Starting phenix.real_space_refine on Sun Sep 13 04:07:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5vn8_8717/09_2026/5vn8_8717.cif Found real_map, /net/cci-nas-00/data/ceres_data/5vn8_8717/09_2026/5vn8_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_8717/09_2026/5vn8_8717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5vn8_8717/09_2026/5vn8_8717.map" restraint_files = "/net/cci-nas-00/data/ceres_data/5vn8_8717/09_2026/5vn8_8717.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5vn8_8717/09_2026/5vn8_8717.cif" model { file = "/net/cci-nas-00/data/ceres_data/5vn8_8717/09_2026/5vn8_8717.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5vn8_8717/09_2026/5vn8_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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 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 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 chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 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 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 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 chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 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 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 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 chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 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 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 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 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 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 chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 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 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 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 chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 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 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 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 chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 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 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 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 chiralities: 4 Time building chain proxies: 4.83, per 1000 atoms: 0.23 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: 2.20 Conformation dependent library (CDL) restraints added in 918.6 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: 0.66 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: 3.56 Time building geometry restraints manager: 2.78 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 - 11.84: 10786 11.84 - 23.68: 623 23.68 - 35.52: 134 35.52 - 47.36: 64 47.36 - 59.20: 15 Dihedral angle restraints: 11622 sinusoidal: 4656 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 11619 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: 0.06 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 19.550 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.090 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 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 : 8.190 50.406 7026 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/Z covalent geometry : bond 0.00730 / 0.34 (20991) covalent geometry : angle 1.17708 / 0.62 (28500) SS BOND : bond 0.01809 / 0.86 ( 36) SS BOND : angle 1.60839 / 1.08 ( 72) hydrogen bonds : bond 0.30664 / 20.47 ( 426) hydrogen bonds : angle 9.91206 / 6.70 ( 1179) Misc. bond : bond 0.00252 / 0.13 ( 6) link_ALPHA1-3 : bond 0.00631 / 0.28 ( 3) link_ALPHA1-3 : angle 1.30721 / 0.74 ( 9) link_BETA1-4 : bond 0.00814 / 0.57 ( 45) link_BETA1-4 : angle 2.62974 / 1.84 ( 135) link_NAG-ASN : bond 0.00827 / 0.52 ( 66) link_NAG-ASN : angle 3.74180 / 2.43 ( 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 : 0.744 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: 0.7580 (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: 0.1687 time to fit residues: 141.9956 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 : 0.745 ------------------------------------------------------------------------------- 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... G 72 HIS G 99 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.121535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.094373 restraints weight = 41730.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.094524 restraints weight = 37193.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.095258 restraints weight = 43164.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.096256 restraints weight = 26823.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.097049 restraints weight = 23533.884| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.095 21147 Z= 0.349 Angle : 0.961 15.356 28914 Z= 0.476 Chirality : 0.055 0.326 3504 Planarity : 0.007 0.073 3510 Dihedral : 4.944 27.462 2604 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.83 % Favored : 87.92 % Rotamer: Outliers : 2.63 % Allowed : 10.27 % Favored : 87.11 % 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: -4.24 (0.15), residues: 2367 helix: -2.83 (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 0.031 0.003 TYR I 98 PHE 0.032 0.003 PHE G 391 TRP 0.025 0.002 TRP G 479 HIS 0.018 0.002 HIS G 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00832 / 0.35 (20991) covalent geometry : angle 0.92028 / 0.47 (28500) SS BOND : bond 0.00780 / 0.41 ( 36) SS BOND : angle 1.86179 / 1.31 ( 72) hydrogen bonds : bond 0.06226 / 4.06 ( 426) hydrogen bonds : angle 6.00109 / 4.02 ( 1179) Misc. bond : bond 0.00146 / 0.08 ( 6) link_ALPHA1-3 : bond 0.01047 / 0.38 ( 3) link_ALPHA1-3 : angle 1.67424 / 1.01 ( 9) link_BETA1-4 : bond 0.00780 / 0.48 ( 45) link_BETA1-4 : angle 2.08526 / 1.45 ( 135) link_NAG-ASN : bond 0.00530 / 0.33 ( 66) link_NAG-ASN : angle 2.91649 / 1.96 ( 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 375 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 320 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 426 MET cc_start: 0.7702 (ttp) cc_final: 0.7431 (ttm) REVERT: H 53 TYR cc_start: 0.8922 (t80) cc_final: 0.8691 (t80) REVERT: L 81 GLU cc_start: 0.7820 (mp0) cc_final: 0.7453 (pp20) REVERT: L 83 PHE cc_start: 0.7729 (m-10) cc_final: 0.6847 (m-80) REVERT: D 383 PHE cc_start: 0.7804 (m-10) cc_final: 0.7594 (m-80) REVERT: B 629 MET cc_start: 0.8813 (mmm) cc_final: 0.8361 (mmm) REVERT: F 1 GLN cc_start: 0.8160 (mm110) cc_final: 0.7829 (mm110) REVERT: F 82 LEU cc_start: 0.8127 (mt) cc_final: 0.7882 (tp) REVERT: J 6 GLN cc_start: 0.6662 (mt0) cc_final: 0.6166 (mt0) REVERT: J 83 PHE cc_start: 0.7950 (m-10) cc_final: 0.7261 (m-10) REVERT: J 100 GLN cc_start: 0.7535 (mt0) cc_final: 0.7251 (mt0) REVERT: E 104 MET cc_start: 0.9090 (ttt) cc_final: 0.8844 (ttt) REVERT: E 427 TRP cc_start: 0.6437 (m100) cc_final: 0.6197 (m100) REVERT: E 434 MET cc_start: 0.7891 (ptm) cc_final: 0.7682 (ttp) REVERT: C 599 SER cc_start: 0.9167 (t) cc_final: 0.8808 (p) REVERT: C 659 GLU cc_start: 0.8118 (pp20) cc_final: 0.7830 (pp20) REVERT: I 47 TRP cc_start: 0.8548 (t60) cc_final: 0.7934 (t60) REVERT: I 54 ASN cc_start: 0.8818 (p0) cc_final: 0.8616 (p0) REVERT: I 72 ASP cc_start: 0.6765 (p0) cc_final: 0.6545 (p0) REVERT: K 1 GLU cc_start: 0.6692 (mt-10) cc_final: 0.6354 (mt-10) REVERT: K 83 PHE cc_start: 0.7740 (m-10) cc_final: 0.6990 (m-80) REVERT: K 97 THR cc_start: 0.7953 (t) cc_final: 0.7626 (p) outliers start: 55 outliers final: 35 residues processed: 363 average time/residue: 0.1620 time to fit residues: 88.4809 Evaluate side-chains 304 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 269 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 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 B residue 621 GLU 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 E residue 414 ILE Chi-restraints excluded: chain C residue 575 GLN 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 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: 0.9980 chunk 94 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 184 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 195 optimal weight: 0.2980 chunk 67 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 99 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** E 363 HIS ** C 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN I 6 GLN I 31 ASN K 6 GLN K 100 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.124639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.096393 restraints weight = 40891.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.097793 restraints weight = 35003.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.098662 restraints weight = 27518.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.099227 restraints weight = 22525.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.100258 restraints weight = 21151.539| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21147 Z= 0.143 Angle : 0.767 14.672 28914 Z= 0.379 Chirality : 0.049 0.325 3504 Planarity : 0.005 0.061 3510 Dihedral : 4.873 35.590 2604 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.08 % Favored : 90.71 % Rotamer: Outliers : 3.01 % Allowed : 12.66 % 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: -3.58 (0.15), residues: 2367 helix: -1.74 (0.23), residues: 390 sheet: -1.88 (0.20), residues: 633 loop : -2.92 (0.15), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 31 TYR 0.027 0.001 TYR I 98 PHE 0.030 0.002 PHE D 391 TRP 0.016 0.001 TRP G 479 HIS 0.016 0.001 HIS G 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (20991) covalent geometry : angle 0.72528 / 0.37 (28500) SS BOND : bond 0.00704 / 0.47 ( 36) SS BOND : angle 2.37157 / 1.82 ( 72) hydrogen bonds : bond 0.04580 / 2.96 ( 426) hydrogen bonds : angle 5.34325 / 3.56 ( 1179) Misc. bond : bond 0.00172 / 0.11 ( 6) link_ALPHA1-3 : bond 0.00750 / 0.32 ( 3) link_ALPHA1-3 : angle 1.31263 / 0.75 ( 9) link_BETA1-4 : bond 0.00466 / 0.28 ( 45) link_BETA1-4 : angle 1.61874 / 1.11 ( 135) link_NAG-ASN : bond 0.00460 / 0.27 ( 66) link_NAG-ASN : angle 2.49315 / 1.69 ( 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 361 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 298 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 447 SER cc_start: 0.8909 (t) cc_final: 0.8695 (m) REVERT: A 566 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8385 (tp) REVERT: H 38 ARG cc_start: 0.7671 (ttp-170) cc_final: 0.7451 (ttp-170) REVERT: H 79 TYR cc_start: 0.8038 (m-80) cc_final: 0.7427 (m-80) REVERT: L 83 PHE cc_start: 0.7695 (m-10) cc_final: 0.6822 (m-80) REVERT: D 100 MET cc_start: 0.8928 (ttm) cc_final: 0.8718 (mtp) REVERT: D 486 TYR cc_start: 0.7093 (p90) cc_final: 0.5890 (p90) REVERT: B 566 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8254 (tp) REVERT: B 629 MET cc_start: 0.8708 (mmm) cc_final: 0.8329 (mmm) REVERT: B 634 GLU cc_start: 0.8422 (tp30) cc_final: 0.7913 (tm-30) REVERT: B 645 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8698 (mm) REVERT: B 656 ASN cc_start: 0.8352 (OUTLIER) cc_final: 0.8152 (t0) REVERT: F 1 GLN cc_start: 0.8096 (mm110) cc_final: 0.7880 (mm110) REVERT: F 80 MET cc_start: 0.7852 (tmm) cc_final: 0.7406 (tmm) REVERT: J 6 GLN cc_start: 0.6745 (mt0) cc_final: 0.6406 (mt0) REVERT: J 29 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.7254 (ptm-80) REVERT: J 81 GLU cc_start: 0.7765 (mp0) cc_final: 0.6601 (tp30) REVERT: J 83 PHE cc_start: 0.7874 (m-10) cc_final: 0.7210 (m-10) REVERT: J 100 GLN cc_start: 0.7556 (mt0) cc_final: 0.7271 (mt0) REVERT: C 599 SER cc_start: 0.9039 (t) cc_final: 0.8678 (p) REVERT: C 629 MET cc_start: 0.8652 (mmm) cc_final: 0.8411 (mtp) REVERT: C 659 GLU cc_start: 0.8144 (pp20) cc_final: 0.7935 (pp20) REVERT: I 47 TRP cc_start: 0.8489 (t60) cc_final: 0.8101 (t60) REVERT: I 54 ASN cc_start: 0.8664 (p0) cc_final: 0.8369 (p0) REVERT: K 31 ARG cc_start: 0.7005 (ttp-170) cc_final: 0.6534 (ttp80) REVERT: K 83 PHE cc_start: 0.7588 (m-10) cc_final: 0.6914 (m-80) REVERT: K 97 THR cc_start: 0.7720 (t) cc_final: 0.7457 (p) outliers start: 63 outliers final: 33 residues processed: 340 average time/residue: 0.1651 time to fit residues: 85.4140 Evaluate side-chains 301 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 263 