Starting phenix.real_space_refine on Sat Jul 4 12:17:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rai_24362/07_2026/7rai_24362.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rai_24362/07_2026/7rai_24362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rai_24362/07_2026/7rai_24362.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rai_24362/07_2026/7rai_24362.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rai_24362/07_2026/7rai_24362.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rai_24362/07_2026/7rai_24362.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7rai_24362/07_2026/7rai_24362.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rai_24362/07_2026/7rai_24362.cif" } resolution = 3.24 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= 0.006 sd= 0.103 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 153 5.16 5 C 12840 2.51 5 N 3429 2.21 5 O 4230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 112 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20652 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 3524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3524 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 3 Chain: "B" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1010 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "H" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 949 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 6, 'TRANS': 117} Chain: "L" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "C" Number of atoms: 3524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3524 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 3 Chain: "D" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1010 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "I" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 949 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 6, 'TRANS': 117} Chain: "M" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "E" Number of atoms: 3524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3524 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 3 Chain: "F" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1010 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "J" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 949 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 6, 'TRANS': 117} Chain: "N" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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 chiralities: 2 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "o" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "L" 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 chiralities: 1 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "M" 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 chiralities: 1 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "N" 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 chiralities: 1 Time building chain proxies: 4.34, per 1000 atoms: 0.21 Number of scatterers: 20652 At special positions: 0 Unit cell: (135.192, 134.144, 132.048, 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 153 16.00 O 4230 8.00 N 3429 7.00 C 12840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, 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=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 97 " - pdb=" SG CYS H 100B" distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 97 " - pdb=" SG CYS I 100B" distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 97 " - pdb=" SG CYS J 100B" distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 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 P 4 " - " MAN P 5 " " MAN P 5 " - " MAN P 6 " " MAN b 4 " - " MAN b 5 " " MAN b 5 " - " MAN b 6 " " MAN n 4 " - " MAN n 5 " " MAN n 5 " - " MAN n 6 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA P 3 " - " MAN P 4 " " BMA Y 3 " - " MAN Y 4 " " BMA b 3 " - " MAN b 4 " " BMA k 3 " - " MAN k 4 " " BMA n 3 " - " MAN n 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA P 3 " - " MAN P 7 " " BMA Y 3 " - " MAN Y 5 " " BMA b 3 " - " MAN b 7 " " BMA k 3 " - " MAN k 5 " " BMA n 3 " - " MAN n 7 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " 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 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 c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 137 " " NAG A 604 " - " ASN A 234 " " NAG A 605 " - " ASN A 339 " " NAG A 606 " - " ASN A 355 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 137 " " NAG C 604 " - " ASN C 234 " " NAG C 605 " - " ASN C 339 " " NAG C 606 " - " ASN C 355 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 133 " " NAG E 603 " - " ASN E 137 " " NAG E 604 " - " ASN E 234 " " NAG E 605 " - " ASN E 339 " " NAG E 606 " - " ASN E 355 " " NAG G 1 " - " ASN A 156 " " NAG K 1 " - " ASN A 160 " " NAG L1001 " - " ASN L 18 " " NAG M1001 " - " ASN M 18 " " NAG N1001 " - " ASN N 18 " " NAG O 1 " - " ASN A 197 " " NAG P 1 " - " ASN A 262 " " NAG Q 1 " - " ASN A 276 " " NAG R 1 " - " ASN A 295 " " NAG S 1 " - " ASN A 301 " " NAG T 1 " - " ASN A 332 " " NAG U 1 " - " ASN A 363 " " NAG V 1 " - " ASN A 386 " " NAG W 1 " - " ASN A 392 " " NAG X 1 " - " ASN A 448 " " NAG Y 1 " - " ASN C 156 " " NAG Z 1 " - " ASN C 160 " " NAG a 1 " - " ASN C 197 " " NAG b 1 " - " ASN C 262 " " NAG c 1 " - " ASN C 276 " " NAG d 1 " - " ASN C 295 " " NAG e 1 " - " ASN C 301 " " NAG f 1 " - " ASN C 332 " " NAG g 1 " - " ASN C 363 " " NAG h 1 " - " ASN C 386 " " NAG i 1 " - " ASN C 392 " " NAG j 1 " - " ASN C 448 " " NAG k 1 " - " ASN E 156 " " NAG l 1 " - " ASN E 160 " " NAG m 1 " - " ASN E 197 " " NAG n 1 " - " ASN E 262 " " NAG o 1 " - " ASN E 276 " " NAG p 1 " - " ASN E 295 " " NAG q 1 " - " ASN E 301 " " NAG r 1 " - " ASN E 332 " " NAG s 1 " - " ASN E 363 " " NAG t 1 " - " ASN E 386 " " NAG u 1 " - " ASN E 392 " " NAG v 1 " - " ASN E 448 " Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 679.5 milliseconds 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4452 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 50 sheets defined 15.3% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 99 through 114 removed outlier: 3.577A pdb=" N HIS A 105 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 349 removed outlier: 3.802A pdb=" N THR A 341 " --> pdb=" O THR A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.800A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 425 through 429' Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.803A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 521 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 543 removed outlier: 3.822A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 583 Processing helix chain 'B' and resid 583 through 596 removed outlier: 3.693A pdb=" N ARG B 588 " --> pdb=" O GLU B 584 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.627A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 663 Processing helix chain 'H' and resid 61 through 65 removed outlier: 4.327A pdb=" N ALA H 65 " --> pdb=" O LYS H 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 114 removed outlier: 3.603A pdb=" N HIS C 105 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 349 removed outlier: 3.804A pdb=" N THR C 341 " --> pdb=" O THR C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.808A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG C 429 " --> pdb=" O MET C 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 425 through 429' Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.779A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 521 Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 537 through 543 removed outlier: 3.833A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 583 Processing helix chain 'D' and resid 583 through 596 removed outlier: 3.691A pdb=" N ARG D 588 " --> pdb=" O GLU D 584 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 636 removed outlier: 3.597A pdb=" N GLU D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 663 Processing helix chain 'I' and resid 61 through 65 removed outlier: 4.373A pdb=" N ALA I 65 " --> pdb=" O LYS I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 removed outlier: 4.064A pdb=" N THR I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 114 removed outlier: 3.543A pdb=" N HIS E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR E 106 " --> pdb=" O GLU E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 349 removed outlier: 3.806A pdb=" N THR E 341 " --> pdb=" O THR E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.837A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 425 through 429' Processing helix chain 'E' and resid 475 through 481 removed outlier: 3.788A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 517 through 521 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 537 through 543 removed outlier: 3.882A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 575 through 583 Processing helix chain 'F' and resid 583 through 596 removed outlier: 3.699A pdb=" N ARG F 588 " --> pdb=" O GLU F 584 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.603A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 641 through 663 Processing helix chain 'J' and resid 61 through 65 removed outlier: 4.348A pdb=" N ALA J 65 " --> pdb=" O LYS J 62 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 5.152A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.430A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 4.065A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 162 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.648A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 