Starting phenix.real_space_refine on Sun Jul 5 06:13:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uoj_26648/07_2026/7uoj_26648.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uoj_26648/07_2026/7uoj_26648.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uoj_26648/07_2026/7uoj_26648.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uoj_26648/07_2026/7uoj_26648.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7uoj_26648/07_2026/7uoj_26648.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uoj_26648/07_2026/7uoj_26648.cif" model { file = "/net/cci-nas-00/data/ceres_data/7uoj_26648/07_2026/7uoj_26648.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uoj_26648/07_2026/7uoj_26648.cif" } resolution = 4.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 150 5.16 5 C 16356 2.51 5 N 4368 2.21 5 O 5259 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s 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: 26133 Number of models: 1 Model: "" Number of chains: 54 Chain: "G" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3559 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Chain: "B" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1029 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "H" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1010 Classifications: {'peptide': 126} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 119} Chain: "L" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 737 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 9, 'TRANS': 88} Chain: "l" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "h" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1031 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain: "A" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3559 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Chain: "C" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1029 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "D" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1010 Classifications: {'peptide': 126} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 119} Chain: "E" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 737 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 9, 'TRANS': 88} Chain: "e" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "d" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1031 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain: "I" Number of atoms: 3559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3559 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Chain: "J" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1029 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "K" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1010 Classifications: {'peptide': 126} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 119} Chain: "M" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 737 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 9, 'TRANS': 88} Chain: "m" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "k" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1031 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 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: "q" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "u" Number of atoms: 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: "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: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 5.67, per 1000 atoms: 0.22 Number of scatterers: 26133 At special positions: 0 Unit cell: (159.796, 161.186, 155.628, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 150 16.00 O 5259 8.00 N 4368 7.00 C 16356 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.05 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.04 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 88 " distance=2.03 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 92 " distance=2.04 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.04 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS C 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS e 23 " - pdb=" SG CYS e 88 " distance=2.03 Simple disulfide: pdb=" SG CYS d 22 " - pdb=" SG CYS d 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.02 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.05 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.02 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS m 23 " - pdb=" SG CYS m 88 " distance=2.03 Simple disulfide: pdb=" SG CYS k 22 " - pdb=" SG CYS k 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN U 4 " - " MAN U 5 " " MAN U 5 " - " MAN U 6 " " MAN i 4 " - " MAN i 5 " " MAN i 5 " - " MAN i 6 " " MAN w 4 " - " MAN w 5 " " MAN w 5 " - " MAN w 6 " ALPHA1-3 " BMA O 3 " - " MAN O 4 " " BMA S 3 " - " MAN S 4 " " BMA U 3 " - " MAN U 4 " " MAN U 7 " - " MAN U 8 " " BMA Z 3 " - " MAN Z 4 " " BMA f 3 " - " MAN f 4 " " BMA i 3 " - " MAN i 4 " " MAN i 7 " - " MAN i 8 " " BMA q 3 " - " MAN q 4 " " BMA u 3 " - " MAN u 4 " " BMA w 3 " - " MAN w 4 " " MAN w 7 " - " MAN w 8 " ALPHA1-6 " BMA S 3 " - " MAN S 5 " " BMA U 3 " - " MAN U 7 " " MAN U 7 " - " MAN U 9 " " BMA f 3 " - " MAN f 5 " " BMA i 3 " - " MAN i 7 " " MAN i 7 " - " MAN i 9 " " BMA u 3 " - " MAN u 5 " " BMA w 3 " - " MAN w 7 " " MAN w 7 " - " MAN w 9 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 197 " " NAG A 604 " - " ASN A 234 " " NAG A 605 " - " ASN A 339 " " NAG F 1 " - " ASN G 156 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 133 " " NAG G 603 " - " ASN G 197 " " NAG G 604 " - " ASN G 234 " " NAG G 605 " - " ASN G 339 " " NAG I 601 " - " ASN I 88 " " NAG I 602 " - " ASN I 133 " " NAG I 603 " - " ASN I 197 " " NAG I 604 " - " ASN I 234 " " NAG I 605 " - " ASN I 339 " " NAG N 1 " - " ASN G 160 " " NAG O 1 " - " ASN G 262 " " NAG P 1 " - " ASN G 295 " " NAG Q 1 " - " ASN G 301 " " NAG R 1 " - " ASN G 363 " " NAG S 1 " - " ASN G 386 " " NAG T 1 " - " ASN G 392 " " NAG U 1 " - " ASN G 332 " " NAG V 1 " - " ASN G 448 " " NAG X 1 " - " ASN A 156 " " NAG Y 1 " - " ASN A 160 " " NAG Z 1 " - " ASN A 262 " " NAG a 1 " - " ASN A 295 " " NAG b 1 " - " ASN A 301 " " NAG c 1 " - " ASN A 363 " " NAG f 1 " - " ASN A 386 " " NAG g 1 " - " ASN A 392 " " NAG i 1 " - " ASN A 332 " " NAG j 1 " - " ASN A 448 " " NAG o 1 " - " ASN I 156 " " NAG p 1 " - " ASN I 160 " " NAG q 1 " - " ASN I 262 " " NAG r 1 " - " ASN I 295 " " NAG s 1 " - " ASN I 301 " " NAG t 1 " - " ASN I 363 " " NAG u 1 " - " ASN I 386 " " NAG v 1 " - " ASN I 392 " " NAG w 1 " - " ASN I 332 " " NAG x 1 " - " ASN I 448 " Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 1.2 seconds 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5766 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 62 sheets defined 15.7% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'G' and resid 57 through 62 removed outlier: 3.673A pdb=" N TYR G 61 " --> pdb=" O ASP G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 115 removed outlier: 3.507A pdb=" N SER G 115 " --> pdb=" O LEU G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 4.134A pdb=" N CYS G 126 " --> pdb=" O THR G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 181 No H-bonds generated for 'chain 'G' and resid 179 through 181' Processing helix chain 'G' and resid 334 through 350 Processing helix chain 'G' and resid 351 through 353 No H-bonds generated for 'chain 'G' and resid 351 through 353' Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.865A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.973A pdb=" N ARG G 429 " --> pdb=" O MET G 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 476 through 481 removed outlier: 4.053A pdb=" N SER G 481 " --> pdb=" O ASP G 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 521 Processing helix chain 'B' and resid 529 through 535 removed outlier: 4.106A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 543 through 545 No H-bonds generated for 'chain 'B' and resid 543 through 545' Processing helix chain 'B' and resid 571 through 595 Processing helix chain 'B' and resid 627 through 635 removed outlier: 4.242A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 664 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.692A pdb=" N ASP H 86 " --> pdb=" O ARG H 83 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR H 87 " --> pdb=" O VAL H 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 83 through 87' Processing helix chain 'L' and resid 25 through 31 removed outlier: 4.503A pdb=" N HIS L 30 " --> pdb=" O GLY L 25 " (cutoff:3.500A) Processing helix chain 'l' and resid 79 through 83 removed outlier: 4.087A pdb=" N GLU l 83 " --> pdb=" O ALA l 80 " (cutoff:3.500A) Processing helix chain 'h' and resid 83 through 87 removed outlier: 3.948A pdb=" N ASP h 86 " --> pdb=" O THR h 83 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER h 87 " --> pdb=" O ALA h 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 83 through 87' Processing helix chain 'h' and resid 100D through 100H Processing helix chain 