Starting phenix.real_space_refine on Thu Mar 5 23:02:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uoj_26648/03_2026/7uoj_26648.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uoj_26648/03_2026/7uoj_26648.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7uoj_26648/03_2026/7uoj_26648.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uoj_26648/03_2026/7uoj_26648.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uoj_26648/03_2026/7uoj_26648.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uoj_26648/03_2026/7uoj_26648.map" } resolution = 4.02 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= 1.000 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 150 5.16 5 C 16356 2.51 5 N 4368 2.21 5 O 5259 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26133 Number of models: 1 Model: "" Number of chains: 54 Chain: "G" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3559 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Chain: "B" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1029 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "H" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1010 Classifications: {'peptide': 126} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 119} Chain: "L" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 737 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 9, 'TRANS': 88} Chain: "l" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "h" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1031 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain: "A" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3559 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Chain: "C" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1029 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "D" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1010 Classifications: {'peptide': 126} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 119} Chain: "E" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 737 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 9, 'TRANS': 88} Chain: "e" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "d" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1031 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain: "I" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3559 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Chain: "J" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1029 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "K" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1010 Classifications: {'peptide': 126} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 119} Chain: "M" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 737 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 9, 'TRANS': 88} Chain: "m" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "k" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1031 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "u" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 6.07, per 1000 atoms: 0.23 Number of scatterers: 26133 At special positions: 0 Unit cell: (159.796, 161.186, 155.628, 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 150 16.00 O 5259 8.00 N 4368 7.00 C 16356 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " 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=2.03 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=2.05 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.04 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 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 l 23 " - pdb=" SG CYS l 88 " distance=2.03 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 92 " distance=2.04 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.04 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS C 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS e 23 " - pdb=" SG CYS e 88 " distance=2.03 Simple disulfide: pdb=" SG CYS d 22 " - pdb=" SG CYS d 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.02 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.05 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.02 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS m 23 " - pdb=" SG CYS m 88 " distance=2.03 Simple disulfide: pdb=" SG CYS k 22 " - pdb=" SG CYS k 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN U 4 " - " MAN U 5 " " MAN U 5 " - " MAN U 6 " " MAN i 4 " - " MAN i 5 " " MAN i 5 " - " MAN i 6 " " MAN w 4 " - " MAN w 5 " " MAN w 5 " - " MAN w 6 " ALPHA1-3 " BMA O 3 " - " MAN O 4 " " BMA S 3 " - " MAN S 4 " " BMA U 3 " - " MAN U 4 " " MAN U 7 " - " MAN U 8 " " BMA Z 3 " - " MAN Z 4 " " BMA f 3 " - " MAN f 4 " " BMA i 3 " - " MAN i 4 " " MAN i 7 " - " MAN i 8 " " BMA q 3 " - " MAN q 4 " " BMA u 3 " - " MAN u 4 " " BMA w 3 " - " MAN w 4 " " MAN w 7 " - " MAN w 8 " ALPHA1-6 " BMA S 3 " - " MAN S 5 " " BMA U 3 " - " MAN U 7 " " MAN U 7 " - " MAN U 9 " " BMA f 3 " - " MAN f 5 " " BMA i 3 " - " MAN i 7 " " MAN i 7 " - " MAN i 9 " " BMA u 3 " - " MAN u 5 " " BMA w 3 " - " MAN w 7 " " MAN w 7 " - " MAN w 9 " BETA1-4 " NAG F 1 " - " NAG F 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 Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG 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 b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " 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 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 w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 197 " " NAG A 604 " - " ASN A 234 " " NAG A 605 " - " ASN A 339 " " NAG F 1 " - " ASN G 156 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 133 " " NAG G 603 " - " ASN G 197 " " NAG G 604 " - " ASN G 234 " " NAG G 605 " - " ASN G 339 " " NAG I 601 " - " ASN I 88 " " NAG I 602 " - " ASN I 133 " " NAG I 603 " - " ASN I 197 " " NAG I 604 " - " ASN I 234 " " NAG I 605 " - " ASN I 339 " " NAG N 1 " - " ASN G 160 " " NAG O 1 " - " ASN G 262 " " NAG P 1 " - " ASN G 295 " " NAG Q 1 " - " ASN G 301 " " NAG R 1 " - " ASN G 363 " " NAG S 1 " - " ASN G 386 " " NAG T 1 " - " ASN G 392 " " NAG U 1 " - " ASN G 332 " " NAG V 1 " - " ASN G 448 " " NAG X 1 " - " ASN A 156 " " NAG Y 1 " - " ASN A 160 " " NAG Z 1 " - " ASN A 262 " " NAG a 1 " - " ASN A 295 " " NAG b 1 " - " ASN A 301 " " NAG c 1 " - " ASN A 363 " " NAG f 1 " - " ASN A 386 " " NAG g 1 " - " ASN A 392 " " NAG i 1 " - " ASN A 332 " " NAG j 1 " - " ASN A 448 " " NAG o 1 " - " ASN I 156 " " NAG p 1 " - " ASN I 160 " " NAG q 1 " - " ASN I 262 " " NAG r 1 " - " ASN I 295 " " NAG s 1 " - " ASN I 301 " " NAG t 1 " - " ASN I 363 " " NAG u 1 " - " ASN I 386 " " NAG v 1 " - " ASN I 392 " " NAG w 1 " - " ASN I 332 " " NAG x 1 " - " ASN I 448 " Time building additional restraints: 2.80 Conformation dependent library (CDL) restraints added in 1.1 seconds 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5766 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 62 sheets defined 15.7% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'G' and resid 57 through 62 removed outlier: 3.673A pdb=" N TYR G 61 " --> pdb=" O ASP G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 115 removed outlier: 3.507A pdb=" N SER G 115 " --> pdb=" O LEU G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 4.134A pdb=" N CYS G 126 " --> pdb=" O THR G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 181 No H-bonds generated for 'chain 'G' and resid 179 through 181' Processing helix chain 'G' and resid 334 through 350 Processing helix chain 'G' and resid 351 through 353 No H-bonds generated for 'chain 'G' and resid 351 through 353' Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.865A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.973A pdb=" N ARG G 429 " --> pdb=" O MET G 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 476 through 481 removed outlier: 4.053A pdb=" N SER G 481 " --> pdb=" O ASP G 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 521 Processing helix chain 'B' and resid 529 through 535 removed outlier: 4.106A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 543 through 545 No H-bonds generated for 'chain 'B' and resid 543 through 545' Processing helix chain 'B' and resid 571 through 595 Processing helix chain 'B' and resid 627 through 635 removed outlier: 4.242A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 664 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.692A pdb=" N ASP H 86 " --> pdb=" O ARG H 83 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR H 87 " --> pdb=" O VAL H 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 83 through 87' Processing helix chain 'L' and resid 25 through 31 removed outlier: 4.503A pdb=" N HIS L 30 " --> pdb=" O GLY L 25 " (cutoff:3.500A) Processing helix chain 'l' and resid 79 through 83 removed outlier: 4.087A pdb=" N GLU l 83 " --> pdb=" O