9.767A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.133A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.695A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.236A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.020A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A 333 " --> pdb=" O ILE A 414 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 315 through 320 removed outlier: 7.047A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER H 100A" --> pdb=" O ALA H 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 393 through 395 removed outlier: 3.662A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB2, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 11 removed outlier: 7.034A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 11 removed outlier: 7.034A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 6 removed outlier: 4.009A pdb=" N ILE L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR L 72 " --> pdb=" O GLY L 65 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.553A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N SER L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.553A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N SER L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE L 86 " --> pdb=" O SER L 102 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 495 through 499 removed outlier: 5.151A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.433A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'C' and resid 91 through 94 removed outlier: 4.071A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 154 through 162 Processing sheet with id=AC5, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AC6, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.622A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 9.814A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.191A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.221A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL C 333 " --> pdb=" O ILE C 414 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 315 through 320 removed outlier: 7.042A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER I 100A" --> pdb=" O ALA I 98 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 393 through 395 removed outlier: 3.627A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 423 through 424 Processing sheet with id=AD1, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AD2, first strand: chain 'I' and resid 10 through 11 removed outlier: 7.023A pdb=" N GLU I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 10 through 11 removed outlier: 7.023A pdb=" N GLU I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N CYS I 92 " --> pdb=" O TRP I 103 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N TRP I 103 " --> pdb=" O CYS I 92 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ARG I 94 " --> pdb=" O ASP I 101 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 4 through 6 Processing sheet with id=AD5, first strand: chain 'M' and resid 4 through 6 removed outlier: 4.005A pdb=" N ILE M 70 " --> pdb=" O SER M 67 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR M 72 " --> pdb=" O GLY M 65 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 53 through 54 removed outlier: 6.513A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N SER M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU M 33 " --> pdb=" O SER M 49 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR M 97 " --> pdb=" O GLN M 90 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 495 through 499 removed outlier: 5.157A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.436A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AE1, first strand: chain 'E' and resid 91 through 94 removed outlier: 4.120A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY E 237 " --> pdb=" O PHE E 93 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 154 through 162 Processing sheet with id=AE3, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AE4, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.623A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 9.843A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.224A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.717A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.235A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.178A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.043A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL E 333 " --> pdb=" O ILE E 414 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS E 385 " --> pdb=" O HIS E 374 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 315 through 320 removed outlier: 7.052A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER J 100A" --> pdb=" O ALA J 98 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 393 through 395 removed outlier: 3.610A pdb=" N SER E 393 " --> pdb=" O PHE E 361 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 423 through 424 Processing sheet with id=AE8, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AE9, first strand: chain 'J' and resid 10 through 11 removed outlier: 7.028A pdb=" N GLU J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 10 through 11 removed outlier: 7.028A pdb=" N GLU J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N CYS J 92 " --> pdb=" O TRP J 103 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N TRP J 103 " --> pdb=" O CYS J 92 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ARG J 94 " --> pdb=" O ASP J 101 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 4 through 6 Processing sheet with id=AF3, first strand: chain 'N' and resid 19 through 20 Processing sheet with id=AF4, first strand: chain 'N' and resid 53 through 54 removed outlier: 6.524A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N SER N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU N 33 " --> pdb=" O SER N 49 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR N 97 " --> pdb=" O GLN N 90 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 53 through 54 removed outlier: 6.524A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N SER N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU N 33 " --> pdb=" O SER N 49 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE N 86 " --> pdb=" O SER N 102 " (cutoff:3.500A) 599 hydrogen bonds defined for protein. 1557 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.02 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6407 1.34 - 1.46: 5219 1.46 - 1.58: 9203 1.58 - 1.70: 0 1.70 - 1.82: 216 Bond restraints: 21045 Sorted by residual: bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.20e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.95e+00 bond pdb=" C1 NAG E 601 " pdb=" O5 NAG E 601 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.93e+00 bond pdb=" C5 MAN P 7 " pdb=" O5 MAN P 7 " ideal model delta sigma weight residual 1.418 1.452 -0.034 2.00e-02 2.50e+03 2.81e+00 bond pdb=" C5 MAN b 7 " pdb=" O5 MAN b 7 " ideal model delta sigma weight residual 1.418 1.451 -0.033 2.00e-02 2.50e+03 2.67e+00 ... (remaining 21040 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 26815 1.62 - 3.24: 1352 3.24 - 4.86: 247 4.86 - 6.48: 72 6.48 - 8.10: 23 Bond angle restraints: 28509 Sorted by residual: angle pdb=" N LEU B 545 " pdb=" CA LEU B 545 " pdb=" C LEU B 545 " ideal model delta sigma weight residual 114.62 110.64 3.98 1.14e+00 7.69e-01 1.22e+01 angle pdb=" N LEU D 545 " pdb=" CA LEU D 545 " pdb=" C LEU D 545 " ideal model delta sigma weight residual 114.62 110.66 3.96 1.14e+00 7.69e-01 1.20e+01 angle pdb=" C CYS E 119 " pdb=" N VAL E 120 " pdb=" CA VAL E 120 " ideal model delta sigma weight residual 120.35 124.55 -4.20 1.39e+00 5.18e-01 9.14e+00 angle pdb=" C CYS C 119 " pdb=" N VAL C 120 " pdb=" CA VAL C 120 " ideal model delta sigma weight residual 120.35 124.39 -4.04 1.39e+00 5.18e-01 8.43e+00 angle pdb=" CA LEU D 545 " pdb=" C LEU D 545 " pdb=" N SER D 546 " ideal model delta sigma weight residual 119.71 116.41 3.30 1.17e+00 7.31e-01 7.98e+00 ... (remaining 28504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 10415 17.97 - 35.95: 872 35.95 - 53.92: 242 53.92 - 71.89: 70 71.89 - 89.86: 29 Dihedral angle restraints: 11628 sinusoidal: 4713 harmonic: 6915 Sorted by residual: dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -121.00 35.00 1 1.00e+01 1.00e-02 1.74e+01 dihedral pdb=" CB CYS E 378 " pdb=" SG CYS E 378 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual -86.00 -120.95 34.95 1 1.00e+01 1.00e-02 1.73e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -120.81 34.81 1 1.00e+01 1.00e-02 1.72e+01 ... (remaining 11625 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2736 0.059 - 0.117: 659 0.117 - 0.175: 111 0.175 - 0.234: 16 0.234 - 0.292: 24 Chirality restraints: 3546 Sorted by residual: chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.43 0.03 2.00e-02 2.50e+03 2.36e+00 chirality pdb=" C5 BMA P 3 " pdb=" C4 BMA P 3 " pdb=" C6 BMA P 3 " pdb=" O5 BMA P 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C5 BMA b 3 " pdb=" C4 BMA b 3 " pdb=" C6 BMA b 3 " pdb=" O5 BMA b 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 3543 not shown) Planarity restraints: 3531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 42 " 0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO A 43 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 42 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO E 43 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO E 43 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 