'A' and resid 57 through 63 removed outlier: 4.159A pdb=" N THR A 63 " --> pdb=" O LYS A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 115 removed outlier: 3.786A pdb=" N HIS A 105 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 4.365A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 334 through 350 Processing helix chain 'A' and resid 351 through 354 removed outlier: 3.922A pdb=" N GLY A 354 " --> pdb=" O LYS A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 351 through 354' Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.037A pdb=" N ARG A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.865A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 520 Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 537 through 542 Processing helix chain 'C' and resid 543 through 545 No H-bonds generated for 'chain 'C' and resid 543 through 545' Processing helix chain 'C' and resid 571 through 595 Processing helix chain 'C' and resid 627 through 635 removed outlier: 4.565A pdb=" N LYS C 633 " --> pdb=" O LEU C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 664 Processing helix chain 'E' and resid 25 through 31 removed outlier: 4.433A pdb=" N HIS E 30 " --> pdb=" O GLY E 25 " (cutoff:3.500A) Processing helix chain 'e' and resid 79 through 83 removed outlier: 4.096A pdb=" N GLU e 83 " --> pdb=" O ALA e 80 " (cutoff:3.500A) Processing helix chain 'd' and resid 100D through 100H removed outlier: 3.599A pdb=" N ASN d 100H" --> pdb=" O VAL d 100E" (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 63 removed outlier: 3.590A pdb=" N TYR I 61 " --> pdb=" O ASP I 57 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N THR I 63 " --> pdb=" O LYS I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 114 Processing helix chain 'I' and resid 115 through 117 No H-bonds generated for 'chain 'I' and resid 115 through 117' Processing helix chain 'I' and resid 122 through 126 removed outlier: 3.988A pdb=" N CYS I 126 " --> pdb=" O THR I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 179 through 181 No H-bonds generated for 'chain 'I' and resid 179 through 181' Processing helix chain 'I' and resid 334 through 350 Processing helix chain 'I' and resid 351 through 353 No H-bonds generated for 'chain 'I' and resid 351 through 353' Processing helix chain 'I' and resid 368 through 373 removed outlier: 3.915A pdb=" N THR I 373 " --> pdb=" O LEU I 369 " (cutoff:3.500A) Processing helix chain 'I' and resid 425 through 429 removed outlier: 3.965A pdb=" N ARG I 429 " --> pdb=" O MET I 426 " (cutoff:3.500A) Processing helix chain 'I' and resid 476 through 481 removed outlier: 4.008A pdb=" N SER I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) Processing helix chain 'J' and resid 514 through 520 removed outlier: 4.542A pdb=" N VAL J 518 " --> pdb=" O GLY J 514 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 536 removed outlier: 3.635A pdb=" N THR J 536 " --> pdb=" O ALA J 532 " (cutoff:3.500A) Processing helix chain 'J' and resid 537 through 542 Processing helix chain 'J' and resid 543 through 545 No H-bonds generated for 'chain 'J' and resid 543 through 545' Processing helix chain 'J' and resid 571 through 595 Processing helix chain 'J' and resid 627 through 638 removed outlier: 4.571A pdb=" N LYS J 633 " --> pdb=" O LEU J 629 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER J 636 " --> pdb=" O ASP J 632 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASN J 637 " --> pdb=" O LYS J 633 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR J 638 " --> pdb=" O GLU J 634 " (cutoff:3.500A) Processing helix chain 'J' and resid 641 through 664 Processing helix chain 'M' and resid 25 through 31 removed outlier: 4.483A pdb=" N HIS M 30 " --> pdb=" O GLY M 25 " (cutoff:3.500A) Processing helix chain 'm' and resid 79 through 83 removed outlier: 4.120A pdb=" N GLU m 83 " --> pdb=" O ALA m 80 " (cutoff:3.500A) Processing helix chain 'k' and resid 100D through 100H Processing sheet with id=AA1, first strand: chain 'G' and resid 495 through 499 removed outlier: 4.982A pdb=" N VAL G 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR B 606 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.720A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR G 244 " --> pdb=" O ILE G 84 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE G 84 " --> pdb=" O THR G 244 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 75 through 76 removed outlier: 4.296A pdb=" N VAL G 75 " --> pdb=" O CYS G 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 91 through 93 removed outlier: 4.057A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 130 through 133 Processing sheet with id=AA6, first strand: chain 'G' and resid 182 through 183 Processing sheet with id=AA7, first strand: chain 'G' and resid 201 through 203 removed outlier: 3.515A pdb=" N TYR G 435 " --> pdb=" O THR G 202 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 271 through 273 removed outlier: 4.119A pdb=" N LEU G 285 " --> pdb=" O ARG G 273 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 271 through 273 removed outlier: 4.119A pdb=" N LEU G 285 " --> pdb=" O ARG G 273 " (cutoff:3.500A) removed outlier: 11.092A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 10.830A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 12.122A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 11.372A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 10.880A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ASN G 300 " --> pdb=" O GLY G 441 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLY G 441 " --> pdb=" O ASN G 300 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 304 through 312 removed outlier: 6.549A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 359 through 360 removed outlier: 3.603A pdb=" N ILE G 359 " --> pdb=" O TRP G 395 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.526A pdb=" N GLY H 76G" --> pdb=" O VAL H 24 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.368A pdb=" N GLY H 10 " --> pdb=" O VAL H 110 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 8 through 13 removed outlier: 3.595A pdb=" N THR L 105 " --> pdb=" O MET L 11 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 19 through 23 Processing sheet with id=AB7, first strand: chain 'l' and resid 9 through 13 removed outlier: 6.059A pdb=" N ILE l 9 " --> pdb=" O THR l 103 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N THR l 105 " --> pdb=" O ILE l 9 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE l 11 " --> pdb=" O THR l 105 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TRP l 35 " --> pdb=" O ILE l 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'l' and resid 19 through 22 Processing sheet with id=AB9, first strand: chain 'h' and resid 4 through 7 removed outlier: 4.082A pdb=" N GLN h 77 " --> pdb=" O ASP h 72 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP h 72 " --> pdb=" O GLN h 77 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'h' and resid 58 through 59 removed outlier: 7.067A pdb=" N TRP h 36 " --> pdb=" O ILE h 48 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N TYR h 50 " --> pdb=" O TRP h 34 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TRP h 34 " --> pdb=" O TYR h 50 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'h' and resid 100 through 100A removed outlier: 4.009A pdb=" N ARG h 100 " --> pdb=" O PHE h 100K" (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE h 100K" --> pdb=" O ARG h 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 495 through 499 removed outlier: 5.040A pdb=" N VAL A 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR C 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.820A pdb=" N THR A 244 " --> pdb=" O ILE A 84 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE A 84 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 75 through 76 removed outlier: 4.439A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 91 through 94 removed outlier: 4.055A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 169 through 177 removed outlier: 4.248A pdb=" N CYS A 131 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS A 189 " --> pdb=" O CYS A 131 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 201 through 203 removed outlier: 3.511A pdb=" N TYR A 435 " --> pdb=" O THR A 202 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 271 through 273 removed outlier: 4.075A pdb=" N LEU A 285 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG A 419 " --> pdb=" O TYR A 384 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 271 through 273 removed outlier: 4.075A pdb=" N LEU A 285 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 11.134A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.852A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.146A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.439A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.927A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.656A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 