Starting phenix.real_space_refine on Thu Mar 5 23:34:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8czz_27103/03_2026/8czz_27103.cif Found real_map, /net/cci-nas-00/data/ceres_data/8czz_27103/03_2026/8czz_27103.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8czz_27103/03_2026/8czz_27103.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8czz_27103/03_2026/8czz_27103.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8czz_27103/03_2026/8czz_27103.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8czz_27103/03_2026/8czz_27103.map" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.033 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 138 5.16 5 C 16491 2.51 5 N 4377 2.21 5 O 5282 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.03s 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: 26288 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 3479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3479 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 23, 'TRANS': 416} Chain breaks: 4 Chain: "B" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 999 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "C" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1003 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "D" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 814 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "E" Number of atoms: 3462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3462 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 23, 'TRANS': 414} Chain breaks: 4 Chain: "F" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 956 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "G" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1003 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "H" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 823 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Chain: "I" Number of atoms: 3455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3455 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 23, 'TRANS': 413} Chain breaks: 4 Chain: "J" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1034 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} Chain breaks: 1 Chain: "K" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1003 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 823 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Chain: "M" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "N" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "O" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "P" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "Q" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "R" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "S" 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: "T" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "U" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 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: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "b" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 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: "i" 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: "j" 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: "k" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 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: 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: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 147 Unusual residues: {'83J': 1, 'NAG': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 147 Unusual residues: {'83J': 1, 'NAG': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 133 Unusual residues: {'83J': 1, 'NAG': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "J" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.86, per 1000 atoms: 0.26 Number of scatterers: 26288 At special positions: 0 Unit cell: (164.521, 165.41, 151.181, 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 138 16.00 O 5282 8.00 N 4377 7.00 C 16491 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 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=2.05 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.63 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.06 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.00 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.05 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.06 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.05 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=1.98 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.52 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.05 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.42 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=1.95 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.06 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.02 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.01 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN S 4 " - " MAN S 5 " " MAN S 5 " - " MAN S 6 " " MAN S 8 " - " MAN S 9 " " MAN T 4 " - " MAN T 5 " " MAN a 4 " - " MAN a 5 " " MAN a 5 " - " MAN a 6 " " MAN a 8 " - " MAN a 9 " " MAN b 4 " - " MAN b 5 " " MAN j 4 " - " MAN j 5 " " MAN j 5 " - " MAN j 6 " " MAN j 8 " - " MAN j 9 " " MAN k 4 " - " MAN k 5 " ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " BMA a 3 " - " MAN a 4 " " MAN a 7 " - " MAN a 10 " " BMA b 3 " - " MAN b 4 " " BMA j 3 " - " MAN j 4 " " BMA k 3 " - " MAN k 4 " " BMA s 3 " - " MAN s 4 " ALPHA1-6 " BMA S 3 " - " MAN S 7 " " MAN S 7 " - " MAN S 8 " " BMA T 3 " - " MAN T 6 " " BMA a 3 " - " MAN a 7 " " MAN a 7 " - " MAN a 8 " " BMA b 3 " - " MAN b 6 " " BMA j 3 " - " MAN j 7 " " MAN j 7 " - " MAN j 8 " " BMA k 3 " - " MAN k 6 " BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " NAG U 3 " " NAG U 3 " - " NAG U 4 " " 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 Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " NAG d 3 " " NAG d 3 " - " NAG d 4 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " NAG n 3 " " NAG n 3 " - " NAG n 4 " " NAG o 1 " - " NAG o 2 " " 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-ASN " NAG A 602 " - " ASN A 160 " " NAG A 603 " - " ASN A 241 " " NAG A 604 " - " ASN A 295 " " NAG A 605 " - " ASN A 301 " " NAG A 606 " - " ASN A 448 " " NAG A 607 " - " ASN A 156 " " NAG A 608 " - " ASN A 289 " " NAG A 609 " - " ASN A 130 " " NAG B 701 " - " ASN B 616 " " NAG B 702 " - " ASN B 625 " " NAG C 301 " - " ASN C 82B" " NAG E 601 " - " ASN E 160 " " NAG E 602 " - " ASN E 241 " " NAG E 603 " - " ASN E 295 " " NAG E 604 " - " ASN E 301 " " NAG E 605 " - " ASN E 355 " " NAG E 606 " - " ASN E 448 " " NAG E 608 " - " ASN E 289 " " NAG E 609 " - " ASN E 130 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 616 " " NAG F 703 " - " ASN F 625 " " NAG G 301 " - " ASN G 82B" " NAG I 601 " - " ASN I 160 " " NAG I 602 " - " ASN I 241 " " NAG I 603 " - " ASN I 295 " " NAG I 604 " - " ASN I 301 " " NAG I 605 " - " ASN I 355 " " NAG I 606 " - " ASN I 448 " " NAG I 608 " - " ASN I 392 " " NAG J 701 " - " ASN J 611 " " NAG J 702 " - " ASN J 616 " " NAG J 703 " - " ASN J 625 " " NAG K 301 " - " ASN K 82B" " NAG S 1 " - " ASN A 234 " " NAG T 1 " - " ASN A 276 " " NAG U 1 " - " ASN A 332 " " NAG V 1 " - " ASN A 386 " " NAG W 1 " - " ASN A 392 " " NAG X 1 " - " ASN A 197 " " NAG Y 1 " - " ASN A 262 " " NAG Z 1 " - " ASN B 637 " " NAG a 1 " - " ASN E 234 " " NAG b 1 " - " ASN E 276 " " NAG c 1 " - " ASN E 156 " " NAG d 1 " - " ASN E 332 " " NAG e 1 " - " ASN E 386 " " NAG f 1 " - " ASN E 392 " " NAG g 1 " - " ASN E 197 " " NAG h 1 " - " ASN E 262 " " NAG i 1 " - " ASN F 637 " " NAG j 1 " - " ASN I 234 " " NAG k 1 " - " ASN I 276 " " NAG l 1 " - " ASN I 156 " " NAG m 1 " - " ASN I 289 " " NAG n 1 " - " ASN I 332 " " NAG o 1 " - " ASN I 386 " " NAG p 1 " - " ASN I 197 " " NAG q 1 " - " ASN I 130 " " NAG r 1 " - " ASN I 262 " " NAG s 1 " - " ASN J 637 " Time building additional restraints: 2.89 Conformation dependent library (CDL) restraints added in 1.1 seconds 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5712 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 68 sheets defined 15.3% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.304A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 334 through 353 removed outlier: 3.549A pdb=" N HIS A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 474 through 481 removed outlier: 4.091A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASN A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 536 removed outlier: 3.928A pdb=" N ILE B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.577A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 removed outlier: 3.619A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TRP B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 662 removed outlier: 3.660A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP B 659 " --> pdb=" O LYS B 655 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 660 " --> pdb=" O ASN B 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'C' and resid 99 through 100C removed outlier: 3.719A pdb=" N SER C 100B" --> pdb=" O ASP C 99 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLY C 100C" --> pdb=" O ARG C 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 99 through 100C' Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.534A pdb=" N PHE D 83 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.240A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 336 through 353 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 427 through 430 removed outlier: 3.877A pdb=" N VAL E 430 " --> pdb=" O TRP E 427 