43 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 42 " -0.025 5.00e-02 4.00e+02 3.87e-02 2.39e+00 pdb=" N PRO C 43 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 43 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 43 " -0.022 5.00e-02 4.00e+02 ... (remaining 3528 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2485 2.74 - 3.28: 19799 3.28 - 3.82: 32058 3.82 - 4.36: 39270 4.36 - 4.90: 69655 Nonbonded interactions: 163267 Sorted by model distance: nonbonded pdb=" N ASP A 167 " pdb=" OD1 ASP A 167 " model vdw 2.199 3.120 nonbonded pdb=" N ASP E 167 " pdb=" OD1 ASP E 167 " model vdw 2.200 3.120 nonbonded pdb=" NE2 GLN C 258 " pdb=" OG1 THR C 387 " model vdw 2.201 3.120 nonbonded pdb=" N ASP C 167 " pdb=" OD1 ASP C 167 " model vdw 2.209 3.120 nonbonded pdb=" NE2 GLN A 258 " pdb=" OG1 THR A 387 " model vdw 2.210 3.120 ... (remaining 163262 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'Y' selection = chain 'k' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'l' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'm' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' } ncs_group { reference = chain 'P' selection = chain 'b' selection = chain 'n' } 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: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 18.290 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 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 : 0.008 0.064 21219 Z= 0.364 Angle : 0.932 11.271 28989 Z= 0.432 Chirality : 0.056 0.292 3546 Planarity : 0.004 0.040 3474 Dihedral : 15.560 89.864 7050 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 7.69 % Allowed : 12.27 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.72 (0.14), residues: 2376 helix: -2.98 (0.20), residues: 432 sheet: -2.86 (0.16), residues: 750 loop : -3.38 (0.14), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 166 TYR 0.024 0.002 TYR L 91 PHE 0.015 0.002 PHE M 98 TRP 0.018 0.002 TRP A 112 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00818 / 0.36 (21045) covalent geometry : angle 0.87835 / 0.42 (28509) SS BOND : bond 0.00443 / 0.24 ( 42) SS BOND : angle 1.40502 / 0.93 ( 84) hydrogen bonds : bond 0.22749 / 14.86 ( 557) hydrogen bonds : angle 10.24541 / 6.83 ( 1557) link_ALPHA1-2 : bond 0.00296 / 0.17 ( 6) link_ALPHA1-2 : angle 2.49024 / 1.35 ( 18) link_ALPHA1-3 : bond 0.00523 / 0.30 ( 6) link_ALPHA1-3 : angle 1.69153 / 0.93 ( 18) link_ALPHA1-6 : bond 0.00261 / 0.15 ( 6) link_ALPHA1-6 : angle 1.93175 / 1.16 ( 18) link_BETA1-4 : bond 0.00772 / 0.47 ( 57) link_BETA1-4 : angle 2.06271 / 1.35 ( 171) link_NAG-ASN : bond 0.00638 / 0.39 ( 57) link_NAG-ASN : angle 3.49249 / 2.35 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 331 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.7346 (ptmt) REVERT: A 271 MET cc_start: 0.7651 (tpt) cc_final: 0.7364 (tpp) REVERT: A 469 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.6588 (mtp85) REVERT: A 475 MET cc_start: 0.8024 (mmm) cc_final: 0.7689 (mmm) REVERT: B 543 ASN cc_start: 0.8804 (m110) cc_final: 0.8444 (m110) REVERT: B 619 LEU cc_start: 0.7980 (mt) cc_final: 0.7763 (mt) REVERT: H 19 ARG cc_start: 0.8272 (ttm170) cc_final: 0.7955 (ttm170) REVERT: H 24 ASP cc_start: 0.8673 (p0) cc_final: 0.8297 (p0) REVERT: H 46 GLU cc_start: 0.8169 (tt0) cc_final: 0.7931 (tt0) REVERT: L 3 GLN cc_start: 0.8094 (mm110) cc_final: 0.7851 (mm-40) REVERT: L 81 ASP cc_start: 0.8002 (t0) cc_final: 0.7739 (t0) REVERT: L 91 TYR cc_start: 0.9152 (OUTLIER) cc_final: 0.8795 (p90) REVERT: L 100 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8265 (pm20) REVERT: C 91 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7859 (tt0) REVERT: C 155 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.7471 (ptmt) REVERT: C 271 MET cc_start: 0.7760 (tpt) cc_final: 0.7499 (tpp) REVERT: C 305 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8120 (ttmm) REVERT: C 475 MET cc_start: 0.8120 (mmm) cc_final: 0.7673 (mmm) REVERT: D 543 ASN cc_start: 0.8847 (m110) cc_final: 0.8469 (m110) REVERT: D 544 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8896 (tt) REVERT: D 654 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7200 (mt-10) REVERT: I 24 ASP cc_start: 0.8753 (p0) cc_final: 0.8503 (p0) REVERT: M 50 ARG cc_start: 0.8245 (mmm-85) cc_final: 0.7978 (mtp85) REVERT: M 100 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8275 (pm20) REVERT: E 155 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.7455 (ptmt) REVERT: E 271 MET cc_start: 0.7691 (tpt) cc_final: 0.7335 (mmp) REVERT: E 475 MET cc_start: 0.8034 (mmm) cc_final: 0.7399 (mmm) REVERT: F 543 ASN cc_start: 0.8888 (m110) cc_final: 0.8504 (m110) REVERT: F 601 LYS cc_start: 0.8445 (ttmt) cc_final: 0.8210 (mtpp) REVERT: F 632 ASP cc_start: 0.8944 (t0) cc_final: 0.8717 (t0) REVERT: F 654 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7105 (mt-10) REVERT: J 23 LYS cc_start: 0.9294 (tttm) cc_final: 0.9041 (tttt) REVERT: J 24 ASP cc_start: 0.8719 (p0) cc_final: 0.8345 (p0) REVERT: J 67 MET cc_start: 0.8695 (ptm) cc_final: 0.8241 (ptm) REVERT: N 61 ARG cc_start: 0.8507 (ptp90) cc_final: 0.8304 (ptt-90) REVERT: N 79 GLN cc_start: 0.8176 (mt0) cc_final: 0.7947 (mt0) outliers start: 161 outliers final: 83 residues processed: 464 average time/residue: 0.1680 time to fit residues: 114.9209 Evaluate side-chains 349 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 256 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 108 GLN Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 54 ASP Chi-restraints excluded: chain I residue 68 LYS Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain I residue 108 GLN Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 100 GLN Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 276 ASN Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 370 GLU Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 655 LYS Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 91 TYR Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 104 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 0.1980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 249 HIS A 302 ASN B 540 GLN B 607 ASN B 618 ASN H 3 GLN H 6 GLN H 108 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN C 66 HIS C 114 GLN C 249 HIS C 302 ASN ** C 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN D 607 ASN D 618 ASN I 3 GLN I 6 GLN I 108 GLN M 6 GLN M 79 GLN M 89 GLN E 66 HIS E 114 GLN E 249 HIS E 302 ASN F 540 GLN F 607 ASN F 618 ASN J 3 GLN J 6 GLN N 6 GLN N 79 GLN N 89 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.109053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.081074 restraints weight = 34998.073| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.49 r_work: 0.2945 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21219 Z= 0.145 Angle : 0.722 10.365 28989 Z= 0.335 Chirality : 0.046 0.254 3546 Planarity : 0.004 0.044 3474 Dihedral : 9.315 69.477 2775 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.92 % Allowed : 15.00 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.55 (0.15), residues: 2376 helix: -2.02 (0.24), residues: 408 sheet: -1.99 (0.17), residues: 735 loop : -2.72 (0.15), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 19 TYR 0.018 0.001 TYR L 91 PHE 0.014 0.001 PHE E 382 TRP 0.011 0.001 TRP A 112 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (21045) covalent geometry : angle 0.67115 / 0.32 (28509) SS BOND : bond 0.00409 / 0.24 ( 42) SS BOND : angle 1.01314 / 0.66 ( 84) hydrogen bonds : bond 0.04316 / 2.90 ( 557) hydrogen bonds : angle 6.34283 / 4.32 ( 1557) link_ALPHA1-2 : bond 0.00233 / 0.13 ( 6) link_ALPHA1-2 : angle 2.14021 / 1.18 ( 18) link_ALPHA1-3 : bond 0.00757 / 0.43 ( 6) link_ALPHA1-3 : angle 1.24346 / 0.69 ( 18) link_ALPHA1-6 : bond 0.00415 / 0.24 ( 6) link_ALPHA1-6 : angle 1.66155 / 0.99 ( 18) link_BETA1-4 : bond 0.00551 / 0.35 ( 57) link_BETA1-4 : angle 1.60711 / 1.06 ( 171) link_NAG-ASN : bond 0.00358 / 0.20 ( 57) link_NAG-ASN : angle 3.05107 / 2.06 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 306 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8547 (mmtp) cc_final: 0.7769 (mmtm) REVERT: A 91 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7955 (tt0) REVERT: A 244 THR cc_start: 0.9232 (OUTLIER) cc_final: 0.8987 (t) REVERT: A 271 MET cc_start: 0.8227 (tpt) cc_final: 0.7945 (mmm) REVERT: A 305 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8093 (ttmm) REVERT: A 434 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8312 (ttp) REVERT: A 469 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7120 (mtp85) REVERT: A 475 MET cc_start: 0.8146 (mmm) cc_final: 0.7538 (mmm) REVERT: B 543 ASN cc_start: 0.8807 (m110) cc_final: 0.8452 (m-40) REVERT: B 626 MET cc_start: 0.7470 (mtp) cc_final: 0.6491 (ttm) REVERT: B 654 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6753 (mt-10) REVERT: H 19 ARG cc_start: 0.8286 (ttm170) cc_final: 0.8001 (ttm170) REVERT: H 24 ASP cc_start: 0.8543 (p0) cc_final: 0.8271 (p0) REVERT: H 46 GLU cc_start: 0.8494 (tt0) cc_final: 0.8261 (tt0) REVERT: L 81 ASP cc_start: 0.8488 (t0) cc_final: 0.8163 (t70) REVERT: L 100 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8513 (pm20) REVERT: C 195 ASN cc_start: 0.8866 (p0) cc_final: 0.8573 (p0) REVERT: C 244 THR cc_start: 0.9181 (OUTLIER) cc_final: 0.8940 (t) REVERT: C 271 MET cc_start: 0.8205 (tpt) cc_final: 0.7642 (tpp) REVERT: C 475 MET cc_start: 0.8204 (mmm) cc_final: 0.7618 (mmm) REVERT: D 535 MET cc_start: 0.8278 (mmt) cc_final: 0.8011 (ttp) REVERT: D 543 ASN cc_start: 0.8793 (m110) cc_final: 0.8449 (m110) REVERT: D 574 LYS cc_start: 0.8182 (mttt) cc_final: 0.7941 (mttt) REVERT: D 654 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7010 (mt-10) REVERT: I 43 GLN cc_start: 0.7697 (pm20) cc_final: 0.7388 (pm20) REVERT: I 100 GLU cc_start: 0.8439 (mp0) cc_final: 0.8224 (mm-30) REVERT: M 50 ARG cc_start: 0.8632 (mmm-85) cc_final: 0.8260 (mtp85) REVERT: M 100 GLN cc_start: 0.8842 (pm20) cc_final: 0.8596 (pm20) REVERT: E 46 LYS cc_start: 0.8543 (mmtp) cc_final: 0.7934 (mttp) REVERT: E 161 MET cc_start: 0.8802 (tpt) cc_final: 0.8478 (tpt) REVERT: E 166 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8426 (mmt180) REVERT: E 271 MET cc_start: 0.8030 (tpt) cc_final: 0.7532 (mmp) REVERT: E 305 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8235 (ttpp) REVERT: E 373 THR cc_start: 0.9239 (OUTLIER) cc_final: 0.9025 (m) REVERT: E 469 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.6464 (ptp90) REVERT: E 475 MET cc_start: 0.8106 (mmm) cc_final: 0.7232 (mmm) REVERT: F 542 ARG cc_start: 0.8630 (ttm110) cc_final: 0.8394 (ttm110) REVERT: F 543 ASN cc_start: 0.8837 (m110) cc_final: 0.8414 (m110) REVERT: F 588 ARG cc_start: 0.8073 (ttm-80) cc_final: 0.7678 (ttm-80) REVERT: F 601 LYS cc_start: 0.8397 (ttmt) cc_final: 0.8161 (mtpp) REVERT: F 654 GLU cc_start: 0.7606 (mm-30) cc_final: 0.6977 (mt-10) REVERT: J 24 ASP cc_start: 0.8662 (p0) cc_final: 0.8462 (p0) REVERT: J 100 GLU cc_start: 0.8412 (mp0) cc_final: 0.8072 (mt-10) REVERT: N 24 ARG cc_start: 0.7815 (mtp-110) cc_final: 0.7511 (ttm110) REVERT: N 81 ASP cc_start: 0.8556 (t0) cc_final: 0.8236 (t0) outliers start: 103 outliers final: 47 residues processed: 389 average time/residue: 0.1509 time to fit residues: 89.1651 Evaluate side-chains 322 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 264 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 54 ASP Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 276 ASN Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 469 ARG Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain N residue 96 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 213 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 193 optimal weight: 0.8980 chunk 231 optimal weight: 1.9990 chunk 152 optimal weight: 8.9990 chunk 192 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 101 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN A 293 GLN B 618 ASN B 625 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 GLN D 618 ASN M 6 GLN M 37 GLN E 258 GLN F 618 ASN N 6 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.107590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.079406 restraints weight = 35495.221| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 3.51 r_work: 0.2914 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 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 : 0.005 0.058 21219 Z= 0.215 Angle : 0.788 18.439 28989 Z= 0.352 Chirality : 0.052 0.790 3546 Planarity : 0.004 0.048 3474 Dihedral : 7.834 57.254 2677 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 5.54 % Allowed : 17.05 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.11 (0.16), residues: 2376 helix: -1.26 (0.27), residues: 384 sheet: -1.76 (0.18), residues: 750 loop : -2.55 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 24 TYR 0.023 0.002 TYR L 91 PHE 0.014 0.002 PHE I 91 TRP 0.014 0.001 TRP A 112 HIS 0.003 0.001 HIS C 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.21 (21045) covalent geometry : angle 0.70761 / 0.33 (28509) SS BOND : bond 0.00418 / 0.23 ( 42) SS BOND : angle 1.28275 / 0.82 ( 84) hydrogen bonds : bond 0.04110 / 2.77 ( 557) hydrogen bonds : angle 5.79753 / 3.98 ( 1557) link_ALPHA1-2 : bond 0.00247 / 0.15 ( 6) link_ALPHA1-2 : angle 2.00983 / 1.11 ( 18) link_ALPHA1-3 : bond 0.00744 / 0.43 ( 6) link_ALPHA1-3 : angle 1.21391 / 0.68 ( 18) link_ALPHA1-6 : bond 0.00317 / 0.18 ( 6) link_ALPHA1-6 : angle 1.67986 / 1.00 ( 18) link_BETA1-4 : bond 0.00483 / 0.30 ( 57) link_BETA1-4 : angle 1.61517 / 1.07 ( 171) link_NAG-ASN : bond 0.00509 / 0.31 ( 57) link_NAG-ASN : angle 4.17491 / 2.80 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 277 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8499 (mmtp) cc_final: 0.7713 (mttm) REVERT: A 244 THR cc_start: 0.9284 (OUTLIER) cc_final: 0.9049 (t) REVERT: A 246 GLN cc_start: 0.8081 (tp40) cc_final: 0.7683 (pm20) REVERT: A 271 MET cc_start: 0.8233 (tpt) cc_final: 0.7923 (mmm) REVERT: A 305 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8150 (ttmm) REVERT: A 469 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7001 (mtp85) REVERT: A 475 MET cc_start: 0.8140 (mmm) cc_final: 0.7566 (mmm) REVERT: B 543 ASN cc_start: 0.8877 (m110) cc_final: 0.8432 (m110) REVERT: B 588 ARG cc_start: 0.8083 (ttm-80) cc_final: 0.7803 (ttm-80) REVERT: B 626 MET cc_start: 0.7149 (mtp) cc_final: 0.6689 (mtp) REVERT: B 654 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6705 (mt-10) REVERT: H 24 ASP cc_start: 0.8698 (p0) cc_final: 0.8445 (p0) REVERT: H 46 GLU cc_start: 0.8492 (tt0) cc_final: 0.8232 (tt0) REVERT: L 81 ASP cc_start: 0.8566 (t0) cc_final: 0.8233 (t70) REVERT: L 100 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8482 (pm20) REVERT: C 211 GLU cc_start: 0.9079 (OUTLIER) cc_final: 0.8757 (tp30) REVERT: C 244 THR cc_start: 0.9257 (OUTLIER) cc_final: 0.9028 (t) REVERT: C 246 GLN cc_start: 0.8008 (tp40) cc_final: 0.7580 (pm20) REVERT: C 271 MET cc_start: 0.8164 (tpt) cc_final: 0.7613 (tpp) REVERT: C 428 GLN cc_start: 0.8571 (mt0) cc_final: 0.7972 (mm-40) REVERT: C 434 MET cc_start: 0.8774 (ttt) cc_final: 0.8547 (ttp) REVERT: C 475 MET cc_start: 0.8301 (mmm) cc_final: 0.7626 (mmm) REVERT: D 535 MET cc_start: 0.8307 (mmt) cc_final: 0.8009 (ttp) REVERT: D 574 LYS cc_start: 0.8118 (mttt) cc_final: 0.7892 (mttt) REVERT: D 654 GLU cc_start: 0.7538 (mm-30) cc_final: 0.6980 (mt-10) REVERT: I 43 GLN cc_start: 0.7655 (pm20) cc_final: 0.7251 (pm20) REVERT: I 100 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8242 (mm-30) REVERT: M 50 ARG cc_start: 0.8617 (mmm-85) cc_final: 0.8276 (mtp85) REVERT: E 153 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8051 (tp30) REVERT: E 211 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.8632 (tp30) REVERT: E 271 MET cc_start: 0.7980 (tpt) cc_final: 0.7459 (mmp) REVERT: E 305 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8236 (ttpp) REVERT: E 434 MET cc_start: 0.8813 (ttp) cc_final: 0.8592 (ttt) REVERT: E 469 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.6529 (ptp90) REVERT: E 475 MET cc_start: 0.8213 (mmm) cc_final: 0.7323 (mmm) REVERT: F 543 ASN cc_start: 0.8811 (m110) cc_final: 0.8366 (m110) REVERT: F 654 GLU cc_start: 0.7620 (mm-30) cc_final: 0.6976 (mt-10) REVERT: J 24 ASP cc_start: 0.8712 (p0) cc_final: 0.8509 (p0) REVERT: J 81 GLU cc_start: 0.7732 (tt0) cc_final: 0.7012 (mp0) REVERT: J 100 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8065 (mt-10) REVERT: N 81 ASP cc_start: 0.8630 (t0) cc_final: 0.8286 (t0) outliers start: 116 outliers final: 67 residues processed: 364 average time/residue: 0.1581 time to fit residues: 86.6559 Evaluate side-chains 344 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 265 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 54 ASP Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 106 MET Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 469 ARG Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 106 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 143 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 170 optimal weight: 0.9990 chunk 222 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 226 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 chunk 40 optimal weight: 10.0000 chunk 135 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 618 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN M 37 GLN N 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.109220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.081168 restraints weight = 35193.069| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.51 r_work: 0.2949 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21219 Z= 0.143 Angle : 0.727 16.634 28989 Z= 0.324 Chirality : 0.049 0.567 3546 Planarity : 0.003 0.035 3474 Dihedral : 7.371 59.849 2663 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 5.30 % Allowed : 18.58 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.85 (0.16), residues: 2376 helix: -1.19 (0.27), residues: 402 sheet: -1.48 (0.18), residues: 747 loop : -2.41 (0.16), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 500 TYR 0.018 0.001 TYR C 486 PHE 0.012 0.001 PHE E 382 TRP 0.013 0.001 TRP A 112 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (21045) covalent geometry : angle 0.65464 / 0.31 (28509) SS BOND : bond 0.00326 / 0.18 ( 42) SS BOND : angle 0.99987 / 0.65 ( 84) hydrogen bonds : bond 0.03562 / 2.39 ( 557) hydrogen bonds : angle 5.34284 / 3.67 ( 1557) link_ALPHA1-2 : bond 0.00235 / 0.14 ( 6) link_ALPHA1-2 : angle 1.91906 / 1.06 ( 18) link_ALPHA1-3 : bond 0.00682 / 0.39 ( 6) link_ALPHA1-3 : angle 1.24221 / 0.70 ( 18) link_ALPHA1-6 : bond 0.00326 / 0.19 ( 6) link_ALPHA1-6 : angle 1.57454 / 0.94 ( 18) link_BETA1-4 : bond 0.00478 / 0.29 ( 57) link_BETA1-4 : angle 1.47983 / 0.99 ( 171) link_NAG-ASN : bond 0.00530 / 0.31 ( 57) link_NAG-ASN : angle 3.81360 / 2.55 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 282 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8509 (mmtp) cc_final: 0.7707 (mttm) REVERT: A 91 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7713 (tt0) REVERT: A 244 THR cc_start: 0.9266 (OUTLIER) cc_final: 0.9058 (t) REVERT: A 246 GLN cc_start: 0.8075 (tp40) cc_final: 