ALA l 80 " (cutoff:3.500A) Processing helix chain 'h' and resid 83 through 87 removed outlier: 3.948A pdb=" N ASP h 86 " --> pdb=" O THR h 83 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER h 87 " --> pdb=" O ALA h 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 83 through 87' Processing helix chain 'h' and resid 100D through 100H Processing helix chain 'A' and resid 57 through 63 removed outlier: 4.159A pdb=" N THR A 63 " --> pdb=" O LYS A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 115 removed outlier: 3.786A pdb=" N HIS A 105 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 4.365A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 334 through 350 Processing helix chain 'A' and resid 351 through 354 removed outlier: 3.922A pdb=" N GLY A 354 " --> pdb=" O LYS A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 351 through 354' Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.037A pdb=" N ARG A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.865A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 520 Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 537 through 542 Processing helix chain 'C' and resid 543 through 545 No H-bonds generated for 'chain 'C' and resid 543 through 545' Processing helix chain 'C' and resid 571 through 595 Processing helix chain 'C' and resid 627 through 635 removed outlier: 4.565A pdb=" N LYS C 633 " --> pdb=" O LEU C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 664 Processing helix chain 'E' and resid 25 through 31 removed outlier: 4.433A pdb=" N HIS E 30 " --> pdb=" O GLY E 25 " (cutoff:3.500A) Processing helix chain 'e' and resid 79 through 83 removed outlier: 4.096A pdb=" N GLU e 83 " --> pdb=" O ALA e 80 " (cutoff:3.500A) Processing helix chain 'd' and resid 100D through 100H removed outlier: 3.599A pdb=" N ASN d 100H" --> pdb=" O VAL d 100E" (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 63 removed outlier: 3.590A pdb=" N TYR I 61 " --> pdb=" O ASP I 57 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N THR I 63 " --> pdb=" O LYS I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 114 Processing helix chain 'I' and resid 115 through 117 No H-bonds generated for 'chain 'I' and resid 115 through 117' Processing helix chain 'I' and resid 122 through 126 removed outlier: 3.988A pdb=" N CYS I 126 " --> pdb=" O THR I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 179 through 181 No H-bonds generated for 'chain 'I' and resid 179 through 181' Processing helix chain 'I' and resid 334 through 350 Processing helix chain 'I' and resid 351 through 353 No H-bonds generated for 'chain 'I' and resid 351 through 353' Processing helix chain 'I' and resid 368 through 373 removed outlier: 3.915A pdb=" N THR I 373 " --> pdb=" O LEU I 369 " (cutoff:3.500A) Processing helix chain 'I' and resid 425 through 429 removed outlier: 3.965A pdb=" N ARG I 429 " --> pdb=" O MET I 426 " (cutoff:3.500A) Processing helix chain 'I' and resid 476 through 481 removed outlier: 4.008A pdb=" N SER I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) Processing helix chain 'J' and resid 514 through 520 removed outlier: 4.542A pdb=" N VAL J 518 " --> pdb=" O GLY J 514 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 536 removed outlier: 3.635A pdb=" N THR J 536 " --> pdb=" O ALA J 532 " (cutoff:3.500A) Processing helix chain 'J' and resid 537 through 542 Processing helix chain 'J' and resid 543 through 545 No H-bonds generated for 'chain 'J' and resid 543 through 545' Processing helix chain 'J' and resid 571 through 595 Processing helix chain 'J' and resid 627 through 638 removed outlier: 4.571A pdb=" N LYS J 633 " --> pdb=" O LEU J 629 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER J 636 " --> pdb=" O ASP J 632 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASN J 637 " --> pdb=" O LYS J 633 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR J 638 " --> pdb=" O GLU J 634 " (cutoff:3.500A) Processing helix chain 'J' and resid 641 through 664 Processing helix chain 'M' and resid 25 through 31 removed outlier: 4.483A pdb=" N HIS M 30 " --> pdb=" O GLY M 25 " (cutoff:3.500A) Processing helix chain 'm' and resid 79 through 83 removed outlier: 4.120A pdb=" N GLU m 83 " --> pdb=" O ALA m 80 " (cutoff:3.500A) Processing helix chain 'k' and resid 100D through 100H Processing sheet with id=AA1, first strand: chain 'G' and resid 495 through 499 removed outlier: 4.982A pdb=" N VAL G 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR B 606 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.720A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR G 244 " --> pdb=" O ILE G 84 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE G 84 " --> pdb=" O THR G 244 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 75 through 76 removed outlier: 4.296A pdb=" N VAL G 75 " --> pdb=" O CYS G 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 91 through 93 removed outlier: 4.057A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 130 through 133 Processing sheet with id=AA6, first strand: chain 'G' and resid 182 through 183 Processing sheet with id=AA7, first strand: chain 'G' and resid 201 through 203 removed outlier: 3.515A pdb=" N TYR G 435 " --> pdb=" O THR G 202 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 271 through 273 removed outlier: 4.119A pdb=" N LEU G 285 " --> pdb=" O ARG G 273 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 271 through 273 removed outlier: 4.119A pdb=" N LEU G 285 " --> pdb=" O ARG G 273 " (cutoff:3.500A) removed outlier: 11.092A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 10.830A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 12.122A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 11.372A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 10.880A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ASN G 300 " --> pdb=" O GLY G 441 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLY G 441 " --> pdb=" O ASN G 300 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 304 through 312 removed outlier: 6.549A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 359 through 360 removed outlier: 3.603A pdb=" N ILE G 359 " --> pdb=" O TRP G 395 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.526A pdb=" N GLY H 76G" --> pdb=" O VAL H 24 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.368A pdb=" N GLY H 10 " --> pdb=" O VAL H 110 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 8 through 13 removed outlier: 3.595A pdb=" N THR L 105 " --> pdb=" O MET L 11 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 19 through 23 Processing sheet with id=AB7, first strand: chain 'l' and resid 9 through 13 removed outlier: 6.059A pdb=" N ILE l 9 " --> pdb=" O THR l 103 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N THR l 105 " --> pdb=" O ILE l 9 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE l 11 " --> pdb=" O THR l 105 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TRP l 35 " --> pdb=" O ILE l 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'l' and resid 19 through 22 Processing sheet with id=AB9, first strand: chain 'h' and resid 4 through 7 removed outlier: 4.082A pdb=" N GLN h 77 " --> pdb=" O ASP h 72 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP h 72 " --> pdb=" O GLN h 77 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'h' and resid 58 through 59 removed outlier: 7.067A pdb=" N TRP h 36 " --> pdb=" O ILE h 48 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N TYR h 50 " --> pdb=" O TRP h 34 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TRP h 34 " --> pdb=" O TYR h 50 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'h' and resid 100 through 100A removed outlier: 4.009A pdb=" N ARG h 100 " --> pdb=" O PHE h 100K" (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE h 100K" --> pdb=" O ARG h 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 495 through 499 removed outlier: 5.040A pdb=" N VAL A 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR C 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.820A pdb=" N THR A 244 " --> pdb=" O ILE A 84 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE A 84 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 75 through 76 removed outlier: 4.439A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 91 through 94 removed outlier: 4.055A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 169 through 177 removed outlier: 4.248A pdb=" N CYS A 131 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS A 189 " --> pdb=" O CYS A 131 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 201 through 203 removed outlier: 3.511A pdb=" N TYR A 435 " --> pdb=" O THR A 202 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 271 through 273 removed outlier: 