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 427 through 430' Processing helix chain 'F' and resid 529 through 536 Processing helix chain 'F' and resid 569 through 596 removed outlier: 3.675A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 626 removed outlier: 3.526A pdb=" N ASN F 625 " --> pdb=" O GLU F 621 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET F 626 " --> pdb=" O ILE F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 removed outlier: 3.512A pdb=" N ARG F 633 " --> pdb=" O ILE F 629 " (cutoff:3.500A) Processing helix chain 'F' and resid 639 through 662 removed outlier: 3.878A pdb=" N LYS F 658 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP F 659 " --> pdb=" O LYS F 655 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.553A pdb=" N THR G 87 " --> pdb=" O SER G 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 74 Processing helix chain 'I' and resid 98 through 117 removed outlier: 4.282A pdb=" N GLU I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 Processing helix chain 'I' and resid 177 through 179 No H-bonds generated for 'chain 'I' and resid 177 through 179' Processing helix chain 'I' and resid 195 through 198 Processing helix chain 'I' and resid 334 through 353 removed outlier: 3.530A pdb=" N HIS I 352 " --> pdb=" O LYS I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'J' and resid 529 through 535 removed outlier: 3.927A pdb=" N ILE J 535 " --> pdb=" O GLY J 531 " (cutoff:3.500A) Processing helix chain 'J' and resid 536 through 542 Processing helix chain 'J' and resid 569 through 595 removed outlier: 3.631A pdb=" N ILE J 573 " --> pdb=" O THR J 569 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS J 574 " --> pdb=" O VAL J 570 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN J 575 " --> pdb=" O TRP J 571 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU J 576 " --> pdb=" O GLY J 572 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL J 580 " --> pdb=" O LEU J 576 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU J 595 " --> pdb=" O LYS J 591 " (cutoff:3.500A) Processing helix chain 'J' and resid 618 through 624 Processing helix chain 'J' and resid 627 through 635 Processing helix chain 'J' and resid 639 through 662 removed outlier: 3.651A pdb=" N LYS J 658 " --> pdb=" O GLU J 654 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP J 659 " --> pdb=" O LYS J 655 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 100C removed outlier: 3.663A pdb=" N SER K 100B" --> pdb=" O ASP K 99 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY K 100C" --> pdb=" O ARG K 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 99 through 100C' Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.751A pdb=" N THR M 87 " --> pdb=" O PRO M 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 84 removed outlier: 3.612A pdb=" N ALA N 84 " --> pdb=" O GLY N 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'P' and resid 80 through 84 removed outlier: 3.629A pdb=" N GLU P 83 " --> pdb=" O ALA P 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 100D through 100H removed outlier: 3.572A pdb=" N PHE Q 100G" --> pdb=" O VAL Q 100D" (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 84 removed outlier: 3.555A pdb=" N GLU R 83 " --> pdb=" O ALA R 80 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA R 84 " --> pdb=" O GLY R 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 80 through 84' Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.791A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 93 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 175 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.726A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 10.278A pdb=" N LYS A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.544A pdb=" N ILE A 294 " --> pdb=" O LYS A 444 " (cutoff:3.500A) removed outlier: 10.284A pdb=" N LEU A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.811A pdb=" N VAL A 292 " --> pdb=" O LEU A 446 " (cutoff:3.500A) removed outlier: 9.730A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.341A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG A 419 " --> pdb=" O TYR A 384 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.806A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.341A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.730A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.811A pdb=" N VAL A 292 " --> pdb=" O LEU A 446 " (cutoff:3.500A) removed outlier: 10.284A pdb=" N LEU A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.544A pdb=" N ILE A 294 " --> pdb=" O LYS A 444 " (cutoff:3.500A) removed outlier: 10.278A pdb=" N LYS A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.460A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.493A pdb=" N GLU C 10 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR C 107 " --> pdb=" O TYR C 90 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE C 109 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR C 95 " --> pdb=" O ALA C 34 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA C 34 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ARG C 38 " --> pdb=" O TYR C 47 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N TYR C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.493A pdb=" N GLU C 10 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR C 107 " --> pdb=" O TYR C 90 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE C 109 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 100E through 100F Processing sheet with id=AB5, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.510A pdb=" N ILE D 75 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE D 21 " --> pdb=" O LEU D 73 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.423A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY D 84 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE D 48 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.423A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY D 84 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 494 through 499 removed outlier: 4.633A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR F 606 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC1, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC2, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC3, first strand: chain 'E' and resid 169 through 175 removed outlier: 3.543A pdb=" N ALA E 174 " --> pdb=" O CYS E 157 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.299A pdb=" N LYS E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.968A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 11.375A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.508A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 11.146A pdb=" N VAL E 292 " --> pdb=" O LEU E 446 " (cutoff:3.500A) removed outlier: 10.184A pdb=" N LEU E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.518A pdb=" N ILE E 294 " --> pdb=" O LYS E 444 " (cutoff:3.500A) removed outlier: 10.248A pdb=" N LYS E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N THR E 357 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N PHE E 468 " --> pdb=" O THR E 357 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER E 393 " --> pdb=" O PHE E 361 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 271 through 273 removed outlier: 3.547A pdb=" N TYR E 330 " --> pdb=" O THR E 297 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 304 through 312 removed outlier: 3.647A pdb=" N THR E 305 " --> pdb=" O LYS E 319 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 374 through 377 removed outlier: 3.503A pdb=" N PHE E 376 " --> pdb=" O PHE E 383 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 3 through 5 removed outlier: 3.743A pdb=" N VAL G 18 " --> pdb=" O ILE G 82 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.369A pdb=" N GLU G 10 " --> pdb=" O SER G 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'G' and resid 56 through 59 removed outlier: 6.598A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLN G 50 " --> pdb=" O VAL G 35 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL G 35 " --> pdb=" O GLN G 50 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N TRP G 52 " --> pdb=" O TYR G 33 " (cutoff:3.500A) removed outlier: 9.430A pdb=" N TYR G 33 " --> pdb=" O TRP G 52 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 100E through 100F Processing sheet with id=AD4, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AD5, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.975A pdb=" N LEU H 11 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N TYR H 49 " --> pdb=" O VAL H 33 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.975A pdb=" N LEU H 11 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR H 97 " --> pdb=" O GLN H 90 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 494 through 499 removed outlier: 4.503A pdb=" N VAL I 36 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR J 606 " --> pdb=" O VAL I 36 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.694A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AE1, first strand: chain 'I' and resid 91 through 94 Processing sheet with id=AE2, first strand: chain 'I' and resid 169 through 175 Processing sheet with id=AE3, first strand: chain 'I' and resid 201 through 203 removed outlier: 6.393A pdb=" N LYS I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 259 through 261 removed outlier: 3.995A pdb=" N GLY I 451 " --> pdb=" O LEU I 260 " (cutoff:3.500A) removed outlier: 10.199A pdb=" N LYS I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 11.573A pdb=" N ILE I 294 " --> pdb=" O LYS I 444 " (cutoff:3.500A) removed