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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 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 565 MET Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 656 ASN 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 29 ARG 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 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 22 SER 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: 0.9980 chunk 34 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 209 optimal weight: 4.9990 chunk 166 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 99 ASN G 363 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN F 35 HIS ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 89 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN I 31 ASN ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.119716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.091435 restraints weight = 41525.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.092816 restraints weight = 35468.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.093642 restraints weight = 27897.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.094173 restraints weight = 22594.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.094448 restraints weight = 21468.310| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 21147 Z= 0.265 Angle : 0.864 12.885 28914 Z= 0.421 Chirality : 0.051 0.306 3504 Planarity : 0.005 0.069 3510 Dihedral : 5.245 35.332 2604 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.62 % Favored : 88.09 % Rotamer: Outliers : 4.58 % Allowed : 12.94 % Favored : 82.47 % 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: -3.45 (0.16), residues: 2367 helix: -1.39 (0.24), residues: 390 sheet: -1.78 (0.20), residues: 630 loop : -2.93 (0.15), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 32 TYR 0.031 0.003 TYR I 98 PHE 0.028 0.003 PHE E 391 TRP 0.019 0.002 TRP F 47 HIS 0.012 0.002 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00626 / 0.26 (20991) covalent geometry : angle 0.82172 / 0.41 (28500) SS BOND : bond 0.00672 / 0.37 ( 36) SS BOND : angle 2.70319 / 1.99 ( 72) hydrogen bonds : bond 0.04877 / 3.12 ( 426) hydrogen bonds : angle 5.27931 / 3.52 ( 1179) Misc. bond : bond 0.00155 / 0.10 ( 6) link_ALPHA1-3 : bond 0.00660 / 0.30 ( 3) link_ALPHA1-3 : angle 1.21305 / 0.69 ( 9) link_BETA1-4 : bond 0.00533 / 0.33 ( 45) link_BETA1-4 : angle 1.83433 / 1.26 ( 135) link_NAG-ASN : bond 0.00490 / 0.30 ( 66) link_NAG-ASN : angle 2.59382 / 1.76 ( 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 358 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 262 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 566 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8457 (tp) REVERT: H 38 ARG cc_start: 0.7794 (ttp-170) cc_final: 0.7466 (ttp-170) REVERT: H 53 TYR cc_start: 0.8908 (t80) cc_final: 0.8362 (t80) REVERT: H 72 ASP cc_start: 0.7896 (p0) cc_final: 0.7623 (p0) REVERT: L 83 PHE cc_start: 0.7766 (m-10) cc_final: 0.6938 (m-80) REVERT: D 108 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8413 (tt) REVERT: D 153 GLU cc_start: 0.6874 (tp30) cc_final: 0.6642 (mm-30) REVERT: B 629 MET cc_start: 0.8762 (mmm) cc_final: 0.8305 (mmm) REVERT: B 645 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8691 (mm) REVERT: F 80 MET cc_start: 0.7869 (tmm) cc_final: 0.7424 (tmm) REVERT: J 6 GLN cc_start: 0.6972 (mt0) cc_final: 0.6769 (mt0) REVERT: J 100 GLN cc_start: 0.7632 (mt0) cc_final: 0.7386 (mt0) REVERT: E 317 PHE cc_start: 0.7027 (t80) cc_final: 0.6822 (t80) REVERT: C 599 SER cc_start: 0.9146 (t) cc_final: 0.8768 (p) REVERT: I 47 TRP cc_start: 0.8518 (t60) cc_final: 0.8312 (t60) REVERT: I 54 ASN cc_start: 0.8884 (p0) cc_final: 0.8569 (p0) REVERT: K 31 ARG cc_start: 0.7177 (ttp-170) cc_final: 0.6809 (ttp80) outliers start: 96 outliers final: 61 residues processed: 327 average time/residue: 0.1616 time to fit residues: 81.4966 Evaluate side-chains 310 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 246 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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 132 ASN Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 414 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 77 THR Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 10 THR 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 75 ILE Chi-restraints excluded: chain D residue 39 TYR 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 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 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 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 107 ASP 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 414 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 491 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 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: 0.9990 chunk 76 optimal weight: 4.9990 chunk 216 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 159 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 212 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 183 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 HIS ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.122138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.093967 restraints weight = 40854.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.094359 restraints weight = 31629.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.095497 restraints weight = 27966.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.096142 restraints weight = 22472.