Starting phenix.real_space_refine on Wed Nov 19 04:24:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5vn8_8717/11_2025/5vn8_8717.cif Found real_map, /net/cci-nas-00/data/ceres_data/5vn8_8717/11_2025/5vn8_8717.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5vn8_8717/11_2025/5vn8_8717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5vn8_8717/11_2025/5vn8_8717.map" model { file = "/net/cci-nas-00/data/ceres_data/5vn8_8717/11_2025/5vn8_8717.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5vn8_8717/11_2025/5vn8_8717.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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 120 5.16 5 C 12840 2.51 5 N 3444 2.21 5 O 4185 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20589 Number of models: 1 Model: "" Number of chains: 51 Chain: "G" Number of atoms: 3393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3393 Classifications: {'peptide': 435} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1104 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 137} Chain breaks: 1 Chain: "H" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1013 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "L" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 836 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "D" Number of atoms: 3393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3393 Classifications: {'peptide': 435} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1104 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 137} Chain breaks: 1 Chain: "F" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1013 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "J" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 836 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "E" Number of atoms: 3393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3393 Classifications: {'peptide': 435} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1104 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 137} Chain breaks: 1 Chain: "I" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1013 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "K" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 836 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 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: "U" 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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 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: "l" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "r" Number of atoms: 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: "G" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.14, per 1000 atoms: 0.25 Number of scatterers: 20589 At special positions: 0 Unit cell: (179.47, 176.85, 117.9, 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 120 16.00 O 4185 8.00 N 3444 7.00 C 12840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.02 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.02 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS A 605 " distance=1.99 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.04 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.02 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS B 605 " distance=2.12 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.02 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS C 605 " distance=2.00 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " 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=6, symmetry=0 Links applied ALPHA1-3 " BMA P 3 " - " MAN P 4 " " BMA a 3 " - " MAN a 4 " " BMA l 3 " - " MAN l 4 " BETA1-4 " 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 S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " 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 i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG A 702 " - " ASN A 616 " " NAG A 703 " - " ASN A 625 " " NAG A 704 " - " ASN A 637 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 616 " " NAG B 703 " - " ASN B 625 " " NAG B 704 " - " ASN B 637 " " NAG C 701 " - " ASN C 611 " " NAG C 702 " - " ASN C 616 " " NAG C 703 " - " ASN C 625 " " NAG C 704 " - " ASN C 637 " " NAG D 601 " - " ASN D 88 " " NAG D 602 " - " ASN D 160 " " NAG D 618 " - " ASN D 301 " " NAG D 621 " - " ASN D 339 " " NAG D 622 " - " ASN D 355 " " NAG D 629 " - " ASN D 392 " " NAG D 630 " - " ASN D 397 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 160 " " NAG E 618 " - " ASN E 301 " " NAG E 621 " - " ASN E 339 " " NAG E 622 " - " ASN E 355 " " NAG E 629 " - " ASN E 392 " " NAG E 630 " - " ASN E 397 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 160 " " NAG G 618 " - " ASN G 301 " " NAG G 621 " - " ASN G 339 " " NAG G 622 " - " ASN G 355 " " NAG G 629 " - " ASN G 392 " " NAG G 630 " - " ASN G 397 " " NAG M 1 " - " ASN G 197 " " NAG N 1 " - " ASN G 234 " " NAG O 1 " - " ASN G 241 " " NAG P 1 " - " ASN G 262 " " NAG Q 1 " - " ASN G 276 " " NAG R 1 " - " ASN G 295 " " NAG S 1 " - " ASN G 332 " " NAG T 1 " - " ASN G 362 " " NAG U 1 " - " ASN G 386 " " NAG V 1 " - " ASN G 413 " " NAG W 1 " - " ASN G 448 " " NAG X 1 " - " ASN D 197 " " NAG Y 1 " - " ASN D 234 " " NAG Z 1 " - " ASN D 241 " " NAG a 1 " - " ASN D 262 " " NAG b 1 " - " ASN D 276 " " NAG c 1 " - " ASN D 295 " " NAG d 1 " - " ASN D 332 " " NAG e 1 " - " ASN D 362 " " NAG f 1 " - " ASN D 386 " " NAG g 1 " - " ASN D 413 " " NAG h 1 " - " ASN D 448 " " NAG i 1 " - " ASN E 197 " " NAG j 1 " - " ASN E 234 " " NAG k 1 " - " ASN E 241 " " NAG l 1 " - " ASN E 262 " " NAG m 1 " - " ASN E 276 " " NAG n 1 " - " ASN E 295 " " NAG o 1 " - " ASN E 332 " " NAG p 1 " - " ASN E 362 " " NAG q 1 " - " ASN E 386 " " NAG r 1 " - " ASN E 413 " " NAG s 1 " - " ASN E 448 " Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 772.1 milliseconds 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4488 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 39 sheets defined 20.1% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'G' and resid 100 through 106 Processing helix chain 'G' and resid 109 through 115 removed outlier: 3.520A pdb=" N SER G 115 " --> pdb=" O LEU G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 185E through 186 removed outlier: 4.348A pdb=" N ASN G 185H" --> pdb=" O ASN G 185E" (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 353 removed outlier: 3.744A pdb=" N GLU G 340 " --> pdb=" O ALA G 336 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU G 351 " --> pdb=" O ALA G 347 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLN G 352 " --> pdb=" O LYS G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.872A pdb=" N VAL G 372 " --> pdb=" O ASP G 368 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR G 373 " --> pdb=" O PRO G 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 368 through 373' Processing helix chain 'G' and resid 476 through 481 removed outlier: 3.975A pdb=" N SER G 481 " --> pdb=" O ASP G 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 546 removed outlier: 3.718A pdb=" N SER A 534 " --> pdb=" O MET A 530 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL A 539 " --> pdb=" O MET A 535 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 544 " --> pdb=" O GLN A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 570 removed outlier: 3.672A pdb=" N VAL A 570 " --> pdb=" O LEU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 593 removed outlier: 3.522A pdb=" N GLN A 575 " --> pdb=" O TRP A 571 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 582 " --> pdb=" O ALA A 578 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN A 591 " --> pdb=" O LEU A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 596 No H-bonds generated for 'chain 'A' and resid 594 through 596' Processing helix chain 'A' and resid 619 through 626 removed outlier: 3.523A pdb=" N TRP A 623 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP A 624 " --> pdb=" O ASN A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 633 Processing helix chain 'A' and resid 638 through 663 removed outlier: 4.033A pdb=" N THR A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU A 647 " --> pdb=" O TYR A 643 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLN A 658 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 660 " --> pdb=" O ASN A 656 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU A 662 " --> pdb=" O GLN A 658 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 663 " --> pdb=" O GLU A 659 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.885A pdb=" N PHE H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 64 removed outlier: 3.533A pdb=" N GLN H 64 " --> pdb=" O ALA H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.620A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.771A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 106 Processing helix chain 'D' and resid 109 through 115 removed outlier: 3.520A pdb=" N SER D 115 " --> pdb=" O LEU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 185E through 186 removed outlier: 4.348A pdb=" N ASN D 185H" --> pdb=" O ASN D 185E" (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 353 removed outlier: 3.743A pdb=" N GLU D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU D 351 " --> pdb=" O ALA D 347 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN D 352 " --> pdb=" O LYS D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 removed outlier: 3.872A pdb=" N