4.075A pdb=" N LEU A 285 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG A 419 " --> pdb=" O TYR A 384 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 271 through 273 removed outlier: 4.075A pdb=" N LEU A 285 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 11.134A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.852A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.146A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.439A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.927A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.656A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 359 through 360 Processing sheet with id=AD4, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AD5, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.969A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 8 through 13 removed outlier: 6.215A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 19 through 23 Processing sheet with id=AD8, first strand: chain 'e' and resid 9 through 13 removed outlier: 5.995A pdb=" N ILE e 9 " --> pdb=" O THR e 103 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N THR e 105 " --> pdb=" O ILE e 9 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE e 11 " --> pdb=" O THR e 105 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N GLN e 37 " --> pdb=" O LEU e 46 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEU e 46 " --> pdb=" O GLN e 37 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'e' and resid 19 through 22 Processing sheet with id=AE1, first strand: chain 'd' and resid 4 through 7 removed outlier: 4.572A pdb=" N GLN d 77 " --> pdb=" O ASP d 72 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP d 72 " --> pdb=" O GLN d 77 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'd' and resid 57 through 59 removed outlier: 7.002A pdb=" N TRP d 36 " --> pdb=" O ILE d 48 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TYR d 50 " --> pdb=" O TRP d 34 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TRP d 34 " --> pdb=" O TYR d 50 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'd' and resid 100 through 100A removed outlier: 3.902A pdb=" N ARG d 100 " --> pdb=" O PHE d 100K" (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE d 100K" --> pdb=" O ARG d 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'I' and resid 495 through 499 removed outlier: 5.025A pdb=" N VAL I 36 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR J 606 " --> pdb=" O VAL I 36 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.717A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR I 244 " --> pdb=" O ILE I 84 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE I 84 " --> pdb=" O THR I 244 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 75 through 76 removed outlier: 4.324A pdb=" N VAL I 75 " --> pdb=" O CYS I 54 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 91 through 94 removed outlier: 4.094A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 130 through 133 Processing sheet with id=AE9, first strand: chain 'I' and resid 182 through 183 Processing sheet with id=AF1, first strand: chain 'I' and resid 201 through 203 Processing sheet with id=AF2, first strand: chain 'I' and resid 271 through 273 removed outlier: 3.895A pdb=" N LEU I 285 " --> pdb=" O ARG I 273 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 271 through 273 removed outlier: 3.895A pdb=" N LEU I 285 " --> pdb=" O ARG I 273 " (cutoff:3.500A) removed outlier: 11.170A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 10.853A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 12.268A pdb=" N PHE I 288 " --> pdb=" O ILE I 453 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N ILE I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 10.808A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ASN I 300 " --> pdb=" O GLY I 441 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N GLY I 441 " --> pdb=" O ASN I 300 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 304 through 308 Processing sheet with id=AF5, first strand: chain 'I' and resid 359 through 360 removed outlier: 3.795A pdb=" N ILE I 359 " --> pdb=" O TRP I 395 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 375 through 377 removed outlier: 4.640A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS I 421 " --> pdb=" O PHE I 382 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AF8, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.693A pdb=" N GLY K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 8 through 13 removed outlier: 3.757A pdb=" N THR M 105 " --> pdb=" O MET M 11 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLN M 37 " --> pdb=" O LEU M 46 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LEU M 46 " --> pdb=" O GLN M 37 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 19 through 23 Processing sheet with id=AG2, first strand: chain 'm' and resid 9 through 13 removed outlier: 6.067A pdb=" N ILE m 9 " --> pdb=" O THR m 103 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N THR m 105 " --> pdb=" O ILE m 9 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE m 11 " --> pdb=" O THR m 105 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN m 37 " --> pdb=" O LEU m 46 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LEU m 46 " --> pdb=" O GLN m 37 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'm' and resid 19 through 22 Processing sheet with id=AG4, first strand: chain 'm' and resid 31 through 32 Processing sheet with id=AG5, first strand: chain 'k' and resid 4 through 7 removed outlier: 4.218A pdb=" N GLN k 77 " --> pdb=" O ASP k 72 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP k 72 " --> pdb=" O GLN k 77 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'k' and resid 58 through 59 removed outlier: 6.984A pdb=" N TRP k 36 " --> pdb=" O ILE k 48 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TYR k 50 " --> pdb=" O TRP k 34 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TRP k 34 " --> pdb=" O TYR k 50 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL k 100R" --> pdb=" O ARG k 94 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU k 96 " --> pdb=" O MET k 100P" (cutoff:3.500A) removed outlier: 6.874A pdb=" N MET k 100P" --> pdb=" O LEU k 96 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'k' and resid 58 through 59 removed outlier: 6.984A pdb=" N TRP k 36 " --> pdb=" O ILE k 48 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TYR k 50 " --> pdb=" O TRP k 34 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TRP k 34 " --> pdb=" O TYR k 50 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'k' and resid 100 through 100A removed outlier: 3.835A pdb=" N ARG k 100 " --> pdb=" O PHE k 100K" (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE k 100K" --> pdb=" O ARG k 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 825 hydrogen bonds defined for protein. 2106 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: 5.49 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 8193 1.34 - 1.47: 7177 1.47 - 1.61: 11119 1.61 - 1.74: 4 1.74 - 1.88: 207 Bond restraints: 26700 Sorted by residual: bond pdb=" C1 MAN w 9 " pdb=" C2 MAN w 9 " ideal model delta sigma weight residual 1.526 1.609 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" C CYS A 385 " pdb=" N ASN A 386 " ideal model delta sigma weight residual 1.328 1.383 -0.055 1.40e-02 5.10e+03 1.55e+01 bond pdb=" N VAL A 208 " pdb=" CA VAL A 208 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.91e+00 bond pdb=" N ILE B 603 " pdb=" CA ILE B 603 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.80e+00 bond pdb=" CB CYS G 296 " pdb=" SG CYS G 296 " ideal model delta sigma weight residual 1.808 1.717 0.091 3.30e-02 9.18e+02 7.67e+00 ... (remaining 26695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 35753 2.90 - 5.81: 450 5.81 - 8.71: 70 8.71 - 11.62: 5 11.62 - 14.52: 4 Bond angle restraints: 36282 Sorted by residual: angle pdb=" N VAL I 371 " pdb=" CA VAL I 371 " pdb=" C VAL I 371 " ideal model delta sigma weight residual 113.71 107.35 6.36 9.50e-01 1.11e+00 4.48e+01 angle pdb=" CA CYS G 296 " pdb=" CB CYS G 296 " pdb=" SG CYS G 296 " ideal model delta sigma weight residual 114.40 128.92 -14.52 2.30e+00 1.89e-01 3.99e+01 angle pdb=" CA CYS I 296 " pdb=" CB CYS I 296 " pdb=" SG CYS I 296 " ideal model delta sigma weight residual 114.40 128.49 -14.09 2.30e+00 1.89e-01 3.75e+01 angle pdb=" C CYS A 385 " pdb=" N ASN A 386 " pdb=" CA ASN A 386 " ideal model delta sigma weight residual 122.67 112.42 10.25 1.73e+00 3.34e-01 3.51e+01 angle pdb=" C CYS G 385 " pdb=" N ASN G 386 " pdb=" CA ASN G 386 " ideal model delta sigma weight residual 122.03 110.26 11.77 2.01e+00 2.48e-01 3.43e+01 ... (remaining 36277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.79: 