359 through 360 Processing sheet with id=AD4, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AD5, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.969A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 8 through 13 removed outlier: 6.215A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 19 through 23 Processing sheet with id=AD8, first strand: chain 'e' and resid 9 through 13 removed outlier: 5.995A pdb=" N ILE e 9 " --> pdb=" O THR e 103 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N THR e 105 " --> pdb=" O ILE e 9 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE e 11 " --> pdb=" O THR e 105 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N GLN e 37 " --> pdb=" O LEU e 46 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEU e 46 " --> pdb=" O GLN e 37 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'e' and resid 19 through 22 Processing sheet with id=AE1, first strand: chain 'd' and resid 4 through 7 removed outlier: 4.572A pdb=" N GLN d 77 " --> pdb=" O ASP d 72 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP d 72 " --> pdb=" O GLN d 77 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'd' and resid 57 through 59 removed outlier: 7.002A pdb=" N TRP d 36 " --> pdb=" O ILE d 48 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TYR d 50 " --> pdb=" O TRP d 34 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TRP d 34 " --> pdb=" O TYR d 50 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'd' and resid 100 through 100A removed outlier: 3.902A pdb=" N ARG d 100 " --> pdb=" O PHE d 100K" (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE d 100K" --> pdb=" O ARG d 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'I' and resid 495 through 499 removed outlier: 5.025A pdb=" N VAL I 36 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR J 606 " --> pdb=" O VAL I 36 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.717A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR I 244 " --> pdb=" O ILE I 84 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE I 84 " --> pdb=" O THR I 244 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 75 through 76 removed outlier: 4.324A pdb=" N VAL I 75 " --> pdb=" O CYS I 54 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 91 through 94 removed outlier: 4.094A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 130 through 133 Processing sheet with id=AE9, first strand: chain 'I' and resid 182 through 183 Processing sheet with id=AF1, first strand: chain 'I' and resid 201 through 203 Processing sheet with id=AF2, first strand: chain 'I' and resid 271 through 273 removed outlier: 3.895A pdb=" N LEU I 285 " --> pdb=" O ARG I 273 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 271 through 273 removed outlier: 3.895A pdb=" N LEU I 285 " --> pdb=" O ARG I 273 " (cutoff:3.500A) removed outlier: 11.170A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 10.853A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 12.268A pdb=" N PHE I 288 " --> pdb=" O ILE I 453 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N ILE I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 10.808A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ASN I 300 " --> pdb=" O GLY I 441 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N GLY I 441 " --> pdb=" O ASN I 300 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 304 through 308 Processing sheet with id=AF5, first strand: chain 'I' and resid 359 through 360 removed outlier: 3.795A pdb=" N ILE I 359 " --> pdb=" O TRP I 395 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 375 through 377 removed outlier: 4.640A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS I 421 " --> pdb=" O PHE I 382 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AF8, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.693A pdb=" N GLY K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 8 through 13 removed outlier: 3.757A pdb=" N THR M 105 " --> pdb=" O MET M 11 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLN M 37 " --> pdb=" O LEU M 46 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LEU M 46 " --> pdb=" O GLN M 37 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 19 through 23 Processing sheet with id=AG2, first strand: chain 'm' and resid 9 through 13 removed outlier: 6.067A pdb=" N ILE m 9 " --> pdb=" O THR m 103 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N THR m 105 " --> pdb=" O ILE m 9 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE m 11 " --> pdb=" O THR m 105 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN m 37 " --> pdb=" O LEU m 46 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LEU m 46 " --> pdb=" O GLN m 37 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'm' and resid 19 through 22 Processing sheet with id=AG4, first strand: chain 'm' and resid 31 through 32 Processing sheet with id=AG5, first strand: chain 'k' and resid 4 through 7 removed outlier: 4.218A pdb=" N GLN k 77 " --> pdb=" O ASP k 72 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP k 72 " --> pdb=" O GLN k 77 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'k' and resid 58 through 59 removed outlier: 6.984A pdb=" N TRP k 36 " --> pdb=" O ILE k 48 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TYR k 50 " --> pdb=" O TRP k 34 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TRP k 34 " --> pdb=" O TYR k 50 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL k 100R" --> pdb=" O ARG k 94 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU k 96 " --> pdb=" O MET k 100P" (cutoff:3.500A) removed outlier: 6.874A pdb=" N MET k 100P" --> pdb=" O LEU k 96 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'k' and resid 58 through 59 removed outlier: 6.984A pdb=" N TRP k 36 " --> pdb=" O ILE k 48 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TYR k 50 " --> pdb=" O TRP k 34 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TRP k 34 " --> pdb=" O TYR k 50 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'k' and resid 100 through 100A removed outlier: 3.835A pdb=" N ARG k 100 " --> pdb=" O PHE k 100K" (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE k 100K" --> pdb=" O ARG k 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 825 hydrogen bonds defined for protein. 2106 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.64 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 8193 1.34 - 1.47: 7177 1.47 - 1.61: 11119 1.61 - 1.74: 4 1.74 - 1.88: 207 Bond restraints: 26700 Sorted by residual: bond pdb=" C1 MAN w 9 " pdb=" C2 MAN w 9 " ideal model delta sigma weight residual 1.526 1.609 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" C CYS A 385 " pdb=" N ASN A 386 " ideal model delta sigma weight residual 1.328 1.383 -0.055 1.40e-02 5.10e+03 1.55e+01 bond pdb=" N VAL A 208 " pdb=" CA VAL A 208 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.91e+00 bond pdb=" N ILE B 603 " pdb=" CA ILE B 603 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.80e+00 bond pdb=" CB CYS G 296 " pdb=" SG CYS G 296 " ideal model delta sigma weight residual 1.808 1.717 0.091 3.30e-02 9.18e+02 7.67e+00 ... (remaining 26695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 35753 2.90 - 5.81: 450 5.81 - 8.71: 70 8.71 - 11.62: 5 11.62 - 14.52: 4 Bond angle restraints: 36282 Sorted by residual: angle pdb=" N VAL I 371 " pdb=" CA VAL I 371 " pdb=" C VAL I 371 " ideal model delta sigma weight residual 113.71 107.35 6.36 9.50e-01 1.11e+00 4.48e+01 angle pdb=" CA CYS G 296 " pdb=" CB CYS G 296 " pdb=" SG CYS G 296 " ideal model delta sigma weight residual 114.40 128.92 -14.52 2.30e+00 1.89e-01 3.99e+01 angle pdb=" CA CYS I 296 " pdb=" CB CYS I 296 " pdb=" SG CYS I 296 " ideal model delta sigma weight residual 114.40 128.49 -14.09 2.30e+00 1.89e-01 3.75e+01 angle pdb=" C CYS A 385 " pdb=" N ASN A 386 " pdb=" CA ASN A 386 " ideal model delta sigma weight residual 122.67 112.42 10.25 1.73e+00 3.34e-01 3.51e+01 angle pdb=" C CYS G 385 " pdb=" N ASN G 386 " pdb=" CA ASN G 386 " ideal model delta sigma weight residual 122.03 110.26 11.77 2.01e+00 2.48e-01 3.43e+01 ... (remaining 36277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 13443 17.80 - 35.59: 1226 35.59 - 53.39: 239 53.39 - 71.19: 40 71.19 - 88.99: 25 Dihedral angle restraints: 14973 sinusoidal: 5979 harmonic: 8994 Sorted by residual: dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 92 " pdb=" CB CYS D 92 " ideal model delta sinusoidal sigma weight residual 93.00 160.33 -67.33 1 1.00e+01 1.00e-02 5.90e+01 dihedral pdb=" CB CYS A 385 " pdb=" SG CYS A 385 " pdb=" SG CYS A 418 " pdb=" CB CYS A 418 " ideal model delta sinusoidal sigma weight residual 93.00 34.75 58.25 1 1.00e+01 1.00e-02 4.55e+01 dihedral pdb=" CB CYS I 296 " pdb=" SG CYS I 296 " pdb=" SG CYS I 331 " pdb=" CB CYS I 331 " ideal model delta sinusoidal sigma weight residual 93.00 39.60 53.40 1 1.00e+01 1.00e-02 3.88e+01 ... (remaining 14970 