VAL D 372 " --> pdb=" O ASP D 368 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR D 373 " --> pdb=" O PRO D 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 368 through 373' Processing helix chain 'D' and resid 476 through 481 removed outlier: 3.976A pdb=" N SER D 481 " --> pdb=" O ASP D 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 546 removed outlier: 3.717A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL B 539 " --> pdb=" O MET B 535 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU B 544 " --> pdb=" O GLN B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 570 removed outlier: 3.673A pdb=" N VAL B 570 " --> pdb=" O LEU B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 593 removed outlier: 3.522A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA B 582 " --> pdb=" O ALA B 578 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN B 591 " --> pdb=" O LEU B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 596 No H-bonds generated for 'chain 'B' and resid 594 through 596' Processing helix chain 'B' and resid 619 through 626 removed outlier: 3.524A pdb=" N TRP B 623 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP B 624 " --> pdb=" O ASN B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 633 Processing helix chain 'B' and resid 638 through 663 removed outlier: 4.033A pdb=" N THR B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLN B 658 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B 660 " --> pdb=" O ASN B 656 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU B 661 " --> pdb=" O GLU B 657 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU B 662 " --> pdb=" O GLN B 658 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 663 " --> pdb=" O GLU B 659 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.884A pdb=" N PHE F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 64 removed outlier: 3.533A pdb=" N GLN F 64 " --> pdb=" O ALA F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.620A pdb=" N THR F 87 " --> pdb=" O SER F 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.771A pdb=" N PHE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 106 Processing helix chain 'E' and resid 109 through 115 removed outlier: 3.519A pdb=" N SER E 115 " --> pdb=" O LEU E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 185E through 186 removed outlier: 4.349A pdb=" N ASN E 185H" --> pdb=" O ASN E 185E" (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 353 removed outlier: 3.744A pdb=" N GLU E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU E 351 " --> pdb=" O ALA E 347 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLN E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.872A pdb=" N VAL E 372 " --> pdb=" O ASP E 368 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR E 373 " --> pdb=" O PRO E 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 368 through 373' Processing helix chain 'E' and resid 476 through 481 removed outlier: 3.975A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 546 removed outlier: 3.718A pdb=" N SER C 534 " --> pdb=" O MET C 530 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL C 539 " --> pdb=" O MET C 535 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU C 544 " --> pdb=" O GLN C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 570 removed outlier: 3.673A pdb=" N VAL C 570 " --> pdb=" O LEU C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 593 removed outlier: 3.523A pdb=" N GLN C 575 " --> pdb=" O TRP C 571 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA C 582 " --> pdb=" O ALA C 578 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN C 591 " --> pdb=" O LEU C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 596 No H-bonds generated for 'chain 'C' and resid 594 through 596' Processing helix chain 'C' and resid 619 through 626 removed outlier: 3.523A pdb=" N TRP C 623 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP C 624 " --> pdb=" O ASN C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 633 Processing helix chain 'C' and resid 638 through 663 removed outlier: 4.032A pdb=" N THR C 644 " --> pdb=" O GLN C 640 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU C 647 " --> pdb=" O TYR C 643 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLN C 658 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU C 660 " --> pdb=" O ASN C 656 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU C 661 " --> pdb=" O GLU C 657 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU C 662 " --> pdb=" O GLN C 658 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU C 663 " --> pdb=" O GLU C 659 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.885A pdb=" N PHE I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 64 removed outlier: 3.533A pdb=" N GLN I 64 " --> pdb=" O ALA I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.619A pdb=" N THR I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.771A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 35 through 40 Processing sheet with id=AA2, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.687A pdb=" N LYS G 487 " --> pdb=" O LEU G 226 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 93 through 94 removed outlier: 3.511A pdb=" N GLY G 237 " --> pdb=" O PHE G 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.543A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N GLY G 441 " --> pdb=" O ASN G 300 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ASN G 300 " --> pdb=" O GLY G 441 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER G 447 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLY G 451 " --> pdb=" O GLU G 290 " (cutoff:3.500A) removed outlier: 9.598A pdb=" N GLU G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 11.590A pdb=" N LEU G 453 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 11.159A pdb=" N LEU G 288 " --> pdb=" O LEU G 453 " (cutoff:3.500A) removed outlier: 10.664A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 10.692A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.543A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR G 357 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N PHE G 468 " --> pdb=" O THR G 357 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE G 359 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 330 through 333 removed outlier: 3.656A pdb=" N LEU G 416 " --> pdb=" O CYS G 331 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE G 333 " --> pdb=" O ILE G 414 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE G 414 " --> pdb=" O ILE G 333 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 423 through 424 Processing sheet with id=AA8, first strand: chain 'H' and resid 20 through 21 Processing sheet with id=AA9, first strand: chain 'H' and resid 56 through 58 removed outlier: 6.365A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 56 through 58 removed outlier: 6.365A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.558A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU L 73 " --> pdb=" O PHE L 21 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 35 through 38 removed outlier: 6.556A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 85 through 86 removed outlier: 3.632A pdb=" N TYR L 86 " --> pdb=" O THR L 102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 35 through 40 Processing sheet with id=AB6, first strand: chain 'D' and resid 45 through 47 removed outlier: 3.688A pdb=" N LYS D 487 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE D 225 " --> pdb=" O VAL D 245 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 93 through 94 removed outlier: 3.511A pdb=" N GLY D 237 " --> pdb=" O PHE D 93 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.543A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N GLY D 441 " --> pdb=" O ASN D 300 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ASN D 300 " --> pdb=" O GLY D 441 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER D 447 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLY D 451 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 9.598A pdb=" N GLU D 290 " --> pdb=" O GLY D 451 " (cutoff:3.500A) removed outlier: 11.591A pdb=" N LEU D 453 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 11.160A pdb=" N LEU D 288 " --> pdb=" O LEU D 453 " (cutoff:3.500A) removed outlier: 10.664A pdb=" N THR D 455 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 10.693A pdb=" N VAL D 286 " --> pdb=" O THR D 455 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.543A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR D 357 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N PHE D 468 " --> pdb=" O THR D 357 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE D 359 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 330 through 333 removed outlier: 3.656A pdb=" N LEU D 416 " --> pdb=" O CYS D 331 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE D 333 " --> pdb=" O ILE D 414 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE D 414 " --> pdb=" O ILE D 333 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 423 through 424 Processing sheet with id=AC3, first strand: chain 'F' and resid 20 through 21 Processing sheet with id=AC4, first strand: chain 'F' and resid 56 through 58 removed outlier: 6.365A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N TRP F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 