16048 24.79 - 49.59: 962 49.59 - 74.38: 206 74.38 - 99.17: 109 99.17 - 123.97: 90 Dihedral angle restraints: 17415 sinusoidal: 8421 harmonic: 8994 Sorted by residual: dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 92 " pdb=" CB CYS D 92 " ideal model delta sinusoidal sigma weight residual 93.00 160.33 -67.33 1 1.00e+01 1.00e-02 5.90e+01 dihedral pdb=" CB CYS A 385 " pdb=" SG CYS A 385 " pdb=" SG CYS A 418 " pdb=" CB CYS A 418 " ideal model delta sinusoidal sigma weight residual 93.00 34.75 58.25 1 1.00e+01 1.00e-02 4.55e+01 dihedral pdb=" CB CYS I 296 " pdb=" SG CYS I 296 " pdb=" SG CYS I 331 " pdb=" CB CYS I 331 " ideal model delta sinusoidal sigma weight residual 93.00 39.60 53.40 1 1.00e+01 1.00e-02 3.88e+01 ... (remaining 17412 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.198: 4324 0.198 - 0.397: 25 0.397 - 0.595: 1 0.595 - 0.794: 1 0.794 - 0.992: 2 Chirality restraints: 4353 Sorted by residual: chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN G 386 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.41 -0.99 2.00e-01 2.50e+01 2.46e+01 chirality pdb=" C1 NAG f 1 " pdb=" ND2 ASN A 386 " pdb=" C2 NAG f 1 " pdb=" O5 NAG f 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.61 -0.79 2.00e-01 2.50e+01 1.58e+01 chirality pdb=" C1 NAG u 1 " pdb=" ND2 ASN I 386 " pdb=" C2 NAG u 1 " pdb=" O5 NAG u 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.62 -0.78 2.00e-01 2.50e+01 1.54e+01 ... (remaining 4350 not shown) Planarity restraints: 4527 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN G 386 " -0.005 2.00e-02 2.50e+03 7.95e-02 7.89e+01 pdb=" CG ASN G 386 " 0.094 2.00e-02 2.50e+03 pdb=" OD1 ASN G 386 " -0.095 2.00e-02 2.50e+03 pdb=" ND2 ASN G 386 " 0.085 2.00e-02 2.50e+03 pdb=" C1 NAG S 1 " -0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN I 386 " -0.000 2.00e-02 2.50e+03 5.46e-02 3.73e+01 pdb=" CG ASN I 386 " -0.066 2.00e-02 2.50e+03 pdb=" OD1 ASN I 386 " 0.066 2.00e-02 2.50e+03 pdb=" ND2 ASN I 386 " -0.055 2.00e-02 2.50e+03 pdb=" C1 NAG u 1 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 386 " -0.000 2.00e-02 2.50e+03 4.85e-02 2.94e+01 pdb=" CG ASN A 386 " -0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN A 386 " 0.058 2.00e-02 2.50e+03 pdb=" ND2 ASN A 386 " -0.052 2.00e-02 2.50e+03 pdb=" C1 NAG f 1 " 0.050 2.00e-02 2.50e+03 ... (remaining 4524 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2452 2.74 - 3.28: 25476 3.28 - 3.82: 40243 3.82 - 4.36: 44846 4.36 - 4.90: 78279 Nonbonded interactions: 191296 Sorted by model distance: nonbonded pdb=" NH1 ARG G 298 " pdb=" OD1 ASN G 302 " model vdw 2.198 3.120 nonbonded pdb=" O GLN k 3 " pdb=" OG SER k 25 " model vdw 2.198 3.040 nonbonded pdb=" OG SER l 30 " pdb=" OG SER l 93 " model vdw 2.202 3.040 nonbonded pdb=" OG SER m 65 " pdb=" OG1 THR m 72 " model vdw 2.203 3.040 nonbonded pdb=" NH1 ARG A 298 " pdb=" OD1 ASN A 302 " model vdw 2.206 3.120 ... (remaining 191291 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'J' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'E' selection = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'F' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'g' selection = chain 'j' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'r' selection = chain 's' selection = chain 'v' selection = chain 'x' selection = chain 'y' } ncs_group { reference = chain 'O' selection = chain 'Z' selection = chain 'q' } ncs_group { reference = chain 'R' selection = chain 'c' selection = chain 't' } ncs_group { reference = chain 'S' selection = chain 'f' selection = chain 'u' } ncs_group { reference = chain 'U' selection = chain 'i' selection = chain 'w' } ncs_group { reference = chain 'd' selection = chain 'h' selection = chain 'k' } ncs_group { reference = chain 'e' selection = chain 'l' selection = chain 'm' } 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: 1.060 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: 0.320 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.410 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 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 : 0.006 0.091 26862 Z= 0.290 Angle : 0.928 17.996 36723 Z= 0.434 Chirality : 0.058 0.992 4353 Planarity : 0.005 0.128 4482 Dihedral : 19.284 123.966 11514 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.93 % Favored : 90.74 % Rotamer: Outliers : 0.11 % Allowed : 0.63 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.15), residues: 3090 helix: 0.71 (0.31), residues: 325 sheet: -0.70 (0.17), residues: 888 loop : -1.87 (0.14), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG l 54 TYR 0.019 0.002 TYR H 91 PHE 0.031 0.002 PHE I 288 TRP 0.026 0.002 TRP G 112 HIS 0.011 0.001 HIS h 97 Details of bonding type rmsd covalent geometry : bond 0.00633 (26700) covalent geometry : angle 0.86268 (36282) SS BOND : bond 0.00522 ( 45) SS BOND : angle 2.05030 ( 90) hydrogen bonds : bond 0.12020 ( 803) hydrogen bonds : angle 6.53172 ( 2106) link_ALPHA1-2 : bond 0.00724 ( 6) link_ALPHA1-2 : angle 1.66064 ( 18) link_ALPHA1-3 : bond 0.00609 ( 12) link_ALPHA1-3 : angle 1.98307 ( 36) link_ALPHA1-6 : bond 0.00871 ( 9) link_ALPHA1-6 : angle 2.24479 ( 27) link_BETA1-4 : bond 0.00647 ( 45) link_BETA1-4 : angle 2.17205 ( 135) link_NAG-ASN : bond 0.00726 ( 45) link_NAG-ASN : angle 4.92766 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 454 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 622 ILE cc_start: 0.8044 (tp) cc_final: 0.7816 (tp) REVERT: B 626 MET cc_start: 0.7067 (pmm) cc_final: 0.6566 (pmm) REVERT: L 87 ILE cc_start: 0.7214 (mt) cc_final: 0.6880 (mt) REVERT: l 62 PHE cc_start: 0.7020 (m-80) cc_final: 0.6696 (m-80) REVERT: A 119 CYS cc_start: 0.5519 (m) cc_final: 0.5241 (m) REVERT: C 626 MET cc_start: 0.6970 (pmm) cc_final: 0.6437 (pmm) REVERT: C 630 GLN cc_start: 0.7707 (mt0) cc_final: 0.7254 (tm-30) REVERT: D 31 ASP cc_start: 0.6770 (p0) cc_final: 0.6558 (p0) REVERT: e 37 GLN cc_start: 0.7925 (tm-30) cc_final: 0.7599 (tm-30) REVERT: e 61 ARG cc_start: 0.6198 (mtm180) cc_final: 0.5728 (mtm-85) REVERT: d 2 MET cc_start: 0.6101 (pmm) cc_final: 0.5800 (pmm) REVERT: I 207 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7573 (mtmm) REVERT: J 603 ILE cc_start: 0.7651 (OUTLIER) cc_final: 0.7447 (tp) REVERT: J 622 ILE cc_start: 0.7971 (tp) cc_final: 0.7582 (tp) REVERT: J 626 MET cc_start: 0.6811 (pmm) cc_final: 0.6414 (pmm) REVERT: K 85 ASP cc_start: 0.6385 (p0) cc_final: 0.5816 (p0) outliers start: 3 outliers final: 0 residues processed: 457 average time/residue: 0.1464 time to fit residues: 110.0740 Evaluate side-chains 360 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 358 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 9.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 GLN B 607 ASN B 616 ASN B 652 GLN H 100 ASN L 77 ASN h 52 HIS h 97 HIS A 99 ASN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 GLN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN E 77 ASN ** e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN I 105 HIS m 34 GLN m 37 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4911 r_free = 0.4911 target = 0.246360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.239617 restraints weight = 34676.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4852 r_free = 0.4852 target = 0.239390 restraints weight = 60630.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4846 r_free = 0.4846 target = 0.238911 restraints weight = 55441.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.238048 restraints weight = 55510.