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.198: 4324 0.198 - 0.397: 25 0.397 - 0.595: 1 0.595 - 0.794: 1 0.794 - 0.992: 2 Chirality restraints: 4353 Sorted by residual: chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN G 386 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.41 -0.99 2.00e-01 2.50e+01 2.46e+01 chirality pdb=" C1 NAG f 1 " pdb=" ND2 ASN A 386 " pdb=" C2 NAG f 1 " pdb=" O5 NAG f 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.61 -0.79 2.00e-01 2.50e+01 1.58e+01 chirality pdb=" C1 NAG u 1 " pdb=" ND2 ASN I 386 " pdb=" C2 NAG u 1 " pdb=" O5 NAG u 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.62 -0.78 2.00e-01 2.50e+01 1.54e+01 ... (remaining 4350 not shown) Planarity restraints: 4527 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN G 386 " -0.005 2.00e-02 2.50e+03 7.95e-02 7.89e+01 pdb=" CG ASN G 386 " 0.094 2.00e-02 2.50e+03 pdb=" OD1 ASN G 386 " -0.095 2.00e-02 2.50e+03 pdb=" ND2 ASN G 386 " 0.085 2.00e-02 2.50e+03 pdb=" C1 NAG S 1 " -0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN I 386 " -0.000 2.00e-02 2.50e+03 5.46e-02 3.73e+01 pdb=" CG ASN I 386 " -0.066 2.00e-02 2.50e+03 pdb=" OD1 ASN I 386 " 0.066 2.00e-02 2.50e+03 pdb=" ND2 ASN I 386 " -0.055 2.00e-02 2.50e+03 pdb=" C1 NAG u 1 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 386 " -0.000 2.00e-02 2.50e+03 4.85e-02 2.94e+01 pdb=" CG ASN A 386 " -0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN A 386 " 0.058 2.00e-02 2.50e+03 pdb=" ND2 ASN A 386 " -0.052 2.00e-02 2.50e+03 pdb=" C1 NAG f 1 " 0.050 2.00e-02 2.50e+03 ... (remaining 4524 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2452 2.74 - 3.28: 25476 3.28 - 3.82: 40243 3.82 - 4.36: 44846 4.36 - 4.90: 78279 Nonbonded interactions: 191296 Sorted by model distance: nonbonded pdb=" NH1 ARG G 298 " pdb=" OD1 ASN G 302 " model vdw 2.198 3.120 nonbonded pdb=" O GLN k 3 " pdb=" OG SER k 25 " model vdw 2.198 3.040 nonbonded pdb=" OG SER l 30 " pdb=" OG SER l 93 " model vdw 2.202 3.040 nonbonded pdb=" OG SER m 65 " pdb=" OG1 THR m 72 " model vdw 2.203 3.040 nonbonded pdb=" NH1 ARG A 298 " pdb=" OD1 ASN A 302 " model vdw 2.206 3.120 ... (remaining 191291 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'J' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'E' selection = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'F' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'g' selection = chain 'j' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'r' selection = chain 's' selection = chain 'v' selection = chain 'x' selection = chain 'y' } ncs_group { reference = chain 'O' selection = chain 'Z' selection = chain 'q' } ncs_group { reference = chain 'R' selection = chain 'c' selection = chain 't' } ncs_group { reference = chain 'S' selection = chain 'f' selection = chain 'u' } ncs_group { reference = chain 'U' selection = chain 'i' selection = chain 'w' } ncs_group { reference = chain 'd' selection = chain 'h' selection = chain 'k' } ncs_group { reference = chain 'e' selection = chain 'l' selection = chain 'm' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 24.930 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 26862 Z= 0.290 Angle : 0.928 17.996 36723 Z= 0.434 Chirality : 0.058 0.992 4353 Planarity : 0.005 0.128 4482 Dihedral : 14.148 88.986 9072 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.93 % Favored : 90.74 % Rotamer: Outliers : 0.11 % Allowed : 0.63 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.15), residues: 3090 helix: 0.71 (0.31), residues: 325 sheet: -0.70 (0.17), residues: 888 loop : -1.87 (0.14), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG l 54 TYR 0.019 0.002 TYR H 91 PHE 0.031 0.002 PHE I 288 TRP 0.026 0.002 TRP G 112 HIS 0.011 0.001 HIS h 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00633 / 0.29 (26700) covalent geometry : angle 0.86268 / 0.42 (36282) SS BOND : bond 0.00522 / 0.32 ( 45) SS BOND : angle 2.05030 / 1.39 ( 90) hydrogen bonds : bond 0.12020 / 8.06 ( 803) hydrogen bonds : angle 6.53172 / 4.50 ( 2106) link_ALPHA1-2 : bond 0.00724 / 0.40 ( 6) link_ALPHA1-2 : angle 1.66064 / 1.08 ( 18) link_ALPHA1-3 : bond 0.00609 / 0.35 ( 12) link_ALPHA1-3 : angle 1.98307 / 1.35 ( 36) link_ALPHA1-6 : bond 0.00871 / 0.64 ( 9) link_ALPHA1-6 : angle 2.24479 / 1.51 ( 27) link_BETA1-4 : bond 0.00647 / 0.43 ( 45) link_BETA1-4 : angle 2.17205 / 1.39 ( 135) link_NAG-ASN : bond 0.00726 / 0.42 ( 45) link_NAG-ASN : angle 4.92766 / 3.40 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 454 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 622 ILE cc_start: 0.8044 (tp) cc_final: 0.7816 (tp) REVERT: B 626 MET cc_start: 0.7067 (pmm) cc_final: 0.6566 (pmm) REVERT: L 87 ILE cc_start: 0.7214 (mt) cc_final: 0.6880 (mt) REVERT: l 62 PHE cc_start: 0.7020 (m-80) cc_final: 0.6696 (m-80) REVERT: A 119 CYS cc_start: 0.5519 (m) cc_final: 0.5241 (m) REVERT: C 626 MET cc_start: 0.6970 (pmm) cc_final: 0.6437 (pmm) REVERT: C 630 GLN cc_start: 0.7707 (mt0) cc_final: 0.7254 (tm-30) REVERT: D 31 ASP cc_start: 0.6770 (p0) cc_final: 0.6558 (p0) REVERT: e 37 GLN cc_start: 0.7925 (tm-30) cc_final: 0.7599 (tm-30) REVERT: e 61 ARG cc_start: 0.6198 (mtm180) cc_final: 0.5728 (mtm-85) REVERT: d 2 MET cc_start: 0.6101 (pmm) cc_final: 0.5800 (pmm) REVERT: I 207 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7573 (mtmm) REVERT: J 603 ILE cc_start: 0.7651 (OUTLIER) cc_final: 0.7447 (tp) REVERT: J 622 ILE cc_start: 0.7971 (tp) cc_final: 0.7582 (tp) REVERT: J 626 MET cc_start: 0.6811 (pmm) cc_final: 0.6414 (pmm) REVERT: K 85 ASP cc_start: 0.6385 (p0) cc_final: 0.5816 (p0) outliers start: 3 outliers final: 0 residues processed: 457 average time/residue: 0.1530 time to fit residues: 114.4954 Evaluate side-chains 360 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 358 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 9.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 GLN B 607 ASN B 616 ASN B 652 GLN H 100 ASN L 77 ASN h 52 HIS h 97 HIS A 99 ASN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 GLN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN E 77 ASN ** e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 HIS m 34 GLN m 37 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.246095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4853 r_free = 0.4853 target = 0.239406 restraints weight = 34649.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.238577 restraints weight = 57315.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.237953 restraints weight = 62242.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.237623 restraints weight = 50865.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4830 r_free = 0.4830 target = 0.237250 restraints weight = 51146.374| |-----------------------------------------------------------------------------| r_work (final): 0.4831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6665 moved from start: 0.0852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 26862 Z= 0.144 Angle : 0.705 13.243 36723 Z= 0.336 Chirality : 0.046 0.368 4353 Planarity : 0.004 0.080 4482 Dihedral : 4.897 26.770 3381 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.38 % Favored : 93.40 % Rotamer: Outliers : 0.22 % Allowed : 5.14 % Favored : 94.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.14), residues: 3090 helix: 1.07 (0.30), residues: 318 sheet: -0.57 (0.17), residues: 816 loop : -1.73 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 54 TYR 0.013 0.001 TYR G 435 PHE 0.022 0.002 PHE G 288 TRP 0.016 0.001 TRP A 112 HIS 0.008 0.001 HIS h 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (26700) covalent geometry : angle 0.65130 / 0.32 (36282) SS BOND : bond 0.00456 / 0.28 ( 45) SS BOND : angle 1.70665 / 1.13 ( 90) hydrogen bonds : bond 0.04188 / 2.82 ( 803) hydrogen bonds : angle 5.60927 / 3.88 ( 2106) link_ALPHA1-2 : bond 0.00933 / 0.50 ( 6) link_ALPHA1-2 : angle 1.59059 / 0.98 ( 18) link_ALPHA1-3 : bond 0.00898 / 0.50 ( 12) link_ALPHA1-3 : angle 1.76651 / 1.14 ( 36) link_ALPHA1-6 : bond 0.00822 / 0.58 ( 9) link_ALPHA1-6 : angle 2.33539 / 1.56 ( 27) link_BETA1-4 : bond 0.00600 / 0.39 ( 45) link_BETA1-4 : angle 1.92318 / 1.26 ( 135) link_NAG-ASN : bond 0.00606 / 0.36 ( 45) link_NAG-ASN : angle 3.65798 / 2.61 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 454 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 201 ILE cc_start: 0.8582 (tp) cc_final: 0.8092 (pt) REVERT: B 626 MET cc_start: 0.7243 (pmm) cc_final: 0.6835 (pmm) REVERT: L 46 LEU cc_start: 0.7502 (tp) cc_final: 0.7270 (tp) REVERT: l 30 SER cc_start: 0.7561 (p) cc_final: 0.7291 (m) REVERT: A 119 CYS cc_start: 0.5423 (m) cc_final: 0.5014 (m) REVERT: A 376 PHE cc_start: 0.8501 (p90) cc_final: 0.8238 (p90) REVERT: A 486 TYR cc_start: 0.7504 (m-10) cc_final: 0.6842 (m-10) REVERT: C 626 MET cc_start: 0.6829 (pmm) cc_final: 0.6513 (pmm) REVERT: D 31 ASP cc_start: 0.6322 (p0) cc_final: 0.6011 (p0) REVERT: e 60 GLU cc_start: 0.6440 (pp20) cc_final: 0.6210 (pp20) REVERT: I 178 ARG cc_start: 0.7937 (tpt90) cc_final: 0.7731 (tpt90) REVERT: I 486 TYR cc_start: 0.7539 (m-10) cc_final: 0.6940 (m-10) REVERT: J 622 ILE cc_start: 0.7278 (tp) cc_final: 0.6728 (tp) REVERT: J 626 MET cc_start: 0.6758 (pmm) cc_final: 0.6467 (pmm) REVERT: K 85 ASP cc_start: 0.6333 (p0) cc_final: 0.5768 (p0) REVERT: m 62 PHE cc_start: 0.6230 (m-80) cc_final: 0.5930 (m-80) outliers start: 6 outliers final: 1 residues processed: 457 average time/residue: 0.1505 time to fit residues: 113.0450 Evaluate side-chains 376 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 375 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 101 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 chunk 239 optimal weight: 6.9990 chunk 275 optimal weight: 3.9990 chunk 157 optimal weight: 10.0000 chunk 259 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 chunk 269 optimal weight: 10.0000 chunk 4 optimal weight: 0.0970 chunk 224 optimal weight: 0.6980 chunk 190 optimal weight: 6.9990 overall best weight: 3.