56 through 58 removed outlier: 6.365A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N TRP F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 4 through 6 removed outlier: 3.558A pdb=" N THR J 5 " --> pdb=" O ARG J 24 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU J 73 " --> pdb=" O PHE J 21 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE J 71 " --> pdb=" O CYS J 23 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 35 through 38 removed outlier: 6.556A pdb=" N TRP J 35 " --> pdb=" O VAL J 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 85 through 86 removed outlier: 3.631A pdb=" N TYR J 86 " --> pdb=" O THR J 102 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 35 through 40 Processing sheet with id=AD1, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.688A pdb=" N LYS E 487 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 93 through 94 removed outlier: 3.511A pdb=" N GLY E 237 " --> pdb=" O PHE E 93 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.543A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER E 447 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 9.598A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.590A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.159A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 10.664A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.693A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.543A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR E 357 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N PHE E 468 " --> pdb=" O THR E 357 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE E 359 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 330 through 333 removed outlier: 3.656A pdb=" N LEU E 416 " --> pdb=" O CYS E 331 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE E 333 " --> pdb=" O ILE E 414 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE E 414 " --> pdb=" O ILE E 333 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 423 through 424 Processing sheet with id=AD7, first strand: chain 'I' and resid 20 through 21 Processing sheet with id=AD8, first strand: chain 'I' and resid 56 through 58 removed outlier: 6.365A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N TRP I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 56 through 58 removed outlier: 6.365A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N TRP I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 4 through 6 removed outlier: 3.558A pdb=" N THR K 5 " --> pdb=" O ARG K 24 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU K 73 " --> pdb=" O PHE K 21 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE K 71 " --> pdb=" O CYS K 23 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 35 through 38 removed outlier: 6.557A pdb=" N TRP K 35 " --> pdb=" O VAL K 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 85 through 86 removed outlier: 3.631A pdb=" N TYR K 86 " --> pdb=" O THR K 102 " (cutoff:3.500A) 450 hydrogen bonds defined for protein. 1179 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: 3.47 Time building geometry restraints manager: 2.67 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: 6435 1.34 - 1.46: 4944 1.46 - 1.58: 9444 1.58 - 1.70: 0 1.70 - 1.81: 168 Bond restraints: 20991 Sorted by residual: bond pdb=" C1 NAG D 630 " pdb=" O5 NAG D 630 " ideal model delta sigma weight residual 1.406 1.510 -0.104 2.00e-02 2.50e+03 2.70e+01 bond pdb=" C1 NAG G 630 " pdb=" O5 NAG G 630 " ideal model delta sigma weight residual 1.406 1.507 -0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" C1 NAG E 630 " pdb=" O5 NAG E 630 " ideal model delta sigma weight residual 1.406 1.506 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" C1 NAG G 602 " pdb=" O5 NAG G 602 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.58e+00 bond pdb=" C THR D 123 " pdb=" N PRO D 124 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.34e-02 1.83e+03 5.80e+00 ... (remaining 20986 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 27348 2.55 - 5.11: 956 5.11 - 7.66: 139 7.66 - 10.22: 41 10.22 - 12.77: 16 Bond angle restraints: 28500 Sorted by residual: angle pdb=" C LEU E 390 " pdb=" N PHE E 391 " pdb=" CA PHE E 391 " ideal model delta sigma weight residual 121.54 134.31 -12.77 1.91e+00 2.74e-01 4.47e+01 angle pdb=" C LEU D 390 " pdb=" N PHE D 391 " pdb=" CA PHE D 391 " ideal model delta sigma weight residual 121.54 134.30 -12.76 1.91e+00 2.74e-01 4.47e+01 angle pdb=" C LEU G 390 " pdb=" N PHE G 391 " pdb=" CA PHE G 391 " ideal model delta sigma weight residual 121.54 134.22 -12.68 1.91e+00 2.74e-01 4.40e+01 angle pdb=" C PHE D 391 " pdb=" N ASN D 392 " pdb=" CA ASN D 392 " ideal model delta sigma weight residual 121.54 131.45 -9.91 1.91e+00 2.74e-01 2.69e+01 angle pdb=" C PHE G 391 " pdb=" N ASN G 392 " pdb=" CA ASN G 392 " ideal model delta sigma weight residual 121.54 131.41 -9.87 1.91e+00 2.74e-01 2.67e+01 ... (remaining 28495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.32: 13381 22.32 - 44.64: 401 44.64 - 66.96: 76 66.96 - 89.28: 71 89.28 - 111.61: 57 Dihedral angle restraints: 13986 sinusoidal: 7020 harmonic: 6966 Sorted by residual: dihedral pdb=" CB CYS E 378 " pdb=" SG CYS E 378 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual 93.00 33.80 59.20 1 1.00e+01 1.00e-02 4.68e+01 dihedral pdb=" CB CYS G 378 " pdb=" SG CYS G 378 " pdb=" SG CYS G 445 " pdb=" CB CYS G 445 " ideal model delta sinusoidal sigma weight residual 93.00 33.83 59.17 1 1.00e+01 1.00e-02 4.68e+01 dihedral pdb=" CB CYS D 378 " pdb=" SG CYS D 378 " pdb=" SG CYS D 445 " pdb=" CB CYS D 445 " ideal model delta sinusoidal sigma weight residual 93.00 33.85 59.15 1 1.00e+01 1.00e-02 4.68e+01 ... (remaining 13983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 3411 0.147 - 0.293: 74 0.293 - 0.440: 15 0.440 - 0.586: 1 0.586 - 0.733: 3 Chirality restraints: 3504 Sorted by residual: chirality pdb=" C1 NAG f 1 " pdb=" ND2 ASN D 386 " pdb=" C2 NAG f 1 " pdb=" O5 NAG f 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.67 -0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" C1 NAG q 1 " pdb=" ND2 ASN E 386 " pdb=" C2 NAG q 1 " pdb=" O5 NAG q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN G 386 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.18e+01 ... (remaining 3501 not shown) Planarity restraints: 3576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 386 " -0.021 2.00e-02 2.50e+03 2.31e-02 6.68e+00 pdb=" CG ASN D 386 " 0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN D 386 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN D 386 " 0.036 2.00e-02 2.50e+03 pdb=" C1 NAG f 1 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 479 " -0.021 2.00e-02 2.50e+03 1.62e-02 6.55e+00 pdb=" CG TRP G 479 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP G 479 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP G 479 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP G 479 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP G 479 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP G 479 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 479 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 479 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP G 479 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 479 " 0.021 2.00e-02 2.50e+03 1.61e-02 6.49e+00 pdb=" CG TRP E 479 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP E 479 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP E 479 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 479 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 479 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 479 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 479 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 479 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP E 479 " 0.003 2.00e-02 2.50e+03 ... (remaining 3573 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3938 2.78 - 3.31: 17932 3.31 - 3.84: 32102 3.84 - 4.37: 36582 4.37 - 4.90: 62960 Nonbonded interactions: 153514 Sorted by model distance: nonbonded pdb=" O VAL E 36 " pdb=" OG1 THR C 606 " model vdw 2.246 3.040 nonbonded pdb=" O VAL G 36 " pdb=" OG1 THR A 606 " model vdw 2.257 3.040 nonbonded pdb=" O VAL D 36 " pdb=" OG1 THR B 606 " model vdw 2.324 3.040 nonbonded pdb=" OG1 THR B 627 " pdb=" OE1 GLN B 630 " model vdw 2.342 3.040 nonbonded pdb=" OG1 THR C 627 " pdb=" OE1 GLN C 630 " model vdw 2.342 3.040 ... (remaining 153509 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'r' selection = chain 's' } ncs_group { reference = chain 'O' selection = chain 'T' selection = chain 'U' selection = chain 'Z' selection = chain 'e' selection = chain 'f' selection = chain 'k' selection = chain 'p' selection = chain 'q' } ncs_group { reference = chain 'P' selection = chain 'a' selection = chain 'l' } 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: 1.500 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: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.840 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 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 : 0.007 0.104 21147 Z= 0.341 Angle : 1.225 14.318 28914 Z= 0.626 Chirality : 0.070 0.733 3504 Planarity : 0.007 0.061 3510 Dihedral : 14.586 111.605 9390 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.63 % Allowed : 12.42 % Favored : 86.95 