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.237727 restraints weight = 58871.570| |-----------------------------------------------------------------------------| r_work (final): 0.4832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6537 moved from start: 0.0910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26862 Z= 0.147 Angle : 0.741 13.110 36723 Z= 0.344 Chirality : 0.048 0.388 4353 Planarity : 0.004 0.079 4482 Dihedral : 16.624 109.528 5823 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.28 % Favored : 93.50 % Rotamer: Outliers : 0.22 % Allowed : 5.28 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.14), residues: 3090 helix: 1.06 (0.30), residues: 318 sheet: -0.57 (0.17), residues: 816 loop : -1.73 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG m 54 TYR 0.013 0.001 TYR G 435 PHE 0.022 0.002 PHE G 288 TRP 0.015 0.001 TRP A 112 HIS 0.008 0.001 HIS h 97 Details of bonding type rmsd covalent geometry : bond 0.00333 (26700) covalent geometry : angle 0.68158 (36282) SS BOND : bond 0.00450 ( 45) SS BOND : angle 1.70938 ( 90) hydrogen bonds : bond 0.04098 ( 803) hydrogen bonds : angle 5.58226 ( 2106) link_ALPHA1-2 : bond 0.00992 ( 6) link_ALPHA1-2 : angle 2.05401 ( 18) link_ALPHA1-3 : bond 0.01284 ( 12) link_ALPHA1-3 : angle 2.30416 ( 36) link_ALPHA1-6 : bond 0.01019 ( 9) link_ALPHA1-6 : angle 2.74375 ( 27) link_BETA1-4 : bond 0.00664 ( 45) link_BETA1-4 : angle 2.32390 ( 135) link_NAG-ASN : bond 0.00573 ( 45) link_NAG-ASN : angle 3.71466 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 458 time to evaluate : 1.150 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 201 ILE cc_start: 0.8587 (tp) cc_final: 0.8103 (pt) REVERT: G 246 GLN cc_start: 0.6630 (tp-100) cc_final: 0.6418 (tp40) REVERT: B 626 MET cc_start: 0.7246 (pmm) cc_final: 0.6844 (pmm) REVERT: L 46 LEU cc_start: 0.7418 (tp) cc_final: 0.7182 (tp) REVERT: l 30 SER cc_start: 0.7548 (p) cc_final: 0.7282 (m) REVERT: A 119 CYS cc_start: 0.5422 (m) cc_final: 0.5023 (m) REVERT: A 376 PHE cc_start: 0.8502 (p90) cc_final: 0.8238 (p90) REVERT: A 486 TYR cc_start: 0.7493 (m-10) cc_final: 0.6902 (m-10) REVERT: C 626 MET cc_start: 0.6943 (pmm) cc_final: 0.6667 (pmm) REVERT: D 31 ASP cc_start: 0.6324 (p0) cc_final: 0.6018 (p0) REVERT: D 85 ASP cc_start: 0.6387 (p0) cc_final: 0.6167 (p0) REVERT: e 30 SER cc_start: 0.7978 (p) cc_final: 0.7564 (m) REVERT: e 60 GLU cc_start: 0.6458 (pp20) cc_final: 0.6214 (pp20) REVERT: I 178 ARG cc_start: 0.7934 (tpt90) cc_final: 0.7732 (tpt90) REVERT: I 486 TYR cc_start: 0.7537 (m-10) cc_final: 0.6918 (m-10) REVERT: J 622 ILE cc_start: 0.7284 (tp) cc_final: 0.6737 (tp) REVERT: J 626 MET cc_start: 0.6764 (pmm) cc_final: 0.6480 (pmm) REVERT: K 85 ASP cc_start: 0.6323 (p0) cc_final: 0.5752 (p0) REVERT: m 62 PHE cc_start: 0.6227 (m-80) cc_final: 0.5929 (m-80) outliers start: 6 outliers final: 2 residues processed: 461 average time/residue: 0.1552 time to fit residues: 117.0951 Evaluate side-chains 380 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 378 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 101 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 239 optimal weight: 5.9990 chunk 275 optimal weight: 5.9990 chunk 157 optimal weight: 8.9990 chunk 259 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 269 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 224 optimal weight: 0.8980 chunk 190 optimal weight: 6.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 478 ASN H 32 GLN ** H 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 GLN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 ASN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN ** e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 GLN m 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.230480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.223244 restraints weight = 35096.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.222844 restraints weight = 68817.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.222632 restraints weight = 67102.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.221996 restraints weight = 61867.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.221853 restraints weight = 56231.054| |-----------------------------------------------------------------------------| r_work (final): 0.4690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.145 26862 Z= 0.413 Angle : 1.052 13.118 36723 Z= 0.500 Chirality : 0.056 0.407 4353 Planarity : 0.007 0.076 4482 Dihedral : 15.925 120.457 5823 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.94 % Favored : 89.84 % Rotamer: Outliers : 0.55 % Allowed : 8.94 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.27 (0.14), residues: 3090 helix: 0.34 (0.29), residues: 329 sheet: -0.94 (0.17), residues: 840 loop : -2.22 (0.13), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 54 TYR 0.032 0.003 TYR K 91 PHE 0.048 0.004 PHE I 288 TRP 0.038 0.003 TRP D 103 HIS 0.016 0.002 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00983 (26700) covalent geometry : angle 0.98313 (36282) SS BOND : bond 0.00751 ( 45) SS BOND : angle 2.27980 ( 90) hydrogen bonds : bond 0.06221 ( 803) hydrogen bonds : angle 6.45019 ( 2106) link_ALPHA1-2 : bond 0.01350 ( 6) link_ALPHA1-2 : angle 2.21953 ( 18) link_ALPHA1-3 : bond 0.01177 ( 12) link_ALPHA1-3 : angle 2.55917 ( 36) link_ALPHA1-6 : bond 0.01009 ( 9) link_ALPHA1-6 : angle 2.93505 ( 27) link_BETA1-4 : bond 0.00888 ( 45) link_BETA1-4 : angle 2.86082 ( 135) link_NAG-ASN : bond 0.01090 ( 45) link_NAG-ASN : angle 5.02472 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 437 time to evaluate : 0.914 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: G 275 GLU cc_start: 0.3947 (OUTLIER) cc_final: 0.3538 (tt0) REVERT: G 427 TRP cc_start: 0.7303 (m-90) cc_final: 0.6880 (m-90) REVERT: G 430 ILE cc_start: 0.7197 (mm) cc_final: 0.6990 (mm) REVERT: B 626 MET cc_start: 0.7210 (pmm) cc_final: 0.6943 (pmm) REVERT: H 85 ASP cc_start: 0.6540 (p0) cc_final: 0.6231 (p0) REVERT: l 30 SER cc_start: 0.7356 (p) cc_final: 0.7106 (m) REVERT: A 361 PHE cc_start: 0.9115 (OUTLIER) cc_final: 0.8374 (m-80) REVERT: C 626 MET cc_start: 0.6658 (pmm) cc_final: 0.6192 (mtm) REVERT: e 95 LYS cc_start: 0.7784 (mttp) cc_final: 0.7405 (mmtp) REVERT: J 622 ILE cc_start: 0.7326 (tp) cc_final: 0.6750 (tp) REVERT: J 626 MET cc_start: 0.6526 (pmm) cc_final: 0.6284 (pmm) REVERT: K 48 MET cc_start: 0.7208 (ptt) cc_final: 0.6990 (ptt) REVERT: K 85 ASP cc_start: 0.6491 (p0) cc_final: 0.5816 (p0) REVERT: M 79 GLN cc_start: 0.8114 (tm-30) cc_final: 0.7088 (tm-30) REVERT: m 62 PHE cc_start: 0.6318 (m-80) cc_final: 0.5961 (m-80) outliers start: 15 outliers final: 10 residues processed: 452 average time/residue: 0.1552 time to fit residues: 114.8370 Evaluate side-chains 373 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 361 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 29 optimal weight: 0.9980 chunk 304 optimal weight: 2.9990 chunk 213 optimal weight: 0.6980 chunk 153 optimal weight: 0.9990 chunk 237 optimal weight: 2.9990 chunk 257 optimal weight: 8.9990 chunk 186 optimal weight: 0.0770 chunk 114 optimal weight: 4.9990 chunk 203 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN H 39 GLN ** H 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 ASN l 50 ASN h 97 HIS ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 640 GLN ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN ** K 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4902 r_free = 0.4902 target = 0.244944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.234425 restraints weight = 34414.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.233077 restraints weight = 59144.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.233038 restraints weight = 66776.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.232519 restraints weight = 50922.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4789 r_free = 0.4789 target = 0.232507 restraints weight = 50229.569| |-----------------------------------------------------------------------------| r_work (final): 0.4788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 26862 Z= 0.150 Angle : 0.795 13.710 36723 Z= 0.366 Chirality : 0.049 0.470 4353 Planarity : 0.004 0.050 4482 Dihedral : 14.557 110.992 5823 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.28 % Favored : 93.50 % Rotamer: Outliers : 0.15 % Allowed : 3.92 % Favored : 95.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.14), residues: 3090 helix: 0.62 (0.29), residues: 330 sheet: -0.74 (0.17), residues: 846 loop : -1.92 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 54 TYR 0.014 0.001 TYR A 318 PHE 0.013 0.002 PHE A 317 TRP 0.021 0.002 TRP D 36 HIS 0.005 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00341 (26700) covalent geometry : angle 0.73096 (36282) SS BOND : bond 0.00528 ( 45) SS BOND : angle 1.89426 ( 90) hydrogen bonds : bond 0.04125 ( 803) hydrogen bonds : angle 5.72311 ( 2106) link_ALPHA1-2 : bond 0.01445 ( 6) link_ALPHA1-2 : angle 1.76293 ( 18) link_ALPHA1-3 : bond 0.01275 ( 12) link_ALPHA1-3 : angle 2.15421 ( 36) link_ALPHA1-6 : bond 0.00975 ( 9) link_ALPHA1-6 : angle 2.51937 ( 27) link_BETA1-4 : bond 0.00646 ( 45) link_BETA1-4 : angle 2.40773 ( 135) link_NAG-ASN : bond 0.00683 ( 45) link_NAG-ASN : angle 4.16015 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 477 time to evaluate : 0.818 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 201 ILE cc_start: 0.8577 (tp) cc_final: 0.8132 (pt) REVERT: B 625 ASN cc_start: 0.7369 (p0) cc_final: 0.7040 (p0) REVERT: H 37 VAL cc_start: 0.9193 (p) cc_final: 0.8930 (m) REVERT: H 85 ASP cc_start: 0.6500 (p0) cc_final: 0.6164 (p0) REVERT: L 46 LEU cc_start: 0.7409 (tp) cc_final: 0.7168 (tp) REVERT: h 70 SER cc_start: 0.6757 (t) cc_final: 0.6469 (m) REVERT: D 31 ASP cc_start: 0.6565 (p0) cc_final: 0.6229 (p0) REVERT: D 85 ASP cc_start: 0.6780 (p0) cc_final: 0.6181 (p0) REVERT: e 30 SER cc_start: 0.7862 (p) cc_final: 0.7506 (m) REVERT: e 61 ARG cc_start: 0.7060 (mtm180) cc_final: 0.6576 (mtm-85) REVERT: d 2 MET cc_start: 0.6560 (pmm) cc_final: 0.6296 (pmm) REVERT: J 622 ILE cc_start: 0.7371 (tp) cc_final: 0.6808 (tp) REVERT: K 85 ASP cc_start: 0.6225 (p0) cc_final: 0.5657 (p0) REVERT: m 62 PHE cc_start: 0.6067 (m-80) cc_final: 0.5830 (m-80) REVERT: k 6 GLU cc_start: 0.5635 (tp30) cc_final: 0.3756 (mt-10) outliers start: 4 outliers final: 0 residues processed: 479 average time/residue: 0.1494 time to fit residues: 117.6732 Evaluate side-chains 365 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 365 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 148 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 227 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 152 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 140 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN ** H 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 97 HIS ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN D 100 ASN ** e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.242602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.235352 restraints weight = 34594.