outlier: 10.360A pdb=" N LEU I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 11.271A pdb=" N VAL I 292 " --> pdb=" O LEU I 446 " (cutoff:3.500A) removed outlier: 9.474A pdb=" N ASN I 448 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 11.015A pdb=" N GLU I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR I 450 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE I 452 " --> pdb=" O VAL I 286 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 284 through 298 current: chain 'I' and resid 357 through 361 Processing sheet with id=AE5, first strand: chain 'I' and resid 271 through 273 removed outlier: 3.573A pdb=" N ILE I 271 " --> pdb=" O HIS I 287 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE I 452 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR I 450 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 11.015A pdb=" N GLU I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 9.474A pdb=" N ASN I 448 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 11.271A pdb=" N VAL I 292 " --> pdb=" O LEU I 446 " (cutoff:3.500A) removed outlier: 10.360A pdb=" N LEU I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 11.573A pdb=" N ILE I 294 " --> pdb=" O LYS I 444 " (cutoff:3.500A) removed outlier: 10.199A pdb=" N LYS I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 443 through 457 current: chain 'I' and resid 414 through 420 removed outlier: 3.667A pdb=" N ARG I 419 " --> pdb=" O TYR I 384 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE I 376 " --> pdb=" O PHE I 383 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 304 through 312 removed outlier: 6.488A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 3 through 5 removed outlier: 3.950A pdb=" N VAL K 18 " --> pdb=" O ILE K 82 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU K 81 " --> pdb=" O LEU K 68 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 10 through 11 removed outlier: 3.622A pdb=" N ILE K 109 " --> pdb=" O ALA K 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL K 37 " --> pdb=" O PHE K 91 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N VAL K 35 " --> pdb=" O GLN K 50 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N GLN K 50 " --> pdb=" O VAL K 35 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 100E through 100F Processing sheet with id=AF1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.701A pdb=" N SER L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.276A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.502A pdb=" N THR M 21 " --> pdb=" O SER M 7 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 11 through 12 Processing sheet with id=AF5, first strand: chain 'M' and resid 45 through 47 removed outlier: 3.811A pdb=" N ARG M 100 " --> pdb=" O PHE M 100K" (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE M 100K" --> pdb=" O ARG M 100 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 50 through 51 Processing sheet with id=AF7, first strand: chain 'M' and resid 68 through 69 Processing sheet with id=AF8, first strand: chain 'N' and resid 21 through 22 removed outlier: 3.621A pdb=" N ILE N 21 " --> pdb=" O LEU N 73 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER N 63 " --> pdb=" O THR N 74 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'N' and resid 45 through 49 removed outlier: 3.529A pdb=" N ILE N 45 " --> pdb=" O GLN N 37 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N TYR N 49 " --> pdb=" O VAL N 33 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'O' and resid 5 through 6 Processing sheet with id=AG2, first strand: chain 'O' and resid 11 through 12 removed outlier: 3.655A pdb=" N VAL O 12 " --> pdb=" O THR O 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'O' and resid 33 through 39 removed outlier: 3.672A pdb=" N GLN O 39 " --> pdb=" O VAL O 89 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG O 96 " --> pdb=" O SER O 100O" (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'O' and resid 49 through 51 Processing sheet with id=AG5, first strand: chain 'P' and resid 21 through 22 Processing sheet with id=AG6, first strand: chain 'P' and resid 31 through 34 Processing sheet with id=AG7, first strand: chain 'P' and resid 36 through 37 Processing sheet with id=AG8, first strand: chain 'P' and resid 86 through 87 Processing sheet with id=AG9, first strand: chain 'Q' and resid 3 through 7 Processing sheet with id=AH1, first strand: chain 'Q' and resid 11 through 12 Processing sheet with id=AH2, first strand: chain 'Q' and resid 45 through 46 Processing sheet with id=AH3, first strand: chain 'Q' and resid 50 through 51 Processing sheet with id=AH4, first strand: chain 'Q' and resid 96 through 100A removed outlier: 3.637A pdb=" N PHE Q 100K" --> pdb=" O ARG Q 100 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'R' and resid 45 through 49 removed outlier: 7.243A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR R 36 " --> pdb=" O TYR R 87 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR R 87 " --> pdb=" O TYR R 36 " (cutoff:3.500A) 756 hydrogen bonds defined for protein. 1935 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: 5.07 Time building geometry restraints manager: 3.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4061 1.30 - 1.44: 7989 1.44 - 1.57: 14627 1.57 - 1.71: 0 1.71 - 1.84: 186 Bond restraints: 26863 Sorted by residual: bond pdb=" C ASN E 156 " pdb=" N CYS E 157 " ideal model delta sigma weight residual 1.330 1.481 -0.151 1.41e-02 5.03e+03 1.15e+02 bond pdb=" C ASN E 130 " pdb=" N CYS E 131 " ideal model delta sigma weight residual 1.330 1.437 -0.108 1.36e-02 5.41e+03 6.28e+01 bond pdb=" C CYS I 331 " pdb=" N ASN I 332 " ideal model delta sigma weight residual 1.330 1.244 0.085 1.32e-02 5.74e+03 4.18e+01 bond pdb=" C ASN E 301 " pdb=" N ASN E 302 " ideal model delta sigma weight residual 1.331 1.237 0.094 1.51e-02 4.39e+03 3.85e+01 bond pdb=" C12 83J E 607 " pdb=" N02 83J E 607 " ideal model delta sigma weight residual 1.339 1.450 -0.111 2.00e-02 2.50e+03 3.10e+01 ... (remaining 26858 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.40: 35770 4.40 - 8.81: 642 8.81 - 13.21: 57 13.21 - 17.62: 5 17.62 - 22.02: 14 Bond angle restraints: 36488 Sorted by residual: angle pdb=" N VAL A 154 " pdb=" CA VAL A 154 " pdb=" C VAL A 154 " ideal model delta sigma weight residual 110.62 123.97 -13.35 1.02e+00 9.61e-01 1.71e+02 angle pdb=" N SER A 365 " pdb=" CA SER A 365 " pdb=" C SER A 365 " ideal model delta sigma weight residual 111.14 122.83 -11.69 1.08e+00 8.57e-01 1.17e+02 angle pdb=" N MET G 100J" pdb=" CA MET G 100J" pdb=" C MET G 100J" ideal model delta sigma weight residual 109.14 123.45 -14.31 1.49e+00 4.50e-01 9.23e+01 angle pdb=" N GLU A 267 " pdb=" CA GLU A 267 " pdb=" C GLU A 267 " ideal model delta sigma weight residual 111.36 121.81 -10.45 1.09e+00 8.42e-01 9.19e+01 angle pdb=" N PRO A 76 " pdb=" CA PRO A 76 " pdb=" C PRO A 76 " ideal model delta sigma weight residual 112.47 93.31 19.16 2.06e+00 2.36e-01 8.65e+01 ... (remaining 36483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.04: 16727 32.04 - 64.09: 634 64.09 - 96.13: 176 96.13 - 128.18: 106 128.18 - 160.22: 8 Dihedral angle restraints: 17651 sinusoidal: 8735 harmonic: 8916 Sorted by residual: dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual -86.00 1.99 -87.99 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" C CYS I 501 " pdb=" N CYS I 501 " pdb=" CA CYS I 501 " pdb=" CB CYS I 501 " ideal model delta harmonic sigma weight residual -122.60 -145.37 22.77 0 2.50e+00 1.60e-01 8.29e+01 dihedral pdb=" CB CYS I 126 " pdb=" SG CYS I 126 " pdb=" SG CYS I 196 " pdb=" CB CYS I 196 " ideal model delta sinusoidal sigma weight residual -86.00 -165.21 79.21 1 1.00e+01 1.00e-02 7.80e+01 ... (remaining 17648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.285: 4317 0.285 - 0.571: 95 0.571 - 0.856: 6 0.856 - 1.141: 3 1.141 - 1.427: 1 Chirality restraints: 4422 Sorted by residual: chirality pdb=" C1 MAN S 9 " pdb=" O2 MAN S 8 " pdb=" C2 MAN S 9 " pdb=" O5 MAN S 9 " both_signs ideal model delta sigma weight residual False 2.40 2.61 -0.21 2.00e-02 2.50e+03 1.10e+02 chirality pdb=" C1 NAG A 609 " pdb=" ND2 ASN A 130 " pdb=" C2 NAG A 609 " pdb=" O5 NAG A 609 " both_signs ideal model delta sigma weight residual False -2.40 -0.97 -1.43 2.00e-01 2.50e+01 5.09e+01 chirality pdb=" CA ASN F 625 " pdb=" N ASN F 625 " pdb=" C ASN F 625 " pdb=" CB ASN F 625 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.36e+01 ... (remaining 4419 not shown) Planarity restraints: 4500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 609 " -0.337 2.00e-02 2.50e+03 2.93e-01 1.07e+03 pdb=" C7 NAG A 609 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG A 609 " -0.100 2.00e-02 2.50e+03 pdb=" N2 NAG A 609 " 0.523 2.00e-02 2.50e+03 pdb=" O7 NAG A 609 " -0.162 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 607 " 0.283 2.00e-02 2.50e+03 2.33e-01 6.81e+02 pdb=" C7 NAG A 607 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG A 607 " 0.192 2.00e-02 2.50e+03 pdb=" N2 NAG A 607 " -0.386 2.00e-02 2.50e+03 pdb=" O7 NAG A 607 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 130 " -0.104 2.00e-02 2.50e+03 1.78e-01 3.97e+02 pdb=" CG ASN A 130 " 0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN A 130 " -0.060 2.00e-02 2.50e+03 pdb=" ND2 ASN A 130 " 0.318 2.00e-02 2.50e+03 pdb=" C1 NAG A 609 " -0.203 2.00e-02 2.50e+03 ... (remaining 4497 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 221 2.54 - 3.13: 19645 3.13 - 3.72: 36653 3.72 - 4.31: 53219 4.31 - 4.90: 89334 Nonbonded interactions: 199072 Sorted by model distance: nonbonded pdb=" O VAL I 154 " pdb=" O ARG I 155 " model