0.7643 (pm20) REVERT: A 271 MET cc_start: 0.8240 (tpt) cc_final: 0.7963 (mmm) REVERT: A 305 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8079 (ttmm) REVERT: A 426 MET cc_start: 0.9001 (mmm) cc_final: 0.8723 (mmm) REVERT: A 469 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7147 (mtp85) REVERT: A 475 MET cc_start: 0.8084 (mmm) cc_final: 0.7445 (mmm) REVERT: B 543 ASN cc_start: 0.8837 (m110) cc_final: 0.8410 (m110) REVERT: B 654 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6673 (mt-10) REVERT: H 24 ASP cc_start: 0.8645 (p0) cc_final: 0.8396 (p0) REVERT: H 46 GLU cc_start: 0.8344 (tt0) cc_final: 0.8091 (tt0) REVERT: H 64 GLN cc_start: 0.8854 (tp40) cc_final: 0.8539 (tp-100) REVERT: L 24 ARG cc_start: 0.7729 (mtp-110) cc_final: 0.7403 (ttm110) REVERT: L 50 ARG cc_start: 0.8646 (mtp85) cc_final: 0.8323 (mtp85) REVERT: L 81 ASP cc_start: 0.8546 (t0) cc_final: 0.8236 (t70) REVERT: C 46 LYS cc_start: 0.8538 (mmtm) cc_final: 0.8268 (mmtm) REVERT: C 150 MET cc_start: 0.8120 (tpt) cc_final: 0.7886 (tpp) REVERT: C 195 ASN cc_start: 0.8771 (p0) cc_final: 0.8511 (p0) REVERT: C 211 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8752 (tp30) REVERT: C 244 THR cc_start: 0.9266 (OUTLIER) cc_final: 0.9042 (t) REVERT: C 246 GLN cc_start: 0.7980 (tp40) cc_final: 0.7531 (pm20) REVERT: C 271 MET cc_start: 0.8168 (tpt) cc_final: 0.7839 (mmm) REVERT: C 428 GLN cc_start: 0.8509 (mt0) cc_final: 0.7904 (mm-40) REVERT: C 475 MET cc_start: 0.8212 (mmm) cc_final: 0.7604 (mmm) REVERT: D 535 MET cc_start: 0.8316 (mmt) cc_final: 0.8065 (ttp) REVERT: D 654 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7034 (mt-10) REVERT: I 19 ARG cc_start: 0.8293 (ttm170) cc_final: 0.8042 (ttm170) REVERT: I 43 GLN cc_start: 0.7692 (pm20) cc_final: 0.7300 (pm20) REVERT: I 48 MET cc_start: 0.8792 (ttm) cc_final: 0.8430 (ttm) REVERT: I 54 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8003 (t0) REVERT: I 100 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8208 (mm-30) REVERT: M 33 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8347 (tp) REVERT: M 50 ARG cc_start: 0.8583 (mmm-85) cc_final: 0.8235 (mtp85) REVERT: M 100 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8509 (pm20) REVERT: E 153 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8164 (tp30) REVERT: E 211 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.8632 (tp30) REVERT: E 246 GLN cc_start: 0.8058 (tp40) cc_final: 0.7712 (pm20) REVERT: E 271 MET cc_start: 0.7973 (tpt) cc_final: 0.7459 (mmp) REVERT: E 469 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.6509 (ptp90) REVERT: E 475 MET cc_start: 0.8106 (mmm) cc_final: 0.7217 (mmm) REVERT: F 535 MET cc_start: 0.8564 (mmm) cc_final: 0.8090 (mmm) REVERT: F 543 ASN cc_start: 0.8762 (m110) cc_final: 0.8341 (m110) REVERT: F 626 MET cc_start: 0.7226 (mtp) cc_final: 0.6450 (ttm) REVERT: F 633 LYS cc_start: 0.9010 (pttm) cc_final: 0.8785 (pttm) REVERT: F 654 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7041 (mt-10) REVERT: J 81 GLU cc_start: 0.7643 (tt0) cc_final: 0.6951 (mp0) REVERT: J 100 GLU cc_start: 0.8406 (mp0) cc_final: 0.8054 (mt-10) REVERT: N 24 ARG cc_start: 0.7618 (mtp-110) cc_final: 0.7277 (ttm110) REVERT: N 81 ASP cc_start: 0.8640 (t0) cc_final: 0.8322 (t0) outliers start: 111 outliers final: 64 residues processed: 368 average time/residue: 0.1594 time to fit residues: 89.3887 Evaluate side-chains 353 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 276 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 54 ASP Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 100 GLN Chi-restraints excluded: chain M residue 106 MET Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 469 ARG Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 67 MET Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 106 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 145 optimal weight: 0.4980 chunk 104 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 229 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 156 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 618 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN D 618 ASN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 618 ASN N 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.107774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.079719 restraints weight = 35163.895| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.50 r_work: 0.2924 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 21219 Z= 0.202 Angle : 0.751 16.804 28989 Z= 0.335 Chirality : 0.049 0.521 3546 Planarity : 0.004 0.038 3474 Dihedral : 7.156 59.249 2650 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 5.11 % Allowed : 19.63 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.67 (0.16), residues: 2376 helix: -0.95 (0.27), residues: 390 sheet: -1.39 (0.18), residues: 750 loop : -2.31 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 24 TYR 0.021 0.002 TYR L 91 PHE 0.014 0.002 PHE I 91 TRP 0.012 0.001 TRP A 112 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.20 (21045) covalent geometry : angle 0.68021 / 0.32 (28509) SS BOND : bond 0.00524 / 0.28 ( 42) SS BOND : angle 1.35534 / 0.87 ( 84) hydrogen bonds : bond 0.03627 / 2.44 ( 557) hydrogen bonds : angle 5.34297 / 3.66 ( 1557) link_ALPHA1-2 : bond 0.00237 / 0.14 ( 6) link_ALPHA1-2 : angle 1.94347 / 1.07 ( 18) link_ALPHA1-3 : bond 0.00704 / 0.41 ( 6) link_ALPHA1-3 : angle 1.20406 / 0.67 ( 18) link_ALPHA1-6 : bond 0.00273 / 0.16 ( 6) link_ALPHA1-6 : angle 1.63051 / 0.97 ( 18) link_BETA1-4 : bond 0.00463 / 0.29 ( 57) link_BETA1-4 : angle 1.49281 / 0.99 ( 171) link_NAG-ASN : bond 0.00554 / 0.33 ( 57) link_NAG-ASN : angle 3.79657 / 2.56 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 272 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8487 (mmtp) cc_final: 0.7702 (mttm) REVERT: A 211 GLU cc_start: 0.9067 (OUTLIER) cc_final: 0.8710 (tp30) REVERT: A 265 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8742 (mp) REVERT: A 271 MET cc_start: 0.8216 (tpt) cc_final: 0.7919 (mmm) REVERT: A 305 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8184 (ttmm) REVERT: A 426 MET cc_start: 0.9026 (mmm) cc_final: 0.8770 (mmm) REVERT: A 469 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7153 (mtp85) REVERT: A 475 MET cc_start: 0.8149 (mmm) cc_final: 0.7540 (mmm) REVERT: B 543 ASN cc_start: 0.8878 (m110) cc_final: 0.8458 (m110) REVERT: B 626 MET cc_start: 0.7305 (mtp) cc_final: 0.6213 (ttm) REVERT: B 654 GLU cc_start: 0.7259 (mm-30) cc_final: 0.6616 (mt-10) REVERT: H 24 ASP cc_start: 0.8674 (p0) cc_final: 0.8432 (p0) REVERT: H 46 GLU cc_start: 0.8453 (tt0) cc_final: 0.8196 (tt0) REVERT: H 64 GLN cc_start: 0.8877 (tp40) cc_final: 0.8583 (tp40) REVERT: L 50 ARG cc_start: 0.8650 (mtp85) cc_final: 0.8384 (mtp85) REVERT: L 74 THR cc_start: 0.8551 (p) cc_final: 0.8322 (t) REVERT: L 81 ASP cc_start: 0.8579 (t0) cc_final: 0.8252 (t70) REVERT: C 46 LYS cc_start: 0.8505 (mmtm) cc_final: 0.8227 (mmtm) REVERT: C 195 ASN cc_start: 0.8762 (p0) cc_final: 0.8521 (p0) REVERT: C 211 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8749 (tp30) REVERT: C 244 THR cc_start: 0.9290 (OUTLIER) cc_final: 0.9081 (t) REVERT: C 246 GLN cc_start: 0.8028 (tp40) cc_final: 0.7587 (pm20) REVERT: C 271 MET cc_start: 0.8182 (tpt) cc_final: 0.7692 (tpp) REVERT: C 428 GLN cc_start: 0.8580 (mt0) cc_final: 0.7953 (mm-40) REVERT: C 475 MET cc_start: 0.8244 (mmm) cc_final: 0.7594 (mmm) REVERT: D 535 MET cc_start: 0.8342 (mmt) cc_final: 0.8093 (ttp) REVERT: D 626 MET cc_start: 0.7100 (mtp) cc_final: 0.6425 (ttm) REVERT: D 654 GLU cc_start: 0.7501 (mm-30) cc_final: 0.6993 (mt-10) REVERT: I 3 GLN cc_start: 0.7043 (tp-100) cc_final: 0.6649 (tp-100) REVERT: I 43 GLN cc_start: 0.7709 (pm20) cc_final: 0.7319 (pm20) REVERT: I 48 MET cc_start: 0.8868 (ttm) cc_final: 0.8414 (ttm) REVERT: I 54 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8151 (t0) REVERT: I 100 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8241 (mm-30) REVERT: M 4 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.7816 (mmm) REVERT: M 33 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8344 (tp) REVERT: M 50 ARG cc_start: 0.8568 (mmm-85) cc_final: 0.8258 (mtp85) REVERT: M 100 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.8519 (pm20) REVERT: E 150 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.8029 (ttm) REVERT: E 153 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8169 (tp30) REVERT: E 211 GLU cc_start: 0.9104 (OUTLIER) cc_final: 0.8624 (tp30) REVERT: E 246 GLN cc_start: 0.8162 (tp40) cc_final: 0.7736 (pm20) REVERT: E 271 MET cc_start: 0.8043 (tpt) cc_final: 0.7497 (mmp) REVERT: E 469 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.6616 (ptp90) REVERT: E 475 MET cc_start: 0.8126 (mmm) cc_final: 0.7308 (mmm) REVERT: F 543 ASN cc_start: 0.8780 (m110) cc_final: 0.8331 (m110) REVERT: F 626 MET cc_start: 0.7256 (mtp) cc_final: 0.6436 (ttm) REVERT: F 633 LYS cc_start: 0.8995 (pttm) cc_final: 0.8766 (pttm) REVERT: F 654 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7068 (mt-10) REVERT: J 81 GLU cc_start: 0.7657 (tt0) cc_final: 0.6966 (mp0) REVERT: J 100 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8066 (mt-10) REVERT: N 24 ARG cc_start: 0.7587 (mtp-110) cc_final: 0.7239 (ttm110) REVERT: N 81 ASP cc_start: 0.8663 (t0) cc_final: 0.8332 (t0) outliers start: 107 outliers final: 66 residues processed: 353 average time/residue: 0.1616 time to fit residues: 86.6752 Evaluate side-chains 346 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 264 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 54 ASP Chi-restraints excluded: chain I residue 76 ARG Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain M residue 4 MET Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 100 GLN Chi-restraints excluded: chain M residue 106 MET Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 469 ARG Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 106 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 14 optimal weight: 2.9990 chunk 233 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 132 optimal weight: 0.4980 chunk 98 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 217 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 232 optimal weight: 0.6980 chunk 208 optimal weight: 6.9990 chunk 200 optimal weight: 0.0030 overall best weight: 0.