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 478 ASN H 32 GLN ** H 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 ASN ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN ** e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 GLN m 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.236476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.229112 restraints weight = 34981.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.228755 restraints weight = 71153.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.228618 restraints weight = 68038.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.228027 restraints weight = 63283.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.227985 restraints weight = 65288.792| |-----------------------------------------------------------------------------| r_work (final): 0.4754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 26862 Z= 0.304 Angle : 0.874 13.267 36723 Z= 0.419 Chirality : 0.051 0.459 4353 Planarity : 0.006 0.063 4482 Dihedral : 5.520 28.606 3381 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.19 % Favored : 90.58 % Rotamer: Outliers : 0.33 % Allowed : 6.61 % Favored : 93.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.14), residues: 3090 helix: 0.65 (0.29), residues: 330 sheet: -0.87 (0.16), residues: 873 loop : -2.00 (0.13), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 54 TYR 0.024 0.002 TYR H 91 PHE 0.038 0.003 PHE I 288 TRP 0.032 0.003 TRP l 35 HIS 0.012 0.002 HIS I 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00724 / 0.30 (26700) covalent geometry : angle 0.81302 / 0.40 (36282) SS BOND : bond 0.00543 / 0.32 ( 45) SS BOND : angle 2.02390 / 1.36 ( 90) hydrogen bonds : bond 0.05247 / 3.55 ( 803) hydrogen bonds : angle 5.99578 / 4.17 ( 2106) link_ALPHA1-2 : bond 0.00901 / 0.49 ( 6) link_ALPHA1-2 : angle 1.66270 / 1.09 ( 18) link_ALPHA1-3 : bond 0.00808 / 0.45 ( 12) link_ALPHA1-3 : angle 2.05369 / 1.37 ( 36) link_ALPHA1-6 : bond 0.00759 / 0.55 ( 9) link_ALPHA1-6 : angle 2.34889 / 1.56 ( 27) link_BETA1-4 : bond 0.00675 / 0.43 ( 45) link_BETA1-4 : angle 2.25916 / 1.48 ( 135) link_NAG-ASN : bond 0.00747 / 0.47 ( 45) link_NAG-ASN : angle 4.46433 / 3.15 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 448 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 626 MET cc_start: 0.7216 (pmm) cc_final: 0.6907 (pmm) REVERT: H 85 ASP cc_start: 0.6381 (p0) cc_final: 0.6138 (p0) REVERT: L 46 LEU cc_start: 0.7538 (tp) cc_final: 0.7265 (tp) REVERT: L 87 ILE cc_start: 0.6894 (mt) cc_final: 0.6632 (mt) REVERT: l 30 SER cc_start: 0.7323 (p) cc_final: 0.7047 (m) REVERT: A 361 PHE cc_start: 0.9041 (OUTLIER) cc_final: 0.8579 (m-10) REVERT: A 374 HIS cc_start: 0.8118 (p-80) cc_final: 0.7751 (p-80) REVERT: C 622 ILE cc_start: 0.7206 (tp) cc_final: 0.6979 (tp) REVERT: C 626 MET cc_start: 0.6653 (pmm) cc_final: 0.6158 (mtm) REVERT: D 31 ASP cc_start: 0.6658 (p0) cc_final: 0.6348 (p0) REVERT: e 60 GLU cc_start: 0.6833 (pp20) cc_final: 0.6478 (pp20) REVERT: J 622 ILE cc_start: 0.7282 (tp) cc_final: 0.6702 (tp) REVERT: J 626 MET cc_start: 0.6526 (pmm) cc_final: 0.6265 (pmm) REVERT: K 85 ASP cc_start: 0.6358 (p0) cc_final: 0.5659 (p0) REVERT: M 79 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7103 (tm-30) REVERT: m 28 LEU cc_start: 0.7375 (mp) cc_final: 0.7103 (mt) REVERT: m 62 PHE cc_start: 0.6380 (m-80) cc_final: 0.6073 (m-80) outliers start: 9 outliers final: 5 residues processed: 456 average time/residue: 0.1495 time to fit residues: 112.8116 Evaluate side-chains 378 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 372 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 29 optimal weight: 0.9990 chunk 304 optimal weight: 2.9990 chunk 213 optimal weight: 0.9980 chunk 153 optimal weight: 0.7980 chunk 237 optimal weight: 0.2980 chunk 257 optimal weight: 20.0000 chunk 186 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 97 HIS ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 37 GLN d 52 HIS I 195 ASN ** K 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4942 r_free = 0.4942 target = 0.245851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.241436 restraints weight = 33652.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.222028 restraints weight = 66448.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.218759 restraints weight = 70233.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.218775 restraints weight = 65199.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.218845 restraints weight = 55414.732| |-----------------------------------------------------------------------------| r_work (final): 0.4613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 26862 Z= 0.149 Angle : 0.735 13.254 36723 Z= 0.348 Chirality : 0.046 0.415 4353 Planarity : 0.004 0.049 4482 Dihedral : 5.092 26.166 3381 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.60 % Favored : 93.17 % Rotamer: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.14), residues: 3090 helix: 0.71 (0.29), residues: 330 sheet: -0.78 (0.16), residues: 894 loop : -1.83 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 54 TYR 0.012 0.001 TYR k 33 PHE 0.017 0.002 PHE G 288 TRP 0.019 0.002 TRP e 35 HIS 0.005 0.001 HIS I 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (26700) covalent geometry : angle 0.67918 / 0.33 (36282) SS BOND : bond 0.00539 / 0.31 ( 45) SS BOND : angle 1.84643 / 1.21 ( 90) hydrogen bonds : bond 0.04095 / 2.79 ( 803) hydrogen bonds : angle 5.63713 / 3.92 ( 2106) link_ALPHA1-2 : bond 0.00992 / 0.53 ( 6) link_ALPHA1-2 : angle 1.42541 / 0.93 ( 18) link_ALPHA1-3 : bond 0.00852 / 0.47 ( 12) link_ALPHA1-3 : angle 1.74298 / 1.15 ( 36) link_ALPHA1-6 : bond 0.00737 / 0.52 ( 9) link_ALPHA1-6 : angle 2.16335 / 1.44 ( 27) link_BETA1-4 : bond 0.00568 / 0.36 ( 45) link_BETA1-4 : angle 1.90257 / 1.25 ( 135) link_NAG-ASN : bond 0.00603 / 0.37 ( 45) link_NAG-ASN : angle 3.87346 / 2.77 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 464 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 201 ILE cc_start: 0.8638 (tp) cc_final: 0.8171 (pt) REVERT: B 625 ASN cc_start: 0.7743 (p0) cc_final: 0.7438 (p0) REVERT: H 85 ASP cc_start: 0.6629 (p0) cc_final: 0.6283 (p0) REVERT: A 119 CYS cc_start: 0.5830 (m) cc_final: 0.5625 (m) REVERT: A 376 PHE cc_start: 0.8771 (p90) cc_final: 0.8386 (p90) REVERT: A 486 TYR cc_start: 0.7669 (m-10) cc_final: 0.7343 (m-10) REVERT: C 626 MET cc_start: 0.6466 (pmm) cc_final: 0.6233 (mtm) REVERT: D 31 ASP cc_start: 0.6754 (p0) cc_final: 0.6327 (p0) REVERT: D 85 ASP cc_start: 0.6939 (p0) cc_final: 0.6668 (p0) REVERT: e 30 SER cc_start: 0.8024 (p) cc_final: 0.7631 (m) REVERT: e 39 ARG cc_start: 0.8357 (mtm180) cc_final: 0.7981 (mtp-110) REVERT: e 61 ARG cc_start: 0.7245 (mtm180) cc_final: 0.6826 (mtm-85) REVERT: d 2 MET cc_start: 0.6294 (pmm) cc_final: 0.5964 (pmm) REVERT: d 94 ARG cc_start: 0.7036 (mtp180) cc_final: 0.6800 (mmm-85) REVERT: J 622 ILE cc_start: 0.7995 (tp) cc_final: 0.7376 (tp) REVERT: J 638 TYR cc_start: 0.6873 (m-80) cc_final: 0.6601 (m-80) REVERT: K 85 ASP cc_start: 0.6246 (p0) cc_final: 0.5555 (p0) REVERT: M 79 GLN cc_start: 0.7620 (tm-30) cc_final: 0.6531 (tm-30) REVERT: m 62 PHE cc_start: 0.6549 (m-80) cc_final: 0.5984 (m-80) outliers start: 0 outliers final: 0 residues processed: 464 average time/residue: 0.1445 time to fit residues: 110.7039 Evaluate side-chains 375 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 148 optimal weight: 3.9990 chunk 27 optimal weight: 0.0000 chunk 244 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 227 optimal weight: 6.9990 chunk 109 optimal weight: 0.1980 chunk 26 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 152 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 140 optimal weight: 0.0030 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 GLN G 425 ASN G 478 ASN B 575 GLN H 32 GLN ** H 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 ASN A 103 GLN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 GLN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN m 37 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4948 r_free = 0.4948 target = 0.250097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.238900 restraints weight = 34546.