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -4.89 (0.14), residues: 2367 helix: -4.80 (0.07), residues: 378 sheet: -2.62 (0.17), residues: 657 loop : -3.17 (0.15), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 273 TYR 0.020 0.003 TYR J 96 PHE 0.035 0.004 PHE E 233 TRP 0.043 0.004 TRP G 479 HIS 0.010 0.002 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00730 (20991) covalent geometry : angle 1.17708 (28500) SS BOND : bond 0.01809 ( 36) SS BOND : angle 1.60839 ( 72) hydrogen bonds : bond 0.30664 ( 426) hydrogen bonds : angle 9.91206 ( 1179) Misc. bond : bond 0.00252 ( 6) link_ALPHA1-3 : bond 0.00631 ( 3) link_ALPHA1-3 : angle 1.30721 ( 9) link_BETA1-4 : bond 0.00814 ( 45) link_BETA1-4 : angle 2.62974 ( 135) link_NAG-ASN : bond 0.00827 ( 66) link_NAG-ASN : angle 3.74180 ( 198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 571 time to evaluate : 0.775 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: G 217 TYR cc_start: 0.8808 (m-10) cc_final: 0.8158 (m-10) REVERT: A 542 ARG cc_start: 0.8365 (mtt90) cc_final: 0.7987 (mtt90) REVERT: A 599 SER cc_start: 0.9080 (t) cc_final: 0.8828 (p) REVERT: H 53 TYR cc_start: 0.8879 (t80) cc_final: 0.8562 (t80) REVERT: H 107 THR cc_start: 0.5861 (t) cc_final: 0.5458 (t) REVERT: L 4 LEU cc_start: 0.8682 (mt) cc_final: 0.8169 (mp) REVERT: L 6 GLN cc_start: 0.6739 (mt0) cc_final: 0.6339 (mt0) REVERT: L 83 PHE cc_start: 0.7430 (m-10) cc_final: 0.6766 (m-80) REVERT: D 104 MET cc_start: 0.8196 (ttm) cc_final: 0.7987 (ttt) REVERT: D 383 PHE cc_start: 0.7579 (m-10) cc_final: 0.7358 (m-80) REVERT: B 629 MET cc_start: 0.8736 (mmm) cc_final: 0.8393 (mmm) REVERT: F 52 ASN cc_start: 0.8762 (t0) cc_final: 0.8189 (t0) REVERT: F 82 LEU cc_start: 0.7513 (mt) cc_final: 0.7295 (tp) REVERT: F 107 THR cc_start: 0.6553 (t) cc_final: 0.6293 (t) REVERT: J 4 LEU cc_start: 0.8272 (mt) cc_final: 0.7977 (mp) REVERT: J 6 GLN cc_start: 0.6866 (mt0) cc_final: 0.6558 (mt0) REVERT: J 104 LEU cc_start: 0.6787 (tp) cc_final: 0.6538 (tp) REVERT: E 80 ASN cc_start: 0.8276 (m-40) cc_final: 0.7953 (m-40) REVERT: E 376 PHE cc_start: 0.7786 (m-80) cc_final: 0.7508 (m-80) REVERT: C 599 SER cc_start: 0.9263 (t) cc_final: 0.8821 (p) REVERT: C 629 MET cc_start: 0.8610 (mmm) cc_final: 0.8351 (mmp) REVERT: K 4 LEU cc_start: 0.8556 (mt) cc_final: 0.8274 (mp) REVERT: K 83 PHE cc_start: 0.7417 (m-10) cc_final: 0.6779 (m-80) REVERT: K 97 THR cc_start: 0.7320 (t) cc_final: 0.6957 (p) outliers start: 0 outliers final: 0 residues processed: 571 average time/residue: 0.1805 time to fit residues: 149.5329 Evaluate side-chains 298 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 72 HIS G 99 ASN G 229 ASN G 363 HIS G 377 ASN G 462 GLN A 653 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 HIS ** L 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 ASN D 462 GLN B 540 GLN B 564 HIS B 653 GLN B 658 GLN F 1 GLN F 100GASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 HIS E 462 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 HIS ** K 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.121544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.094223 restraints weight = 41713.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.094703 restraints weight = 37010.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.095224 restraints weight = 43671.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.096423 restraints weight = 26896.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.096872 restraints weight = 23003.284| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 21147 Z= 0.348 Angle : 0.986 14.781 28914 Z= 0.482 Chirality : 0.055 0.299 3504 Planarity : 0.007 0.071 3510 Dihedral : 13.630 106.427 4968 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.83 % Favored : 87.92 % Rotamer: Outliers : 2.72 % Allowed : 10.03 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -4.25 (0.15), residues: 2367 helix: -2.85 (0.20), residues: 384 sheet: -2.38 (0.18), residues: 657 loop : -3.12 (0.15), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 31 TYR 0.029 0.003 TYR I 98 PHE 0.033 0.003 PHE G 391 TRP 0.024 0.002 TRP G 479 HIS 0.018 0.002 HIS G 363 Details of bonding type rmsd covalent geometry : bond 0.00828 (20991) covalent geometry : angle 0.93589 (28500) SS BOND : bond 0.00659 ( 36) SS BOND : angle 2.09997 ( 72) hydrogen bonds : bond 0.06514 ( 426) hydrogen bonds : angle 6.02642 ( 1179) Misc. bond : bond 0.00233 ( 6) link_ALPHA1-3 : bond 0.00963 ( 3) link_ALPHA1-3 : angle 2.03254 ( 9) link_BETA1-4 : bond 0.00677 ( 45) link_BETA1-4 : angle 2.52970 ( 135) link_NAG-ASN : bond 0.00557 ( 66) link_NAG-ASN : angle 3.10737 ( 198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 319 time to evaluate : 0.846 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: H 53 TYR cc_start: 0.8919 (t80) cc_final: 0.8688 (t80) REVERT: L 81 GLU cc_start: 0.7815 (mp0) cc_final: 0.7439 (pp20) REVERT: L 83 PHE cc_start: 0.7721 (m-10) cc_final: 0.6832 (m-80) REVERT: D 383 PHE cc_start: 0.7798 (m-10) cc_final: 0.7589 (m-80) REVERT: B 629 MET cc_start: 0.8810 (mmm) cc_final: 0.8338 (mmm) REVERT: F 1 GLN cc_start: 0.8157 (mm110) cc_final: 0.7830 (mm110) REVERT: F 82 LEU cc_start: 0.8120 (mt) cc_final: 0.7882 (tp) REVERT: J 6 GLN cc_start: 0.6661 (mt0) cc_final: 0.6153 (mt0) REVERT: J 83 PHE cc_start: 0.7951 (m-10) cc_final: 0.7270 (m-10) REVERT: J 100 GLN cc_start: 0.7532 (mt0) cc_final: 0.7261 (mt0) REVERT: E 104 MET cc_start: 0.9091 (ttt) cc_final: 0.8843 (ttt) REVERT: E 427 TRP cc_start: 0.6440 (m100) cc_final: 0.6192 (m100) REVERT: E 434 MET cc_start: 0.7879 (ptm) cc_final: 0.7678 (ttp) REVERT: C 599 SER cc_start: 0.9163 (t) cc_final: 0.8800 (p) REVERT: C 659 GLU cc_start: 0.8107 (pp20) cc_final: 0.7824 (pp20) REVERT: I 47 TRP cc_start: 0.8551 (t60) cc_final: 0.7949 (t60) REVERT: I 54 ASN cc_start: 0.8814 (p0) cc_final: 0.8611 (p0) REVERT: I 72 ASP cc_start: 0.6917 (p0) cc_final: 0.6669 (p0) REVERT: K 1 GLU cc_start: 0.6691 (mt-10) cc_final: 0.6353 (mt-10) REVERT: K 83 PHE cc_start: 0.7728 (m-10) cc_final: 0.6977 (m-80) REVERT: K 97 THR cc_start: 0.7948 (t) cc_final: 0.7621 (p) outliers start: 57 outliers final: 34 residues processed: 362 average time/residue: 0.1689 time to fit residues: 90.6036 Evaluate side-chains 302 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 268 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 132 ASN Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 414 ILE Chi-restraints excluded: chain A residue 620 ASN Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 375 SER Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain F residue 59 PHE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain J residue 29 ARG Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain I residue 59 PHE Chi-restraints excluded: chain I residue 105 LYS Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 53 ASN Chi-restraints excluded: chain K residue 56 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 66 optimal weight: 3.9990 chunk 227 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 99 ASN G 302 ASN G 363 HIS A 658 GLN H 43 GLN D 99 ASN F 43 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 ASN K 6 GLN K 100 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.123372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.095014 restraints weight = 41042.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.094981 restraints weight = 35564.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.096035 restraints weight = 35611.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.097024 restraints weight = 25159.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.097812 restraints weight = 22869.116| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 21147 Z= 0.172 Angle : 0.820 16.126 28914 Z= 0.398 Chirality : 0.051 0.294 3504 Planarity : 0.005 0.064 3510 Dihedral : 11.246 101.940 4968 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.63 % Favored : 90.11 % Rotamer: Outliers : 3.25 % Allowed : 12.42 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -3.63 (0.15), residues: 2367 helix: -1.78 (0.23), residues: 390 sheet: -1.89 (0.20), residues: 603 loop : -2.95 (0.15), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 77 TYR 0.028 0.002 TYR I 98 PHE 0.030 0.002 PHE D 391 TRP 0.017 0.001 TRP G 479 HIS 0.016 0.002 HIS G 363 Details of bonding type rmsd covalent geometry : bond 0.00395 (20991) covalent geometry : angle 0.76939 (28500) SS BOND : bond 0.00297 ( 36) SS BOND : angle 2.49586 ( 72) hydrogen bonds : bond 0.04776 ( 426) hydrogen bonds : angle 5.41826 ( 1179) Misc. bond : bond 0.00147 ( 6) link_ALPHA1-3 : bond 0.01077 ( 3) link_ALPHA1-3 : angle 1.10045 ( 9) link_BETA1-4 : bond 0.00556 ( 45) link_BETA1-4 : angle 2.19377 ( 135) link_NAG-ASN : bond 0.00475 ( 66) link_NAG-ASN : angle 2.72505 ( 198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 295 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 566 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8435 (tp) REVERT: H 38 ARG cc_start: 0.7729 (ttp-170) cc_final: 0.7513 (ttp-170) REVERT: H 53 TYR cc_start: 0.8853 (t80) cc_final: 0.8590 (t80) REVERT: L 81 GLU cc_start: 0.7602 (mp0) cc_final: 0.7324 (pp20) REVERT: L 83 PHE cc_start: 0.7807 (m-10) cc_final: 0.7031 (m-80) REVERT: D 486 TYR cc_start: 0.7264 (p90) cc_final: 0.5954 (p90) REVERT: B 564 HIS cc_start: 0.6825 (OUTLIER) cc_final: 0.6622 (t-90) REVERT: B 629 MET cc_start: 0.8757 (mmm) cc_final: 0.8358 (mmm) REVERT: B 645 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8691 (mm) REVERT: F 1 GLN cc_start: 0.8138 (mm110) cc_final: 0.7918 (mm110) REVERT: F 80 MET cc_start: 0.7887 (tmm) cc_final: 0.7403 (tmm) REVERT: J 6 GLN cc_start: 0.6798 (mt0) cc_final: 0.6452 (mt0) REVERT: J 29 ARG cc_start: 0.6952 (OUTLIER) cc_final: 0.6676 (ptm-80) REVERT: J 81 GLU cc_start: 0.7857 (mp0) cc_final: 0.6638 (tp30) REVERT: J 83 PHE cc_start: 0.7950 (m-10) cc_final: 0.7672 (m-10) REVERT: J 100 GLN cc_start: 0.7613 (mt0) cc_final: 0.7301 (mt0) REVERT: C 599 SER cc_start: 0.9083 (t) cc_final: 0.8720 (p) REVERT: C 629 MET cc_start: 0.8719 (mmm) cc_final: 0.8512 (mtp) REVERT: C 659 GLU cc_start: 0.8146 (pp20) cc_final: 0.7931 (pp20) REVERT: I 47 TRP cc_start: 0.8557 (t60) cc_final: 0.8165 (t60) REVERT: I 54 ASN cc_start: 0.8718 (p0) cc_final: 0.8438 (p0) REVERT: K 4 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8104 (mm) REVERT: K 31 ARG cc_start: 0.7147 (ttp-170) cc_final: 0.6655 (ttp80) REVERT: K 83 PHE cc_start: 0.7695 (m-10) cc_final: 0.6990 (m-80) REVERT: K 97 THR cc_start: 0.7815 (t) cc_final: 0.7543 (p) outliers start: 68 outliers final: 41 residues processed: 343 average time/residue: 0.1633 time to fit residues: 84.8741 Evaluate side-chains 309 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 263 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 375 SER Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 59 PHE Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 29 ARG Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 59 PHE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 53 ASN Chi-restraints excluded: chain K residue 56 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 214 optimal weight: 6.9990 chunk 197 optimal weight: 0.6980 chunk 34 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 216 optimal weight: 2.9990 chunk 209 optimal weight: 0.6980 chunk 166 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 99 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 363 HIS ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN I 6 GLN ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN K 89 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.123390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.094797 restraints weight = 40992.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.094668 restraints weight = 37354.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.095891 restraints weight = 33431.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.097431 restraints weight = 24546.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.097644 restraints weight = 22135.858| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21147 Z= 0.151 Angle : 0.760 11.156 28914 Z= 0.366 Chirality : 0.049 0.286 3504 Planarity : 0.005 0.061 3510 Dihedral : 9.180 94.580 4968 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.14 % Favored : 89.73 % Rotamer: Outliers : 3.82 % Allowed : 12.94 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -3.33 (0.16), residues: 2367 helix: -1.22 (0.24), residues: 393 sheet: -1.69 (0.20), residues: 621 loop : -2.88 (0.15), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 61 TYR 0.029 0.002 TYR I 98 PHE 0.028 0.002 PHE D 391 TRP 0.015 0.001 TRP D 479 HIS 0.006 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00344 (20991) covalent geometry : angle 0.71072 (28500) SS BOND : bond 0.00314 ( 36) SS BOND : angle 2.27701 ( 72) hydrogen bonds : bond 0.04058 ( 426) hydrogen bonds : angle 5.05702 ( 1179) Misc. bond : bond 0.00128 ( 6) link_ALPHA1-3 : bond 0.01387 ( 3) link_ALPHA1-3 : angle 1.30873 ( 9) link_BETA1-4 : bond 0.00526 ( 45) link_BETA1-4 : angle 2.08518 ( 135) link_NAG-ASN : bond 0.00432 ( 66) link_NAG-ASN : angle 2.59530 ( 198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 267 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 566 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8443 (tp) REVERT: H 38 ARG cc_start: 0.7643 (ttp-170) cc_final: 0.7392 (ttp-170) REVERT: H 53 TYR cc_start: 0.8840 (t80) cc_final: 0.8552 (t80) REVERT: L 32 ARG cc_start: 0.6119 (mtt180) cc_final: 0.5742 (mtt-85) REVERT: L 83 PHE cc_start: 0.8032 (m-10) cc_final: 0.7142 (m-80) REVERT: D 486 TYR cc_start: 0.7433 (p90) cc_final: 0.6199 (p90) REVERT: B 566 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8229 (tp) REVERT: B 629 MET cc_start: 0.8634 (mmm) cc_final: 0.8260 (mmm) REVERT: B 634 GLU cc_start: 0.8435 (tp30) cc_final: 0.7972 (tm-30) REVERT: B 645 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8715 (mm) REVERT: F 65 ASP cc_start: 0.7316 (t0) cc_final: 0.6942 (p0) REVERT: F 80 MET cc_start: 0.7776 (tmm) cc_final: 0.7353 (tmm) REVERT: J 6 GLN cc_start: 0.6875 (mt0) cc_final: 0.6533 (mt0) REVERT: J 100 GLN cc_start: 0.7551 (mt0) cc_final: 0.7271 (mt0) REVERT: C 599 SER cc_start: 0.9057 (t) cc_final: 0.8704 (p) REVERT: I 54 ASN cc_start: 0.8763 (p0) cc_final: 0.8431 (p0) REVERT: K 31 ARG cc_start: 0.7022 (ttp-170) cc_final: 0.6631 (ttp80) REVERT: K 83 PHE cc_start: 0.7803 (m-10) cc_final: 0.7159 (m-80) REVERT: K 97 THR cc_start: 0.7962 (t) cc_final: 0.7663 (p) outliers start: 80 outliers final: 51 residues processed: 319 average time/residue: 0.1660 time to fit residues: 80.3011 Evaluate side-chains 308 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 254 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 107 ASP Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 132 ASN Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 414 ILE Chi-restraints excluded: chain G residue 494 LEU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 375 SER Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 447 SER Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain F residue 59 PHE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 58 ILE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 59 PHE Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 56 SER Chi-restraints excluded: chain K residue 58 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 115 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 216 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 chunk 159 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 212 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 183 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 GLN E 363 HIS ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 ASN ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.120376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.092274 restraints weight = 40950.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.093741 restraints weight = 34993.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.094529 restraints weight = 27259.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.095082 restraints weight = 22413.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.095964 restraints weight = 21074.042| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 21147 Z= 0.221 Angle : 0.804 11.331 28914 Z= 0.389 Chirality : 0.050 0.277 3504 Planarity : 0.005 0.066 3510 Dihedral : 8.154 87.505 4968 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.41 % Favored : 88.47 % Rotamer: Outliers : 4.68 % Allowed : 13.23 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -3.25 (0.16), residues: 2367 helix: -1.00 (0.25), residues: 390 sheet: -1.80 (0.20), residues: 621 loop : -2.79 (0.15), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 32 TYR 0.029 0.002 TYR I 98 PHE 0.029 0.002 PHE D 391 TRP 0.030 0.002 TRP H 47 HIS 0.008 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00522 (20991) covalent geometry : angle 0.75718 (28500) SS BOND : bond 0.00404 ( 36) SS BOND : angle 2.27599 ( 72) hydrogen bonds : bond 0.04368 ( 426) hydrogen bonds : angle 5.06433 ( 1179) Misc. bond : bond 0.00125 ( 6) link_ALPHA1-3 : bond 0.01262 ( 3) link_ALPHA1-3 : angle 0.94876 ( 9) link_BETA1-4 : bond 0.00508 ( 45) link_BETA1-4 : angle 1.94422 ( 135) link_NAG-ASN : bond 0.00459 ( 66) link_NAG-ASN : angle 2.70114 ( 198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 263 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 318 TYR cc_start: 0.7922 (m-80) cc_final: 0.7315 (m-80) REVERT: A 566 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8565 (tp) REVERT: H 38 ARG cc_start: 0.7794 (ttp-170) cc_final: 0.7578 (ttp-170) REVERT: H 53 TYR cc_start: 0.8820 (t80) cc_final: 0.8547 (t80) REVERT: H 83 ARG cc_start: 0.7406 (mtt90) cc_final: 0.7122 (mtt90) REVERT: L 32 ARG cc_start: 0.5988 (mtt180) cc_final: 0.5687 (mtt-85) REVERT: D 486 TYR cc_start: 0.7823 (p90) cc_final: 0.6139 (p90) REVERT: B 629 MET cc_start: 0.8693 (mmm) cc_final: 0.8240 (mmm) REVERT: B 645 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8780 (mm) REVERT: F 1 GLN cc_start: 0.8050 (mm110) cc_final: 0.7485 (pt0) REVERT: F 80 MET cc_start: 0.7815 (tmm) cc_final: 0.7411 (tmm) REVERT: F 98 TYR cc_start: 0.8704 (t80) cc_final: 0.8260 (t80) REVERT: J 6 GLN cc_start: 0.7035 (mt0) cc_final: 0.6712 (mt0) REVERT: J 81 GLU cc_start: 0.7785 (mp0) cc_final: 0.6723 (tp30) REVERT: J 100 GLN cc_start: 0.7638 (mt0) cc_final: 0.7406 (mt0) REVERT: E 486 TYR cc_start: 0.7508 (OUTLIER) cc_final: 0.5908 (p90) REVERT: C 599 SER cc_start: 0.9093 (t) cc_final: 0.8840 (p) REVERT: C 629 MET cc_start: 0.8966 (mtp) cc_final: 0.8664 (mtp) REVERT: I 46 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8185 (pt0) REVERT: I 47 