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.234363 restraints weight = 59545.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.233695 restraints weight = 64517.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.233097 restraints weight = 60262.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.232992 restraints weight = 56748.393| |-----------------------------------------------------------------------------| r_work (final): 0.4803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 26862 Z= 0.180 Angle : 0.800 13.994 36723 Z= 0.371 Chirality : 0.050 0.405 4353 Planarity : 0.005 0.052 4482 Dihedral : 13.896 113.813 5823 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.73 % Favored : 92.04 % Rotamer: Outliers : 0.07 % Allowed : 3.18 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.14), residues: 3090 helix: 0.69 (0.29), residues: 330 sheet: -0.74 (0.17), residues: 840 loop : -1.97 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 54 TYR 0.014 0.002 TYR k 100B PHE 0.025 0.002 PHE G 53 TRP 0.019 0.002 TRP A 112 HIS 0.007 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00422 (26700) covalent geometry : angle 0.73731 (36282) SS BOND : bond 0.00513 ( 45) SS BOND : angle 1.97034 ( 90) hydrogen bonds : bond 0.04189 ( 803) hydrogen bonds : angle 5.61085 ( 2106) link_ALPHA1-2 : bond 0.01366 ( 6) link_ALPHA1-2 : angle 1.72570 ( 18) link_ALPHA1-3 : bond 0.01201 ( 12) link_ALPHA1-3 : angle 2.21304 ( 36) link_ALPHA1-6 : bond 0.00840 ( 9) link_ALPHA1-6 : angle 2.48692 ( 27) link_BETA1-4 : bond 0.00663 ( 45) link_BETA1-4 : angle 2.35074 ( 135) link_NAG-ASN : bond 0.00629 ( 45) link_NAG-ASN : angle 4.12819 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 447 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 201 ILE cc_start: 0.8594 (tp) cc_final: 0.8257 (pt) REVERT: G 369 LEU cc_start: 0.9044 (tp) cc_final: 0.8681 (tt) REVERT: B 625 ASN cc_start: 0.7039 (p0) cc_final: 0.6682 (p0) REVERT: H 85 ASP cc_start: 0.6508 (p0) cc_final: 0.6220 (p0) REVERT: L 46 LEU cc_start: 0.7508 (tp) cc_final: 0.7243 (tp) REVERT: h 53 LYS cc_start: 0.7540 (mmmm) cc_final: 0.6868 (mmmt) REVERT: A 119 CYS cc_start: 0.5646 (m) cc_final: 0.5228 (m) REVERT: C 586 TYR cc_start: 0.8623 (t80) cc_final: 0.8383 (t80) REVERT: D 31 ASP cc_start: 0.6333 (p0) cc_final: 0.6027 (p0) REVERT: D 85 ASP cc_start: 0.6829 (p0) cc_final: 0.6223 (p0) REVERT: e 30 SER cc_start: 0.7890 (p) cc_final: 0.7519 (m) REVERT: e 60 GLU cc_start: 0.6698 (pp20) cc_final: 0.6285 (pp20) REVERT: e 61 ARG cc_start: 0.6980 (mtm180) cc_final: 0.6433 (mtm-85) REVERT: J 622 ILE cc_start: 0.7502 (tp) cc_final: 0.6973 (tp) REVERT: J 626 MET cc_start: 0.6564 (pmm) cc_final: 0.6193 (pmm) REVERT: K 85 ASP cc_start: 0.6103 (p0) cc_final: 0.5455 (p0) REVERT: M 46 LEU cc_start: 0.7581 (tp) cc_final: 0.7309 (tp) REVERT: m 62 PHE cc_start: 0.6036 (m-80) cc_final: 0.5798 (m-80) REVERT: k 6 GLU cc_start: 0.5620 (tp30) cc_final: 0.3766 (mt-10) outliers start: 2 outliers final: 0 residues processed: 447 average time/residue: 0.1477 time to fit residues: 109.4162 Evaluate side-chains 365 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 365 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 101 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 298 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 86 optimal weight: 20.0000 chunk 117 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 262 optimal weight: 0.9980 chunk 296 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 425 ASN ** H 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 ASN l 37 GLN h 97 HIS ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN ** e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN ** m 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.244979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.234448 restraints weight = 34429.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4805 r_free = 0.4805 target = 0.233577 restraints weight = 58063.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.233427 restraints weight = 61311.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.232456 restraints weight = 55845.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.232432 restraints weight = 58366.764| |-----------------------------------------------------------------------------| r_work (final): 0.4791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 26862 Z= 0.152 Angle : 0.777 13.542 36723 Z= 0.360 Chirality : 0.049 0.469 4353 Planarity : 0.004 0.055 4482 Dihedral : 13.255 110.250 5823 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.50 % Favored : 93.27 % Rotamer: Outliers : 0.07 % Allowed : 2.77 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.14), residues: 3090 helix: 0.73 (0.30), residues: 324 sheet: -0.82 (0.16), residues: 891 loop : -1.85 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 54 TYR 0.015 0.001 TYR A 217 PHE 0.022 0.002 PHE I 53 TRP 0.014 0.001 TRP A 112 HIS 0.006 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00349 (26700) covalent geometry : angle 0.71640 (36282) SS BOND : bond 0.00592 ( 45) SS BOND : angle 2.01544 ( 90) hydrogen bonds : bond 0.03925 ( 803) hydrogen bonds : angle 5.52570 ( 2106) link_ALPHA1-2 : bond 0.01352 ( 6) link_ALPHA1-2 : angle 1.50978 ( 18) link_ALPHA1-3 : bond 0.01235 ( 12) link_ALPHA1-3 : angle 2.19258 ( 36) link_ALPHA1-6 : bond 0.00892 ( 9) link_ALPHA1-6 : angle 2.28505 ( 27) link_BETA1-4 : bond 0.00654 ( 45) link_BETA1-4 : angle 2.31047 ( 135) link_NAG-ASN : bond 0.00581 ( 45) link_NAG-ASN : angle 3.95252 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 455 time to evaluate : 0.984 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 201 ILE cc_start: 0.8564 (tp) cc_final: 0.8215 (pt) REVERT: G 369 LEU cc_start: 0.8990 (tp) cc_final: 0.8588 (tt) REVERT: B 625 ASN cc_start: 0.7060 (p0) cc_final: 0.6639 (p0) REVERT: H 85 ASP cc_start: 0.6393 (p0) cc_final: 0.6094 (p0) REVERT: L 46 LEU cc_start: 0.7453 (tp) cc_final: 0.7213 (tp) REVERT: l 92 ASP cc_start: 0.7772 (p0) cc_final: 0.7531 (p0) REVERT: h 53 LYS cc_start: 0.7590 (mmmm) cc_final: 0.6855 (mtpt) REVERT: C 586 TYR cc_start: 0.8635 (t80) cc_final: 0.8361 (t80) REVERT: D 31 ASP cc_start: 0.6353 (p0) cc_final: 0.6010 (p0) REVERT: D 85 ASP cc_start: 0.6637 (p0) cc_final: 0.6039 (p0) REVERT: e 30 SER cc_start: 0.7829 (p) cc_final: 0.7542 (t) REVERT: e 60 GLU cc_start: 0.6786 (pp20) cc_final: 0.6232 (pp20) REVERT: e 61 ARG cc_start: 0.7047 (mtm180) cc_final: 0.6543 (mtm-85) REVERT: d 2 MET cc_start: 0.6068 (pmm) cc_final: 0.5868 (pmm) REVERT: J 622 ILE cc_start: 0.7568 (tp) cc_final: 0.7008 (tp) REVERT: J 626 MET cc_start: 0.6655 (pmm) cc_final: 0.6392 (pmm) REVERT: K 85 ASP cc_start: 0.6009 (p0) cc_final: 0.5368 (p0) REVERT: m 62 PHE cc_start: 0.6023 (m-80) cc_final: 0.5790 (m-80) REVERT: k 6 GLU cc_start: 0.5904 (tp30) cc_final: 0.4089 (mt-10) outliers start: 2 outliers final: 1 residues processed: 456 average time/residue: 0.1408 time to fit residues: 107.9278 Evaluate side-chains 364 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 363 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 35 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 173 optimal weight: 7.9990 chunk 255 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 280 optimal weight: 20.0000 chunk 286 optimal weight: 4.9990 chunk 184 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 ASN h 97 HIS ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN e 37 GLN ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 52 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4848 r_free = 0.4848 target = 0.238294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4789 r_free = 0.4789 target = 0.231449 restraints weight = 34629.