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4845 r_free = 0.4845 target = 0.238074 restraints weight = 57632.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4839 r_free = 0.4839 target = 0.237724 restraints weight = 58791.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4831 r_free = 0.4831 target = 0.236912 restraints weight = 55072.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.236706 restraints weight = 56428.362| |-----------------------------------------------------------------------------| r_work (final): 0.4828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 26862 Z= 0.118 Angle : 0.700 14.560 36723 Z= 0.327 Chirality : 0.046 0.386 4353 Planarity : 0.004 0.048 4482 Dihedral : 4.745 24.927 3381 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.02 % Favored : 93.75 % Rotamer: Outliers : 0.11 % Allowed : 3.14 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.14), residues: 3090 helix: 0.86 (0.30), residues: 330 sheet: -0.49 (0.17), residues: 852 loop : -1.80 (0.13), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 54 TYR 0.015 0.001 TYR J 586 PHE 0.020 0.001 PHE G 53 TRP 0.025 0.001 TRP l 35 HIS 0.004 0.001 HIS L 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (26700) covalent geometry : angle 0.64745 / 0.31 (36282) SS BOND : bond 0.00541 / 0.32 ( 45) SS BOND : angle 1.70423 / 1.08 ( 90) hydrogen bonds : bond 0.03593 / 2.44 ( 803) hydrogen bonds : angle 5.37033 / 3.71 ( 2106) link_ALPHA1-2 : bond 0.00967 / 0.51 ( 6) link_ALPHA1-2 : angle 1.33541 / 0.88 ( 18) link_ALPHA1-3 : bond 0.00856 / 0.47 ( 12) link_ALPHA1-3 : angle 1.66635 / 1.09 ( 36) link_ALPHA1-6 : bond 0.00645 / 0.44 ( 9) link_ALPHA1-6 : angle 2.07483 / 1.38 ( 27) link_BETA1-4 : bond 0.00606 / 0.40 ( 45) link_BETA1-4 : angle 1.75420 / 1.15 ( 135) link_NAG-ASN : bond 0.00597 / 0.38 ( 45) link_NAG-ASN : angle 3.73499 / 2.63 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 461 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 161 MET cc_start: 0.8324 (tpt) cc_final: 0.7787 (tpt) REVERT: G 201 ILE cc_start: 0.8558 (tp) cc_final: 0.8176 (pt) REVERT: B 622 ILE cc_start: 0.7556 (tp) cc_final: 0.7343 (tp) REVERT: B 625 ASN cc_start: 0.7150 (p0) cc_final: 0.6862 (p0) REVERT: H 85 ASP cc_start: 0.6534 (p0) cc_final: 0.6264 (p0) REVERT: L 46 LEU cc_start: 0.7456 (tp) cc_final: 0.7245 (tp) REVERT: h 6 GLU cc_start: 0.4771 (tp30) cc_final: 0.3368 (mt-10) REVERT: A 117 LYS cc_start: 0.8295 (mmtm) cc_final: 0.7848 (mmtp) REVERT: A 486 TYR cc_start: 0.7507 (m-10) cc_final: 0.6960 (m-10) REVERT: C 586 TYR cc_start: 0.8609 (t80) cc_final: 0.8339 (t80) REVERT: C 626 MET cc_start: 0.6477 (pmm) cc_final: 0.5802 (mtm) REVERT: C 630 GLN cc_start: 0.6686 (mt0) cc_final: 0.6276 (tt0) REVERT: D 31 ASP cc_start: 0.6330 (p0) cc_final: 0.6051 (p0) REVERT: D 85 ASP cc_start: 0.6627 (p0) cc_final: 0.6348 (p0) REVERT: e 30 SER cc_start: 0.7986 (p) cc_final: 0.7757 (t) REVERT: e 61 ARG cc_start: 0.7121 (mtm180) cc_final: 0.6630 (mtm-85) REVERT: d 2 MET cc_start: 0.6437 (pmm) cc_final: 0.6182 (pmm) REVERT: d 94 ARG cc_start: 0.6871 (mtp180) cc_final: 0.6619 (mmm-85) REVERT: J 622 ILE cc_start: 0.7553 (tp) cc_final: 0.7008 (tp) REVERT: J 626 MET cc_start: 0.6575 (pmm) cc_final: 0.6165 (pmm) REVERT: K 85 ASP cc_start: 0.6019 (p0) cc_final: 0.5460 (p0) REVERT: m 62 PHE cc_start: 0.6001 (m-80) cc_final: 0.5765 (m-80) outliers start: 3 outliers final: 1 residues processed: 462 average time/residue: 0.1481 time to fit residues: 112.8752 Evaluate side-chains 380 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 379 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 101 optimal weight: 9.9990 chunk 1 optimal weight: 0.0050 chunk 298 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 83 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 262 optimal weight: 1.9990 chunk 296 optimal weight: 5.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN B 656 ASN ** H 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 GLN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4928 r_free = 0.4928 target = 0.247731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4848 r_free = 0.4848 target = 0.238133 restraints weight = 34521.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.236414 restraints weight = 57440.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.235435 restraints weight = 62311.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.235112 restraints weight = 60532.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.234932 restraints weight = 52255.255| |-----------------------------------------------------------------------------| r_work (final): 0.4813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 26862 Z= 0.137 Angle : 0.699 13.542 36723 Z= 0.330 Chirality : 0.046 0.383 4353 Planarity : 0.004 0.052 4482 Dihedral : 4.759 27.287 3381 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.02 % Favored : 92.78 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.14), residues: 3090 helix: 0.93 (0.30), residues: 324 sheet: -0.49 (0.16), residues: 861 loop : -1.84 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 54 TYR 0.012 0.001 TYR J 586 PHE 0.015 0.002 PHE G 288 TRP 0.016 0.001 TRP l 35 HIS 0.005 0.001 HIS h 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (26700) covalent geometry : angle 0.64694 / 0.32 (36282) SS BOND : bond 0.00487 / 0.29 ( 45) SS BOND : angle 1.77486 / 1.15 ( 90) hydrogen bonds : bond 0.03779 / 2.58 ( 803) hydrogen bonds : angle 5.33955 / 3.69 ( 2106) link_ALPHA1-2 : bond 0.00809 / 0.43 ( 6) link_ALPHA1-2 : angle 1.38737 / 0.92 ( 18) link_ALPHA1-3 : bond 0.00823 / 0.45 ( 12) link_ALPHA1-3 : angle 1.73239 / 1.14 ( 36) link_ALPHA1-6 : bond 0.00591 / 0.40 ( 9) link_ALPHA1-6 : angle 2.03955 / 1.35 ( 27) link_BETA1-4 : bond 0.00556 / 0.36 ( 45) link_BETA1-4 : angle 1.76704 / 1.15 ( 135) link_NAG-ASN : bond 0.00547 / 0.34 ( 45) link_NAG-ASN : angle 3.62960 / 2.56 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 459 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 201 ILE cc_start: 0.8544 (tp) cc_final: 0.8024 (pt) REVERT: G 369 LEU cc_start: 0.8902 (tp) cc_final: 0.8563 (tt) REVERT: B 622 ILE cc_start: 0.7656 (tp) cc_final: 0.7438 (tp) REVERT: B 625 ASN cc_start: 0.7078 (p0) cc_final: 0.6703 (p0) REVERT: H 85 ASP cc_start: 0.6183 (p0) cc_final: 0.5881 (p0) REVERT: L 46 LEU cc_start: 0.7408 (tp) cc_final: 0.7192 (tp) REVERT: l 39 ARG cc_start: 0.7563 (mtm180) cc_final: 0.7250 (mtm180) REVERT: A 117 LYS cc_start: 0.8330 (mmtm) cc_final: 0.7880 (mmtp) REVERT: A 119 CYS cc_start: 0.5335 (m) cc_final: 0.4996 (m) REVERT: A 486 TYR cc_start: 0.7591 (m-10) cc_final: 0.7034 (m-10) REVERT: D 31 ASP cc_start: 0.6192 (p0) cc_final: 0.5791 (p0) REVERT: D 85 ASP cc_start: 0.6628 (p0) cc_final: 0.6357 (p0) REVERT: e 30 SER cc_start: 0.7901 (p) cc_final: 0.7557 (t) REVERT: e 60 GLU cc_start: 0.6741 (pp20) cc_final: 0.6297 (pp20) REVERT: e 61 ARG cc_start: 0.7065 (mtm180) cc_final: 0.6558 (mtm-85) REVERT: d 2 MET cc_start: 0.6470 (pmm) cc_final: 0.6203 (pmm) REVERT: d 94 ARG cc_start: 0.6866 (mtp180) cc_final: 0.6624 (mmm-85) REVERT: J 622 ILE cc_start: 0.7559 (tp) cc_final: 0.7039 (tp) REVERT: J 626 MET cc_start: 0.6807 (pmm) cc_final: 0.6306 (pmm) REVERT: K 85 ASP cc_start: 0.6023 (p0) cc_final: 0.5481 (p0) REVERT: m 62 PHE cc_start: 0.6045 (m-80) cc_final: 0.5763 (m-80) outliers start: 0 outliers final: 0 residues processed: 459 average time/residue: 0.1385 time to fit residues: 105.4467 Evaluate side-chains 373 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 35 optimal weight: 0.8980 chunk 81 optimal weight: 8.9990 chunk 84 optimal weight: 8.9990 chunk 173 optimal weight: 9.9990 chunk 255 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 chunk 280 optimal weight: 7.9990 chunk 286 optimal weight: 0.9990 chunk 184 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 GLN ** H 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 ASN A 374 HIS ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN E 37 GLN ** e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4924 r_free = 0.4924 target = 0.247221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4835 r_free = 0.4835 target = 0.236730 restraints weight = 34429.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.235563 restraints weight = 60307.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.235231 restraints weight = 67090.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.234232 restraints weight = 59653.