TRP cc_start: 0.8400 (t60) cc_final: 0.7902 (t60) REVERT: I 54 ASN cc_start: 0.8767 (p0) cc_final: 0.8518 (p0) REVERT: K 31 ARG cc_start: 0.7179 (ttp-170) cc_final: 0.6742 (tmm-80) REVERT: K 58 ILE cc_start: 0.7531 (OUTLIER) cc_final: 0.7273 (tt) REVERT: K 106 ARG cc_start: 0.6449 (ptp90) cc_final: 0.6083 (ptt-90) outliers start: 98 outliers final: 67 residues processed: 327 average time/residue: 0.1618 time to fit residues: 80.5304 Evaluate side-chains 323 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 251 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 39 TYR Chi-restraints excluded: chain G residue 107 ASP Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 391 PHE Chi-restraints excluded: chain G residue 414 ILE Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain D residue 39 TYR Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 375 SER Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 59 PHE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 58 ILE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 391 PHE Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 486 TYR Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 59 PHE Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 53 ASN Chi-restraints excluded: chain K residue 56 SER Chi-restraints excluded: chain K residue 58 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 211 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 225 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 172 optimal weight: 0.0670 chunk 125 optimal weight: 2.9990 chunk 227 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN D 363 HIS ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 ASN E 363 HIS ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.123632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.094934 restraints weight = 40525.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.095100 restraints weight = 36176.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.096327 restraints weight = 32828.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.097159 restraints weight = 24208.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.097569 restraints weight = 22410.885| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21147 Z= 0.121 Angle : 0.711 11.643 28914 Z= 0.342 Chirality : 0.047 0.283 3504 Planarity : 0.005 0.079 3510 Dihedral : 7.550 83.865 4968 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.82 % Favored : 92.06 % Rotamer: Outliers : 3.06 % Allowed : 15.04 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.88 (0.16), residues: 2367 helix: -0.54 (0.26), residues: 393 sheet: -1.33 (0.21), residues: 591 loop : -2.71 (0.15), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 77 TYR 0.027 0.001 TYR I 98 PHE 0.029 0.002 PHE D 391 TRP 0.035 0.001 TRP H 47 HIS 0.005 0.001 HIS B 641 Details of bonding type rmsd covalent geometry : bond 0.00268 (20991) covalent geometry : angle 0.66745 (28500) SS BOND : bond 0.00421 ( 36) SS BOND : angle 1.78167 ( 72) hydrogen bonds : bond 0.03537 ( 426) hydrogen bonds : angle 4.81874 ( 1179) Misc. bond : bond 0.00085 ( 6) link_ALPHA1-3 : bond 0.01085 ( 3) link_ALPHA1-3 : angle 1.17981 ( 9) link_BETA1-4 : bond 0.00462 ( 45) link_BETA1-4 : angle 1.67848 ( 135) link_NAG-ASN : bond 0.00436 ( 66) link_NAG-ASN : angle 2.54671 ( 198) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 277 time to evaluate : 0.803 Fit side-chains revert: symmetry clash REVERT: G 318 TYR cc_start: 0.7745 (m-80) cc_final: 0.7316 (m-80) REVERT: G 383 PHE cc_start: 0.8110 (m-80) cc_final: 0.7903 (m-80) REVERT: A 566 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8402 (tp) REVERT: H 38 ARG cc_start: 0.7619 (ttp-170) cc_final: 0.7391 (ttp-170) REVERT: H 47 TRP cc_start: 0.7824 (t60) cc_final: 0.7504 (t60) REVERT: H 53 TYR cc_start: 0.8787 (t80) cc_final: 0.8481 (t80) REVERT: H 83 ARG cc_start: 0.7253 (mtt90) cc_final: 0.6947 (mtt90) REVERT: L 32 ARG cc_start: 0.5889 (mtt180) cc_final: 0.5578 (mtt-85) REVERT: L 106 ARG cc_start: 0.6195 (ptt-90) cc_final: 0.5745 (ptt-90) REVERT: D 153 GLU cc_start: 0.6925 (tp30) cc_final: 0.6535 (mm-30) REVERT: D 318 TYR cc_start: 0.6911 (m-80) cc_final: 0.6503 (m-80) REVERT: B 629 MET cc_start: 0.8537 (mmm) cc_final: 0.8057 (mmm) REVERT: B 634 GLU cc_start: 0.8242 (tp30) cc_final: 0.7941 (tm-30) REVERT: B 645 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8735 (mm) REVERT: F 1 GLN cc_start: 0.7998 (mm110) cc_final: 0.7491 (pt0) REVERT: F 80 MET cc_start: 0.7773 (tmm) cc_final: 0.7352 (tmm) REVERT: F 98 TYR cc_start: 0.8736 (t80) cc_final: 0.8280 (t80) REVERT: J 6 GLN cc_start: 0.6962 (mt0) cc_final: 0.6541 (mt0) REVERT: J 58 ILE cc_start: 0.7800 (tp) cc_final: 0.7446 (tt) REVERT: J 100 GLN cc_start: 0.7579 (mt0) cc_final: 0.7343 (mt0) REVERT: C 599 SER cc_start: 0.8997 (t) cc_final: 0.8662 (p) REVERT: I 38 ARG cc_start: 0.7356 (ttp-170) cc_final: 0.6947 (ttp-170) REVERT: I 46 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7653 (pt0) REVERT: I 54 ASN cc_start: 0.8726 (p0) cc_final: 0.8486 (p0) REVERT: I 80 MET cc_start: 0.7781 (ttp) cc_final: 0.7167 (tmm) REVERT: K 31 ARG cc_start: 0.7172 (ttp-170) cc_final: 0.6727 (tmm-80) REVERT: K 58 ILE cc_start: 0.7408 (OUTLIER) cc_final: 0.7152 (tt) REVERT: K 106 ARG cc_start: 0.6610 (ptp90) cc_final: 0.6375 (ptt-90) outliers start: 64 outliers final: 50 residues processed: 316 average time/residue: 0.1663 time to fit residues: 79.4353 Evaluate side-chains 317 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 263 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 107 ASP Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 391 PHE Chi-restraints excluded: chain G residue 414 ILE Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain A residue 564 HIS Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 376 PHE Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 59 PHE Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 391 PHE Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 59 PHE Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 53 ASN Chi-restraints excluded: chain K residue 58 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 233 optimal weight: 0.5980 chunk 132 optimal weight: 2.9990 chunk 230 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 209 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 12 optimal weight: 0.0980 chunk 94 optimal weight: 3.9990 chunk 118 optimal weight: 0.2980 chunk 189 optimal weight: 5.9990 chunk 158 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN L 89 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 ASN ** 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 = 0.3758 r_free = 0.3758 target = 0.124420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.091878 restraints weight = 40823.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.094522 restraints weight = 24378.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.096188 restraints weight = 17941.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.097218 restraints weight = 15001.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.097683 restraints weight = 13467.992| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21147 Z= 0.114 Angle : 0.696 12.044 28914 Z= 0.333 Chirality : 0.046 0.270 3504 Planarity : 0.005 0.075 3510 Dihedral : 6.911 76.652 4968 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.83 % Favored : 91.04 % Rotamer: Outliers : 3.49 % Allowed : 14.90 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.73 (0.16), residues: 2367 helix: -0.13 (0.26), residues: 390 sheet: -1.35 (0.21), residues: 624 loop : -2.67 (0.15), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 61 TYR 0.023 0.001 TYR I 98 PHE 0.029 0.002 PHE G 391 TRP 0.020 0.001 TRP H 47 HIS 0.005 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00254 (20991) covalent geometry : angle 0.65166 (28500) SS BOND : bond 0.00256 ( 36) SS BOND : angle 1.55231 ( 72) hydrogen bonds : bond 0.03319 ( 426) hydrogen bonds : angle 4.65007 ( 1179) Misc. bond : bond 0.00265 ( 6) link_ALPHA1-3 : bond 0.01027 ( 3) link_ALPHA1-3 : angle 1.16799 ( 9) link_BETA1-4 : bond 0.00452 ( 45) link_BETA1-4 : angle 1.59917 ( 135) link_NAG-ASN : bond 0.00417 ( 66) link_NAG-ASN : angle 2.62134 ( 198) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 279 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 215 ILE cc_start: 0.8742 (mm) cc_final: 0.8459 (pt) REVERT: G 318 TYR cc_start: 0.7754 (m-80) cc_final: 0.7373 (m-80) REVERT: G 383 PHE cc_start: 0.7941 (m-80) cc_final: 0.7725 (m-80) REVERT: A 566 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8398 (tp) REVERT: H 38 ARG cc_start: 0.7528 (ttp-170) cc_final: 0.7310 (ttp-170) REVERT: H 47 TRP cc_start: 0.7749 (t60) cc_final: 0.7307 (t60) REVERT: H 53 TYR cc_start: 0.8781 (t80) cc_final: 0.8442 (t80) REVERT: L 58 ILE cc_start: 0.7654 (OUTLIER) cc_final: 0.7453 (tt) REVERT: L 106 ARG cc_start: 0.6163 (ptt-90) cc_final: 0.5760 (ptt-90) REVERT: D 318 TYR cc_start: 0.6975 (m-80) cc_final: 0.6588 (m-80) REVERT: B 629 MET cc_start: 0.8449 (mmm) cc_final: 0.7981 (mmm) REVERT: F 1 GLN cc_start: 0.8146 (mm110) cc_final: 0.7555 (pt0) REVERT: F 80 MET cc_start: 0.7740 (tmm) cc_final: 0.7356 (tmm) REVERT: F 98 TYR cc_start: 0.8785 (t80) cc_final: 0.8366 (t80) REVERT: J 6 GLN cc_start: 0.6997 (mt0) cc_final: 0.6423 (mt0) REVERT: J 31 ARG cc_start: 0.6667 (tmm160) cc_final: 0.6199 (tmm160) REVERT: J 