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.231318 restraints weight = 55390.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.231054 restraints weight = 54460.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.230428 restraints weight = 51590.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.230217 restraints weight = 56205.384| |-----------------------------------------------------------------------------| r_work (final): 0.4776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 26862 Z= 0.247 Angle : 0.879 14.880 36723 Z= 0.410 Chirality : 0.052 0.376 4353 Planarity : 0.005 0.057 4482 Dihedral : 13.196 114.783 5823 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.00 % Favored : 90.78 % Rotamer: Outliers : 0.04 % Allowed : 2.44 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.14), residues: 3090 helix: 0.69 (0.30), residues: 324 sheet: -0.79 (0.17), residues: 843 loop : -1.95 (0.13), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG l 54 TYR 0.017 0.002 TYR k 100B PHE 0.026 0.003 PHE I 159 TRP 0.027 0.002 TRP A 112 HIS 0.011 0.002 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00586 (26700) covalent geometry : angle 0.81036 (36282) SS BOND : bond 0.00640 ( 45) SS BOND : angle 2.27430 ( 90) hydrogen bonds : bond 0.04738 ( 803) hydrogen bonds : angle 5.83140 ( 2106) link_ALPHA1-2 : bond 0.01279 ( 6) link_ALPHA1-2 : angle 1.68054 ( 18) link_ALPHA1-3 : bond 0.01204 ( 12) link_ALPHA1-3 : angle 2.40259 ( 36) link_ALPHA1-6 : bond 0.00852 ( 9) link_ALPHA1-6 : angle 2.31752 ( 27) link_BETA1-4 : bond 0.00694 ( 45) link_BETA1-4 : angle 2.52366 ( 135) link_NAG-ASN : bond 0.00713 ( 45) link_NAG-ASN : angle 4.55927 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 440 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 201 ILE cc_start: 0.8563 (tp) cc_final: 0.8185 (pt) REVERT: G 369 LEU cc_start: 0.9034 (tp) cc_final: 0.8546 (tt) REVERT: B 625 ASN cc_start: 0.6956 (p0) cc_final: 0.6542 (p0) REVERT: B 626 MET cc_start: 0.7172 (pmm) cc_final: 0.6953 (pmm) REVERT: H 85 ASP cc_start: 0.6589 (p0) cc_final: 0.6313 (p0) REVERT: L 46 LEU cc_start: 0.7541 (tp) cc_final: 0.7312 (tp) REVERT: l 92 ASP cc_start: 0.7917 (p0) cc_final: 0.7707 (p0) REVERT: h 53 LYS cc_start: 0.7649 (mmmm) cc_final: 0.6942 (mtpt) REVERT: A 119 CYS cc_start: 0.5432 (m) cc_final: 0.5131 (m) REVERT: D 31 ASP cc_start: 0.6686 (p0) cc_final: 0.6366 (p0) REVERT: D 85 ASP cc_start: 0.6767 (p0) cc_final: 0.6171 (p0) REVERT: e 60 GLU cc_start: 0.6829 (pp20) cc_final: 0.6499 (pp20) REVERT: e 61 ARG cc_start: 0.6960 (mtm180) cc_final: 0.6409 (mtm-85) REVERT: I 119 CYS cc_start: 0.5988 (m) cc_final: 0.5759 (m) REVERT: J 622 ILE cc_start: 0.7671 (tp) cc_final: 0.7159 (tp) REVERT: J 626 MET cc_start: 0.6712 (pmm) cc_final: 0.6412 (pmm) REVERT: K 85 ASP cc_start: 0.6006 (p0) cc_final: 0.5329 (p0) REVERT: M 46 LEU cc_start: 0.7545 (tp) cc_final: 0.7339 (tp) REVERT: m 62 PHE cc_start: 0.6028 (m-80) cc_final: 0.5781 (m-80) outliers start: 1 outliers final: 1 residues processed: 440 average time/residue: 0.1442 time to fit residues: 105.9126 Evaluate side-chains 361 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 360 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 54 optimal weight: 0.9980 chunk 279 optimal weight: 9.9990 chunk 93 optimal weight: 0.0870 chunk 34 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 238 optimal weight: 0.8980 chunk 218 optimal weight: 3.9990 chunk 232 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 186 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 302 ASN ** H 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 97 HIS ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN ** m 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 52 HIS k 97 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4915 r_free = 0.4915 target = 0.246050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.235845 restraints weight = 34664.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.234258 restraints weight = 53405.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.234053 restraints weight = 62947.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.233022 restraints weight = 55576.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.233066 restraints weight = 59570.164| |-----------------------------------------------------------------------------| r_work (final): 0.4797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 26862 Z= 0.139 Angle : 0.790 15.049 36723 Z= 0.364 Chirality : 0.050 0.585 4353 Planarity : 0.004 0.055 4482 Dihedral : 12.621 110.211 5823 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.50 % Favored : 93.27 % Rotamer: Outliers : 0.04 % Allowed : 1.26 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.14), residues: 3090 helix: 0.95 (0.30), residues: 312 sheet: -0.75 (0.17), residues: 858 loop : -1.74 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 54 TYR 0.014 0.001 TYR A 486 PHE 0.017 0.002 PHE I 288 TRP 0.021 0.001 TRP D 36 HIS 0.010 0.001 HIS k 52 Details of bonding type rmsd covalent geometry : bond 0.00313 (26700) covalent geometry : angle 0.72355 (36282) SS BOND : bond 0.00571 ( 45) SS BOND : angle 1.99240 ( 90) hydrogen bonds : bond 0.03852 ( 803) hydrogen bonds : angle 5.54989 ( 2106) link_ALPHA1-2 : bond 0.01255 ( 6) link_ALPHA1-2 : angle 1.58852 ( 18) link_ALPHA1-3 : bond 0.01226 ( 12) link_ALPHA1-3 : angle 2.16779 ( 36) link_ALPHA1-6 : bond 0.00838 ( 9) link_ALPHA1-6 : angle 2.12783 ( 27) link_BETA1-4 : bond 0.00682 ( 45) link_BETA1-4 : angle 2.34229 ( 135) link_NAG-ASN : bond 0.00638 ( 45) link_NAG-ASN : angle 4.29491 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 445 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 161 MET cc_start: 0.8303 (tpt) cc_final: 0.7982 (tpt) REVERT: G 201 ILE cc_start: 0.8439 (tp) cc_final: 0.8072 (pt) REVERT: G 369 LEU cc_start: 0.8970 (tp) cc_final: 0.8536 (tt) REVERT: B 625 ASN cc_start: 0.7082 (p0) cc_final: 0.6638 (p0) REVERT: H 36 TRP cc_start: 0.8170 (m100) cc_final: 0.7706 (m100) REVERT: H 85 ASP cc_start: 0.6368 (p0) cc_final: 0.6069 (p0) REVERT: L 46 LEU cc_start: 0.7443 (tp) cc_final: 0.7211 (tp) REVERT: h 53 LYS cc_start: 0.7507 (mmmm) cc_final: 0.6855 (mmmt) REVERT: A 119 CYS cc_start: 0.5508 (m) cc_final: 0.5165 (m) REVERT: D 31 ASP cc_start: 0.6330 (p0) cc_final: 0.6000 (p0) REVERT: D 85 ASP cc_start: 0.6502 (p0) cc_final: 0.6221 (p0) REVERT: e 30 SER cc_start: 0.7861 (p) cc_final: 0.7567 (t) REVERT: e 60 GLU cc_start: 0.6755 (pp20) cc_final: 0.6263 (pp20) REVERT: e 61 ARG cc_start: 0.7082 (mtm180) cc_final: 0.6628 (mtm-85) REVERT: d 2 MET cc_start: 0.6146 (pmm) cc_final: 0.5727 (pmm) REVERT: J 622 ILE cc_start: 0.7754 (tp) cc_final: 0.7227 (tp) REVERT: J 626 MET cc_start: 0.6716 (pmm) cc_final: 0.6435 (pmm) REVERT: K 85 ASP cc_start: 0.5922 (p0) cc_final: 0.5521 (p0) REVERT: k 6 GLU cc_start: 0.5308 (tp30) cc_final: 0.3532 (mt-10) outliers start: 1 outliers final: 0 residues processed: 446 average time/residue: 0.1474 time to fit residues: 110.3024 Evaluate side-chains 355 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 284 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 267 optimal weight: 2.9990 chunk 304 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 282 optimal weight: 4.9990 chunk 211 optimal weight: 3.9990 chunk 224 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 ASN l 37 GLN h 52 HIS h 97 HIS ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 37 GLN ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 52 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.242980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.235695 restraints weight = 34702.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.235033 restraints weight = 60075.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4815 r_free = 0.4815 target = 0.234603 restraints weight = 60374.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.234074 restraints weight = 57943.