.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.056394 restraints weight = 30826.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.056843 restraints weight = 27215.159| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 23161 Z= 0.245 Angle : 0.777 12.494 31693 Z= 0.368 Chirality : 0.047 0.247 3921 Planarity : 0.004 0.059 3804 Dihedral : 7.684 58.913 5667 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.13 % Favored : 93.80 % Rotamer: Outliers : 3.10 % Allowed : 18.10 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.16), residues: 2612 helix: 1.11 (0.27), residues: 393 sheet: -0.54 (0.17), residues: 892 loop : -1.22 (0.16), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 66 TYR 0.027 0.002 TYR L 94 PHE 0.023 0.002 PHE K 67 TRP 0.032 0.002 TRP H 35 HIS 0.011 0.001 HIS G 100A Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.25 (22973) covalent geometry : angle 0.73068 / 0.36 (31179) SS BOND : bond 0.00453 / 0.28 ( 50) SS BOND : angle 1.70359 / 1.16 ( 100) hydrogen bonds : bond 0.04038 / 2.64 ( 603) hydrogen bonds : angle 5.10491 / 3.66 ( 1563) link_ALPHA1-2 : bond 0.00375 / 0.23 ( 11) link_ALPHA1-2 : angle 2.07625 / 1.18 ( 33) link_ALPHA1-3 : bond 0.00728 / 0.37 ( 11) link_ALPHA1-3 : angle 2.28159 / 1.40 ( 33) link_ALPHA1-6 : bond 0.00585 / 0.35 ( 11) link_ALPHA1-6 : angle 2.39079 / 1.48 ( 33) link_BETA1-4 : bond 0.00357 / 0.21 ( 42) link_BETA1-4 : angle 1.62157 / 1.18 ( 126) link_NAG-ASN : bond 0.00569 / 0.38 ( 63) link_NAG-ASN : angle 2.69891 / 1.97 ( 189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 168 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASN cc_start: 0.8667 (OUTLIER) cc_final: 0.8232 (t0) REVERT: C 479 TRP cc_start: 0.8545 (m-90) cc_final: 0.8001 (m-90) REVERT: K 75 ARG cc_start: 0.8643 (ptp90) cc_final: 0.8108 (ptp90) REVERT: K 82 ASN cc_start: 0.7458 (p0) cc_final: 0.6902 (p0) REVERT: L 93 ASN cc_start: 0.7076 (t0) cc_final: 0.6011 (p0) REVERT: M 101 ASP cc_start: 0.9056 (t0) cc_final: 0.8797 (t0) REVERT: M 103 TRP cc_start: 0.7742 (m100) cc_final: 0.7354 (m-90) REVERT: N 4 MET cc_start: 0.7311 (tmm) cc_final: 0.6994 (tmm) REVERT: N 48 ILE cc_start: 0.9086 (mm) cc_final: 0.8746 (tp) REVERT: N 93 ASN cc_start: 0.9257 (t0) cc_final: 0.8587 (p0) REVERT: B 589 ASP cc_start: 0.8620 (m-30) cc_final: 0.8376 (m-30) REVERT: D 137 ASN cc_start: 0.6844 (OUTLIER) cc_final: 0.6445 (m110) REVERT: E 69 ILE cc_start: 0.7409 (tp) cc_final: 0.7119 (mt) REVERT: F 93 ASN cc_start: 0.7209 (t0) cc_final: 0.6796 (t0) REVERT: H 61 ARG cc_start: 0.6571 (OUTLIER) cc_final: 0.6185 (pmt-80) REVERT: H 78 LEU cc_start: 0.7723 (mp) cc_final: 0.6724 (tt) REVERT: I 625 ASN cc_start: 0.8604 (OUTLIER) cc_final: 0.8359 (p0) REVERT: I 647 GLU cc_start: 0.8872 (tt0) cc_final: 0.8553 (tm-30) outliers start: 72 outliers final: 52 residues processed: 227 average time/residue: 0.1475 time to fit residues: 54.9980 Evaluate side-chains 212 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 156 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain M residue 3 HIS Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 94 TYR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain E residue 3 HIS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain G residue 83 ARG Chi-restraints excluded: chain G residue 98 CYS Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain I residue 570 VAL Chi-restraints excluded: chain I residue 604 CYS Chi-restraints excluded: chain I residue 625 ASN Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 333 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 108 optimal weight: 0.0040 chunk 217 optimal weight: 7.9990 chunk 247 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 153 optimal weight: 0.0770 chunk 43 optimal weight: 0.0070 chunk 92 optimal weight: 9.9990 chunk 235 optimal weight: 0.8980 overall best weight: 0.3368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 625 ASN J 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.072456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.054642 restraints weight = 101369.