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.234302 restraints weight = 61553.777| |-----------------------------------------------------------------------------| r_work (final): 0.4809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 26862 Z= 0.146 Angle : 0.718 14.911 36723 Z= 0.339 Chirality : 0.047 0.492 4353 Planarity : 0.004 0.054 4482 Dihedral : 4.779 27.991 3381 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.89 % Favored : 92.94 % Rotamer: Outliers : 0.04 % Allowed : 1.77 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.14), residues: 3090 helix: 1.02 (0.30), residues: 318 sheet: -0.49 (0.16), residues: 873 loop : -1.81 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG l 54 TYR 0.016 0.001 TYR h 90 PHE 0.016 0.002 PHE G 288 TRP 0.020 0.001 TRP m 35 HIS 0.005 0.001 HIS I 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (26700) covalent geometry : angle 0.66319 / 0.33 (36282) SS BOND : bond 0.00500 / 0.30 ( 45) SS BOND : angle 1.81677 / 1.19 ( 90) hydrogen bonds : bond 0.03832 / 2.60 ( 803) hydrogen bonds : angle 5.36417 / 3.71 ( 2106) link_ALPHA1-2 : bond 0.00818 / 0.43 ( 6) link_ALPHA1-2 : angle 1.38378 / 0.92 ( 18) link_ALPHA1-3 : bond 0.00814 / 0.45 ( 12) link_ALPHA1-3 : angle 1.73946 / 1.15 ( 36) link_ALPHA1-6 : bond 0.00554 / 0.37 ( 9) link_ALPHA1-6 : angle 1.99737 / 1.32 ( 27) link_BETA1-4 : bond 0.00562 / 0.36 ( 45) link_BETA1-4 : angle 1.77319 / 1.15 ( 135) link_NAG-ASN : bond 0.00615 / 0.37 ( 45) link_NAG-ASN : angle 3.85130 / 2.70 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 462 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 201 ILE cc_start: 0.8534 (tp) cc_final: 0.8073 (pt) REVERT: G 369 LEU cc_start: 0.8938 (tp) cc_final: 0.8585 (tt) REVERT: B 622 ILE cc_start: 0.7561 (tp) cc_final: 0.7265 (tp) REVERT: B 625 ASN cc_start: 0.7082 (p0) cc_final: 0.6688 (p0) REVERT: H 85 ASP cc_start: 0.6144 (p0) cc_final: 0.5901 (p0) REVERT: L 46 LEU cc_start: 0.7404 (tp) cc_final: 0.7142 (tp) REVERT: l 39 ARG cc_start: 0.7669 (mtm180) cc_final: 0.6988 (mtm180) REVERT: A 119 CYS cc_start: 0.5627 (m) cc_final: 0.5401 (m) REVERT: A 486 TYR cc_start: 0.7548 (m-10) cc_final: 0.7014 (m-10) REVERT: C 626 MET cc_start: 0.6775 (pmm) cc_final: 0.6410 (pmm) REVERT: D 31 ASP cc_start: 0.6239 (p0) cc_final: 0.5867 (p0) REVERT: D 85 ASP cc_start: 0.6605 (p0) cc_final: 0.6309 (p0) REVERT: e 30 SER cc_start: 0.7866 (p) cc_final: 0.7548 (t) REVERT: e 60 GLU cc_start: 0.6701 (pp20) cc_final: 0.6294 (pp20) REVERT: e 61 ARG cc_start: 0.7023 (mtm180) cc_final: 0.6521 (mtm-85) REVERT: d 2 MET cc_start: 0.6480 (pmm) cc_final: 0.6237 (pmm) REVERT: d 94 ARG cc_start: 0.6895 (mtp180) cc_final: 0.6630 (mmm-85) REVERT: J 622 ILE cc_start: 0.7520 (tp) cc_final: 0.7012 (tp) REVERT: J 626 MET cc_start: 0.6675 (pmm) cc_final: 0.6405 (pmm) REVERT: K 85 ASP cc_start: 0.5985 (p0) cc_final: 0.5382 (p0) REVERT: m 62 PHE cc_start: 0.6016 (m-80) cc_final: 0.5757 (m-80) outliers start: 1 outliers final: 1 residues processed: 462 average time/residue: 0.1375 time to fit residues: 105.9229 Evaluate side-chains 380 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 379 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 54 optimal weight: 2.9990 chunk 279 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 34 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 238 optimal weight: 0.8980 chunk 218 optimal weight: 2.9990 chunk 232 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 186 optimal weight: 0.0970 chunk 42 optimal weight: 5.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN B 656 ASN ** H 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 103 GLN m 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4926 r_free = 0.4926 target = 0.247457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.238232 restraints weight = 34697.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.236748 restraints weight = 60811.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4823 r_free = 0.4823 target = 0.236122 restraints weight = 62802.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.235671 restraints weight = 61256.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.235602 restraints weight = 57473.911| |-----------------------------------------------------------------------------| r_work (final): 0.4819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 26862 Z= 0.141 Angle : 0.715 15.016 36723 Z= 0.337 Chirality : 0.047 0.573 4353 Planarity : 0.004 0.056 4482 Dihedral : 4.769 27.147 3381 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.12 % Favored : 92.72 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.14), residues: 3090 helix: 1.04 (0.30), residues: 318 sheet: -0.41 (0.17), residues: 837 loop : -1.79 (0.13), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG l 54 TYR 0.012 0.001 TYR k 59 PHE 0.019 0.002 PHE G 53 TRP 0.018 0.001 TRP m 35 HIS 0.005 0.001 HIS I 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (26700) covalent geometry : angle 0.66179 / 0.32 (36282) SS BOND : bond 0.00497 / 0.30 ( 45) SS BOND : angle 1.79948 / 1.18 ( 90) hydrogen bonds : bond 0.03772 / 2.56 ( 803) hydrogen bonds : angle 5.33075 / 3.69 ( 2106) link_ALPHA1-2 : bond 0.00799 / 0.42 ( 6) link_ALPHA1-2 : angle 1.38029 / 0.92 ( 18) link_ALPHA1-3 : bond 0.00809 / 0.44 ( 12) link_ALPHA1-3 : angle 1.73361 / 1.15 ( 36) link_ALPHA1-6 : bond 0.00557 / 0.37 ( 9) link_ALPHA1-6 : angle 1.93720 / 1.27 ( 27) link_BETA1-4 : bond 0.00588 / 0.39 ( 45) link_BETA1-4 : angle 1.75421 / 1.14 ( 135) link_NAG-ASN : bond 0.00617 / 0.36 ( 45) link_NAG-ASN : angle 3.78117 / 2.66 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 461 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 201 ILE cc_start: 0.8599 (tp) cc_final: 0.8137 (pt) REVERT: G 369 LEU cc_start: 0.9006 (tp) cc_final: 0.8664 (tt) REVERT: B 622 ILE cc_start: 0.7613 (tp) cc_final: 0.7375 (tp) REVERT: B 625 ASN cc_start: 0.7083 (p0) cc_final: 0.6675 (p0) REVERT: H 85 ASP cc_start: 0.6248 (p0) cc_final: 0.5969 (p0) REVERT: L 46 LEU cc_start: 0.7401 (tp) cc_final: 0.7149 (tp) REVERT: l 39 ARG cc_start: 0.7673 (mtm180) cc_final: 0.6959 (mtm180) REVERT: A 119 CYS cc_start: 0.6101 (m) cc_final: 0.5851 (m) REVERT: A 486 TYR cc_start: 0.7556 (m-10) cc_final: 0.7052 (m-10) REVERT: C 622 ILE cc_start: 0.7328 (tp) cc_final: 0.7030 (tp) REVERT: D 31 ASP cc_start: 0.6296 (p0) cc_final: 0.5895 (p0) REVERT: D 85 ASP cc_start: 0.6538 (p0) cc_final: 0.6283 (p0) REVERT: E 46 LEU cc_start: 0.7411 (tp) cc_final: 0.7171 (tp) REVERT: e 30 SER cc_start: 0.7859 (p) cc_final: 0.7534 (t) REVERT: e 60 GLU cc_start: 0.6765 (pp20) cc_final: 0.6486 (pp20) REVERT: e 61 ARG cc_start: 0.6951 (mtm180) cc_final: 0.6451 (mtm-85) REVERT: d 2 MET cc_start: 0.6473 (pmm) cc_final: 0.6251 (pmm) REVERT: d 94 ARG cc_start: 0.6864 (mtp180) cc_final: 0.6619 (mmm-85) REVERT: I 434 MET cc_start: 0.8244 (ptp) cc_final: 0.7997 (ptm) REVERT: J 622 ILE cc_start: 0.7500 (tp) cc_final: 0.6991 (tp) REVERT: J 626 MET cc_start: 0.6682 (pmm) cc_final: 0.6415 (pmm) REVERT: K 85 ASP cc_start: 0.5853 (p0) cc_final: 0.5262 (p0) REVERT: m 62 PHE cc_start: 0.5979 (m-80) cc_final: 0.5742 (m-80) REVERT: m 92 ASP cc_start: 0.7536 (p0) cc_final: 0.7320 (p0) outliers start: 0 outliers final: 0 residues processed: 461 average time/residue: 0.1493 time to fit residues: 114.7750 Evaluate side-chains 380 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 380 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 284 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 267 optimal weight: 1.9990 chunk 304 optimal weight: 5.9990 chunk 168 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 282 optimal weight: 4.9990 chunk 211 optimal weight: 4.9990 chunk 224 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 GLN G 302 ASN ** H 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 ASN h 97 HIS A 374 HIS ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN ** e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 103 GLN ** J 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4885 r_free = 0.4885 target = 0.242761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.232856 restraints weight = 34622.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.231600 restraints weight = 54406.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.230844 restraints weight = 64449.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.230378 restraints weight = 52995.