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.234046 restraints weight = 59048.770| |-----------------------------------------------------------------------------| r_work (final): 0.4808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 26862 Z= 0.179 Angle : 0.819 15.814 36723 Z= 0.379 Chirality : 0.051 0.651 4353 Planarity : 0.005 0.059 4482 Dihedral : 12.406 111.246 5823 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.77 % Favored : 92.01 % Rotamer: Outliers : 0.07 % Allowed : 1.07 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.14), residues: 3090 helix: 0.98 (0.31), residues: 312 sheet: -0.61 (0.17), residues: 828 loop : -1.79 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 54 TYR 0.022 0.002 TYR A 40 PHE 0.017 0.002 PHE I 376 TRP 0.018 0.002 TRP D 103 HIS 0.011 0.001 HIS k 52 Details of bonding type rmsd covalent geometry : bond 0.00419 (26700) covalent geometry : angle 0.75069 (36282) SS BOND : bond 0.00581 ( 45) SS BOND : angle 2.08715 ( 90) hydrogen bonds : bond 0.04173 ( 803) hydrogen bonds : angle 5.62090 ( 2106) link_ALPHA1-2 : bond 0.01116 ( 6) link_ALPHA1-2 : angle 1.71277 ( 18) link_ALPHA1-3 : bond 0.01259 ( 12) link_ALPHA1-3 : angle 2.26214 ( 36) link_ALPHA1-6 : bond 0.00816 ( 9) link_ALPHA1-6 : angle 2.12512 ( 27) link_BETA1-4 : bond 0.00683 ( 45) link_BETA1-4 : angle 2.41094 ( 135) link_NAG-ASN : bond 0.00599 ( 45) link_NAG-ASN : angle 4.43254 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 438 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 201 ILE cc_start: 0.8490 (tp) cc_final: 0.8124 (pt) REVERT: G 369 LEU cc_start: 0.9014 (tp) cc_final: 0.8420 (tt) REVERT: B 625 ASN cc_start: 0.6889 (p0) cc_final: 0.6526 (p0) REVERT: B 626 MET cc_start: 0.7159 (pmm) cc_final: 0.6891 (pmm) REVERT: H 36 TRP cc_start: 0.8161 (m100) cc_final: 0.7652 (m100) REVERT: H 85 ASP cc_start: 0.6129 (p0) cc_final: 0.5820 (p0) REVERT: L 46 LEU cc_start: 0.7497 (tp) cc_final: 0.7251 (tp) REVERT: h 53 LYS cc_start: 0.7181 (mmmm) cc_final: 0.6847 (mmmt) REVERT: A 119 CYS cc_start: 0.5298 (m) cc_final: 0.5002 (m) REVERT: D 31 ASP cc_start: 0.6352 (p0) cc_final: 0.6051 (p0) REVERT: D 85 ASP cc_start: 0.6460 (p0) cc_final: 0.6205 (p0) REVERT: e 30 SER cc_start: 0.7884 (p) cc_final: 0.7552 (t) REVERT: e 60 GLU cc_start: 0.6794 (pp20) cc_final: 0.6453 (pp20) REVERT: e 61 ARG cc_start: 0.7014 (mtm180) cc_final: 0.6531 (mtm-85) REVERT: d 2 MET cc_start: 0.6173 (pmm) cc_final: 0.5744 (pmm) REVERT: I 119 CYS cc_start: 0.5991 (m) cc_final: 0.5774 (m) REVERT: I 217 TYR cc_start: 0.8110 (m-80) cc_final: 0.7293 (m-80) REVERT: I 425 ASN cc_start: 0.7809 (m-40) cc_final: 0.7580 (m110) REVERT: J 622 ILE cc_start: 0.7638 (tp) cc_final: 0.7133 (tp) REVERT: J 626 MET cc_start: 0.6632 (pmm) cc_final: 0.6355 (pmm) REVERT: K 85 ASP cc_start: 0.5777 (p0) cc_final: 0.5339 (p0) REVERT: k 6 GLU cc_start: 0.5344 (tp30) cc_final: 0.3564 (mt-10) outliers start: 2 outliers final: 0 residues processed: 439 average time/residue: 0.1439 time to fit residues: 106.4006 Evaluate side-chains 366 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 66 optimal weight: 8.9990 chunk 189 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 chunk 248 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 165 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 chunk 257 optimal weight: 8.9990 chunk 259 optimal weight: 0.0270 chunk 296 optimal weight: 5.9990 overall best weight: 0.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 52 HIS h 97 HIS ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 246 GLN ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 52 HIS k 97 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4920 r_free = 0.4920 target = 0.246670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.236386 restraints weight = 34564.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.235266 restraints weight = 60359.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.235217 restraints weight = 64704.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.234466 restraints weight = 54273.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.234367 restraints weight = 57943.977| |-----------------------------------------------------------------------------| r_work (final): 0.4810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6590 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 26862 Z= 0.140 Angle : 0.784 14.610 36723 Z= 0.362 Chirality : 0.049 0.523 4353 Planarity : 0.004 0.059 4482 Dihedral : 11.979 108.967 5823 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.54 % Favored : 93.24 % Rotamer: Outliers : 0.04 % Allowed : 0.59 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.14), residues: 3090 helix: 0.93 (0.30), residues: 312 sheet: -0.57 (0.17), residues: 843 loop : -1.74 (0.13), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 54 TYR 0.011 0.001 TYR A 486 PHE 0.021 0.002 PHE A 288 TRP 0.018 0.001 TRP D 36 HIS 0.012 0.001 HIS k 52 Details of bonding type rmsd covalent geometry : bond 0.00320 (26700) covalent geometry : angle 0.72201 (36282) SS BOND : bond 0.00547 ( 45) SS BOND : angle 1.92667 ( 90) hydrogen bonds : bond 0.03842 ( 803) hydrogen bonds : angle 5.47825 ( 2106) link_ALPHA1-2 : bond 0.01140 ( 6) link_ALPHA1-2 : angle 1.64607 ( 18) link_ALPHA1-3 : bond 0.01207 ( 12) link_ALPHA1-3 : angle 2.11608 ( 36) link_ALPHA1-6 : bond 0.00832 ( 9) link_ALPHA1-6 : angle 2.00873 ( 27) link_BETA1-4 : bond 0.00683 ( 45) link_BETA1-4 : angle 2.36003 ( 135) link_NAG-ASN : bond 0.00566 ( 45) link_NAG-ASN : angle 4.07241 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 447 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 161 MET cc_start: 0.8314 (tpt) cc_final: 0.8042 (tpt) REVERT: G 201 ILE cc_start: 0.8449 (tp) cc_final: 0.8091 (pt) REVERT: G 369 LEU cc_start: 0.9023 (tp) cc_final: 0.8453 (tt) REVERT: B 625 ASN cc_start: 0.6891 (p0) cc_final: 0.6512 (p0) REVERT: B 626 MET cc_start: 0.7155 (pmm) cc_final: 0.6920 (pmm) REVERT: H 36 TRP cc_start: 0.8107 (m100) cc_final: 0.7717 (m100) REVERT: H 85 ASP cc_start: 0.6333 (p0) cc_final: 0.6022 (p0) REVERT: L 46 LEU cc_start: 0.7430 (tp) cc_final: 0.7184 (tp) REVERT: h 53 LYS cc_start: 0.7143 (mmmm) cc_final: 0.6755 (mmmt) REVERT: A 119 CYS cc_start: 0.5465 (m) cc_final: 0.5121 (m) REVERT: D 31 ASP cc_start: 0.6391 (p0) cc_final: 0.5996 (p0) REVERT: D 85 ASP cc_start: 0.6352 (p0) cc_final: 0.6087 (p0) REVERT: e 30 SER cc_start: 0.7865 (p) cc_final: 0.7551 (t) REVERT: e 60 GLU cc_start: 0.6775 (pp20) cc_final: 0.6495 (pp20) REVERT: d 2 MET cc_start: 0.6095 (pmm) cc_final: 0.5616 (pmm) REVERT: I 119 CYS cc_start: 0.6037 (m) cc_final: 0.5782 (m) REVERT: I 425 ASN cc_start: 0.7760 (m-40) cc_final: 0.7531 (m110) REVERT: I 434 MET cc_start: 0.8278 (ptp) cc_final: 0.8018 (ptm) REVERT: J 622 ILE cc_start: 0.7659 (tp) cc_final: 0.7165 (tp) REVERT: J 626 MET cc_start: 0.6660 (pmm) cc_final: 0.6395 (pmm) REVERT: K 85 ASP cc_start: 0.5904 (p0) cc_final: 0.5419 (p0) outliers start: 1 outliers final: 0 residues processed: 448 average time/residue: 0.1434 time to fit residues: 108.3629 Evaluate side-chains 367 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 102 optimal weight: 0.8980 chunk 217 optimal weight: 0.8980 chunk 104 optimal weight: 9.9990 chunk 165 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 158 optimal weight: 4.9990 chunk 241 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 305 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 ASN l 37 GLN l 50 ASN h 52 HIS h 97 HIS ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 52 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.245348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.238171 restraints weight = 34636.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.236918 restraints weight = 60559.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.236161 restraints weight = 67930.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4821 r_free = 0.4821 target = 0.235690 restraints weight = 62643.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.235596 restraints weight = 62221.340| |-----------------------------------------------------------------------------| r_work (final): 0.4820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 26862 Z= 0.157 Angle : 0.792 14.384 36723 Z= 0.367 Chirality : 0.049 0.443 4353 Planarity : 0.004 0.058 4482 Dihedral : 11.785 109.380 5823 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.38 % Favored : 92.39 % Rotamer: Outliers : 0.07 % Allowed : 0.67 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.14), residues: 3090 helix: 0.89 (0.31), residues: 314 sheet: -0.52 (0.17), residues: 840 loop : -1.73 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 54 TYR 0.027 0.001 TYR k 59 PHE 0.023 0.002 PHE I 468 TRP 0.029 0.002 TRP m 35 HIS 0.012 0.001 HIS k 52 Details of bonding type rmsd covalent geometry : bond 0.00366 (26700) covalent geometry : angle 0.73184 (36282) SS BOND : bond 0.00552 ( 45) SS BOND : angle 1.94866 ( 90) hydrogen bonds : bond 0.03951 ( 803) hydrogen bonds : angle 5.52795 ( 2106) link_ALPHA1-2 : bond 0.01122 ( 6) link_ALPHA1-2 : angle 1.70545 ( 18) link_ALPHA1-3 : bond 0.01200 ( 12) link_ALPHA1-3 : angle 2.14510 ( 36) link_ALPHA1-6 : bond 0.00797 ( 9) link_ALPHA1-6 : angle 1.99665 ( 27) link_BETA1-4 : bond 0.00677 ( 45) link_BETA1-4 : angle 2.38937 ( 135) link_NAG-ASN : bond 0.00560 ( 45) link_NAG-ASN : angle 4.02761 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3313.53 seconds wall clock time: 58 minutes 42.02 seconds (3522.02 seconds total)