vdw 1.950 3.040 nonbonded pdb=" O THR A 198 " pdb=" OG SER A 199 " model vdw 1.955 3.040 nonbonded pdb=" N ASN A 302 " pdb=" OD1 ASN A 302 " model vdw 2.163 3.120 nonbonded pdb=" O ARG R 61 " pdb=" OG1 THR R 74 " model vdw 2.218 3.040 nonbonded pdb=" O SER F 612 " pdb=" O SER F 615 " model vdw 2.221 3.040 ... (remaining 199067 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 134 or resid 152 through 396 or resid 408 throu \ gh 504 or resid 602 through 606 or resid 608)) selection = (chain 'E' and (resid 33 through 134 or resid 152 through 504 or resid 602 throu \ gh 606 or resid 608)) selection = (chain 'I' and (resid 33 through 504 or resid 602 through 606 or resid 608)) } ncs_group { reference = (chain 'B' and (resid 522 through 542 or resid 566 through 702)) selection = (chain 'F' and resid 522 through 702) selection = (chain 'J' and (resid 522 through 542 or resid 566 through 702)) } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 1 through 106) selection = (chain 'L' and resid 1 through 106) } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' } ncs_group { reference = (chain 'S' and (resid 1 or resid 4 through 9)) selection = (chain 'a' and (resid 2 or resid 5 through 10)) selection = (chain 'j' and (resid 1 or resid 4 through 9)) } ncs_group { reference = chain 'T' selection = chain 'b' selection = chain 'k' } ncs_group { reference = (chain 'U' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'n' and resid 1 through 2) selection = (chain 's' and resid 1 through 2) } ncs_group { reference = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'c' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'l' selection = chain 'm' selection = chain 'o' selection = chain 'p' selection = chain 'q' } ncs_group { reference = chain 'Y' selection = chain 'Z' selection = chain 'h' selection = chain 'i' selection = chain 'r' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.660 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: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 25.710 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 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 : 0.011 0.594 27043 Z= 0.687 Angle : 1.494 39.018 36983 Z= 0.867 Chirality : 0.102 1.427 4422 Planarity : 0.009 0.293 4439 Dihedral : 19.738 160.223 11804 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.90 % Favored : 95.96 % Rotamer: Outliers : 2.12 % Allowed : 4.92 % Favored : 92.96 % Cbeta Deviations : 0.67 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.15), residues: 3048 helix: 1.39 (0.26), residues: 396 sheet: 0.19 (0.18), residues: 893 loop : -0.93 (0.14), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 579 TYR 0.040 0.002 TYR D 91 PHE 0.029 0.002 PHE I 391 TRP 0.041 0.002 TRP P 35 HIS 0.007 0.001 HIS I 216 Details of bonding type rmsd covalent geometry : bond 0.00932 (26863) covalent geometry : angle 1.40647 (36488) SS BOND : bond 0.12965 ( 45) SS BOND : angle 6.68773 ( 90) hydrogen bonds : bond 0.25441 ( 736) hydrogen bonds : angle 8.81604 ( 1935) link_ALPHA1-2 : bond 0.00767 ( 12) link_ALPHA1-2 : angle 2.49079 ( 36) link_ALPHA1-3 : bond 0.00317 ( 8) link_ALPHA1-3 : angle 1.81541 ( 24) link_ALPHA1-6 : bond 0.00299 ( 9) link_ALPHA1-6 : angle 1.87850 ( 27) link_BETA1-4 : bond 0.00460 ( 45) link_BETA1-4 : angle 1.95280 ( 135) link_NAG-ASN : bond 0.01142 ( 61) link_NAG-ASN : angle 5.43994 ( 183) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 431 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ASP cc_start: 0.7758 (t0) cc_final: 0.7414 (m-30) REVERT: A 229 ASN cc_start: 0.6901 (m110) cc_final: 0.6295 (m110) REVERT: A 303 THR cc_start: 0.8611 (p) cc_final: 0.8235 (t) REVERT: A 304 ARG cc_start: 0.7815 (ptm160) cc_final: 0.7519 (ptp-170) REVERT: A 354 ASN cc_start: 0.7857 (t0) cc_final: 0.7271 (t0) REVERT: A 413 THR cc_start: 0.8889 (m) cc_final: 0.8685 (p) REVERT: A 466 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7062 (mm-30) REVERT: A 492 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7847 (mt-10) REVERT: A 496 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8243 (mp) REVERT: B 656 ASN cc_start: 0.7872 (t0) cc_final: 0.7445 (t0) REVERT: C 23 LYS cc_start: 0.6937 (mtpt) cc_final: 0.6547 (mttt) REVERT: C 38 ARG cc_start: 0.6932 (OUTLIER) cc_final: 0.6678 (ttt180) REVERT: D 3 GLN cc_start: 0.7365 (mp10) cc_final: 0.6919 (mp10) REVERT: E 117 LYS cc_start: 0.7195 (mttt) cc_final: 0.6965 (mmtp) REVERT: F 577 GLN cc_start: 0.7753 (tp-100) cc_final: 0.7552 (tp-100) REVERT: F 632 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8355 (mm-30) REVERT: G 35 ASN cc_start: 0.8196 (m-40) cc_final: 0.7839 (m110) REVERT: G 56 LYS cc_start: 0.7530 (mmmt) cc_final: 0.7060 (tttp) REVERT: H 33 VAL cc_start: 0.6639 (m) cc_final: 0.6417 (t) REVERT: H 65 SER cc_start: 0.8747 (t) cc_final: 0.8448 (p) REVERT: I 161 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.7100 (ttm) REVERT: I 211 ASP cc_start: 0.7165 (t70) cc_final: 0.6769 (m-30) REVERT: I 246 GLN cc_start: 0.7196 (tp40) cc_final: 0.6861 (tp-100) REVERT: I 303 THR cc_start: 0.8587 (p) cc_final: 0.8336 (t) REVERT: I 354 ASN cc_start: 0.7932 (m110) cc_final: 0.7722 (m110) REVERT: I 377 ASN cc_start: 0.8095 (p0) cc_final: 0.7731 (p0) REVERT: I 440 LYS cc_start: 0.7671 (tmtt) cc_final: 0.7306 (tptp) REVERT: K 23 LYS cc_start: 0.6859 (mtpt) cc_final: 0.6528 (mttt) REVERT: M 100 ILE cc_start: 0.7157 (pt) cc_final: 0.6909 (pt) REVERT: Q 100 MET cc_start: 0.3907 (mmm) cc_final: 0.3427 (mtm) outliers start: 57 outliers final: 24 residues processed: 480 average time/residue: 0.1691 time to fit residues: 127.6224 Evaluate side-chains 326 residues out of total 2684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 299 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain F residue 617 LYS Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 277 LEU Chi-restraints excluded: chain I residue 302 ASN Chi-restraints excluded: chain I residue 323 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.0870 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 195 ASN A 203 GLN A 339 HIS A 425 ASN A 478 ASN C 50 GLN C 61 HIS D 27 GLN D 38 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 ASN E 72 HIS E 99 ASN E 203 GLN E 229 ASN G 6 GLN I 99 ASN I 195 ASN I 302 ASN K 35AASN ** O 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.231047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.179661 restraints weight = 30853.834| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 3.63 r_work: 0.3839 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27043 Z= 0.141 Angle : 0.762 11.467 36983 Z= 0.358 Chirality : 0.051 0.443 4422 Planarity : 0.005 0.048 4439 Dihedral : 16.712 157.136 6236 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.16 % Allowed : 10.95 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.15), residues: 3048 helix: 1.42 (0.26), residues: 403 sheet: 0.32 (0.18), residues: 861 loop : -0.82 (0.15), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 469 TYR 0.017 0.001 TYR D 91 PHE 0.023 0.001 PHE Q 100K TRP 0.022 0.001 TRP O 47 HIS 0.005 0.001 HIS E 72 Details of bonding type rmsd covalent geometry : bond 0.00299 (26863) covalent geometry : angle 0.69494 (36488) SS BOND : bond 0.00408 ( 45) SS BOND : angle 1.45874 ( 90) hydrogen bonds : bond 0.05686 ( 736) hydrogen bonds : angle 6.53399 ( 1935) link_ALPHA1-2 : bond 0.01151 ( 12) link_ALPHA1-2 : angle 1.63161 ( 36) link_ALPHA1-3 : bond 0.00868 ( 8) link_ALPHA1-3 : angle 1.89336 ( 24) link_ALPHA1-6 : bond 0.00613 ( 9) link_ALPHA1-6 : angle 1.73363 ( 27) link_BETA1-4 : bond 0.00523 ( 45) link_BETA1-4 : angle 2.10574 ( 135) link_NAG-ASN : bond 0.00546 ( 61) link_NAG-ASN : angle 3.90029 ( 183) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 316 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 SER cc_start: 0.8818 (t) cc_final: 0.8429 (m) REVERT: A 211 ASP cc_start: 0.8042 (t0) cc_final: 0.7577 (m-30) REVERT: A 348 LYS cc_start: 0.7451 (tppt) cc_final: 0.7189 (tptp) REVERT: A 354 ASN cc_start: 0.7963 (t0) cc_final: 0.7390 (t0) REVERT: A 492 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8182 (mt-10) REVERT: C 23 LYS cc_start: 0.6805 (mtpt) cc_final: 0.6416 (mttt) REVERT: C 99 ASP cc_start: 0.7688 (p0) cc_final: 0.7484 (p0) REVERT: E 110 SER cc_start: 0.8824 (t) cc_final: 0.8402 (m) REVERT: G 28 ASN cc_start: 0.8415 (p0) cc_final: 0.8185 (p0) REVERT: G 56 LYS cc_start: 0.7418 (mmmt) cc_final: 0.6932 (tttp) REVERT: G 87 THR cc_start: 0.8663 (p) cc_final: 0.8460 (t) REVERT: I 61 TYR cc_start: 0.4519 (OUTLIER) cc_final: 0.2288 (t80) REVERT: I 110 SER cc_start: 0.8882 (t) cc_final: 0.8470 (m) REVERT: I 211 ASP cc_start: 0.7252 (t70) cc_final: 0.6803 (m-30) REVERT: K 56 LYS cc_start: 0.7414 (mmmt) cc_final: 0.6792 (tttp) REVERT: K 99 ASP cc_start: 0.7759 (p0) cc_final: 0.7531 (p0) REVERT: M 29 MET cc_start: 0.3471 (tpp) cc_final: 0.2293 (ttt) outliers start: 58 outliers final: 34 residues processed: 353 average time/residue: 0.1599 time to fit residues: 92.9091 Evaluate side-chains 312 residues out of total 2684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 277 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 61 HIS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 320 THR Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain I residue 323 ILE Chi-restraints excluded: chain I residue 448 ASN Chi-restraints excluded: chain K residue 61 HIS Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain Q residue 25 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 199 optimal weight: 8.9990 chunk 209 optimal weight: 2.9990 chunk 230 optimal weight: 8.9990 chunk 267 optimal weight: 8.9990 chunk 219 optimal weight: 0.9990 