58 ILE cc_start: 0.7806 (tp) cc_final: 0.7439 (tt) REVERT: J 81 GLU cc_start: 0.7395 (mp0) cc_final: 0.6446 (tp30) REVERT: J 100 GLN cc_start: 0.7603 (mt0) cc_final: 0.7328 (mt0) REVERT: E 149 MET cc_start: 0.6657 (mtp) cc_final: 0.6336 (mtp) REVERT: E 317 PHE cc_start: 0.6839 (t80) cc_final: 0.6618 (t80) REVERT: E 318 TYR cc_start: 0.7571 (m-80) cc_final: 0.6747 (m-80) REVERT: C 599 SER cc_start: 0.8989 (t) cc_final: 0.8598 (p) REVERT: I 38 ARG cc_start: 0.7312 (ttp-170) cc_final: 0.6984 (ttp-170) REVERT: I 46 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7713 (pt0) REVERT: I 47 TRP cc_start: 0.8241 (t60) cc_final: 0.7693 (t60) REVERT: I 54 ASN cc_start: 0.8879 (p0) cc_final: 0.8600 (p0) REVERT: I 80 MET cc_start: 0.7742 (ttp) cc_final: 0.7042 (tmm) REVERT: K 58 ILE cc_start: 0.7280 (OUTLIER) cc_final: 0.7032 (tt) REVERT: K 106 ARG cc_start: 0.6811 (ptp90) cc_final: 0.6602 (ptt-90) outliers start: 73 outliers final: 55 residues processed: 326 average time/residue: 0.1637 time to fit residues: 80.8515 Evaluate side-chains 323 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 264 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 107 ASP Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 391 PHE Chi-restraints excluded: chain G residue 414 ILE Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain A residue 564 HIS Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 375 SER Chi-restraints excluded: chain D residue 376 PHE Chi-restraints excluded: chain D residue 391 PHE Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 59 PHE Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 29 ARG Chi-restraints excluded: chain J residue 32 ARG Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 391 PHE Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 59 PHE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 53 ASN Chi-restraints excluded: chain K residue 58 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 158 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 193 optimal weight: 6.9990 chunk 206 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 176 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 192 optimal weight: 6.9990 chunk 76 optimal weight: 0.5980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.122584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.094653 restraints weight = 40882.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.096244 restraints weight = 35014.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.097087 restraints weight = 26824.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.097624 restraints weight = 21825.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.098625 restraints weight = 20613.082| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21147 Z= 0.169 Angle : 0.755 12.740 28914 Z= 0.363 Chirality : 0.048 0.267 3504 Planarity : 0.005 0.089 3510 Dihedral : 6.788 68.214 4968 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.10 % Favored : 89.78 % Rotamer: Outliers : 3.25 % Allowed : 15.14 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.69 (0.16), residues: 2367 helix: -0.10 (0.26), residues: 393 sheet: -1.33 (0.21), residues: 624 loop : -2.64 (0.15), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 77 TYR 0.030 0.002 TYR I 98 PHE 0.031 0.002 PHE D 391 TRP 0.019 0.001 TRP H 47 HIS 0.009 0.001 HIS B 641 Details of bonding type rmsd covalent geometry : bond 0.00396 (20991) covalent geometry : angle 0.70316 (28500) SS BOND : bond 0.00326 ( 36) SS BOND : angle 2.00644 ( 72) hydrogen bonds : bond 0.03660 ( 426) hydrogen bonds : angle 4.72417 ( 1179) Misc. bond : bond 0.00571 ( 6) link_ALPHA1-3 : bond 0.01016 ( 3) link_ALPHA1-3 : angle 1.12826 ( 9) link_BETA1-4 : bond 0.00449 ( 45) link_BETA1-4 : angle 1.61226 ( 135) link_NAG-ASN : bond 0.00379 ( 66) link_NAG-ASN : angle 2.96284 ( 198) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 259 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 318 TYR cc_start: 0.7820 (m-80) cc_final: 0.7451 (m-80) REVERT: G 368 ASP cc_start: 0.7996 (m-30) cc_final: 0.7656 (m-30) REVERT: G 383 PHE cc_start: 0.8044 (m-80) cc_final: 0.7810 (m-80) REVERT: A 566 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8472 (tp) REVERT: H 47 TRP cc_start: 0.7853 (t60) cc_final: 0.7416 (t60) REVERT: H 53 TYR cc_start: 0.8776 (t80) cc_final: 0.8446 (t80) REVERT: H 83 ARG cc_start: 0.7170 (mtt90) cc_final: 0.6939 (mtt90) REVERT: L 106 ARG cc_start: 0.6177 (ptt-90) cc_final: 0.5750 (ptt-90) REVERT: D 153 GLU cc_start: 0.6971 (tp30) cc_final: 0.6562 (mm-30) REVERT: D 318 TYR cc_start: 0.7044 (m-80) cc_final: 0.6673 (m-80) REVERT: B 629 MET cc_start: 0.8561 (mmm) cc_final: 0.7984 (mmm) REVERT: F 1 GLN cc_start: 0.8111 (mm110) cc_final: 0.7663 (pt0) REVERT: F 80 MET cc_start: 0.7811 (tmm) cc_final: 0.7399 (tmm) REVERT: F 98 TYR cc_start: 0.8782 (t80) cc_final: 0.8392 (t80) REVERT: F 100 ASP cc_start: 0.6816 (m-30) cc_final: 0.6572 (m-30) REVERT: J 6 GLN cc_start: 0.7187 (mt0) cc_final: 0.6683 (mt0) REVERT: J 31 ARG cc_start: 0.6748 (tmm160) cc_final: 0.6352 (tmm160) REVERT: J 58 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7403 (tt) REVERT: J 100 GLN cc_start: 0.7602 (mt0) cc_final: 0.7389 (mt0) REVERT: E 149 MET cc_start: 0.6581 (mtp) cc_final: 0.6372 (mtp) REVERT: E 317 PHE cc_start: 0.6983 (t80) cc_final: 0.6759 (t80) REVERT: E 318 TYR cc_start: 0.7633 (m-80) cc_final: 0.6927 (m-80) REVERT: E 363 HIS cc_start: 0.6364 (t-170) cc_final: 0.6115 (t-170) REVERT: C 599 SER cc_start: 0.9129 (t) cc_final: 0.8730 (p) REVERT: I 46 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8210 (pt0) REVERT: I 47 TRP cc_start: 0.8304 (t60) cc_final: 0.7621 (t60) REVERT: I 54 ASN cc_start: 0.8855 (p0) cc_final: 0.8603 (p0) REVERT: K 58 ILE cc_start: 0.7356 (OUTLIER) cc_final: 0.7066 (tt) outliers start: 68 outliers final: 57 residues processed: 300 average time/residue: 0.1659 time to fit residues: 75.7821 Evaluate side-chains 309 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 248 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 107 ASP Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 391 PHE Chi-restraints excluded: chain G residue 414 ILE Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 375 SER Chi-restraints excluded: chain D residue 376 PHE Chi-restraints excluded: chain D residue 391 PHE Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 428 GLN Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 59 PHE Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 32 ARG Chi-restraints excluded: chain J residue 58 ILE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 391 PHE Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 59 PHE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 53 ASN Chi-restraints excluded: chain K residue 58 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 48 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 178 optimal weight: 5.9990 chunk 204 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 220 optimal weight: 9.9990 chunk 211 optimal weight: 1.9990 chunk 202 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 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 = 0.3748 r_free = 0.3748 target = 0.123689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.090985 restraints weight = 40758.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.093712 restraints weight = 24147.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.095420 restraints weight = 17674.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.096372 restraints weight = 14720.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.097034 restraints weight = 13252.856| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21147 Z= 0.132 Angle : 0.727 12.648 28914 Z= 0.352 Chirality : 0.047 0.265 3504 Planarity : 0.005 0.080 3510 Dihedral : 6.446 52.755 4968 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.79 % Favored : 91.09 % Rotamer: Outliers : 2.96 % Allowed : 15.62 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.56 (0.16), residues: 2367 helix: 0.11 (0.27), residues: 387 sheet: -1.18 (0.21), residues: 618 loop : -2.61 (0.15), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 61 TYR 0.024 0.001 TYR H 98 PHE 0.030 0.002 PHE D 391 TRP 0.016 0.001 TRP H 47 HIS 0.008 0.001 HIS B 641 Details of bonding type rmsd covalent geometry : bond 0.00304 (20991) covalent geometry : angle 0.67784 (28500) SS BOND : bond 0.00282 ( 36) SS BOND : angle 1.78993 ( 72) hydrogen bonds : bond 0.03417 ( 426) hydrogen bonds : angle 4.65102 ( 1179) Misc. bond : bond 0.00595 ( 6) link_ALPHA1-3 : bond 0.00986 ( 3) link_ALPHA1-3 : angle 1.21816 ( 9) link_BETA1-4 : bond 0.00453 ( 45) link_BETA1-4 : angle 1.55107 ( 135) link_NAG-ASN : bond 0.00367 ( 66) link_NAG-ASN : angle 2.85180 ( 198) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 261 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 318 TYR cc_start: 0.7807 (m-80) cc_final: 0.7413 (m-80) REVERT: G 383 PHE cc_start: 0.7931 (m-80) cc_final: 0.7684 (m-80) REVERT: A 566 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8427 (tp) REVERT: H 47 TRP cc_start: 0.7848 (t60) cc_final: 0.7284 (t60) REVERT: H 53 TYR cc_start: 0.8782 (t80) cc_final: 0.8427 (t80) REVERT: H 83 ARG cc_start: 0.7143 (mtt90) cc_final: 0.6941 (mtt90) REVERT: L 106 ARG cc_start: 0.6165 (ptt-90) cc_final: 0.5815 (ptt-90) REVERT: D 153 GLU cc_start: 0.7023 (tp30) cc_final: 0.6613 (mm-30) REVERT: D 318 TYR cc_start: 0.7052 (m-80) cc_final: 0.6624 (m-80) REVERT: B 629 MET cc_start: 0.8542 (mmm) cc_final: 0.8056 (mmm) REVERT: F 1 GLN cc_start: 0.8110 (mm110) cc_final: 0.7590 (pt0) REVERT: F 46 GLU cc_start: 0.7688 (mp0) cc_final: 0.7259 (mp0) REVERT: F 80 MET cc_start: 0.7822 (tmm) cc_final: 0.7404 (tmm) REVERT: F 98 TYR cc_start: 0.8842 (t80) cc_final: 0.8418 (t80) REVERT: J 6 GLN cc_start: 0.7051 (mt0) cc_final: 0.6148 (mt0) REVERT: J 31 ARG cc_start: 0.6732 (tmm160) cc_final: 0.6350 (tmm160) REVERT: J 32 ARG cc_start: 0.5786 (ptp-170) cc_final: 0.5580 (ptp-170) REVERT: J 58 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7496 (tt) REVERT: J 81 GLU cc_start: 0.7277 (mp0) cc_final: 0.6469 (tp30) REVERT: J 100 GLN cc_start: 0.7637 (mt0) cc_final: 0.7427 (mp10) REVERT: E 149 MET cc_start: 0.6566 (mtp) cc_final: 0.6357 (mtp) REVERT: E 317 PHE cc_start: 0.6864 (t80) cc_final: 0.6567 (t80) REVERT: E 318 TYR cc_start: 0.7530 (m-80) cc_final: 0.6779 (m-80) REVERT: E 363 HIS cc_start: 0.6238 (t-170) cc_final: 0.5969 (t-170) REVERT: C 599 SER cc_start: 0.9034 (t) cc_final: 0.8651 (p) REVERT: I 38 ARG cc_start: 0.7316 (ttp-170) cc_final: 0.6917 (ttp-170) REVERT: I 46 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.7686 (pt0) REVERT: I 47 TRP cc_start: 0.8274 (t60) cc_final: 0.7576 (t60) REVERT: I 54 ASN cc_start: 0.8915 (p0) cc_final: 0.8646 (p0) REVERT: I 80 MET cc_start: 0.7751 (ttp) cc_final: 0.7246 (tmm) REVERT: K 58 ILE cc_start: 0.7410 (OUTLIER) cc_final: 0.7105 (tt) outliers start: 62 outliers final: 54 residues processed: 298 average time/residue: 0.1624 time to fit residues: 73.8090 Evaluate side-chains 310 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 252 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 107 ASP Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 391 PHE Chi-restraints excluded: chain G residue 414 ILE Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain A residue 564 HIS Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 375 SER Chi-restraints excluded: chain D residue 376 PHE Chi-restraints excluded: chain D residue 391 PHE Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 59 PHE Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 58 ILE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 391 PHE Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 59 PHE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 53 ASN Chi-restraints excluded: chain K residue 58 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 77 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 142 optimal weight: 9.9990 chunk 183 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 chunk 155 optimal weight: 0.5980 chunk 91 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 215 optimal weight: 4.9990 chunk 202 optimal weight: 2.9990 chunk 206 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.121757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.093781 restraints weight = 41102.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.095270 restraints weight = 35495.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.096052 restraints weight = 27577.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.096624 restraints weight = 22507.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.097686 restraints weight = 21070.155| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21147 Z= 0.184 Angle : 0.760 12.479 28914 Z= 0.371 Chirality : 0.048 0.264 3504 Planarity : 0.005 0.082 3510 Dihedral : 6.470 49.973 4968 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.22 % Favored : 89.65 % Rotamer: Outliers : 3.20 % Allowed : 15.57 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.57 (0.16), residues: 2367 helix: 0.20 (0.27), residues: 372 sheet: -1.28 (0.21), residues: 642 loop : -2.59 (0.15), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 106 TYR 0.025 0.002 TYR H 98 PHE 0.031 0.002 PHE D 391 TRP 0.019 0.001 TRP H 47 HIS 0.008 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00433 (20991) covalent geometry : angle 0.70938 (28500) SS BOND : bond 0.00336 ( 36) SS BOND : angle 1.96018 ( 72) hydrogen bonds : bond 0.03725 ( 426) hydrogen bonds : angle 4.72426 ( 1179) Misc. bond : bond 0.00618 ( 6) link_ALPHA1-3 : bond 0.00886 ( 3) link_ALPHA1-3 : angle 1.13956 ( 9) link_BETA1-4 : bond 0.00452 ( 45) link_BETA1-4 : angle 1.58567 ( 135) link_NAG-ASN : bond 0.00364 ( 66) link_NAG-ASN : angle 2.94846 ( 198) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4734 Ramachandran restraints generated. 2367 Oldfield, 0 Emsley, 2367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 250 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: G 318 TYR cc_start: 0.7849 (m-80) cc_final: 0.7554 (m-80) REVERT: A 566 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8371 (tp) REVERT: H 53 TYR cc_start: 0.8769 (t80) cc_final: 0.8413 (t80) REVERT: D 318 TYR cc_start: 0.7143 (m-80) cc_final: 0.6801 (m-80) REVERT: B 629 MET cc_start: 0.8594 (mmm) cc_final: 0.8012 (mmm) REVERT: F 1 GLN cc_start: 0.8144 (mm110) cc_final: 0.7686 (pt0) REVERT: F 46 GLU cc_start: 0.7734 (mp0) cc_final: 0.7366 (mp0) REVERT: F 80 MET cc_start: 0.7861 (tmm) cc_final: 0.7391 (tmm) REVERT: F 98 TYR cc_start: 0.8804 (t80) cc_final: 0.8457 (t80) REVERT: J 6 GLN cc_start: 0.7185 (mt0) cc_final: 0.6404 (mt0) REVERT: J 58 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7395 (tt) REVERT: J 81 GLU cc_start: 0.7268 (mp0) cc_final: 0.6480 (tp30) REVERT: E 149 MET cc_start: 0.6494 (mtp) cc_final: 0.6264 (mtp) REVERT: E 317 PHE cc_start: 0.6971 (t80) cc_final: 0.6701 (t80) REVERT: E 318 TYR cc_start: 0.7560 (m-80) cc_final: 0.6879 (m-80) REVERT: E 363 HIS cc_start: 0.6427 (t-170) cc_final: 0.6183 (t-170) REVERT: E 486 TYR cc_start: 0.7709 (OUTLIER) cc_final: 0.5988 (p90) REVERT: C 599 SER cc_start: 0.9047 (t) cc_final: 0.8798 (p) REVERT: I 46 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8169 (pt0) REVERT: I 47 TRP cc_start: 0.8350 (t60) cc_final: 0.7613 (t60) REVERT: I 54 ASN cc_start: 0.8956 (p0) cc_final: 0.8679 (p0) REVERT: I 80 MET cc_start: 0.7864 (ttp) cc_final: 0.7278 (tmm) REVERT: K 58 ILE cc_start: 0.7381 (OUTLIER) cc_final: 0.7081 (tt) outliers start: 67 outliers final: 58 residues processed: 290 average time/residue: 0.1649 time to fit residues: 73.2108 Evaluate side-chains 308 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 245 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 107 ASP Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 391 PHE Chi-restraints excluded: chain G residue 414 ILE Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain A residue 564 HIS Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 375 SER Chi-restraints excluded: chain D residue 376 PHE Chi-restraints excluded: chain D residue 391 PHE Chi-restraints excluded: chain D residue 414 ILE Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 59 PHE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 58 ILE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 391 PHE Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 486 TYR Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 59 PHE Chi-restraints excluded: chain I residue 83 ARG Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 53 ASN Chi-restraints excluded: chain K residue 58 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 175 optimal weight: 0.8980 chunk 73 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 142 optimal weight: 10.0000 chunk 232 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 201 optimal weight: 0.9980 chunk 131 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 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 = 0.3759 r_free = 0.3759 target = 0.123731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.096127 restraints weight = 41413.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.097565 restraints weight = 35564.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.098667 restraints weight = 27529.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.099281 restraints weight = 21969.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.099605 restraints weight = 21087.427| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21147 Z= 0.126 Angle : 0.711 12.417 28914 Z= 0.348 Chirality : 0.046 0.261 3504 Planarity : 0.005 0.057 3510 Dihedral : 6.156 50.595 4968 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.07 % Favored : 91.80 % Rotamer: Outliers : 2.82 % Allowed : 15.85 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.44 (0.17), residues: 2367 helix: 0.21 (0.27), residues: 393 sheet: -1.15 (0.20), residues: 642 loop : -2.54 (0.15), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 61 TYR 0.025 0.001 TYR H 98 PHE 0.029 0.002 PHE D 391 TRP 0.017 0.001 TRP H 47 HIS 0.008 0.001 HIS B 641 Details of bonding type rmsd covalent geometry : bond 0.00289 (20991) covalent geometry : angle 0.66554 (28500) SS BOND : bond 0.00289 ( 36) SS BOND : angle 1.65502 ( 72) hydrogen bonds : bond 0.03349 ( 426) hydrogen bonds : angle 4.58178 ( 1179) Misc. bond : bond 0.00505 ( 6) link_ALPHA1-3 : bond 0.00874 ( 3) link_ALPHA1-3 : angle 1.24678 ( 9) link_BETA1-4 : bond 0.00452 ( 45) link_BETA1-4 : angle 1.49969 ( 135) link_NAG-ASN : bond 0.00390 ( 66) link_NAG-ASN : angle 2.73492 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3470.63 seconds wall clock time: 60 minutes 58.67 seconds (3658.67 seconds total)