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.230224 restraints weight = 51162.562| |-----------------------------------------------------------------------------| r_work (final): 0.4774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 26862 Z= 0.202 Angle : 0.787 14.739 36723 Z= 0.374 Chirality : 0.048 0.396 4353 Planarity : 0.005 0.057 4482 Dihedral : 5.100 30.042 3381 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.03 % Favored : 91.78 % Rotamer: Outliers : 0.04 % Allowed : 0.96 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.14), residues: 3090 helix: 0.76 (0.30), residues: 330 sheet: -0.55 (0.17), residues: 810 loop : -1.84 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 54 TYR 0.018 0.002 TYR A 217 PHE 0.020 0.002 PHE G 159 TRP 0.024 0.002 TRP m 35 HIS 0.007 0.001 HIS I 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.20 (26700) covalent geometry : angle 0.73035 / 0.36 (36282) SS BOND : bond 0.00569 / 0.36 ( 45) SS BOND : angle 2.07147 / 1.46 ( 90) hydrogen bonds : bond 0.04313 / 2.92 ( 803) hydrogen bonds : angle 5.54254 / 3.86 ( 2106) link_ALPHA1-2 : bond 0.00788 / 0.42 ( 6) link_ALPHA1-2 : angle 1.50255 / 0.99 ( 18) link_ALPHA1-3 : bond 0.00808 / 0.44 ( 12) link_ALPHA1-3 : angle 1.82604 / 1.21 ( 36) link_ALPHA1-6 : bond 0.00540 / 0.37 ( 9) link_ALPHA1-6 : angle 1.97650 / 1.30 ( 27) link_BETA1-4 : bond 0.00553 / 0.34 ( 45) link_BETA1-4 : angle 1.91989 / 1.26 ( 135) link_NAG-ASN : bond 0.00638 / 0.39 ( 45) link_NAG-ASN : angle 4.07534 / 2.80 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 453 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 201 ILE cc_start: 0.8514 (tp) cc_final: 0.8059 (pt) REVERT: G 369 LEU cc_start: 0.8980 (tp) cc_final: 0.8546 (tt) REVERT: B 622 ILE cc_start: 0.7851 (tp) cc_final: 0.7571 (tp) REVERT: B 625 ASN cc_start: 0.6901 (p0) cc_final: 0.6565 (p0) REVERT: H 85 ASP cc_start: 0.6325 (p0) cc_final: 0.6079 (p0) REVERT: L 46 LEU cc_start: 0.7514 (tp) cc_final: 0.7270 (tp) REVERT: l 39 ARG cc_start: 0.7659 (mtm180) cc_final: 0.6935 (mtm180) REVERT: A 486 TYR cc_start: 0.7689 (m-10) cc_final: 0.7102 (m-10) REVERT: C 622 ILE cc_start: 0.7314 (tp) cc_final: 0.7013 (tp) REVERT: D 31 ASP cc_start: 0.6561 (p0) cc_final: 0.6209 (p0) REVERT: D 85 ASP cc_start: 0.6667 (p0) cc_final: 0.6383 (p0) REVERT: e 60 GLU cc_start: 0.6784 (pp20) cc_final: 0.6513 (pp20) REVERT: e 61 ARG cc_start: 0.7040 (mtm180) cc_final: 0.6559 (mtm-85) REVERT: d 2 MET cc_start: 0.6527 (pmm) cc_final: 0.6319 (pmm) REVERT: I 434 MET cc_start: 0.8241 (ptp) cc_final: 0.8030 (ptm) REVERT: J 622 ILE cc_start: 0.7670 (tp) cc_final: 0.7198 (tp) REVERT: J 626 MET cc_start: 0.6723 (pmm) cc_final: 0.6452 (pmm) REVERT: K 85 ASP cc_start: 0.5836 (p0) cc_final: 0.5182 (p0) REVERT: m 62 PHE cc_start: 0.6017 (m-80) cc_final: 0.5769 (m-80) REVERT: m 92 ASP cc_start: 0.7583 (p0) cc_final: 0.7356 (p0) outliers start: 1 outliers final: 0 residues processed: 453 average time/residue: 0.1433 time to fit residues: 108.3013 Evaluate side-chains 371 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 371 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 66 optimal weight: 5.9990 chunk 189 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 248 optimal weight: 0.9980 chunk 2 optimal weight: 7.9990 chunk 165 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 257 optimal weight: 0.4980 chunk 259 optimal weight: 5.9990 chunk 296 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 ASN h 97 HIS ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4928 r_free = 0.4928 target = 0.247608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4868 r_free = 0.4868 target = 0.240355 restraints weight = 34536.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4853 r_free = 0.4853 target = 0.239155 restraints weight = 58232.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4847 r_free = 0.4847 target = 0.238517 restraints weight = 65170.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.237988 restraints weight = 64024.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4839 r_free = 0.4839 target = 0.237837 restraints weight = 63155.834| |-----------------------------------------------------------------------------| r_work (final): 0.4840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 26862 Z= 0.140 Angle : 0.760 18.035 36723 Z= 0.354 Chirality : 0.050 0.876 4353 Planarity : 0.004 0.057 4482 Dihedral : 4.886 31.987 3381 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.47 % Favored : 93.33 % Rotamer: Outliers : 0.04 % Allowed : 0.41 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.14), residues: 3090 helix: 0.95 (0.31), residues: 318 sheet: -0.38 (0.17), residues: 801 loop : -1.74 (0.13), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 54 TYR 0.011 0.001 TYR d 33 PHE 0.012 0.001 PHE I 376 TRP 0.017 0.001 TRP e 91 HIS 0.005 0.001 HIS h 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (26700) covalent geometry : angle 0.69113 / 0.34 (36282) SS BOND : bond 0.00500 / 0.32 ( 45) SS BOND : angle 1.96553 / 1.39 ( 90) hydrogen bonds : bond 0.03820 / 2.59 ( 803) hydrogen bonds : angle 5.38533 / 3.74 ( 2106) link_ALPHA1-2 : bond 0.00806 / 0.43 ( 6) link_ALPHA1-2 : angle 1.37115 / 0.91 ( 18) link_ALPHA1-3 : bond 0.00830 / 0.46 ( 12) link_ALPHA1-3 : angle 1.69477 / 1.12 ( 36) link_ALPHA1-6 : bond 0.00539 / 0.36 ( 9) link_ALPHA1-6 : angle 1.86161 / 1.22 ( 27) link_BETA1-4 : bond 0.00594 / 0.39 ( 45) link_BETA1-4 : angle 1.78518 / 1.16 ( 135) link_NAG-ASN : bond 0.00624 / 0.37 ( 45) link_NAG-ASN : angle 4.61987 / 3.08 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 456 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 161 MET cc_start: 0.8231 (tpt) cc_final: 0.7958 (tpt) REVERT: G 201 ILE cc_start: 0.8565 (tp) cc_final: 0.8102 (pt) REVERT: G 369 LEU cc_start: 0.8982 (tp) cc_final: 0.8454 (tt) REVERT: B 622 ILE cc_start: 0.7754 (tp) cc_final: 0.7459 (tp) REVERT: B 625 ASN cc_start: 0.6775 (p0) cc_final: 0.6509 (p0) REVERT: H 48 MET cc_start: 0.5853 (mtp) cc_final: 0.5610 (mtp) REVERT: H 85 ASP cc_start: 0.6200 (p0) cc_final: 0.5915 (p0) REVERT: L 46 LEU cc_start: 0.7388 (tp) cc_final: 0.7113 (tp) REVERT: l 39 ARG cc_start: 0.7580 (mtm180) cc_final: 0.6879 (mtm180) REVERT: A 119 CYS cc_start: 0.5399 (m) cc_final: 0.5122 (m) REVERT: A 486 TYR cc_start: 0.7546 (m-10) cc_final: 0.7042 (m-10) REVERT: C 622 ILE cc_start: 0.7181 (tp) cc_final: 0.6976 (tp) REVERT: D 31 ASP cc_start: 0.6290 (p0) cc_final: 0.5874 (p0) REVERT: D 85 ASP cc_start: 0.6496 (p0) cc_final: 0.6226 (p0) REVERT: e 30 SER cc_start: 0.7795 (p) cc_final: 0.7522 (t) REVERT: e 60 GLU cc_start: 0.6697 (pp20) cc_final: 0.6447 (pp20) REVERT: e 61 ARG cc_start: 0.6901 (mtm180) cc_final: 0.6356 (mtm-85) REVERT: J 622 ILE cc_start: 0.7429 (tp) cc_final: 0.6958 (tp) REVERT: J 626 MET cc_start: 0.6764 (pmm) cc_final: 0.6433 (pmm) REVERT: K 85 ASP cc_start: 0.6096 (p0) cc_final: 0.5636 (p0) outliers start: 1 outliers final: 1 residues processed: 456 average time/residue: 0.1490 time to fit residues: 113.0327 Evaluate side-chains 374 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 373 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 102 optimal weight: 3.9990 chunk 217 optimal weight: 2.9990 chunk 104 optimal weight: 9.9990 chunk 165 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 158 optimal weight: 9.9990 chunk 241 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 79 optimal weight: 0.0970 chunk 59 optimal weight: 4.9990 chunk 305 optimal weight: 4.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 GLN ** H 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 97 HIS ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 37 GLN ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4906 r_free = 0.4906 target = 0.245149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4846 r_free = 0.4846 target = 0.238000 restraints weight = 34598.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4835 r_free = 0.4835 target = 0.237049 restraints weight = 58647.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.236722 restraints weight = 61572.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.236202 restraints weight = 55413.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4823 r_free = 0.4823 target = 0.235831 restraints weight = 57512.012| |-----------------------------------------------------------------------------| r_work (final): 0.4822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 26862 Z= 0.167 Angle : 0.769 14.472 36723 Z= 0.361 Chirality : 0.049 0.705 4353 Planarity : 0.004 0.072 4482 Dihedral : 4.966 31.597 3381 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.86 % Favored : 91.94 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.14), residues: 3090 helix: 0.96 (0.30), residues: 318 sheet: -0.45 (0.17), residues: 807 loop : -1.74 (0.13), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 54 TYR 0.023 0.002 TYR k 59 PHE 0.021 0.002 PHE A 353 TRP 0.020 0.002 TRP D 36 HIS 0.006 0.001 HIS I 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (26700) covalent geometry : angle 0.70469 / 0.35 (36282) SS BOND : bond 0.00537 / 0.34 ( 45) SS BOND : angle 1.96503 / 1.39 ( 90) hydrogen bonds : bond 0.04016 / 2.73 ( 803) hydrogen bonds : angle 5.45442 / 3.78 ( 2106) link_ALPHA1-2 : bond 0.00765 / 0.41 ( 6) link_ALPHA1-2 : angle 1.45699 / 0.96 ( 18) link_ALPHA1-3 : bond 0.00794 / 0.43 ( 12) link_ALPHA1-3 : angle 1.75127 / 1.16 ( 36) link_ALPHA1-6 : bond 0.00542 / 0.36 ( 9) link_ALPHA1-6 : angle 1.86273 / 1.22 ( 27) link_BETA1-4 : bond 0.00554 / 0.36 ( 45) link_BETA1-4 : angle 1.81253 / 1.18 ( 135) link_NAG-ASN : bond 0.00587 / 0.35 ( 45) link_NAG-ASN : angle 4.44906 / 3.02 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3587.10 seconds wall clock time: 63 minutes 41.85 seconds (3821.85 seconds total)