chunk 197 optimal weight: 4.9990 chunk 156 optimal weight: 5.9990 chunk 212 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 299 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 195 ASN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN D 6 GLN D 27 GLN E 229 ASN E 352 HIS G 105 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 HIS ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.222031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.170322 restraints weight = 30952.329| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 3.71 r_work: 0.3704 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 27043 Z= 0.255 Angle : 0.830 13.263 36983 Z= 0.394 Chirality : 0.054 0.439 4422 Planarity : 0.005 0.044 4439 Dihedral : 15.027 153.437 6205 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.98 % Allowed : 13.52 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.15), residues: 3048 helix: 0.96 (0.26), residues: 396 sheet: 0.36 (0.19), residues: 805 loop : -1.01 (0.14), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 20 TYR 0.032 0.002 TYR D 91 PHE 0.034 0.002 PHE E 382 TRP 0.023 0.002 TRP O 47 HIS 0.008 0.002 HIS C 61 Details of bonding type rmsd covalent geometry : bond 0.00616 (26863) covalent geometry : angle 0.76017 (36488) SS BOND : bond 0.00674 ( 45) SS BOND : angle 1.83241 ( 90) hydrogen bonds : bond 0.06777 ( 736) hydrogen bonds : angle 6.29020 ( 1935) link_ALPHA1-2 : bond 0.01139 ( 12) link_ALPHA1-2 : angle 1.78639 ( 36) link_ALPHA1-3 : bond 0.00902 ( 8) link_ALPHA1-3 : angle 1.96475 ( 24) link_ALPHA1-6 : bond 0.00606 ( 9) link_ALPHA1-6 : angle 1.77955 ( 27) link_BETA1-4 : bond 0.00513 ( 45) link_BETA1-4 : angle 2.21099 ( 135) link_NAG-ASN : bond 0.00551 ( 61) link_NAG-ASN : angle 4.15007 ( 183) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 268 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8647 (ttt) cc_final: 0.8444 (ttt) REVERT: A 110 SER cc_start: 0.8946 (t) cc_final: 0.8461 (m) REVERT: A 166 ARG cc_start: 0.8139 (ttp80) cc_final: 0.7935 (ttp80) REVERT: A 211 ASP cc_start: 0.8260 (t0) cc_final: 0.7792 (m-30) REVERT: A 304 ARG cc_start: 0.8257 (ptm160) cc_final: 0.8052 (ptp-170) REVERT: A 348 LYS cc_start: 0.7565 (tppt) cc_final: 0.7351 (tptp) REVERT: A 354 ASN cc_start: 0.8030 (t0) cc_final: 0.7510 (t0) REVERT: A 444 LYS cc_start: 0.8586 (ttmt) cc_final: 0.8218 (tttp) REVERT: A 492 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8126 (mt-10) REVERT: B 577 GLN cc_start: 0.8081 (tp-100) cc_final: 0.7712 (tp40) REVERT: B 662 GLU cc_start: 0.5873 (OUTLIER) cc_final: 0.5065 (mt-10) REVERT: C 23 LYS cc_start: 0.6952 (mtpt) cc_final: 0.6553 (mttt) REVERT: C 82 LEU cc_start: 0.8065 (tt) cc_final: 0.7861 (tt) REVERT: D 3 GLN cc_start: 0.7588 (mp10) cc_final: 0.7282 (mp10) REVERT: E 110 SER cc_start: 0.8892 (t) cc_final: 0.8448 (m) REVERT: E 316 VAL cc_start: 0.8820 (p) cc_final: 0.8540 (t) REVERT: E 444 LYS cc_start: 0.8513 (ttmt) cc_final: 0.8298 (tttp) REVERT: G 23 LYS cc_start: 0.6852 (mtpt) cc_final: 0.6394 (mttt) REVERT: G 56 LYS cc_start: 0.7642 (mmmt) cc_final: 0.7199 (tttp) REVERT: G 87 THR cc_start: 0.8653 (p) cc_final: 0.8445 (t) REVERT: I 61 TYR cc_start: 0.5034 (OUTLIER) cc_final: 0.2994 (t80) REVERT: I 65 VAL cc_start: 0.8374 (t) cc_final: 0.7426 (p) REVERT: I 110 SER cc_start: 0.8973 (t) cc_final: 0.8531 (m) REVERT: I 275 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7563 (tp30) REVERT: K 56 LYS cc_start: 0.7632 (mmmt) cc_final: 0.7032 (tttp) REVERT: K 64 ARG cc_start: 0.8002 (mtm110) cc_final: 0.7550 (ttm-80) REVERT: M 29 MET cc_start: 0.3841 (tpp) cc_final: 0.2808 (ttt) REVERT: Q 29 MET cc_start: 0.4601 (tpp) cc_final: 0.4398 (tpp) REVERT: R 50 ASN cc_start: 0.6882 (t0) cc_final: 0.6305 (t0) outliers start: 80 outliers final: 56 residues processed: 329 average time/residue: 0.1587 time to fit residues: 85.6094 Evaluate side-chains 307 residues out of total 2684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 248 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 662 GLU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 61 HIS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 413 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 236 THR Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain I residue 274 SER Chi-restraints excluded: chain I residue 275 GLU Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 320 THR Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain I residue 448 ASN Chi-restraints excluded: chain I residue 500 LYS Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 61 HIS Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain Q residue 25 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 273 optimal weight: 0.0970 chunk 76 optimal weight: 9.9990 chunk 217 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 259 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 262 optimal weight: 40.0000 chunk 142 optimal weight: 5.9990 chunk 267 optimal weight: 9.9990 chunk 158 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 229 ASN A 302 ASN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN I 82 GLN I 432 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 HIS L 3 GLN ** O 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 89 HIS ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.225393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.174471 restraints weight = 30791.287| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 3.31 r_work: 0.3756 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 27043 Z= 0.147 Angle : 0.712 11.498 36983 Z= 0.334 Chirality : 0.050 0.549 4422 Planarity : 0.004 0.045 4439 Dihedral : 13.659 156.642 6197 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.31 % Allowed : 14.98 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.15), residues: 3048 helix: 1.28 (0.27), residues: 386 sheet: 0.35 (0.19), residues: 827 loop : -1.05 (0.14), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 20 TYR 0.020 0.001 TYR D 91 PHE 0.021 0.001 PHE Q 100K TRP 0.017 0.001 TRP O 47 HIS 0.011 0.001 HIS K 61 Details of bonding type rmsd covalent geometry : bond 0.00336 (26863) covalent geometry : angle 0.64862 (36488) SS BOND : bond 0.00524 ( 45) SS BOND : angle 1.73500 ( 90) hydrogen bonds : bond 0.05157 ( 736) hydrogen bonds : angle 5.85947 ( 1935) link_ALPHA1-2 : bond 0.01124 ( 12) link_ALPHA1-2 : angle 1.77055 ( 36) link_ALPHA1-3 : bond 0.01029 ( 8) link_ALPHA1-3 : angle 1.89012 ( 24) link_ALPHA1-6 : bond 0.00657 ( 9) link_ALPHA1-6 : angle 1.77490 ( 27) link_BETA1-4 : bond 0.00460 ( 45) link_BETA1-4 : angle 2.00535 ( 135) link_NAG-ASN : bond 0.00457 ( 61) link_NAG-ASN : angle 3.54916 ( 183) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 268 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 TRP cc_start: 0.9153 (p90) cc_final: 0.8884 (p90) REVERT: A 110 SER cc_start: 0.8888 (t) cc_final: 0.8462 (m) REVERT: A 155 ARG cc_start: 0.5819 (OUTLIER) cc_final: 0.5520 (ttm170) REVERT: A 211 ASP cc_start: 0.8237 (t0) cc_final: 0.7706 (m-30) REVERT: A 304 ARG cc_start: 0.8194 (ptm160) cc_final: 0.7850 (ptp-170) REVERT: A 348 LYS cc_start: 0.7461 (tppt) cc_final: 0.7116 (tptp) REVERT: A 354 ASN cc_start: 0.7958 (t0) cc_final: 0.7656 (t0) REVERT: A 492 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8086 (mt-10) REVERT: B 577 GLN cc_start: 0.7883 (tp-100) cc_final: 0.7453 (tp40) REVERT: D 3 GLN cc_start: 0.7594 (mp10) cc_final: 0.7309 (mp10) REVERT: D 79 GLN cc_start: 0.6740 (mp10) cc_final: 0.5984 (mp10) REVERT: E 110 SER cc_start: 0.8906 (t) cc_final: 0.8527 (m) REVERT: E 444 LYS cc_start: 0.8466 (ttmt) cc_final: 0.8188 (ttmm) REVERT: F 656 ASN cc_start: 0.8109 (t0) cc_final: 0.7646 (t0) REVERT: G 56 LYS cc_start: 0.7601 (mmmt) cc_final: 0.7119 (tttp) REVERT: G 87 THR cc_start: 0.8613 (p) cc_final: 0.8407 (m) REVERT: I 61 TYR cc_start: 0.4956 (OUTLIER) cc_final: 0.2877 (t80) REVERT: I 65 VAL cc_start: 0.8335 (t) cc_final: 0.7379 (p) REVERT: I 110 SER cc_start: 0.8924 (t) cc_final: 0.8524 (m) REVERT: I 275 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7930 (tp30) REVERT: K 56 LYS cc_start: 0.7621 (mmmt) cc_final: 0.7018 (tttp) REVERT: K 64 ARG cc_start: 0.7951 (mtm110) cc_final: 0.7270 (ttm-80) REVERT: M 29 MET cc_start: 0.3777 (tpp) cc_final: 0.2829 (ttt) REVERT: O 100 MET cc_start: 0.4063 (tpt) cc_final: 0.3386 (mtt) REVERT: R 50 ASN cc_start: 0.6903 (t0) cc_final: 0.6325 (t0) outliers start: 62 outliers final: 41 residues processed: 318 average time/residue: 0.1560 time to fit residues: 81.0616 Evaluate side-chains 295 residues out of total 2684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 251 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain I residue 274 SER Chi-restraints excluded: chain I residue 275 GLU Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 320 THR Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain I residue 448 ASN Chi-restraints excluded: chain I residue 500 LYS Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain M residue 65 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 174 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 51 optimal weight: 0.5980 chunk 148 optimal weight: 3.9990 chunk 231 optimal weight: 9.