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN A 258 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN N 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.110551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.082625 restraints weight = 34898.730| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.50 r_work: 0.2974 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21219 Z= 0.124 Angle : 0.697 16.207 28989 Z= 0.309 Chirality : 0.047 0.448 3546 Planarity : 0.003 0.034 3474 Dihedral : 6.844 59.902 2648 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.44 % Allowed : 20.34 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.16), residues: 2376 helix: -0.70 (0.27), residues: 384 sheet: -1.10 (0.19), residues: 738 loop : -2.14 (0.16), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 24 TYR 0.015 0.001 TYR A 486 PHE 0.011 0.001 PHE E 382 TRP 0.011 0.001 TRP E 112 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (21045) covalent geometry : angle 0.63365 / 0.29 (28509) SS BOND : bond 0.00385 / 0.20 ( 42) SS BOND : angle 0.94339 / 0.62 ( 84) hydrogen bonds : bond 0.03212 / 2.15 ( 557) hydrogen bonds : angle 4.98497 / 3.43 ( 1557) link_ALPHA1-2 : bond 0.00256 / 0.15 ( 6) link_ALPHA1-2 : angle 1.79931 / 1.00 ( 18) link_ALPHA1-3 : bond 0.00637 / 0.37 ( 6) link_ALPHA1-3 : angle 1.26320 / 0.72 ( 18) link_ALPHA1-6 : bond 0.00345 / 0.19 ( 6) link_ALPHA1-6 : angle 1.53289 / 0.92 ( 18) link_BETA1-4 : bond 0.00483 / 0.30 ( 57) link_BETA1-4 : angle 1.37403 / 0.92 ( 171) link_NAG-ASN : bond 0.00517 / 0.30 ( 57) link_NAG-ASN : angle 3.50846 / 2.34 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 289 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8494 (mmtp) cc_final: 0.7704 (mttm) REVERT: A 211 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8684 (tp30) REVERT: A 265 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8670 (mt) REVERT: A 271 MET cc_start: 0.8179 (tpt) cc_final: 0.7911 (mmm) REVERT: A 469 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.6973 (mtp85) REVERT: A 475 MET cc_start: 0.8063 (mmm) cc_final: 0.7373 (mmm) REVERT: B 543 ASN cc_start: 0.8847 (m110) cc_final: 0.8456 (m110) REVERT: B 626 MET cc_start: 0.6968 (mtp) cc_final: 0.6262 (ttm) REVERT: B 654 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6547 (mt-10) REVERT: H 24 ASP cc_start: 0.8635 (p0) cc_final: 0.8403 (p0) REVERT: H 46 GLU cc_start: 0.8368 (tt0) cc_final: 0.8117 (tt0) REVERT: H 64 GLN cc_start: 0.8902 (tp40) cc_final: 0.8583 (tp-100) REVERT: L 24 ARG cc_start: 0.7654 (mtp-110) cc_final: 0.7390 (ttm110) REVERT: L 50 ARG cc_start: 0.8626 (mtp85) cc_final: 0.8344 (mtp85) REVERT: L 74 THR cc_start: 0.8580 (p) cc_final: 0.8373 (t) REVERT: L 81 ASP cc_start: 0.8519 (t0) cc_final: 0.8192 (t70) REVERT: C 35 TRP cc_start: 0.8530 (m100) cc_final: 0.8084 (m-90) REVERT: C 46 LYS cc_start: 0.8546 (mmtm) cc_final: 0.8215 (mmtm) REVERT: C 155 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.7224 (ptmt) REVERT: C 211 GLU cc_start: 0.9106 (OUTLIER) cc_final: 0.8708 (mm-30) REVERT: C 246 GLN cc_start: 0.7948 (tp40) cc_final: 0.7571 (pm20) REVERT: C 271 MET cc_start: 0.8247 (tpt) cc_final: 0.7961 (mmm) REVERT: C 428 GLN cc_start: 0.8589 (mt0) cc_final: 0.7954 (mm-40) REVERT: C 475 MET cc_start: 0.8033 (mmm) cc_final: 0.7450 (mmm) REVERT: D 535 MET cc_start: 0.8337 (mmt) cc_final: 0.8105 (ttp) REVERT: D 626 MET cc_start: 0.6945 (mtp) cc_final: 0.6556 (ttm) REVERT: D 654 GLU cc_start: 0.7431 (mm-30) cc_final: 0.6981 (mt-10) REVERT: I 3 GLN cc_start: 0.7094 (tp-100) cc_final: 0.6573 (tp-100) REVERT: I 43 GLN cc_start: 0.7713 (pm20) cc_final: 0.7363 (pm20) REVERT: I 48 MET cc_start: 0.8810 (ttm) cc_final: 0.8415 (ttm) REVERT: I 54 ASP cc_start: 0.8514 (OUTLIER) cc_final: 0.8261 (t0) REVERT: I 80 MET cc_start: 0.8459 (tmm) cc_final: 0.8202 (tmm) REVERT: I 100 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8195 (mm-30) REVERT: M 24 ARG cc_start: 0.7756 (mtp-110) cc_final: 0.7449 (ttm110) REVERT: M 33 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8311 (tp) REVERT: M 50 ARG cc_start: 0.8563 (mmm-85) cc_final: 0.8237 (mtp85) REVERT: E 153 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8183 (tp30) REVERT: E 211 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.8647 (tp30) REVERT: E 246 GLN cc_start: 0.8180 (tp40) cc_final: 0.7735 (pm20) REVERT: E 271 MET cc_start: 0.8040 (tpt) cc_final: 0.7476 (mmp) REVERT: E 469 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.6427 (ptp90) REVERT: E 475 MET cc_start: 0.8034 (mmm) cc_final: 0.7204 (mmm) REVERT: F 535 MET cc_start: 0.8494 (mmm) cc_final: 0.8258 (mmm) REVERT: F 542 ARG cc_start: 0.8462 (ttm110) cc_final: 0.8261 (ttm110) REVERT: F 543 ASN cc_start: 0.8691 (m110) cc_final: 0.8283 (m110) REVERT: F 626 MET cc_start: 0.7196 (mtp) cc_final: 0.6892 (ttm) REVERT: F 633 LYS cc_start: 0.9013 (pttm) cc_final: 0.8793 (pttm) REVERT: F 654 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7029 (mt-10) REVERT: J 52 ILE cc_start: 0.8242 (mp) cc_final: 0.7991 (mt) REVERT: J 81 GLU cc_start: 0.7610 (tt0) cc_final: 0.6937 (mp0) REVERT: J 100 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8041 (mt-10) REVERT: N 24 ARG cc_start: 0.7509 (mtp-110) cc_final: 0.7220 (ttm110) REVERT: N 81 ASP cc_start: 0.8649 (t0) cc_final: 0.8338 (t0) outliers start: 93 outliers final: 53 residues processed: 360 average time/residue: 0.1590 time to fit residues: 86.5356 Evaluate side-chains 340 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 275 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 54 ASP Chi-restraints excluded: chain I residue 76 ARG Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain M residue 6 GLN Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 106 MET Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 469 ARG Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain J residue 67 MET Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain N residue 6 GLN Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 106 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 198 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 211 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 184 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 159 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 618 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 618 ASN F 618 ASN N 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.111018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.086380 restraints weight = 34941.357| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.90 r_work: 0.3034 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21219 Z= 0.141 Angle : 0.713 16.225 28989 Z= 0.318 Chirality : 0.048 0.503 3546 Planarity : 0.003 0.035 3474 Dihedral : 6.594 59.470 2637 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.11 % Allowed : 20.68 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.16), residues: 2376 helix: -0.69 (0.27), residues: 390 sheet: -1.02 (0.19), residues: 738 loop : -2.06 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 24 TYR 0.014 0.001 TYR A 486 PHE 0.012 0.001 PHE C 382 TRP 0.010 0.001 TRP A 112 HIS 0.004 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (21045) covalent geometry : angle 0.64891 / 0.30 (28509) SS BOND : bond 0.00405 / 0.21 ( 42) SS BOND : angle 1.49374 / 0.93 ( 84) hydrogen bonds : bond 0.03216 / 2.15 ( 557) hydrogen bonds : angle 4.94674 / 3.40 ( 1557) link_ALPHA1-2 : bond 0.00212 / 0.12 ( 6) link_ALPHA1-2 : angle 1.80752 / 1.00 ( 18) link_ALPHA1-3 : bond 0.00645 / 0.37 ( 6) link_ALPHA1-3 : angle 1.23017 / 0.69 ( 18) link_ALPHA1-6 : bond 0.00320 / 0.18 ( 6) link_ALPHA1-6 : angle 1.54316 / 0.92 ( 18) link_BETA1-4 : bond 0.00473 / 0.29 ( 57) link_BETA1-4 : angle 1.37601 / 0.91 ( 171) link_NAG-ASN : bond 0.00480 / 0.27 ( 57) link_NAG-ASN : angle 3.49211 / 2.34 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 275 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8594 (mmm) cc_final: 0.7975 (mmm) REVERT: A 265 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8902 (mt) REVERT: A 469 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7757 (mtp85) REVERT: A 475 MET cc_start: 0.7992 (mmm) cc_final: 0.7736 (mmm) REVERT: B 543 ASN cc_start: 0.8894 (m110) cc_final: 0.8572 (m110) REVERT: B 626 MET cc_start: 0.7124 (mtp) cc_final: 0.6817 (ttm) REVERT: B 654 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6762 (mt-10) REVERT: H 24 ASP cc_start: 0.8389 (p0) cc_final: 0.8165 (p0) REVERT: H 64 GLN cc_start: 0.8840 (tp40) cc_final: 0.8603 (tp-100) REVERT: L 81 ASP cc_start: 0.8144 (t0) cc_final: 0.7852 (t70) REVERT: C 35 TRP cc_start: 0.8710 (m100) cc_final: 0.8331 (m-90) REVERT: C 155 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.7720 (ptmt) REVERT: C 428 GLN cc_start: 0.8493 (mt0) cc_final: 0.8162 (mm-40) REVERT: C 475 MET cc_start: 0.8108 (mmm) cc_final: 