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.096524 restraints weight = 21675.377| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21147 Z= 0.145 Angle : 0.730 11.131 28914 Z= 0.356 Chirality : 0.048 0.315 3504 Planarity : 0.005 0.063 3510 Dihedral : 5.066 32.809 2604 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.53 % Favored : 91.34 % Rotamer: Outliers : 3.72 % Allowed : 14.52 % Favored : 81.76 % 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: -3.17 (0.16), residues: 2367 helix: -0.96 (0.25), residues: 393 sheet: -1.61 (0.20), residues: 618 loop : -2.80 (0.15), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 61 TYR 0.029 0.002 TYR I 98 PHE 0.029 0.002 PHE D 391 TRP 0.018 0.001 TRP H 47 HIS 0.005 0.001 HIS B 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (20991) covalent geometry : angle 0.69235 / 0.35 (28500) SS BOND : bond 0.00454 / 0.30 ( 36) SS BOND : angle 2.01922 / 1.48 ( 72) hydrogen bonds : bond 0.03971 / 2.55 ( 426) hydrogen bonds : angle 4.99535 / 3.32 ( 1179) Misc. bond : bond 0.00121 / 0.07 ( 6) link_ALPHA1-3 : bond 0.00669 / 0.30 ( 3) link_ALPHA1-3 : angle 1.28953 / 0.73 ( 9) link_BETA1-4 : bond 0.00444 / 0.28 ( 45) link_BETA1-4 : angle 1.56554 / 1.07 ( 135) link_NAG-ASN : bond 0.00422 / 0.24 ( 66) link_NAG-ASN : angle 2.36593 / 1.60 ( 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 342 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 264 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 318 TYR cc_start: 0.7824 (m-80) cc_final: 0.7277 (m-80) REVERT: A 566 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8481 (tp) REVERT: H 38 ARG cc_start: 0.7769 (ttp-170) cc_final: 0.7546 (ttp-170) REVERT: H 53 TYR cc_start: 0.8775 (t80) cc_final: 0.8238 (t80) REVERT: H 72 ASP cc_start: 0.7808 (p0) cc_final: 0.7513 (p0) REVERT: L 106 ARG cc_start: 0.6371 (ptt-90) cc_final: 0.5949 (ptt-90) REVERT: D 153 GLU cc_start: 0.7024 (tp30) cc_final: 0.6626 (mm-30) REVERT: B 629 MET cc_start: 0.8622 (mmm) cc_final: 0.8184 (mmm) REVERT: B 645 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8787 (mm) REVERT: F 46 GLU cc_start: 0.7907 (mp0) cc_final: 0.7539 (mp0) REVERT: F 54 ASN cc_start: 0.8983 (p0) cc_final: 0.8706 (p0) REVERT: F 80 MET cc_start: 0.7716 (tmm) cc_final: 0.7286 (tmm) REVERT: F 98 TYR cc_start: 0.8702 (t80) cc_final: 0.8215 (t80) REVERT: J 6 GLN cc_start: 0.6957 (mt0) cc_final: 0.6606 (mt0) REVERT: J 29 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.6296 (ptm-80) REVERT: J 81 GLU cc_start: 0.7677 (mp0) cc_final: 0.6531 (tp30) REVERT: J 100 GLN cc_start: 0.7568 (mt0) cc_final: 0.7271 (mt0) REVERT: E 317 PHE cc_start: 0.6958 (t80) cc_final: 0.6706 (t80) REVERT: C 599 SER cc_start: 0.9046 (t) cc_final: 0.8679 (p) REVERT: I 46 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8164 (pt0) REVERT: I 54 ASN cc_start: 0.8739 (p0) cc_final: 0.8441 (p0) REVERT: K 31 ARG cc_start: 0.7187 (ttp-170) cc_final: 0.6715 (tmm-80) REVERT: K 106 ARG cc_start: 0.6405 (ptp90) cc_final: 0.6130 (ptt-90) outliers start: 78 outliers final: 55 residues processed: 315 average time/residue: 0.1608 time to fit residues: 77.8724 Evaluate side-chains 310 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 251 time to evaluate : 0.677 ------------------------------------------------------------------------------- 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 494 LEU Chi-restraints excluded: chain A residue 548 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 73 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 81 GLU 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 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 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 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 13 LEU Chi-restraints excluded: chain J residue 29 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 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 I residue 37 VAL Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 59 PHE Chi-restraints excluded: chain I residue 107 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 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: 0.7980 chunk 107 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 225 optimal weight: 5.9990 chunk 139 optimal weight: 0.9980 chunk 141 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 172 optimal weight: 0.8980 chunk 125 optimal weight: 0.6980 chunk 227 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 6 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 GLN ** 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 = 0.3739 r_free = 0.3739 target = 0.123015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.094330 restraints weight = 40744.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.094924 restraints weight = 34292.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.096044 restraints weight = 31788.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.096768 restraints weight = 23394.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.097099 restraints weight = 22069.242| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4346 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= 0.127 Angle : 0.697 11.102 28914 Z= 0.341 Chirality : 0.047 0.321 3504 Planarity : 0.005 0.058 3510 Dihedral : 4.899 31.763 2604 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.29 % Favored : 90.58 % Rotamer: Outliers : 3.39 % Allowed : 14.76 % Favored : 81.85 % 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: -2.98 (0.16), residues: 2367 helix: -0.60 (0.25), residues: 393 sheet: -1.49 (0.20), residues: 621 loop : -2.75 (0.15), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 61 TYR 0.027 0.001 TYR I 98 PHE 0.029 0.002 PHE D 391 TRP 0.040 0.001 TRP H 47 HIS 0.005 0.001 HIS B 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (20991) covalent geometry : angle 0.66149 / 0.33 (28500) SS BOND : bond 0.00304 / 0.18 ( 36) SS BOND : angle 1.84889 / 1.38 ( 72) hydrogen bonds : bond 0.03641 / 2.34 ( 426) hydrogen bonds : angle 4.82797 / 3.20 ( 1179) Misc. bond : bond 0.00265 / 0.21 ( 6) link_ALPHA1-3 : bond 0.00698 / 0.30 ( 3) link_ALPHA1-3 : angle 1.35164 / 0.77 ( 9) link_BETA1-4 : bond 0.00442 / 0.28 ( 45) link_BETA1-4 : angle 1.52191 / 1.04 ( 135) link_NAG-ASN : bond 0.00424 / 0.24 ( 66) link_NAG-ASN : angle 2.26938 / 1.54 ( 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 335 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 264 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 318 TYR cc_start: 0.7758 (m-80) cc_final: 0.7310 (m-80) REVERT: A 566 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8420 (tp) REVERT: H 38 ARG cc_start: 0.7623 (ttp-170) cc_final: 0.7412 (ttp-170) REVERT: H 47 TRP cc_start: 0.7937 (t60) cc_final: 0.7654 (t60) REVERT: H 53 TYR cc_start: 0.8778 (t80) cc_final: 0.8551 (t80) REVERT: H 64 GLN cc_start: 0.7907 (mm110) cc_final: 0.7687 (mm110) REVERT: H 72 ASP cc_start: 0.7826 (p0) cc_final: 0.7563 (p0) REVERT: H 80 MET cc_start: 0.7764 (ttp) cc_final: 0.7082 (tmm) REVERT: L 106 ARG cc_start: 0.6248 (ptt-90) cc_final: 0.5859 (ptt-90) REVERT: D 318 TYR cc_start: 0.6972 (m-80) cc_final: 0.6505 (m-80) REVERT: D 486 TYR cc_start: 0.7324 (p90) cc_final: 0.6119 (p90) REVERT: B 629 MET cc_start: 0.8526 (mmm) cc_final: 0.8058 (mmm) REVERT: B 645 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8756 (mm) REVERT: F 1 GLN cc_start: 0.8080 (mm110) cc_final: 0.7627 (pt0) REVERT: F 46 GLU cc_start: 0.7914 (mp0) cc_final: 0.7540 (mp0) REVERT: F 80 MET cc_start: 0.7775 (tmm) cc_final: 0.7174 (tmm) REVERT: F 98 TYR cc_start: 0.8755 (t80) cc_final: 0.8268 (t80) REVERT: J 6 GLN cc_start: 0.6971 (mt0) cc_final: 0.6543 (mt0) REVERT: J 29 ARG cc_start: 0.7124 (OUTLIER) cc_final: 0.6279 (ptm-80) REVERT: J 58 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.7419 (tt) REVERT: J 100 GLN cc_start: 0.7578 (mt0) cc_final: 0.7346 (mt0) REVERT: E 107 ASP cc_start: 0.7294 (OUTLIER) cc_final: 0.7055 (t0) REVERT: E 317 PHE cc_start: 0.6915 (t80) cc_final: 0.6505 (t80) REVERT: E 318 TYR cc_start: 0.7564 (m-80) cc_final: 0.6819 (m-80) REVERT: C 599 SER cc_start: 0.8999 (t) cc_final: 0.8660 (p) REVERT: I 46 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8214 (pt0) REVERT: I 54 ASN cc_start: 0.8736 (p0) cc_final: 0.8477 (p0) REVERT: K 58 ILE cc_start: 0.7353 (OUTLIER) cc_final: 0.7117 (tt) REVERT: K 106 ARG cc_start: 0.6329 (ptp90) cc_final: 0.6059 (ptt-90) outliers start: 71 outliers final: 50 residues processed: 306 average time/residue: 0.1535 time to fit residues: 72.6812 Evaluate side-chains 313 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 256 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 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 65 ASP Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 77 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 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 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 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 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 13 LEU Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 29 ARG Chi-restraints excluded: chain J residue 58 ILE 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 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 59 PHE Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 22 SER 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: 0.8980 chunk 132 optimal weight: 0.8980 chunk 230 optimal weight: 10.0000 chunk 150 optimal weight: 5.9990 chunk 209 optimal weight: 0.4980 chunk 51 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 94 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 189 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 89 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN ** 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 = 0.3751 r_free = 0.3751 target = 0.123816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.095024 restraints weight = 41051.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.095275 restraints weight = 35689.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.096426 restraints weight = 33190.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.097405 restraints weight = 24405.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.097718 restraints weight = 22567.450| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.4445 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= 0.120 Angle : 0.679 11.136 28914 Z= 0.332 Chirality : 0.046 0.322 3504 Planarity : 0.004 0.054 3510 Dihedral : 4.754 30.027 2604 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.15 % Favored : 91.72 % Rotamer: Outliers : 3.63 % Allowed : 14.47 % 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: -2.77 (0.16), residues: 2367 helix: -0.19 (0.26), residues: 390 sheet: -1.38 (0.20), residues: 651 loop : -2.70 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 32 TYR 0.026 0.001 TYR I 98 PHE 0.030 0.002 PHE D 391 TRP 0.018 0.001 TRP H 47 HIS 0.005 0.001 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (20991) covalent geometry : angle 0.64613 / 0.32 (28500) SS BOND : bond 0.00276 / 0.16 ( 36) SS BOND : angle 1.58738 / 1.18 ( 72) hydrogen bonds : bond 0.03425 / 2.20 ( 426) hydrogen bonds : angle 4.67989 / 3.11 ( 1179) Misc. bond : bond 0.00351 / 0.28 ( 6) link_ALPHA1-3 : bond 0.00667 / 0.30 ( 3) link_ALPHA1-3 : angle 1.35393 / 0.77 ( 9) link_BETA1-4 : bond 0.00414 / 0.26 ( 45) link_BETA1-4 : angle 1.45205 / 0.99 ( 135) link_NAG-ASN : bond 0.00417 / 0.24 ( 66) link_NAG-ASN : angle 2.20941 / 1.49 ( 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 348 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 272 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 215 ILE cc_start: 0.8754 (mm) cc_final: 0.8513 (pt) REVERT: G 318 TYR cc_start: 0.7761 (m-80) cc_final: 0.7365 (m-80) REVERT: G 368 ASP cc_start: 0.7833 (m-30) cc_final: 0.7513 (m-30) REVERT: A 566 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8407 (tp) REVERT: H 38 ARG cc_start: 0.7568 (ttp-170) cc_final: 0.7367 (ttp-170) REVERT: H 47 TRP cc_start: 0.7910 (t60) cc_final: 0.7473 (t60) REVERT: H 72 ASP cc_start: 0.7687 (p0) cc_final: 0.7400 (p0) REVERT: H 80 MET cc_start: 0.7687 (ttp) cc_final: 0.7050 (tmm) REVERT: L 106 ARG cc_start: 0.6263 (ptt-90) cc_final: 0.5921 (ptt-90) REVERT: D 153 GLU cc_start: 0.6869 (tp30) cc_final: 0.6552 (mm-30) REVERT: D 318 TYR cc_start: 0.6975 (m-80) cc_final: 0.6585 (m-80) REVERT: D 376 PHE cc_start: 0.7669 (OUTLIER) cc_final: 0.7005 (t80) REVERT: D 486 TYR cc_start: 0.7411 (p90) cc_final: 0.6191 (p90) REVERT: B 629 MET cc_start: 0.8475 (mmm) cc_final: 0.8008 (mmm) REVERT: B 645 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8694 (mm) REVERT: F 1 GLN cc_start: 0.8132 (mm110) cc_final: 0.7628 (pt0) REVERT: F 46 GLU cc_start: 0.7985 (mp0) cc_final: 0.7756 (mp0) REVERT: F 80 MET cc_start: 0.7780 (tmm) cc_final: 0.7190 (tmm) REVERT: F 98 TYR cc_start: 0.8734 (t80) cc_final: 0.8269 (t80) REVERT: J 6 GLN cc_start: 0.6929 (mt0) cc_final: 0.6482 (mt0) REVERT: J 58 ILE cc_start: 0.7785 (OUTLIER) cc_final: 0.7434 (tt) REVERT: J 100 GLN cc_start: 0.7553 (mt0) cc_final: 0.7322 (mt0) REVERT: E 317 PHE cc_start: 0.6915 (t80) cc_final: 0.6579 (t80) REVERT: E 486 TYR cc_start: 0.7396 (OUTLIER) cc_final: 0.5615 (p90) REVERT: C 599 SER cc_start: 0.9035 (t) cc_final: 0.8643 (p) REVERT: I 38 ARG cc_start: 0.7348 (ttp-170) cc_final: 0.6954 (ttp-170) REVERT: I 46 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7677 (pt0) REVERT: I 47 TRP cc_start: 0.8244 (t60) cc_final: 0.7734 (t60) REVERT: I 54 ASN cc_start: 0.8723 (p0) cc_final: 0.8458 (p0) REVERT: K 58 ILE cc_start: 0.7228 (OUTLIER) cc_final: 0.6981 (tt) REVERT: K 106 ARG cc_start: 0.6852 (ptp90) cc_final: 0.6617 (ptt-90) outliers start: 76 outliers final: 54 residues processed: 321 average time/residue: 0.1558 time to fit residues: 77.4264 Evaluate side-chains 321 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 260 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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 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 73 THR Chi-restraints excluded: chain H residue 77 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 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 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 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 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 81 GLU Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain J residue 5 THR 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 108 ILE 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 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 59 PHE Chi-restraints excluded: chain I residue 73 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: 0.7980 chunk 63 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 chunk 193 optimal weight: 7.9990 chunk 206 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 176 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 192 optimal weight: 10.0000 chunk 76 optimal weight: 0.6980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 35 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 = 0.3717 r_free = 0.3717 target = 0.121425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.092951 restraints weight = 40935.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.093516 restraints weight = 33826.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.094193 restraints weight = 34755.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.095360 restraints weight = 24443.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.095696 restraints weight = 21585.473| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 21147 Z= 0.197 Angle : 0.762 11.126 28914 Z= 0.371 Chirality : 0.049 0.306 3504 Planarity : 0.005 0.091 3510 Dihedral : 4.929 32.112 2604 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.39 % Favored : 89.48 % Rotamer: Outliers : 3.53 % Allowed : 14.57 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.80 (0.16), residues: 2367 helix: -0.17 (0.26), residues: 390 sheet: -1.41 (0.21), residues: 615 loop : -2.71 (0.15), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 77 TYR 0.019 0.002 TYR H 98 PHE 0.031 0.002 PHE D 391 TRP 0.018 0.001 TRP H 47 HIS 0.009 0.001 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 (20991) covalent geometry : angle 0.72385 / 0.36 (28500) SS BOND : bond 0.00340 / 0.20 ( 36) SS BOND : angle 2.03078 / 1.51 ( 72) hydrogen bonds : bond 0.03848 / 2.46 ( 426) hydrogen bonds : angle 4.79099 / 3.18 ( 1179) Misc. bond : bond 0.00656 / 0.39 ( 6) link_ALPHA1-3 : bond 0.00682 / 0.30 ( 3) link_ALPHA1-3 : angle 1.29835 / 0.74 ( 9) link_BETA1-4 : bond 0.00439 / 0.27 ( 45) link_BETA1-4 : angle 1.54765 / 1.06 ( 135) link_NAG-ASN : bond 0.00453 / 0.27 ( 66) link_NAG-ASN : angle 2.47817 / 1.63 ( 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 328 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 254 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 318 TYR cc_start: 0.7830 (m-80) cc_final: 0.7352 (m-80) REVERT: G 368 ASP cc_start: 0.7910 (m-30) cc_final: 0.7592 (m-30) REVERT: G 383 PHE cc_start: 0.8180 (m-80) cc_final: 0.7872 (m-10) REVERT: A 566 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8498 (tp) REVERT: H 47 TRP cc_start: 0.7977 (t60) cc_final: 0.7570 (t60) REVERT: L 106 ARG cc_start: 0.6232 (ptt-90) cc_final: 0.5866 (ptt-90) REVERT: D 318 TYR cc_start: 0.7056 (m-80) cc_final: 0.6653 (m-80) REVERT: B 629 MET cc_start: 0.8550 (mmm) cc_final: 0.8030 (mmm) REVERT: B 645 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8814 (mm) REVERT: F 1 GLN cc_start: 0.8132 (mm110) cc_final: 0.7653 (pt0) REVERT: F 80 MET cc_start: 0.7825 (tmm) cc_final: 0.7185 (tmm) REVERT: F 98 TYR cc_start: 0.8797 (t80) cc_final: 0.8381 (t80) REVERT: J 6 GLN cc_start: 0.7060 (mt0) cc_final: 0.6602 (mt0) REVERT: J 58 ILE cc_start: 0.7825 (OUTLIER) cc_final: 0.7470 (tt) REVERT: J 100 GLN cc_start: 0.7625 (mt0) cc_final: 0.7384 (mt0) REVERT: E 318 TYR cc_start: 0.7604 (m-80) cc_final: 0.6823 (m-80) REVERT: E 363 HIS cc_start: 0.6412 (t-170) cc_final: 0.6202 (t-170) REVERT: E 486 TYR cc_start: 0.7670 (OUTLIER) cc_final: 0.5962 (p90) REVERT: C 599 SER cc_start: 0.9028 (t) cc_final: 0.8815 (p) REVERT: I 46 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8187 (pt0) REVERT: I 47 TRP cc_start: 0.8320 (t60) cc_final: 0.7728 (t60) REVERT: I 54 ASN cc_start: 0.8863 (p0) cc_final: 0.8630 (p0) REVERT: K 58 ILE cc_start: 0.7336 (OUTLIER) cc_final: 0.7037 (tt) outliers start: 74 outliers final: 61 residues processed: 299 average time/residue: 0.1602 time to fit residues: 73.6867 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 : 0.734 ------------------------------------------------------------------------------- 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 A residue 566 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 77 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 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 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 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 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 5 THR 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 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 59 PHE Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 83 ARG 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: 2.9990 chunk 13 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 204 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 220 optimal weight: 10.0000 chunk 211 optimal weight: 1.9990 chunk 202 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 35 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.122238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.094005 restraints weight = 40781.