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 HIS E 354 ASN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** O 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.224506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.173306 restraints weight = 30658.226| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 3.40 r_work: 0.3745 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 27043 Z= 0.184 Angle : 0.733 12.043 36983 Z= 0.343 Chirality : 0.050 0.374 4422 Planarity : 0.004 0.046 4439 Dihedral : 12.988 155.724 6196 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.91 % Allowed : 15.91 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.15), residues: 3048 helix: 1.16 (0.27), residues: 386 sheet: 0.25 (0.18), residues: 844 loop : -1.10 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 20 TYR 0.026 0.002 TYR D 91 PHE 0.024 0.002 PHE I 383 TRP 0.018 0.001 TRP O 47 HIS 0.005 0.001 HIS C 61 Details of bonding type rmsd covalent geometry : bond 0.00440 (26863) covalent geometry : angle 0.67143 (36488) SS BOND : bond 0.00492 ( 45) SS BOND : angle 1.62730 ( 90) hydrogen bonds : bond 0.05471 ( 736) hydrogen bonds : angle 5.78015 ( 1935) link_ALPHA1-2 : bond 0.01024 ( 12) link_ALPHA1-2 : angle 1.78429 ( 36) link_ALPHA1-3 : bond 0.00986 ( 8) link_ALPHA1-3 : angle 1.96083 ( 24) link_ALPHA1-6 : bond 0.00629 ( 9) link_ALPHA1-6 : angle 1.86297 ( 27) link_BETA1-4 : bond 0.00461 ( 45) link_BETA1-4 : angle 2.05738 ( 135) link_NAG-ASN : bond 0.00425 ( 61) link_NAG-ASN : angle 3.55231 ( 183) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 257 time to evaluate : 0.926 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: A 110 SER cc_start: 0.8804 (t) cc_final: 0.8327 (m) REVERT: A 211 ASP cc_start: 0.8360 (t0) cc_final: 0.7690 (m-30) REVERT: A 304 ARG cc_start: 0.8252 (ptm160) cc_final: 0.7892 (ptp-170) REVERT: A 348 LYS cc_start: 0.7379 (tppt) cc_final: 0.6968 (tptp) REVERT: A 354 ASN cc_start: 0.8038 (t0) cc_final: 0.7670 (t0) REVERT: A 492 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8137 (mt-10) REVERT: B 577 GLN cc_start: 0.7953 (tp-100) cc_final: 0.7449 (tp40) REVERT: B 656 ASN cc_start: 0.7989 (t0) cc_final: 0.7495 (t0) REVERT: B 662 GLU cc_start: 0.5089 (OUTLIER) cc_final: 0.4471 (mt-10) REVERT: C 64 ARG cc_start: 0.7918 (mtm110) cc_final: 0.7486 (mtm-85) REVERT: D 3 GLN cc_start: 0.7631 (mp10) cc_final: 0.7276 (mp10) REVERT: E 110 SER cc_start: 0.8826 (t) cc_final: 0.8384 (m) REVERT: E 444 LYS cc_start: 0.8514 (ttmt) cc_final: 0.8164 (tttp) REVERT: F 621 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7803 (mt-10) REVERT: G 56 LYS cc_start: 0.7527 (mmmt) cc_final: 0.6959 (tttp) REVERT: I 61 TYR cc_start: 0.5080 (OUTLIER) cc_final: 0.3016 (t80) REVERT: I 65 VAL cc_start: 0.8336 (t) cc_final: 0.7271 (p) REVERT: I 110 SER cc_start: 0.8887 (t) cc_final: 0.8443 (m) REVERT: I 275 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.8072 (tp30) REVERT: I 287 HIS cc_start: 0.9196 (OUTLIER) cc_final: 0.8977 (t-170) REVERT: I 449 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7727 (mt) REVERT: J 656 ASN cc_start: 0.8080 (t0) cc_final: 0.7694 (t0) REVERT: K 56 LYS cc_start: 0.7610 (mmmt) cc_final: 0.6934 (tttp) REVERT: M 29 MET cc_start: 0.3844 (tpp) cc_final: 0.3040 (ttt) REVERT: O 100 MET cc_start: 0.4172 (tpt) cc_final: 0.3539 (mtt) REVERT: R 50 ASN cc_start: 0.6927 (t0) cc_final: 0.6346 (t0) outliers start: 78 outliers final: 58 residues processed: 320 average time/residue: 0.1501 time to fit residues: 78.9203 Evaluate side-chains 308 residues out of total 2684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 245 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 662 GLU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain I residue 274 SER Chi-restraints excluded: chain I residue 275 GLU Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 287 HIS Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 320 THR Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 448 ASN Chi-restraints excluded: chain I residue 449 ILE Chi-restraints excluded: chain I residue 500 LYS Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain Q residue 25 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 287 optimal weight: 0.0770 chunk 223 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 145 optimal weight: 9.9990 chunk 82 optimal weight: 0.0000 chunk 166 optimal weight: 9.9990 chunk 15 optimal weight: 0.7980 chunk 235 optimal weight: 40.0000 chunk 91 optimal weight: 0.9980 chunk 295 optimal weight: 10.0000 chunk 234 optimal weight: 40.0000 overall best weight: 0.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.227691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.177295 restraints weight = 30844.359| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 3.32 r_work: 0.3791 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 27043 Z= 0.116 Angle : 0.653 11.696 36983 Z= 0.304 Chirality : 0.047 0.341 4422 Planarity : 0.004 0.044 4439 Dihedral : 12.037 158.421 6194 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.42 % Allowed : 17.21 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.15), residues: 3048 helix: 1.37 (0.27), residues: 392 sheet: 0.26 (0.18), residues: 837 loop : -1.03 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG R 31 TYR 0.015 0.001 TYR D 91 PHE 0.023 0.001 PHE Q 100K TRP 0.025 0.001 TRP G 36 HIS 0.003 0.001 HIS E 287 Details of bonding type rmsd covalent geometry : bond 0.00255 (26863) covalent geometry : angle 0.59729 (36488) SS BOND : bond 0.00415 ( 45) SS BOND : angle 1.61508 ( 90) hydrogen bonds : bond 0.04217 ( 736) hydrogen bonds : angle 5.39941 ( 1935) link_ALPHA1-2 : bond 0.01051 ( 12) link_ALPHA1-2 : angle 1.76358 ( 36) link_ALPHA1-3 : bond 0.01033 ( 8) link_ALPHA1-3 : angle 1.87559 ( 24) link_ALPHA1-6 : bond 0.00652 ( 9) link_ALPHA1-6 : angle 1.72737 ( 27) link_BETA1-4 : bond 0.00482 ( 45) link_BETA1-4 : angle 1.84312 ( 135) link_NAG-ASN : bond 0.00412 ( 61) link_NAG-ASN : angle 3.10025 ( 183) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 267 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 SER cc_start: 0.8936 (t) cc_final: 0.8549 (m) REVERT: A 166 ARG cc_start: 0.8058 (ttp-110) cc_final: 0.7791 (mtm110) REVERT: A 211 ASP cc_start: 0.8143 (t0) cc_final: 0.7598 (m-30) REVERT: A 304 ARG cc_start: 0.8125 (ptm160) cc_final: 0.7726 (ptp-170) REVERT: A 348 LYS cc_start: 0.7478 (tppt) cc_final: 0.7192 (tptp) REVERT: A 354 ASN cc_start: 0.7994 (t0) cc_final: 0.7704 (t0) REVERT: A 492 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8118 (mt-10) REVERT: B 577 GLN cc_start: 0.7757 (tp-100) cc_final: 0.7317 (tp40) REVERT: B 656 ASN cc_start: 0.8027 (t0) cc_final: 0.7598 (t0) REVERT: D 3 GLN cc_start: 0.7668 (mp10) cc_final: 0.7396 (mp10) REVERT: E 110 SER cc_start: 0.8876 (t) cc_final: 0.8520 (m) REVERT: E 444 LYS cc_start: 0.8460 (ttmt) cc_final: 0.8226 (ttmm) REVERT: F 656 ASN cc_start: 0.8042 (t0) cc_final: 0.7582 (t0) REVERT: G 56 LYS cc_start: 0.7608 (mmmt) cc_final: 0.7144 (tttp) REVERT: H 38 GLN cc_start: 0.6769 (pt0) cc_final: 0.6433 (tt0) REVERT: I 61 TYR cc_start: 0.4812 (OUTLIER) cc_final: 0.2649 (t80) REVERT: I 65 VAL cc_start: 0.8319 (t) cc_final: 0.7280 (p) REVERT: I 110 SER cc_start: 0.8948 (t) cc_final: 0.8568 (m) REVERT: I 275 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7928 (tp30) REVERT: J 656 ASN cc_start: 0.8220 (t0) cc_final: 0.7829 (t0) REVERT: K 32 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7987 (pp) REVERT: K 56 LYS cc_start: 0.7767 (mmmt) cc_final: 0.7143 (tttp) REVERT: K 64 ARG cc_start: 0.7836 (mtm-85) cc_final: 0.7546 (mtm-85) REVERT: M 29 MET cc_start: 0.3934 (tpp) cc_final: 0.3187 (ttt) REVERT: N 66 ILE cc_start: 0.5691 (OUTLIER) cc_final: 0.5466 (mp) REVERT: O 100 MET cc_start: 0.4203 (tpt) cc_final: 0.3529 (mtt) REVERT: R 50 ASN cc_start: 0.6963 (t0) cc_final: 0.6384 (t0) outliers start: 65 outliers final: 41 residues processed: 320 average time/residue: 0.1593 time to fit residues: 83.6292 Evaluate side-chains 294 residues out of total 2684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 249 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 61 HIS Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 100 HIS Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 236 THR Chi-restraints excluded: chain I residue 274 SER Chi-restraints excluded: chain I residue 275 GLU Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 320 THR Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 448 ASN Chi-restraints excluded: chain I residue 500 LYS Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain Q residue 25 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 100 optimal weight: 0.6980 chunk 120 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 285 optimal weight: 30.0000 chunk 11 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 263 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 233 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.229198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.176875 restraints weight = 30501.477| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 3.61 r_work: 0.3815 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 27043 Z= 0.116 Angle : 0.646 11.821 36983 Z= 0.301 Chirality : 0.047 0.343 4422 Planarity : 0.004 0.044 4439 Dihedral : 11.583 159.313 6192 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.61 % Allowed : 17.29 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.15), residues: 3048 helix: 1.53 (0.27), residues: 392 sheet: 0.29 (0.18), residues: 845 loop : -0.97 (0.14), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 20 TYR 0.017 0.001 TYR L 94 PHE 0.022 0.001 PHE Q 100K TRP 0.013 0.001 TRP O 47 HIS 0.003 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00256 (26863) covalent geometry : angle 0.59115 (36488) SS BOND : bond 0.00461 ( 45) SS BOND : angle 1.53314 ( 90) hydrogen bonds : bond 0.04080 ( 736) hydrogen bonds : angle 5.25804 ( 1935) link_ALPHA1-2 : bond 0.01066 ( 12) link_ALPHA1-2 : angle 1.80969 ( 36) link_ALPHA1-3 : bond 0.01024 ( 8) link_ALPHA1-3 : angle 1.97802 ( 24) link_ALPHA1-6 : bond 0.00583 ( 9) link_ALPHA1-6 : angle 1.62864 ( 27) link_BETA1-4 : bond 0.00509 ( 45) link_BETA1-4 : angle 1.88220 ( 135) link_NAG-ASN : bond 0.00445 ( 61) link_NAG-ASN : angle 3.04320 ( 183) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 248 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 SER cc_start: 0.8800 (t) cc_final: 0.8379 (m) REVERT: A 166 ARG cc_start: 0.8016 (ttp-110) cc_final: 0.7668 (mtm110) REVERT: A 211 ASP cc_start: 0.8239 (t0) cc_final: 0.7546 (m-30) REVERT: A 230 ASP cc_start: 0.8686 (OUTLIER) cc_final: 0.8363 (m-30) REVERT: A 348 LYS cc_start: 0.7301 (tppt) cc_final: 0.6905 (tptp) REVERT: A 354 ASN cc_start: 0.8039 (t0) cc_final: 0.7674 (t0) REVERT: A 492 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8101 (mt-10) REVERT: B 530 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7426 (mtt) REVERT: B 577 GLN cc_start: 0.7755 (tp-100) cc_final: 0.7489 (tp-100) REVERT: B 656 ASN cc_start: 0.7868 (t0) cc_final: 0.7409 (t0) REVERT: D 3 GLN cc_start: 0.7613 (mp10) cc_final: 0.7248 (mp10) REVERT: E 110 SER cc_start: 0.8749 (t) cc_final: 0.8347 (m) REVERT: E 195 ASN cc_start: 0.7309 (m110) cc_final: 0.7050 (m-40) REVERT: E 198 THR cc_start: 0.9029 (m) cc_final: 0.8746 (p) REVERT: E 444 LYS cc_start: 0.8520 (ttmt) cc_final: 0.8156 (ttmm) REVERT: F 656 ASN cc_start: 0.7873 (t0) cc_final: 0.7392 (t0) REVERT: G 56 LYS cc_start: 0.7479 (mmmt) cc_final: 0.6903 (tttp) REVERT: H 38 GLN cc_start: 0.6695 (pt0) cc_final: 0.6368 (tt0) REVERT: I 61 TYR cc_start: 0.4922 (OUTLIER) cc_final: 0.2741 (t80) REVERT: I 65 VAL cc_start: 0.8277 (t) cc_final: 0.7107 (p) REVERT: I 110 SER cc_start: 0.8823 (t) cc_final: 0.8434 (m) REVERT: I 275 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8039 (tp30) REVERT: J 656 ASN cc_start: 0.8105 (t0) cc_final: 0.7731 (t0) REVERT: K 32 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7892 (pp) REVERT: K 56 LYS cc_start: 0.7626 (mmmt) cc_final: 0.6911 (tttp) REVERT: O 100 MET cc_start: 0.4115 (tpt) cc_final: 0.3484 (mtt) REVERT: R 50 ASN cc_start: 0.6883 (t0) cc_final: 0.6326 (t0) REVERT: R 66 ILE cc_start: 0.5756 (OUTLIER) cc_final: 0.5516 (mm) outliers start: 70 outliers final: 51 residues processed: 302 average time/residue: 0.1525 time to fit residues: 77.0759 Evaluate side-chains 303 residues out of total 2684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 246 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 61 HIS Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 100 HIS Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 236 THR Chi-restraints excluded: chain I residue 274 SER Chi-restraints excluded: chain I residue 275 GLU Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 320 THR Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 448 ASN Chi-restraints excluded: chain I residue 500 LYS Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain R residue 66 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 122 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 295 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 299 optimal weight: 0.2980 chunk 259 optimal weight: 50.0000 chunk 193 optimal weight: 4.9990 chunk 276 optimal weight: 1.9990 chunk 228 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 89 HIS ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.226214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.173053 restraints weight = 30868.629| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 4.30 r_work: 0.3746 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 27043 Z= 0.167 Angle : 0.706 11.603 36983 Z= 0.330 Chirality : 0.049 0.364 4422 Planarity : 0.004 0.045 4439 Dihedral : 11.362 156.824 6192 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.61 % Allowed : 17.40 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.15), residues: 3048 helix: 1.30 (0.27), residues: 392 sheet: 0.26 (0.18), residues: 827 loop : -1.05 (0.14), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 20 TYR 0.025 0.001 TYR D 91 PHE 0.024 0.002 PHE I 383 TRP 0.016 0.001 TRP O 47 HIS 0.004 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00395 (26863) covalent geometry : angle 0.64856 (36488) SS BOND : bond 0.00472 ( 45) SS BOND : angle 1.63375 ( 90) hydrogen bonds : bond 0.05010 ( 736) hydrogen bonds : angle 5.40886 ( 1935) link_ALPHA1-2 : bond 0.01056 ( 12) link_ALPHA1-2 : angle 1.87422 ( 36) link_ALPHA1-3 : bond 0.01008 ( 8) link_ALPHA1-3 : angle 2.03176 ( 24) link_ALPHA1-6 : bond 0.00503 ( 9) link_ALPHA1-6 : angle 1.68919 ( 27) link_BETA1-4 : bond 0.00485 ( 45) link_BETA1-4 : angle 2.06648 ( 135) link_NAG-ASN : bond 0.00469 ( 61) link_NAG-ASN : angle 3.28766 ( 183) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 256 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8614 (ttt) cc_final: 0.8396 (ttt) REVERT: A 110 SER cc_start: 0.8779 (t) cc_final: 0.8310 (m) REVERT: A 166 ARG cc_start: 0.8141 (ttp-110) cc_final: 0.7694 (mtm110) REVERT: A 211 ASP cc_start: 0.8276 (t0) cc_final: 0.7599 (m-30) REVERT: A 304 ARG cc_start: 0.8251 (ptm160) cc_final: 0.7788 (ptp-170) REVERT: A 348 LYS cc_start: 0.7336 (tppt) cc_final: 0.6899 (tptp) REVERT: A 354 ASN cc_start: 0.8110 (t0) cc_final: 0.7703 (t0) REVERT: A 444 LYS cc_start: 0.8515 (ttmt) cc_final: 0.8037 (tttp) REVERT: A 492 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8248 (mt-10) REVERT: B 530 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7603 (mtt) REVERT: B 577 GLN cc_start: 0.7959 (tp-100) cc_final: 0.7408 (tp40) REVERT: B 656 ASN cc_start: 0.7855 (t0) cc_final: 0.7366 (t0) REVERT: D 3 GLN cc_start: 0.7693 (mp10) cc_final: 0.7336 (mp10) REVERT: E 110 SER cc_start: 0.8822 (t) cc_final: 0.8396 (m) REVERT: E 444 LYS cc_start: 0.8571 (ttmt) cc_final: 0.8221 (ttmm) REVERT: F 656 ASN cc_start: 0.7865 (t0) cc_final: 0.7352 (t0) REVERT: G 56 LYS cc_start: 0.7511 (mmmt) cc_final: 0.6915 (tttp) REVERT: H 38 GLN cc_start: 0.6819 (pt0) cc_final: 0.6434 (tt0) REVERT: I 61 TYR cc_start: 0.4819 (OUTLIER) cc_final: 0.2662 (t80) REVERT: I 65 VAL cc_start: 0.8274 (t) cc_final: 0.7370 (p) REVERT: I 110 SER cc_start: 0.8888 (t) cc_final: 0.8448 (m) REVERT: J 656 ASN cc_start: 0.8018 (t0) cc_final: 0.7650 (t0) REVERT: K 32 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7989 (pp) REVERT: K 56 LYS cc_start: 0.7619 (mmmt) cc_final: 0.6947 (tttp) REVERT: K 64 ARG cc_start: 0.7611 (mtm-85) cc_final: 0.7126 (mtm-85) REVERT: M 29 MET cc_start: 0.2781 (tpt) cc_final: 0.1942 (ttt) REVERT: O 100 MET cc_start: 0.3869 (tpt) cc_final: 0.3420 (mtt) REVERT: R 50 ASN cc_start: 0.6978 (t0) cc_final: 0.6403 (t0) REVERT: R 66 ILE cc_start: 0.5716 (OUTLIER) cc_final: 0.5484 (mm) outliers start: 70 outliers final: 54 residues processed: 309 average time/residue: 0.1628 time to fit residues: 82.7088 Evaluate side-chains 309 residues out of total 2684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 251 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 61 HIS Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 100 HIS Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 230 ASP Chi-restraints excluded: chain I residue 236 THR Chi-restraints excluded: chain I residue 274 SER Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 320 THR Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 500 LYS Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain J residue 583 VAL Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 61 HIS Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain R residue 66 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 94 optimal weight: 0.8980 chunk 286 optimal weight: 40.0000 chunk 29 optimal weight: 2.9990 chunk 224 optimal weight: 10.0000 chunk 293 optimal weight: 6.9990 chunk 183 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 60 optimal weight: 0.0980 chunk 95 optimal weight: 6.9990 chunk 196 optimal weight: 1.9990 chunk 249 optimal weight: 8.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.228446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.175612 restraints weight = 30795.302| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 4.42 r_work: 0.3774 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27043 Z= 0.124 Angle : 0.658 11.980 36983 Z= 0.307 Chirality : 0.047 0.349 4422 Planarity : 0.004 0.047 4439 Dihedral : 10.987 158.290 6192 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.53 % Allowed : 17.66 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.15), residues: 3048 helix: 1.42 (0.27), residues: 392 sheet: 0.28 (0.18), residues: 815 loop : -1.01 (0.14), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 20 TYR 0.017 0.001 TYR D 91 PHE 0.022 0.001 PHE Q 100K TRP 0.013 0.001 TRP O 47 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00279 (26863) covalent geometry : angle 0.60317 (36488) SS BOND : bond 0.00451 ( 45) SS BOND : angle 1.55615 ( 90) hydrogen bonds : bond 0.04310 ( 736) hydrogen bonds : angle 5.25208 ( 1935) link_ALPHA1-2 : bond 0.01035 ( 12) link_ALPHA1-2 : angle 1.85189 ( 36) link_ALPHA1-3 : bond 0.01024 ( 8) link_ALPHA1-3 : angle 1.92202 ( 24) link_ALPHA1-6 : bond 0.00533 ( 9) link_ALPHA1-6 : angle 1.65420 ( 27) link_BETA1-4 : bond 0.00482 ( 45) link_BETA1-4 : angle 1.88624 ( 135) link_NAG-ASN : bond 0.00435 ( 61) link_NAG-ASN : angle 3.08339 ( 183) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 254 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 SER cc_start: 0.8826 (t) cc_final: 0.8383 (m) REVERT: A 166 ARG cc_start: 0.8073 (ttp-110) cc_final: 0.7580 (mtm110) REVERT: A 211 ASP cc_start: 0.8251 (t0) cc_final: 0.7544 (m-30) REVERT: A 230 ASP cc_start: 0.8693 (OUTLIER) cc_final: 0.8361 (m-30) REVERT: A 304 ARG cc_start: 0.8210 (ptm160) cc_final: 0.7747 (ptp-170) REVERT: A 348 LYS cc_start: 