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.056665 restraints weight = 50180.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.057939 restraints weight = 34058.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.058728 restraints weight = 27162.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.059206 restraints weight = 23677.282| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23161 Z= 0.117 Angle : 0.707 12.233 31693 Z= 0.334 Chirality : 0.045 0.278 3921 Planarity : 0.004 0.065 3804 Dihedral : 7.142 59.436 5667 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.59 % Favored : 95.29 % Rotamer: Outliers : 2.59 % Allowed : 19.09 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.16), residues: 2612 helix: 1.26 (0.27), residues: 393 sheet: -0.37 (0.17), residues: 924 loop : -1.05 (0.17), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 43 TYR 0.020 0.001 TYR F 94 PHE 0.021 0.001 PHE E 58 TRP 0.054 0.001 TRP H 35 HIS 0.004 0.001 HIS G 100A Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (22973) covalent geometry : angle 0.66324 / 0.32 (31179) SS BOND : bond 0.00308 / 0.18 ( 50) SS BOND : angle 1.43507 / 0.97 ( 100) hydrogen bonds : bond 0.03496 / 2.27 ( 603) hydrogen bonds : angle 4.86481 / 3.49 ( 1563) link_ALPHA1-2 : bond 0.00533 / 0.29 ( 11) link_ALPHA1-2 : angle 1.90364 / 1.13 ( 33) link_ALPHA1-3 : bond 0.01072 / 0.62 ( 11) link_ALPHA1-3 : angle 2.00104 / 1.12 ( 33) link_ALPHA1-6 : bond 0.00785 / 0.45 ( 11) link_ALPHA1-6 : angle 2.12919 / 1.22 ( 33) link_BETA1-4 : bond 0.00447 / 0.27 ( 42) link_BETA1-4 : angle 1.48690 / 1.08 ( 126) link_NAG-ASN : bond 0.00524 / 0.35 ( 63) link_NAG-ASN : angle 2.54579 / 1.86 ( 189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 177 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASN cc_start: 0.8822 (OUTLIER) cc_final: 0.8280 (t0) REVERT: C 173 TYR cc_start: 0.8569 (p90) cc_final: 0.8326 (p90) REVERT: C 475 MET cc_start: 0.7385 (pmm) cc_final: 0.6145 (ptp) REVERT: C 479 TRP cc_start: 0.8442 (m-90) cc_final: 0.7784 (m-90) REVERT: K 90 TYR cc_start: 0.7154 (m-10) cc_final: 0.6881 (m-10) REVERT: L 93 ASN cc_start: 0.6939 (t0) cc_final: 0.5924 (p0) REVERT: M 101 ASP cc_start: 0.9050 (t0) cc_final: 0.8787 (t0) REVERT: M 103 TRP cc_start: 0.7769 (m100) cc_final: 0.7312 (m-90) REVERT: N 4 MET cc_start: 0.7507 (tmm) cc_final: 0.6933 (tmm) REVERT: N 48 ILE cc_start: 0.9044 (mm) cc_final: 0.8666 (tp) REVERT: N 93 ASN cc_start: 0.9308 (t0) cc_final: 0.8659 (p0) REVERT: B 589 ASP cc_start: 0.8814 (m-30) cc_final: 0.8517 (m-30) REVERT: D 112 TRP cc_start: 0.8869 (t-100) cc_final: 0.8475 (t60) REVERT: D 137 ASN cc_start: 0.6817 (OUTLIER) cc_final: 0.6471 (m110) REVERT: D 434 MET cc_start: 0.8067 (tpt) cc_final: 0.7703 (tpt) REVERT: E 69 ILE cc_start: 0.7375 (tp) cc_final: 0.7075 (mt) REVERT: F 93 ASN cc_start: 0.7100 (t0) cc_final: 0.6637 (t0) REVERT: G 29 PHE cc_start: 0.7751 (t80) cc_final: 0.7524 (t80) REVERT: G 31 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7145 (t0) REVERT: G 97 TYR cc_start: 0.7621 (t80) cc_final: 0.7276 (t80) REVERT: H 4 MET cc_start: 0.6893 (tpp) cc_final: 0.6320 (tpp) REVERT: H 61 ARG cc_start: 0.6402 (OUTLIER) cc_final: 0.6082 (pmt-80) REVERT: H 78 LEU cc_start: 0.7808 (mp) cc_final: 0.6866 (tt) REVERT: I 625 ASN cc_start: 0.8714 (OUTLIER) cc_final: 0.8445 (p0) REVERT: I 647 GLU cc_start: 0.9040 (tt0) cc_final: 0.8630 (tm-30) REVERT: J 161 MET cc_start: 0.8526 (mmm) cc_final: 0.8211 (mmm) outliers start: 60 outliers final: 43 residues processed: 222 average time/residue: 0.1540 time to fit residues: 55.1995 Evaluate side-chains 212 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 164 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain M residue 3 HIS Chi-restraints excluded: chain N residue 94 TYR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 83 ARG Chi-restraints excluded: chain G residue 98 CYS Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain I residue 530 MET Chi-restraints excluded: chain I residue 570 VAL