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.093953 restraints weight = 34249.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.094980 restraints weight = 34327.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.095969 restraints weight = 24751.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.096813 restraints weight = 22388.333| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21147 Z= 0.149 Angle : 0.718 11.155 28914 Z= 0.352 Chirality : 0.047 0.309 3504 Planarity : 0.005 0.059 3510 Dihedral : 4.893 31.405 2604 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.08 % Favored : 90.79 % Rotamer: Outliers : 3.49 % Allowed : 14.47 % Favored : 82.04 % 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: -2.63 (0.16), residues: 2367 helix: 0.13 (0.27), residues: 372 sheet: -1.24 (0.21), residues: 615 loop : -2.64 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 77 TYR 0.020 0.002 TYR F 53 PHE 0.031 0.002 PHE D 391 TRP 0.014 0.001 TRP H 50 HIS 0.005 0.001 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (20991) covalent geometry : angle 0.68468 / 0.34 (28500) SS BOND : bond 0.00292 / 0.17 ( 36) SS BOND : angle 1.78597 / 1.33 ( 72) hydrogen bonds : bond 0.03584 / 2.30 ( 426) hydrogen bonds : angle 4.69611 / 3.11 ( 1179) Misc. bond : bond 0.00534 / 0.34 ( 6) link_ALPHA1-3 : bond 0.00675 / 0.30 ( 3) link_ALPHA1-3 : angle 1.34201 / 0.76 ( 9) link_BETA1-4 : bond 0.00411 / 0.26 ( 45) link_BETA1-4 : angle 1.45789 / 1.00 ( 135) link_NAG-ASN : bond 0.00411 / 0.24 ( 66) link_NAG-ASN : angle 2.27762 / 1.52 ( 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 336 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 263 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 318 TYR cc_start: 0.7837 (m-80) cc_final: 0.7426 (m-80) REVERT: G 368 ASP cc_start: 0.7875 (m-30) cc_final: 0.7350 (m-30) REVERT: A 566 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8458 (tp) REVERT: H 47 TRP cc_start: 0.8011 (t60) cc_final: 0.7519 (t60) REVERT: L 106 ARG cc_start: 0.6268 (ptt-90) cc_final: 0.5907 (ptt-90) REVERT: D 153 GLU cc_start: 0.6906 (tp30) cc_final: 0.6625 (mm-30) REVERT: D 318 TYR cc_start: 0.7090 (m-80) cc_final: 0.6678 (m-80) REVERT: B 629 MET cc_start: 0.8514 (mmm) cc_final: 0.8006 (mmm) REVERT: B 645 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8759 (mm) REVERT: F 1 GLN cc_start: 0.8180 (mm110) cc_final: 0.7660 (pt0) REVERT: F 72 ASP cc_start: 0.6916 (p0) cc_final: 0.6667 (p0) REVERT: F 80 MET cc_start: 0.7840 (tmm) cc_final: 0.7373 (tmm) REVERT: F 98 TYR cc_start: 0.8761 (t80) cc_final: 0.8369 (t80) REVERT: J 6 GLN cc_start: 0.7118 (mt0) cc_final: 0.6638 (mt0) REVERT: J 58 ILE cc_start: 0.7798 (OUTLIER) cc_final: 0.7446 (tt) REVERT: J 100 GLN cc_start: 0.7598 (mt0) cc_final: 0.7360 (mt0) REVERT: E 318 TYR cc_start: 0.7624 (m-80) cc_final: 0.6901 (m-80) REVERT: E 363 HIS cc_start: 0.6397 (t-170) cc_final: 0.6149 (t-170) REVERT: E 486 TYR cc_start: 0.7674 (OUTLIER) cc_final: 0.5831 (p90) REVERT: C 599 SER cc_start: 0.9011 (t) cc_final: 0.8690 (p) REVERT: I 46 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8206 (pt0) REVERT: I 47 TRP cc_start: 0.8298 (t60) cc_final: 0.7685 (t60) REVERT: I 54 ASN cc_start: 0.8920 (p0) cc_final: 0.8652 (p0) REVERT: I 80 MET cc_start: 0.7819 (ttp) cc_final: 0.7245 (tmm) REVERT: I 98 TYR cc_start: 0.8293 (t80) cc_final: 0.8089 (t80) REVERT: K 58 ILE cc_start: 0.7329 (OUTLIER) cc_final: 0.7045 (tt) outliers start: 73 outliers final: 61 residues processed: 308 average time/residue: 0.1517 time to fit residues: 72.2806 Evaluate side-chains 319 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 252 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 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 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 48 MET 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 47 VAL 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 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 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 5 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 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 37 VAL Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 59 PHE Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 22 SER 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: 0.7980 chunk 112 optimal weight: 0.3980 chunk 142 optimal weight: 10.0000 chunk 183 optimal weight: 0.8980 chunk 173 optimal weight: 0.7980 chunk 155 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 202 optimal weight: 0.0670 chunk 206 optimal weight: 2.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3755 r_free = 0.3755 target = 0.124070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.091376 restraints weight = 41009.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.094127 restraints weight = 24097.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.095851 restraints weight = 17586.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.096878 restraints weight = 14624.