0.7316 (tppt) cc_final: 0.6879 (tptp) REVERT: A 354 ASN cc_start: 0.8090 (t0) cc_final: 0.7678 (t0) REVERT: A 444 LYS cc_start: 0.8495 (ttmt) cc_final: 0.8003 (tttp) REVERT: A 492 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8187 (mt-10) REVERT: B 530 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7500 (mtt) REVERT: B 577 GLN cc_start: 0.7796 (tp-100) cc_final: 0.7227 (tp40) REVERT: B 656 ASN cc_start: 0.7830 (t0) cc_final: 0.7365 (t0) REVERT: B 662 GLU cc_start: 0.4493 (OUTLIER) cc_final: 0.4142 (mt-10) REVERT: D 3 GLN cc_start: 0.7649 (mp10) cc_final: 0.7306 (mp10) REVERT: E 110 SER cc_start: 0.8806 (t) cc_final: 0.8395 (m) REVERT: F 577 GLN cc_start: 0.7771 (tp-100) cc_final: 0.7521 (tp-100) REVERT: F 656 ASN cc_start: 0.7834 (t0) cc_final: 0.7305 (t0) REVERT: G 56 LYS cc_start: 0.7480 (mmmt) cc_final: 0.6871 (tttp) REVERT: H 38 GLN cc_start: 0.6680 (pt0) cc_final: 0.6419 (tt0) REVERT: I 61 TYR cc_start: 0.4755 (OUTLIER) cc_final: 0.2421 (t80) REVERT: I 65 VAL cc_start: 0.8218 (t) cc_final: 0.7163 (p) REVERT: I 110 SER cc_start: 0.8845 (t) cc_final: 0.8454 (m) REVERT: I 193 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7783 (mp) REVERT: J 656 ASN cc_start: 0.8017 (t0) cc_final: 0.7653 (t0) REVERT: K 32 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7958 (pp) REVERT: K 56 LYS cc_start: 0.7581 (mmmt) cc_final: 0.6910 (tttp) REVERT: K 64 ARG cc_start: 0.7635 (mtm-85) cc_final: 0.7127 (mtm-85) REVERT: M 29 MET cc_start: 0.2839 (tpt) cc_final: 0.2004 (ttt) REVERT: O 100 MET cc_start: 0.4081 (tpt) cc_final: 0.3396 (mtt) REVERT: R 50 ASN cc_start: 0.7004 (t0) cc_final: 0.6432 (t0) REVERT: R 66 ILE cc_start: 0.5716 (OUTLIER) cc_final: 0.5476 (mm) outliers start: 68 outliers final: 54 residues processed: 305 average time/residue: 0.1632 time to fit residues: 81.8536 Evaluate side-chains 312 residues out of total 2684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 251 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 662 GLU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 61 HIS Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 100 HIS Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain I residue 230 ASP Chi-restraints excluded: chain I residue 236 THR Chi-restraints excluded: chain I residue 274 SER Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 292 VAL Chi-restraints excluded: chain I residue 320 THR Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 448 ASN Chi-restraints excluded: chain I residue 500 LYS Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain J residue 583 VAL Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain O residue 100 ILE Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain R residue 66 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 165 optimal weight: 0.8980 chunk 240 optimal weight: 0.9990 chunk 295 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 152 optimal weight: 9.9990 chunk 225 optimal weight: 9.9990 chunk 289 optimal weight: 40.0000 chunk 292 optimal weight: 7.9990 chunk 97 optimal weight: 0.8980 chunk 68 optimal weight: 8.9990 chunk 159 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN E 352 HIS G 61 HIS ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.223713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.172007 restraints weight = 30513.043| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 3.46 r_work: 0.3752 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 27043 Z= 0.207 Angle : 0.748 12.629 36983 Z= 0.350 Chirality : 0.050 0.377 4422 Planarity : 0.004 0.047 4439 Dihedral : 11.207 155.513 6192 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.65 % Allowed : 17.70 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.15), residues: 3048 helix: 1.06 (0.27), residues: 392 sheet: 0.20 (0.18), residues: 829 loop : -1.11 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 20 TYR 0.027 0.002 TYR D 91 PHE 0.027 0.002 PHE I 383 TRP 0.017 0.002 TRP O 47 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00501 (26863) covalent geometry : angle 0.68874 (36488) SS BOND : bond 0.00455 ( 45) SS BOND : angle 1.76698 ( 90) hydrogen bonds : bond 0.05530 ( 736) hydrogen bonds : angle 5.52879 ( 1935) link_ALPHA1-2 : bond 0.01046 ( 12) link_ALPHA1-2 : angle 1.93906 ( 36) link_ALPHA1-3 : bond 0.00975 ( 8) link_ALPHA1-3 : angle 2.02408 ( 24) link_ALPHA1-6 : bond 0.00467 ( 9) link_ALPHA1-6 : angle 1.68603 ( 27) link_BETA1-4 : bond 0.00467 ( 45) link_BETA1-4 : angle 2.14083 ( 135) link_NAG-ASN : bond 0.00433 ( 61) link_NAG-ASN : angle 3.45923 ( 183) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 249 time to evaluate : 0.927 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: A 104 MET cc_start: 0.8655 (ttt) cc_final: 0.8436 (ttt) REVERT: A 110 SER cc_start: 0.8792 (t) cc_final: 0.8287 (m) REVERT: A 166 ARG cc_start: 0.8155 (ttp-110) cc_final: 0.7669 (mtm110) REVERT: A 211 ASP cc_start: 0.8252 (t0) cc_final: 0.7668 (m-30) REVERT: A 304 ARG cc_start: 0.8324 (ptm160) cc_final: 0.7865 (ptp-170) REVERT: A 348 LYS cc_start: 0.7434 (tppt) cc_final: 0.7180 (tptp) REVERT: A 354 ASN cc_start: 0.8132 (t0) cc_final: 0.7591 (t0) REVERT: A 444 LYS cc_start: 0.8554 (ttmt) cc_final: 0.8092 (tttp) REVERT: A 492 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8253 (mt-10) REVERT: B 530 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7649 (mtt) REVERT: B 577 GLN cc_start: 0.8048 (tp-100) cc_final: 0.7529 (tp40) REVERT: B 656 ASN cc_start: 0.7944 (t0) cc_final: 0.7436 (t0) REVERT: B 662 GLU cc_start: 0.4815 (OUTLIER) cc_final: 0.4248 (mt-10) REVERT: D 3 GLN cc_start: 0.7705 (mp10) cc_final: 0.7378 (mp10) REVERT: E 110 SER cc_start: 0.8847 (t) cc_final: 0.8400 (m) REVERT: E 444 LYS cc_start: 0.8486 (ttmt) cc_final: 0.8206 (ttmm) REVERT: F 621 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7895 (mp0) REVERT: G 56 LYS cc_start: 0.7582 (mmmt) cc_final: 0.7044 (tttp) REVERT: I 61 TYR cc_start: 0.5008 (OUTLIER) cc_final: 0.2933 (t80) REVERT: I 65 VAL cc_start: 0.8282 (t) cc_final: 0.7170 (p) REVERT: I 110 SER cc_start: 0.8878 (t) cc_final: 0.8430 (m) REVERT: I 193 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8025 (mp) REVERT: I 275 GLU cc_start: 0.7993 (tp30) cc_final: 0.7529 (tp30) REVERT: J 656 ASN cc_start: 0.8117 (t0) cc_final: 0.7746 (t0) REVERT: K 32 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8013 (pp) REVERT: K 56 LYS cc_start: 0.7718 (mmmt) cc_final: 0.7076 (tttp) REVERT: K 64 ARG cc_start: 0.7688 (mtm-85) cc_final: 0.7203 (mtm-85) REVERT: O 100 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7311 (mt-10) REVERT: O 100 MET cc_start: 0.3958 (tpt) cc_final: 0.3450 (mtt) REVERT: R 50 ASN cc_start: 0.7023 (t0) cc_final: 0.6450 (t0) REVERT: R 66 ILE cc_start: 0.5990 (OUTLIER) cc_final: 0.5773 (mm) outliers start: 71 outliers final: 56 residues processed: 301 average time/residue: 0.1589 time to fit residues: 78.8629 Evaluate side-chains 309 residues out of total 2684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 246 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 662 GLU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 61 HIS Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 100 HIS Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain I residue 230 ASP Chi-restraints excluded: chain I residue 236 THR Chi-restraints excluded: chain I residue 274 SER Chi-restraints excluded: chain I residue 283 THR Chi-restraints excluded: chain I residue 320 THR Chi-restraints excluded: chain I residue 322 ILE Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 448 ASN Chi-restraints excluded: chain I residue 500 LYS Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain J residue 583 VAL Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain R residue 66 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 199 optimal weight: 4.9990 chunk 182 optimal weight: 0.9990 chunk 297 optimal weight: 20.0000 chunk 157 optimal weight: 0.6980 chunk 184 optimal weight: 0.7980 chunk 229 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 292 optimal weight: 50.0000 chunk 142 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN ** O 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.227088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.173506 restraints weight = 30659.083| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 3.50 r_work: 0.3806 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 27043 Z= 0.129 Angle : 0.673 12.205 36983 Z= 0.315 Chirality : 0.047 0.352 4422 Planarity : 0.004 0.047 4439 Dihedral : 10.855 157.448 6190 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.42 % Allowed : 18.14 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.15), residues: 3048 helix: 1.22 (0.27), residues: 392 sheet: 0.23 (0.18), residues: 815 loop : -1.08 (0.14), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 20 TYR 0.020 0.001 TYR D 91 PHE 0.020 0.001 PHE Q 100K TRP 0.014 0.001 TRP O 47 HIS 0.007 0.001 HIS G 62 Details of bonding type rmsd covalent geometry : bond 0.00293 (26863) covalent geometry : angle 0.61878 (36488) SS BOND : bond 0.00428 ( 45) SS BOND : angle 1.45031 ( 90) hydrogen bonds : bond 0.04588 ( 736) hydrogen bonds : angle 5.35140 ( 1935) link_ALPHA1-2 : bond 0.00977 ( 12) link_ALPHA1-2 : angle 1.85506 ( 36) link_ALPHA1-3 : bond 0.01018 ( 8) link_ALPHA1-3 : angle 1.88130 ( 24) link_ALPHA1-6 : bond 0.00519 ( 9) link_ALPHA1-6 : angle 1.63833 ( 27) link_BETA1-4 : bond 0.00472 ( 45) link_BETA1-4 : angle 1.93314 ( 135) link_NAG-ASN : bond 0.00415 ( 61) link_NAG-ASN : angle 3.15661 ( 183) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6739.45 seconds wall clock time: 116 minutes 9.68 seconds (6969.68 seconds total)