0.7885 (mmm) REVERT: D 654 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7325 (mt-10) REVERT: I 3 GLN cc_start: 0.7179 (tp-100) cc_final: 0.6950 (tp-100) REVERT: M 33 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8467 (tp) REVERT: M 50 ARG cc_start: 0.8487 (mmm-85) cc_final: 0.8240 (mtp85) REVERT: M 100 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8384 (pm20) REVERT: E 153 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8315 (tp30) REVERT: E 211 GLU cc_start: 0.9096 (OUTLIER) cc_final: 0.8839 (tp30) REVERT: E 271 MET cc_start: 0.8132 (tpt) cc_final: 0.7752 (mmp) REVERT: E 469 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7070 (ptp90) REVERT: E 475 MET cc_start: 0.7877 (mmm) cc_final: 0.7505 (mmm) REVERT: F 543 ASN cc_start: 0.8684 (m110) cc_final: 0.8356 (m110) REVERT: F 654 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7349 (mt-10) REVERT: J 81 GLU cc_start: 0.7655 (tt0) cc_final: 0.7348 (mp0) REVERT: J 100 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7990 (mt-10) REVERT: N 24 ARG cc_start: 0.7710 (mtp-110) cc_final: 0.7498 (ttm110) REVERT: N 81 ASP cc_start: 0.8398 (t0) cc_final: 0.8141 (t0) outliers start: 86 outliers final: 58 residues processed: 340 average time/residue: 0.1548 time to fit residues: 78.9975 Evaluate side-chains 337 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 270 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 70 ILE Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 76 ARG Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 100 GLN Chi-restraints excluded: chain M residue 106 MET Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 469 ARG Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain J residue 67 MET Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 106 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 119 optimal weight: 4.9990 chunk 207 optimal weight: 0.0270 chunk 3 optimal weight: 2.9990 chunk 195 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 233 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 overall best weight: 1.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.110685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.086099 restraints weight = 35066.642| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.91 r_work: 0.3042 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21219 Z= 0.152 Angle : 0.727 16.495 28989 Z= 0.325 Chirality : 0.048 0.452 3546 Planarity : 0.003 0.036 3474 Dihedral : 6.573 59.829 2634 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 4.20 % Allowed : 20.77 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.17), residues: 2376 helix: -0.59 (0.27), residues: 390 sheet: -0.97 (0.19), residues: 747 loop : -2.00 (0.16), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 24 TYR 0.017 0.001 TYR A 486 PHE 0.012 0.001 PHE C 382 TRP 0.011 0.001 TRP A 112 HIS 0.006 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (21045) covalent geometry : angle 0.66666 / 0.31 (28509) SS BOND : bond 0.00363 / 0.19 ( 42) SS BOND : angle 1.45117 / 0.90 ( 84) hydrogen bonds : bond 0.03259 / 2.18 ( 557) hydrogen bonds : angle 4.93828 / 3.38 ( 1557) link_ALPHA1-2 : bond 0.00227 / 0.13 ( 6) link_ALPHA1-2 : angle 1.81142 / 1.00 ( 18) link_ALPHA1-3 : bond 0.00651 / 0.38 ( 6) link_ALPHA1-3 : angle 1.22816 / 0.69 ( 18) link_ALPHA1-6 : bond 0.00307 / 0.18 ( 6) link_ALPHA1-6 : angle 1.56180 / 0.93 ( 18) link_BETA1-4 : bond 0.00463 / 0.29 ( 57) link_BETA1-4 : angle 1.36912 / 0.91 ( 171) link_NAG-ASN : bond 0.00516 / 0.30 ( 57) link_NAG-ASN : angle 3.44651 / 2.30 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 273 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8597 (mmm) cc_final: 0.8017 (mmm) REVERT: A 265 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8892 (mt) REVERT: A 469 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.7397 (mtp85) REVERT: A 475 MET cc_start: 0.8048 (mmm) cc_final: 0.7732 (mmm) REVERT: B 543 ASN cc_start: 0.8917 (m110) cc_final: 0.8592 (m110) REVERT: B 626 MET cc_start: 0.7069 (mtp) cc_final: 0.6695 (ttm) REVERT: B 654 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6740 (mt-10) REVERT: H 24 ASP cc_start: 0.8421 (p0) cc_final: 0.8108 (p0) REVERT: H 57 LYS cc_start: 0.9294 (OUTLIER) cc_final: 0.9093 (mmtp) REVERT: H 64 GLN cc_start: 0.8834 (tp40) cc_final: 0.8588 (tp40) REVERT: L 81 ASP cc_start: 0.8196 (t0) cc_final: 0.7917 (t0) REVERT: C 155 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.7995 (ptmt) REVERT: C 246 GLN cc_start: 0.8430 (pm20) cc_final: 0.8070 (tp-100) REVERT: C 428 GLN cc_start: 0.8519 (mt0) cc_final: 0.8129 (mm-40) REVERT: C 475 MET cc_start: 0.8154 (mmm) cc_final: 0.7851 (mmm) REVERT: D 654 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7331 (mt-10) REVERT: I 3 GLN cc_start: 0.7207 (tp-100) cc_final: 0.6938 (tp-100) REVERT: I 43 GLN cc_start: 0.7762 (pm20) cc_final: 0.7346 (pm20) REVERT: M 24 ARG cc_start: 0.7832 (mtp-110) cc_final: 0.7619 (ttm110) REVERT: M 33 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8401 (tp) REVERT: M 50 ARG cc_start: 0.8506 (mmm-85) cc_final: 0.8243 (mtp85) REVERT: M 76 LYS cc_start: 0.8317 (mmmm) cc_final: 0.8045 (mmmm) REVERT: M 100 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8432 (pm20) REVERT: E 46 LYS cc_start: 0.8685 (mmtp) cc_final: 0.7836 (mttp) REVERT: E 153 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8311 (tp30) REVERT: E 211 GLU cc_start: 0.9114 (OUTLIER) cc_final: 0.8814 (tp30) REVERT: E 246 GLN cc_start: 0.8428 (pm20) cc_final: 0.8077 (tp-100) REVERT: E 271 MET cc_start: 0.8132 (tpt) cc_final: 0.7724 (mmp) REVERT: E 469 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7080 (ptp90) REVERT: E 475 MET cc_start: 0.7959 (mmm) cc_final: 0.7530 (mmm) REVERT: F 543 ASN cc_start: 0.8680 (m110) cc_final: 0.8360 (m110) REVERT: F 654 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7415 (mt-10) REVERT: J 81 GLU cc_start: 0.7653 (tt0) cc_final: 0.7296 (mp0) REVERT: J 100 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8039 (mt-10) REVERT: N 24 ARG cc_start: 0.7640 (mtp-110) cc_final: 0.7420 (ttm110) REVERT: N 81 ASP cc_start: 0.8332 (t0) cc_final: 0.8081 (t0) outliers start: 88 outliers final: 64 residues processed: 339 average time/residue: 0.1498 time to fit residues: 76.4020 Evaluate side-chains 340 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 266 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 76 ARG Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain M residue 6 GLN Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 100 GLN Chi-restraints excluded: chain M residue 106 MET Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 469 ARG Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain J residue 67 MET Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 106 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 119 optimal weight: 4.9990 chunk 190 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 73 optimal weight: 0.0020 chunk 89 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 618 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 618 ASN ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.109901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.083966 restraints weight = 34708.873| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 3.13 r_work: 0.2998 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21219 Z= 0.152 Angle : 0.741 16.338 28989 Z= 0.331 Chirality : 0.050 0.809 3546 Planarity : 0.003 0.040 3474 Dihedral : 6.560 59.965 2634 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.96 % Allowed : 21.06 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.17), residues: 2376 helix: -0.44 (0.27), residues: 384 sheet: -0.90 (0.19), residues: 738 loop : -1.95 (0.16), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 24 TYR 0.018 0.001 TYR C 486 PHE 0.014 0.001 PHE L 14 TRP 0.011 0.001 TRP E 112 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (21045) covalent geometry : angle 0.67761 / 0.32 (28509) SS BOND : bond 0.00425 / 0.24 ( 42) SS BOND : angle 1.39133 / 0.87 ( 84) hydrogen bonds : bond 0.03242 / 2.17 ( 557) hydrogen bonds : angle 4.91438 / 3.36 ( 1557) link_ALPHA1-2 : bond 0.00228 / 0.13 ( 6) link_ALPHA1-2 : angle 1.80496 / 1.00 ( 18) link_ALPHA1-3 : bond 0.00640 / 0.37 ( 6) link_ALPHA1-3 : angle 1.22672 / 0.69 ( 18) link_ALPHA1-6 : bond 0.00307 / 0.18 ( 6) link_ALPHA1-6 : angle 1.55930 / 0.93 ( 18) link_BETA1-4 : bond 0.00460 / 0.29 ( 57) link_BETA1-4 : angle 1.35806 / 0.90 ( 171) link_NAG-ASN : bond 0.00514 / 0.31 ( 57) link_NAG-ASN : angle 3.61655 / 2.38 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 265 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8786 (mmm) cc_final: 0.8102 (mmm) REVERT: A 265 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8723 (mt) REVERT: A 469 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.6601 (mtp85) REVERT: A 475 MET cc_start: 0.8063 (mmm) cc_final: 0.7477 (mmm) REVERT: B 543 ASN cc_start: 0.8834 (m110) cc_final: 0.8422 (m110) REVERT: B 626 MET cc_start: 0.6992 (mtp) cc_final: 0.6254 (ttm) REVERT: B 654 GLU cc_start: 0.7163 (mm-30) cc_final: 0.6786 (mt-10) REVERT: H 24 ASP cc_start: 0.8666 (p0) cc_final: 0.8306 (p0) REVERT: H 64 GLN cc_start: 0.8912 (tp40) cc_final: 0.8581 (tp-100) REVERT: L 24 ARG cc_start: 0.7765 (ttm110) cc_final: 0.7533 (ttm110) REVERT: L 81 ASP cc_start: 0.8408 (t0) cc_final: 0.8130 (t0) REVERT: C 46 LYS cc_start: 0.8456 (mmtm) cc_final: 0.8204 (mmtm) REVERT: C 155 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.7735 (ptmt) REVERT: C 246 GLN cc_start: 0.8353 (pm20) cc_final: 0.7869 (tp-100) REVERT: C 265 