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.097427 restraints weight = 13126.539| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.4759 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= 0.119 Angle : 0.705 11.111 28914 Z= 0.345 Chirality : 0.047 0.323 3504 Planarity : 0.005 0.100 3510 Dihedral : 4.807 29.243 2604 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.62 % Favored : 91.25 % Rotamer: Outliers : 3.01 % Allowed : 15.00 % Favored : 82.00 % 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: -2.45 (0.17), residues: 2367 helix: 0.45 (0.28), residues: 369 sheet: -1.18 (0.21), residues: 633 loop : -2.57 (0.15), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 61 TYR 0.026 0.001 TYR H 98 PHE 0.030 0.002 PHE D 391 TRP 0.017 0.001 TRP H 50 HIS 0.004 0.001 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (20991) covalent geometry : angle 0.67380 / 0.34 (28500) SS BOND : bond 0.00253 / 0.15 ( 36) SS BOND : angle 1.57301 / 1.17 ( 72) hydrogen bonds : bond 0.03309 / 2.14 ( 426) hydrogen bonds : angle 4.54547 / 3.01 ( 1179) Misc. bond : bond 0.00585 / 0.33 ( 6) link_ALPHA1-3 : bond 0.00651 / 0.29 ( 3) link_ALPHA1-3 : angle 1.37504 / 0.78 ( 9) link_BETA1-4 : bond 0.00408 / 0.25 ( 45) link_BETA1-4 : angle 1.40020 / 0.95 ( 135) link_NAG-ASN : bond 0.00432 / 0.25 ( 66) link_NAG-ASN : angle 2.19605 / 1.48 ( 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 334 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 271 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 318 TYR cc_start: 0.7676 (m-80) cc_final: 0.7425 (m-80) REVERT: G 368 ASP cc_start: 0.7794 (m-30) cc_final: 0.7583 (m-30) REVERT: A 566 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8411 (tp) REVERT: H 47 TRP cc_start: 0.8078 (t60) cc_final: 0.7566 (t60) REVERT: H 100 MET cc_start: 0.7568 (mpp) cc_final: 0.6406 (mmt) REVERT: L 106 ARG cc_start: 0.6197 (ptt-90) cc_final: 0.5924 (ptt-90) REVERT: D 153 GLU cc_start: 0.7075 (tp30) cc_final: 0.6624 (mm-30) REVERT: D 318 TYR cc_start: 0.7017 (m-80) cc_final: 0.6592 (m-80) REVERT: D 376 PHE cc_start: 0.7650 (OUTLIER) cc_final: 0.7063 (t80) REVERT: B 629 MET cc_start: 0.8380 (mmm) cc_final: 0.7949 (mmm) REVERT: F 1 GLN cc_start: 0.8126 (mm110) cc_final: 0.7615 (pt0) REVERT: F 72 ASP cc_start: 0.6956 (p0) cc_final: 0.6663 (p0) REVERT: F 80 MET cc_start: 0.7830 (tmm) cc_final: 0.7411 (tmm) REVERT: F 98 TYR cc_start: 0.8846 (t80) cc_final: 0.8459 (t80) REVERT: J 6 GLN cc_start: 0.7005 (mt0) cc_final: 0.6117 (mt0) REVERT: J 31 ARG cc_start: 0.6983 (tmm160) cc_final: 0.6758 (ttp80) REVERT: J 32 ARG cc_start: 0.6101 (ptt-90) cc_final: 0.5892 (ptt-90) REVERT: J 58 ILE cc_start: 0.7805 (OUTLIER) cc_final: 0.7449 (tt) REVERT: E 317 PHE cc_start: 0.6809 (t80) cc_final: 0.6238 (t80) REVERT: E 318 TYR cc_start: 0.7538 (m-80) cc_final: 0.6876 (m-80) REVERT: E 363 HIS cc_start: 0.6245 (t-170) cc_final: 0.5993 (t-170) REVERT: E 486 TYR cc_start: 0.7448 (OUTLIER) cc_final: 0.5642 (p90) REVERT: C 599 SER cc_start: 0.8955 (t) cc_final: 0.8590 (p) REVERT: I 38 ARG cc_start: 0.7351 (ttp-170) cc_final: 0.6908 (ttp-170) REVERT: I 46 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7690 (pt0) REVERT: I 47 TRP cc_start: 0.8249 (t60) cc_final: 0.7584 (t60) REVERT: I 54 ASN cc_start: 0.8963 (p0) cc_final: 0.8723 (p0) REVERT: I 80 MET cc_start: 0.7564 (ttp) cc_final: 0.6974 (tmm) REVERT: K 58 ILE cc_start: 0.7359 (OUTLIER) cc_final: 0.7029 (tt) outliers start: 63 outliers final: 52 residues processed: 312 average time/residue: 0.1569 time to fit residues: 75.3748 Evaluate side-chains 308 residues out of total 2097 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 250 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 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 48 MET Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain H residue 107 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 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 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 13 LEU 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 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 37 VAL Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 59 PHE Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 22 SER 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: 0.9990 chunk 73 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 142 optimal weight: 0.7980 chunk 232 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 201 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 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 = 0.3756 r_free = 0.3756 target = 0.123995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.093454 restraints weight = 41211.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.094197 restraints weight = 26842.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.094208 restraints weight = 20592.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.094543 restraints weight = 21098.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.094903 restraints weight = 19347.476| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21147 Z= 0.130 Angle : 0.709 11.103 28914 Z= 0.350 Chirality : 0.047 0.317 3504 Planarity : 0.005 0.109 3510 Dihedral : 4.827 28.567 2604 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.70 % Favored : 91.17 % Rotamer: Outliers : 2.96 % Allowed : 15.47 % Favored : 81.57 % 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: -2.42 (0.17), residues: 2367 helix: 0.38 (0.27), residues: 387 sheet: -1.16 (0.20), residues: 651 loop : -2.56 (0.16), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 61 TYR 0.030 0.001 TYR H 98 PHE 0.031 0.002 PHE D 391 TRP 0.014 0.001 TRP H 47 HIS 0.008 0.001 HIS B 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (20991) covalent geometry : angle 0.67875 / 0.34 (28500) SS BOND : bond 0.00277 / 0.17 ( 36) SS BOND : angle 1.58639 / 1.18 ( 72) hydrogen bonds : bond 0.03381 / 2.19 ( 426) hydrogen bonds : angle 4.55075 / 3.01 ( 1179) Misc. bond : bond 0.00617 / 0.35 ( 6) link_ALPHA1-3 : bond 0.00657 / 0.29 ( 3) link_ALPHA1-3 : angle 1.36682 / 0.78 ( 9) link_BETA1-4 : bond 0.00420 / 0.26 ( 45) link_BETA1-4 : angle 1.40889 / 0.96 ( 135) link_NAG-ASN : bond 0.00407 / 0.24 ( 66) link_NAG-ASN : angle 2.19896 / 1.48 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3379.97 seconds wall clock time: 59 minutes 30.51 seconds (3570.51 seconds total)