Chi-restraints excluded: chain I residue 604 CYS Chi-restraints excluded: chain I residue 625 ASN Chi-restraints excluded: chain J residue 33 ASN Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 126 CYS Chi-restraints excluded: chain J residue 135 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 57 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 215 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 chunk 111 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 217 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 81 GLN G 100AHIS J 33 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.072295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.054405 restraints weight = 102197.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.056346 restraints weight = 53021.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.057581 restraints weight = 36914.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.058333 restraints weight = 29833.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.058777 restraints weight = 26204.793| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23161 Z= 0.141 Angle : 0.705 11.851 31693 Z= 0.332 Chirality : 0.045 0.249 3921 Planarity : 0.004 0.061 3804 Dihedral : 7.123 58.999 5667 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.44 % Favored : 94.49 % Rotamer: Outliers : 2.54 % Allowed : 19.27 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.81 % 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: -0.72 (0.16), residues: 2612 helix: 1.23 (0.27), residues: 393 sheet: -0.36 (0.18), residues: 896 loop : -1.05 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 75 TYR 0.030 0.001 TYR F 94 PHE 0.015 0.001 PHE L 71 TRP 0.048 0.001 TRP H 35 HIS 0.003 0.001 HIS G 100A Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (22973) covalent geometry : angle 0.66207 / 0.32 (31179) SS BOND : bond 0.00338 / 0.21 ( 50) SS BOND : angle 1.46533 / 1.00 ( 100) hydrogen bonds : bond 0.03521 / 2.30 ( 603) hydrogen bonds : angle 4.85006 / 3.48 ( 1563) link_ALPHA1-2 : bond 0.00434 / 0.25 ( 11) link_ALPHA1-2 : angle 1.91443 / 1.12 ( 33) link_ALPHA1-3 : bond 0.00935 / 0.53 ( 11) link_ALPHA1-3 : angle 2.02007 / 1.17 ( 33) link_ALPHA1-6 : bond 0.00680 / 0.40 ( 11) link_ALPHA1-6 : angle 2.14793 / 1.28 ( 33) link_BETA1-4 : bond 0.00376 / 0.22 ( 42) link_BETA1-4 : angle 1.49358 / 1.08 ( 126) link_NAG-ASN : bond 0.00503 / 0.33 ( 63) link_NAG-ASN : angle 2.52046 / 1.85 ( 189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 168 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASN cc_start: 0.8776 (OUTLIER) cc_final: 0.8281 (t0) REVERT: C 173 TYR cc_start: 0.8595 (p90) cc_final: 0.8312 (p90) REVERT: C 475 MET cc_start: 0.7199 (pmm) cc_final: 0.6040 (ptp) REVERT: C 479 TRP cc_start: 0.8459 (m-90) cc_final: 0.7922 (m-90) REVERT: K 75 ARG cc_start: 0.8617 (ptp90) cc_final: 0.8040 (ptp90) REVERT: L 93 ASN cc_start: 0.7054 (t0) cc_final: 0.6072 (p0) REVERT: M 101 ASP cc_start: 0.9025 (t0) cc_final: 0.8752 (t0) REVERT: M 103 TRP cc_start: 0.7755 (m100) cc_final: 0.7336 (m-90) REVERT: N 4 MET cc_start: 0.7555 (tmm) cc_final: 0.6607 (tmm) REVERT: N 48 ILE cc_start: 0.9061 (mm) cc_final: 0.8693 (tp) REVERT: N 93 ASN cc_start: 0.9282 (t0) cc_final: 0.8674 (p0) REVERT: B 589 ASP cc_start: 0.8661 (m-30) cc_final: 0.8380 (m-30) REVERT: D 137 ASN cc_start: 0.6859 (OUTLIER) cc_final: 0.6528 (m110) REVERT: E 69 ILE cc_start: 0.7307 (tp) cc_final: 0.6981 (mt) REVERT: E 82 MET cc_start: 0.5610 (tmm) cc_final: 0.5116 (ppp) REVERT: F 93 ASN cc_start: 0.7288 (t0) cc_final: 0.6799 (t0) REVERT: G 29 PHE cc_start: 0.7907 (t80) cc_final: 0.7705 (t80) REVERT: H 4 MET cc_start: 0.7139 (tpp) cc_final: 0.6805 (tpp) REVERT: H 33 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8496 (tp) REVERT: H 61 ARG cc_start: 0.6543 (OUTLIER) cc_final: 0.6135 (pmt-80) REVERT: H 78 LEU cc_start: 0.7786 (mp) cc_final: 0.6843 (tt) REVERT: I 625 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.8359 (p0) REVERT: I 647 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8539 (tm-30) REVERT: J 161 MET cc_start: 0.8444 (mmm) cc_final: 0.8142 (mmm) outliers start: 59 outliers final: 42 residues processed: 212 average time/residue: 0.1544 time to fit residues: 52.6258 Evaluate side-chains 212 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 164 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain M residue 3 HIS Chi-restraints excluded: chain N residue 94 TYR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 23 CYS Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 83 ARG Chi-restraints excluded: chain G residue 98 CYS Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain I residue 530 MET Chi-restraints excluded: chain I residue 604 CYS Chi-restraints excluded: chain I residue 625 ASN Chi-restraints excluded: chain I residue 647 GLU Chi-restraints excluded: chain J residue 33 ASN Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 126 CYS Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 333 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 115 optimal weight: 3.9990 chunk 237 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 chunk 40 optimal weight: 8.9990 chunk 186 optimal weight: 0.9980 chunk 241 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 211 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 81 GLN J 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.072228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.054350 restraints weight = 102966.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.056291 restraints weight = 53245.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.057525 restraints weight = 37057.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.058276 restraints weight = 29915.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.058742 restraints weight = 26304.650| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23161 Z= 0.142 Angle : 0.720 11.813 31693 Z= 0.340 Chirality : 0.045 0.250 3921 Planarity : 0.003 0.063 3804 Dihedral : 7.076 58.554 5667 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.36 % Favored : 94.56 % Rotamer: Outliers : 2.24 % Allowed : 19.57 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.81 % 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: -0.70 (0.16), residues: 2612 helix: 1.23 (0.27), residues: 393 sheet: -0.33 (0.18), residues: 896 loop : -1.04 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 75 TYR 0.029 0.001 TYR F 94 PHE 0.020 0.001 PHE B 519 TRP 0.046 0.001 TRP H 35 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (22973) covalent geometry : angle 0.67477 / 0.33 (31179) SS BOND : bond 0.00404 / 0.18 ( 50) SS BOND : angle 1.90440 / 1.20 ( 100) hydrogen bonds : bond 0.03483 / 2.27 ( 603) hydrogen bonds : angle 4.82033 / 3.46 ( 1563) link_ALPHA1-2 : bond 0.00423 / 0.24 ( 11) link_ALPHA1-2 : angle 1.89833 / 1.11 ( 33) link_ALPHA1-3 : bond 0.00948 / 0.53 ( 11) link_ALPHA1-3 : angle 2.01381 / 1.17 ( 33) link_ALPHA1-6 : bond 0.00687 / 0.40 ( 11) link_ALPHA1-6 : angle 2.13968 / 1.26 ( 33) link_BETA1-4 : bond 0.00372 / 0.22 ( 42) link_BETA1-4 : angle 1.47497 / 1.07 ( 126) link_NAG-ASN : bond 0.00490 / 0.32 ( 63) link_NAG-ASN : angle 2.50992 / 1.85 ( 189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 164 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 ASN cc_start: 0.8841 (OUTLIER) cc_final: 0.8273 (t0) REVERT: C 173 TYR cc_start: 0.8637 (p90) cc_final: 0.8392 (p90) REVERT: C 475 MET cc_start: 0.7186 (pmm) cc_final: 0.6036 (ptp) REVERT: C 479 TRP cc_start: 0.8517 (m-90) cc_final: 0.7881 (m-90) REVERT: K 86 ASP cc_start: 0.7339 (m-30) cc_final: 0.6168 (p0) REVERT: L 93 ASN cc_start: 0.7031 (t0) cc_final: 0.6035 (p0) REVERT: M 101 ASP cc_start: 0.9073 (t0) cc_final: 0.8803 (t0) REVERT: M 103 TRP cc_start: 0.7789 (m100) cc_final: 0.7330 (m-90) REVERT: N 4 MET cc_start: 0.7589 (tmm) cc_final: 0.6635 (tmm) REVERT: N 48 ILE cc_start: 0.9098 (mm) cc_final: 0.8717 (tp) REVERT: N 93 ASN cc_start: 0.9295 (t0) cc_final: 0.8669 (p0) REVERT: B 589 ASP cc_start: 0.8792 (m-30) cc_final: 0.8494 (m-30) REVERT: D 137 ASN cc_start: 0.6909 (OUTLIER) cc_final: 0.6574 (m110) REVERT: E 69 ILE cc_start: 0.7361 (tp) cc_final: 0.7068 (mt) REVERT: E 82 MET cc_start: 0.5645 (tmm) cc_final: 0.5342 (ppp) REVERT: F 93 ASN cc_start: 0.7263 (t0) cc_final: 0.6763 (t0) REVERT: G 29 PHE cc_start: 0.7903 (t80) cc_final: 0.7657 (t80) REVERT: G 31 ASP cc_start: 0.8015 (t0) cc_final: 0.7705 (t0) REVERT: H 4 MET cc_start: 0.7180 (tpp) cc_final: 0.6904 (tpp) REVERT: H 33 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8469 (tp) REVERT: H 61 ARG cc_start: 0.6640 (OUTLIER) cc_final: 0.6281 (pmt-80) REVERT: H 78 LEU cc_start: 0.7782 (mp) cc_final: 0.6846 (tt) REVERT: I 625 ASN cc_start: 0.8720 (OUTLIER) cc_final: 0.8402 (p0) REVERT: I 647 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8646 (tm-30) REVERT: J 161 MET cc_start: 0.8541 (mmm) cc_final: 0.8283 (mmm) outliers start: 52 outliers final: 42 residues processed: 202 average time/residue: 0.1537 time to fit residues: 50.2630 Evaluate side-chains 210 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 162 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain K residue 3 HIS Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain M residue 3 HIS Chi-restraints excluded: chain N residue 94 TYR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 137 ASN Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 94 TYR Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 83 ARG Chi-restraints excluded: chain G residue 98 CYS Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain I residue 604 CYS Chi-restraints excluded: chain I residue 625 ASN Chi-restraints excluded: chain I residue 647 GLU Chi-restraints excluded: chain J residue 33 ASN Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 126 CYS Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 333 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 50 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 213 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 228 optimal weight: 0.0570 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 81 GLN E 46 GLN ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.070966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.052973 restraints weight = 103007.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.054873 restraints weight = 53742.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.056073 restraints weight = 37620.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.056802 restraints weight = 30539.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.057258 restraints weight = 26947.508| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 23161 Z= 0.212 Angle : 0.759 11.323 31693 Z= 0.359 Chirality : 0.046 0.231 3921 Planarity : 0.004 0.061 3804 Dihedral : 7.326 58.111 5665 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.90 % Favored : 94.07 % Rotamer: Outliers : 2.20 % Allowed : 19.66 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.16), residues: 2612 helix: 1.14 (0.27), residues: 393 sheet: -0.41 (0.18), residues: 892 loop : -1.10 (0.16), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 66 TYR 0.028 0.002 TYR F 94 PHE 0.016 0.002 PHE H 36 TRP 0.057 0.002 TRP H 35 HIS 0.005 0.001 HIS J 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.21 (22973) covalent geometry : angle 0.71292 / 0.35 (31179) SS BOND : bond 0.00400 / 0.21 ( 50) SS BOND : angle 2.03761 / 1.30 ( 100) hydrogen bonds : bond 0.03876 / 2.53 ( 603) hydrogen bonds : angle 5.02131 / 3.61 ( 1563) link_ALPHA1-2 : bond 0.00334 / 0.20 ( 11) link_ALPHA1-2 : angle 1.95988 / 1.13 ( 33) link_ALPHA1-3 : bond 0.00811 / 0.46 ( 11) link_ALPHA1-3 : angle 2.13402 / 1.30 ( 33) link_ALPHA1-6 : bond 0.00642 / 0.36 ( 11) link_ALPHA1-6 : angle 2.31078 / 1.42 ( 33) link_BETA1-4 : bond 0.00341 / 0.20 ( 42) link_BETA1-4 : angle 1.52563 / 1.10 ( 126) link_NAG-ASN : bond 0.00515 / 0.34 ( 63) link_NAG-ASN : angle 2.56477 / 1.88 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4035.53 seconds wall clock time: 70 minutes 52.03 seconds (4252.03 seconds total)