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8774 (mt) REVERT: C 428 GLN cc_start: 0.8574 (mt0) cc_final: 0.7967 (mm-40) REVERT: C 475 MET cc_start: 0.8155 (mmm) cc_final: 0.7568 (mmm) REVERT: D 654 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7116 (mt-10) REVERT: I 3 GLN cc_start: 0.7164 (tp-100) cc_final: 0.6738 (tp-100) REVERT: I 43 GLN cc_start: 0.7570 (pm20) cc_final: 0.7055 (pm20) REVERT: I 100 GLU cc_start: 0.8401 (mm-30) cc_final: 0.7882 (mt-10) REVERT: M 24 ARG cc_start: 0.7792 (mtp-110) cc_final: 0.7496 (ttm110) REVERT: M 33 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8222 (tp) REVERT: M 50 ARG cc_start: 0.8500 (mmm-85) cc_final: 0.8197 (mtp85) REVERT: M 100 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8484 (pm20) REVERT: E 46 LYS cc_start: 0.8564 (mmtp) cc_final: 0.7654 (mttp) REVERT: E 211 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.8655 (tp30) REVERT: E 246 GLN cc_start: 0.8343 (pm20) cc_final: 0.7856 (tp-100) REVERT: E 271 MET cc_start: 0.8051 (tpt) cc_final: 0.7492 (mmp) REVERT: E 469 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.6766 (ptp90) REVERT: E 475 MET cc_start: 0.7995 (mmm) cc_final: 0.7278 (mmm) REVERT: F 543 ASN cc_start: 0.8695 (m110) cc_final: 0.8317 (m110) REVERT: F 654 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7216 (mt-10) REVERT: J 81 GLU cc_start: 0.7612 (tt0) cc_final: 0.6963 (mp0) REVERT: J 100 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8032 (mt-10) REVERT: N 24 ARG cc_start: 0.7537 (mtp-110) cc_final: 0.7263 (ttm110) REVERT: N 81 ASP cc_start: 0.8520 (t0) cc_final: 0.8227 (t0) outliers start: 83 outliers final: 62 residues processed: 326 average time/residue: 0.1519 time to fit residues: 74.8243 Evaluate side-chains 331 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 260 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 76 ARG Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 100 GLN Chi-restraints excluded: chain M residue 106 MET Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 469 ARG Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain J residue 67 MET Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 93 ASP Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 106 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 16 optimal weight: 0.7980 chunk 218 optimal weight: 0.9990 chunk 198 optimal weight: 1.9990 chunk 160 optimal weight: 0.0170 chunk 11 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.111226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.085427 restraints weight = 34861.661| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.13 r_work: 0.3023 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21219 Z= 0.125 Angle : 0.714 15.578 28989 Z= 0.318 Chirality : 0.048 0.762 3546 Planarity : 0.003 0.036 3474 Dihedral : 6.279 58.940 2633 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.20 % Allowed : 21.59 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.17), residues: 2376 helix: -0.33 (0.27), residues: 384 sheet: -0.79 (0.19), residues: 738 loop : -1.87 (0.16), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 24 TYR 0.015 0.001 TYR A 486 PHE 0.011 0.001 PHE E 382 TRP 0.017 0.001 TRP E 112 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (21045) covalent geometry : angle 0.65408 / 0.30 (28509) SS BOND : bond 0.00377 / 0.20 ( 42) SS BOND : angle 1.23305 / 0.78 ( 84) hydrogen bonds : bond 0.03123 / 2.08 ( 557) hydrogen bonds : angle 4.78600 / 3.27 ( 1557) link_ALPHA1-2 : bond 0.00241 / 0.13 ( 6) link_ALPHA1-2 : angle 1.73305 / 0.97 ( 18) link_ALPHA1-3 : bond 0.00618 / 0.36 ( 6) link_ALPHA1-3 : angle 1.25155 / 0.71 ( 18) link_ALPHA1-6 : bond 0.00345 / 0.20 ( 6) link_ALPHA1-6 : angle 1.51496 / 0.91 ( 18) link_BETA1-4 : bond 0.00466 / 0.29 ( 57) link_BETA1-4 : angle 1.31465 / 0.87 ( 171) link_NAG-ASN : bond 0.00514 / 0.31 ( 57) link_NAG-ASN : angle 3.44741 / 2.32 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 269 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8751 (mmm) cc_final: 0.8073 (mmm) REVERT: A 265 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8701 (mt) REVERT: A 469 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.6772 (mtp85) REVERT: A 475 MET cc_start: 0.7967 (mmm) cc_final: 0.7269 (mmm) REVERT: B 543 ASN cc_start: 0.8787 (m110) cc_final: 0.8411 (m110) REVERT: B 626 MET cc_start: 0.6969 (mtp) cc_final: 0.6368 (ttm) REVERT: B 654 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6759 (mt-10) REVERT: H 24 ASP cc_start: 0.8653 (p0) cc_final: 0.8277 (p0) REVERT: H 64 GLN cc_start: 0.8878 (tp40) cc_final: 0.8553 (tp-100) REVERT: L 81 ASP cc_start: 0.8418 (t0) cc_final: 0.8155 (t0) REVERT: C 46 LYS cc_start: 0.8447 (mmtm) cc_final: 0.8188 (mmtm) REVERT: C 155 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.7701 (ptmt) REVERT: C 246 GLN cc_start: 0.8261 (pm20) cc_final: 0.7760 (tp-100) REVERT: C 265 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8787 (mt) REVERT: C 428 GLN cc_start: 0.8536 (mt0) cc_final: 0.7938 (mm-40) REVERT: C 475 MET cc_start: 0.8026 (mmm) cc_final: 0.7440 (mmm) REVERT: C 502 LYS cc_start: 0.8800 (tttt) cc_final: 0.8478 (tttp) REVERT: D 654 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7140 (mt-10) REVERT: I 3 GLN cc_start: 0.7136 (tp-100) cc_final: 0.6793 (tp-100) REVERT: I 43 GLN cc_start: 0.7513 (pm20) cc_final: 0.7061 (pm20) REVERT: I 69 MET cc_start: 0.8837 (mtm) cc_final: 0.8394 (mtm) REVERT: I 100 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7821 (mt-10) REVERT: M 24 ARG cc_start: 0.7739 (mtp-110) cc_final: 0.7465 (ttm110) REVERT: M 33 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8181 (tp) REVERT: M 50 ARG cc_start: 0.8483 (mmm-85) cc_final: 0.8167 (mtp85) REVERT: M 96 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.7133 (mm-30) REVERT: M 100 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8499 (pm20) REVERT: E 211 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.8655 (tp30) REVERT: E 246 GLN cc_start: 0.8406 (pm20) cc_final: 0.7899 (tp-100) REVERT: E 271 MET cc_start: 0.7977 (tpt) cc_final: 0.7444 (mmp) REVERT: E 469 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.6510 (ptp90) REVERT: E 475 MET cc_start: 0.7917 (mmm) cc_final: 0.7182 (mmm) REVERT: F 543 ASN cc_start: 0.8665 (m110) cc_final: 0.8290 (m110) REVERT: F 654 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7026 (mt-10) REVERT: J 81 GLU cc_start: 0.7575 (tt0) cc_final: 0.6943 (mp0) REVERT: J 100 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7989 (mt-10) REVERT: N 24 ARG cc_start: 0.7462 (mtp-110) cc_final: 0.7201 (ttm110) REVERT: N 50 ARG cc_start: 0.8558 (mmm-85) cc_final: 0.8180 (mtp85) REVERT: N 81 ASP cc_start: 0.8536 (t0) cc_final: 0.8279 (t0) outliers start: 67 outliers final: 52 residues processed: 320 average time/residue: 0.1477 time to fit residues: 70.9451 Evaluate side-chains 327 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 265 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 96 GLU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 76 ARG Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 96 GLU Chi-restraints excluded: chain M residue 100 GLN Chi-restraints excluded: chain M residue 106 MET Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 469 ARG Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 544 LEU Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain J residue 67 MET Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 96 GLU Chi-restraints excluded: chain N residue 106 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 25 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 218 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 193 optimal weight: 0.0060 chunk 168 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 150 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 226 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 618 ASN L 6 GLN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 618 ASN ** E 94 ASN ** 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 = 0.3581 r_free = 0.3581 target = 0.111564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.085734 restraints weight = 34921.443| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.15 r_work: 0.3027 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21219 Z= 0.124 Angle : 0.719 16.062 28989 Z= 0.320 Chirality : 0.048 0.625 3546 Planarity : 0.003 0.037 3474 Dihedral : 6.218 59.561 2632 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.30 % Allowed : 21.30 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.17), residues: 2376 helix: -0.16 (0.28), residues: 378 sheet: -0.68 (0.19), residues: 735 loop : -1.83 (0.16), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 24 TYR 0.023 0.001 TYR C 486 PHE 0.023 0.001 PHE L 83 TRP 0.015 0.001 TRP E 112 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (21045) covalent geometry : angle 0.66076 / 0.31 (28509) SS BOND : bond 0.00354 / 0.19 ( 42) SS BOND : angle 1.43918 / 0.91 ( 84) hydrogen bonds : bond 0.03113 / 2.08 ( 557) hydrogen bonds : angle 4.76008 / 3.26 ( 1557) link_ALPHA1-2 : bond 0.00249 / 0.14 ( 6) link_ALPHA1-2 : angle 1.73596 / 0.97 ( 18) link_ALPHA1-3 : bond 0.00613 / 0.35 ( 6) link_ALPHA1-3 : angle 1.25579 / 0.71 ( 18) link_ALPHA1-6 : bond 0.00352 / 0.20 ( 6) link_ALPHA1-6 : angle 1.50495 / 0.90 ( 18) link_BETA1-4 : bond 0.00462 / 0.29 ( 57) link_BETA1-4 : angle 1.30586 / 0.86 ( 171) link_NAG-ASN : bond 0.00511 / 0.30 ( 57) link_NAG-ASN : angle 3.37585 / 2.27 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4087.16 seconds wall clock time: 71 minutes 17.99 seconds (4277.99 seconds total)