Starting phenix.real_space_refine on Sun Sep 13 03:30:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6dfg_7875/09_2026/6dfg_7875.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dfg_7875/09_2026/6dfg_7875.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6dfg_7875/09_2026/6dfg_7875.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6dfg_7875/09_2026/6dfg_7875.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6dfg_7875/09_2026/6dfg_7875.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dfg_7875/09_2026/6dfg_7875.map" model { file = "/net/cci-nas-00/data/ceres_data/6dfg_7875/09_2026/6dfg_7875.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dfg_7875/09_2026/6dfg_7875.cif" } resolution = 4.42 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 123 5.16 5 C 12570 2.51 5 N 3303 2.21 5 O 4194 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20190 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 3427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3427 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 5 Chain: "B" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 917 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 1, 'TRANS': 113} Chain breaks: 1 Chain: "H" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1007 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "L" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 806 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "C" Number of atoms: 3427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3427 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 5 Chain: "E" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 917 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 1, 'TRANS': 113} Chain breaks: 1 Chain: "G" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1007 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "J" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 806 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "D" Number of atoms: 3427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3427 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 5 Chain: "F" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 917 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 1, 'TRANS': 113} Chain breaks: 1 Chain: "I" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1007 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "K" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 806 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "M" 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: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 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: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 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: 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: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 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: 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: "c" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 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: "g" 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: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "l" 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: "m" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 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: "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: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 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: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.59, per 1000 atoms: 0.23 Number of scatterers: 20190 At special positions: 0 Unit cell: (158.62, 166.86, 142.14, 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 123 16.00 O 4194 8.00 N 3303 7.00 C 12570 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.02 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=1.95 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.02 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=1.99 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.02 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.02 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.14 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN P 4 " - " MAN P 5 " " MAN S 4 " - " MAN S 5 " " MAN S 5 " - " MAN S 6 " " MAN S 8 " - " MAN S 9 " " MAN U 4 " - " MAN U 5 " " MAN U 5 " - " MAN U 6 " " MAN Z 4 " - " MAN Z 5 " " MAN c 4 " - " MAN c 5 " " MAN c 5 " - " MAN c 6 " " MAN c 8 " - " MAN c 9 " " MAN e 4 " - " MAN e 5 " " MAN e 5 " - " MAN e 6 " " MAN j 4 " - " MAN j 5 " " MAN m 4 " - " MAN m 5 " " MAN m 5 " - " MAN m 6 " " MAN m 8 " - " MAN m 9 " " MAN o 4 " - " MAN o 5 " " MAN o 5 " - " MAN o 6 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA P 3 " - " MAN P 4 " " BMA S 3 " - " MAN S 4 " " MAN S 7 " - " MAN S 10 " " BMA U 3 " - " MAN U 4 " " BMA W 3 " - " MAN W 4 " " BMA Z 3 " - " MAN Z 4 " " BMA c 3 " - " MAN c 4 " " MAN c 7 " - " MAN c 10 " " BMA e 3 " - " MAN e 4 " " BMA g 3 " - " MAN g 4 " " BMA j 3 " - " MAN j 4 " " BMA m 3 " - " MAN m 4 " " MAN m 7 " - " MAN m 10 " " BMA o 3 " - " MAN o 4 " ALPHA1-6 " BMA P 3 " - " MAN P 6 " " BMA S 3 " - " MAN S 7 " " MAN S 7 " - " MAN S 8 " " BMA Z 3 " - " MAN Z 6 " " BMA c 3 " - " MAN c 7 " " MAN c 7 " - " MAN c 8 " " BMA j 3 " - " MAN j 6 " " BMA m 3 " - " MAN m 7 " " MAN m 7 " - " MAN m 8 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG 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 W 2 " - " BMA W 3 " " 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 b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " 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-ASN " NAG A 605 " - " ASN A 137 " " NAG A 608 " - " ASN A 160 " " NAG A 611 " - " ASN A 234 " " NAG A 623 " - " ASN A 301 " " NAG A 634 " - " ASN A 339 " " NAG C 605 " - " ASN C 137 " " NAG C 608 " - " ASN C 160 " " NAG C 611 " - " ASN C 234 " " NAG C 623 " - " ASN C 301 " " NAG C 634 " - " ASN C 339 " " NAG D 605 " - " ASN D 137 " " NAG D 608 " - " ASN D 160 " " NAG D 611 " - " ASN D 234 " " NAG D 623 " - " ASN D 301 " " NAG D 634 " - " ASN D 339 " " NAG G 301 " - " ASN G 26 " " NAG H 301 " - " ASN H 26 " " NAG I 301 " - " ASN I 26 " " NAG M 1 " - " ASN A 133 " " NAG N 1 " - " ASN A 156 " " NAG O 1 " - " ASN A 197 " " NAG P 1 " - " ASN A 262 " " NAG Q 1 " - " ASN A 276 " " NAG R 1 " - " ASN A 295 " " NAG S 1 " - " ASN A 332 " " NAG T 1 " - " ASN A 386 " " NAG U 1 " - " ASN A 392 " " NAG V 1 " - " ASN A 448 " " NAG W 1 " - " ASN C 133 " " NAG X 1 " - " ASN C 156 " " NAG Y 1 " - " ASN C 197 " " NAG Z 1 " - " ASN C 262 " " NAG a 1 " - " ASN C 276 " " NAG b 1 " - " ASN C 295 " " NAG c 1 " - " ASN C 332 " " NAG d 1 " - " ASN C 386 " " NAG e 1 " - " ASN C 392 " " NAG f 1 " - " ASN C 448 " " NAG g 1 " - " ASN D 133 " " NAG h 1 " - " ASN D 156 " " NAG i 1 " - " ASN D 197 " " NAG j 1 " - " ASN D 262 " " NAG k 1 " - " ASN D 276 " " NAG l 1 " - " ASN D 295 " " NAG m 1 " - " ASN D 332 " " NAG n 1 " - " ASN D 386 " " NAG o 1 " - " ASN D 392 " " NAG p 1 " - " ASN D 448 " Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 736.4 milliseconds 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4386 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 51 sheets defined 16.1% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.009A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 108 " --> pdb=" O MET A 104 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 354 removed outlier: 4.090A pdb=" N LYS A 344 " --> pdb=" O GLU A 340 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A 345 " --> pdb=" O THR A 341 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 removed outlier: 3.517A pdb=" N LEU A 390 " --> pdb=" O THR A 387 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE A 391 " --> pdb=" O SER A 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 387 through 391' Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.647A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 425 through 429' Processing helix chain 'A' and resid 475 through 482 removed outlier: 3.697A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 537 removed outlier: 3.701A pdb=" N LEU B 537 " --> pdb=" O SER B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 543 removed outlier: 4.450A pdb=" N ARG B 542 " --> pdb=" O THR B 538 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 538 through 543' Processing helix chain 'B' and resid 580 through 585 Processing helix chain 'B' and resid 587 through 597 removed outlier: 3.557A pdb=" N LEU B 592 " --> pdb=" O ARG B 588 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE B 595 " --> pdb=" O GLN B 591 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY B 597 " --> pdb=" O LEU B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 639 through 646 Processing helix chain 'B' and resid 648 through 653 removed outlier: 3.920A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 657 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 27 through 30 Processing helix chain 'C' and resid 98 through 116 removed outlier: 4.009A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE C 108 " --> pdb=" O MET C 104 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 354 removed outlier: 4.091A pdb=" N LYS C 344 " --> pdb=" O GLU C 340 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL C 345 " --> pdb=" O THR C 341 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 391 removed outlier: 3.517A pdb=" N LEU C 390 " --> pdb=" O THR C 387 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE C 391 " --> pdb=" O SER C 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 387 through 391' Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.648A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG C 429 " --> pdb=" O MET C 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 425 through 429' Processing helix chain 'C' and resid 475 through 482 removed outlier: 3.697A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 531 through 537 removed outlier: 3.700A pdb=" N LEU E 537 " --> pdb=" O SER E 534 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 543 removed outlier: 4.450A pdb=" N ARG E 542 " --> pdb=" O THR E 538 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 538 through 543' Processing helix chain 'E' and resid 580 through 585 Processing helix chain 'E' and resid 587 through 597 removed outlier: 3.558A pdb=" N LEU E 592 " --> pdb=" O ARG E 588 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE E 595 " --> pdb=" O GLN E 591 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY E 597 " --> pdb=" O LEU E 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 635 Processing helix chain 'E' and resid 639 through 646 Processing helix chain 'E' and resid 648 through 653 removed outlier: 3.921A pdb=" N GLN E 653 " --> pdb=" O SER E 649 " (cutoff:3.500A) Processing helix chain 'E' and resid 654 through 657 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'J' and resid 27 through 30 Processing helix chain 'D' and resid 98 through 116 removed outlier: 4.009A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE D 108 " --> pdb=" O MET D 104 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE D 109 " --> pdb=" O HIS D 105 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU D 116 " --> pdb=" O TRP D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 354 removed outlier: 4.090A pdb=" N LYS D 344 " --> pdb=" O GLU D 340 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL D 345 " --> pdb=" O THR D 341 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LYS D 351 " --> pdb=" O LYS D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 391 removed outlier: 3.517A pdb=" N LEU D 390 " --> pdb=" O THR D 387 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE D 391 " --> pdb=" O SER D 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 387 through 391' Processing helix chain 'D' and resid 425 through 429 removed outlier: 3.647A pdb=" N GLN D 428 " --> pdb=" O ASN D 425 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG D 429 " --> pdb=" O MET D 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 425 through 429' Processing helix chain 'D' and resid 475 through 482 removed outlier: 3.697A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 537 removed outlier: 3.701A pdb=" N LEU F 537 " --> pdb=" O SER F 534 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 543 removed outlier: 4.449A pdb=" N ARG F 542 " --> pdb=" O THR F 538 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 538 through 543' Processing helix chain 'F' and resid 580 through 585 Processing helix chain 'F' and resid 587 through 597 removed outlier: 3.558A pdb=" N LEU F 592 " --> pdb=" O ARG F 588 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE F 595 " --> pdb=" O GLN F 591 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY F 597 " --> pdb=" O LEU F 593 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 635 Processing helix chain 'F' and resid 639 through 646 Processing helix chain 'F' and resid 648 through 653 removed outlier: 3.920A pdb=" N GLN F 653 " --> pdb=" O SER F 649 " (cutoff:3.500A) Processing helix chain 'F' and resid 654 through 657 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'K' and resid 27 through 30 Processing sheet with id=AA1, first strand: chain 'A' and resid 498 through 499 removed outlier: 6.002A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR B 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 38 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N CYS B 604 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 47 removed outlier: 4.060A pdb=" N LYS A 46 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 224 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.726A pdb=" N PHE A 53 " --> pdb=" O CYS A 218 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 93 removed outlier: 3.625A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 133 removed outlier: 3.586A pdb=" N SER A 174 " --> pdb=" O CYS A 157 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'A' and resid 200 through 203 removed outlier: 5.835A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET A 434 " --> pdb=" O ILE A 424 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 3.584A pdb=" N ILE A 271 " --> pdb=" O GLN A 287 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 374 through 378 removed outlier: 3.519A pdb=" N CYS A 331 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN A 295 " --> pdb=" O ASN A 332 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 302 through 308 removed outlier: 6.223A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.557A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.557A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.711A pdb=" N TRP H 35 " --> pdb=" O ASP H 50 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP H 50 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.991A pdb=" N CYS H 92 " --> pdb=" O VAL H 102 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL H 102 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG H 94 " --> pdb=" O MET H 100M" (cutoff:3.500A) removed outlier: 4.439A pdb=" N MET H 100M" --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ALA H 96 " --> pdb=" O TYR H 100K" (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AB7, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.198A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N TRP L 35 " --> pdb=" O ILE L 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.198A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER L 90 " --> pdb=" O MET L 97 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 498 through 499 removed outlier: 5.883A pdb=" N VAL C 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR E 606 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N CYS E 604 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 46 through 47 removed outlier: 4.060A pdb=" N LYS C 46 " --> pdb=" O LYS C 490 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA C 224 " --> pdb=" O VAL C 489 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.726A pdb=" N PHE C 53 " --> pdb=" O CYS C 218 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 91 through 93 removed outlier: 3.626A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 130 through 133 removed outlier: 3.586A pdb=" N SER C 174 " --> pdb=" O CYS C 157 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AC6, first strand: chain 'C' and resid 200 through 203 removed outlier: 5.835A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N MET C 434 " --> pdb=" O ILE C 424 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 271 through 273 removed outlier: 3.586A pdb=" N ILE C 271 " --> pdb=" O GLN C 287 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.518A pdb=" N CYS C 331 " --> pdb=" O LEU C 416 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN C 295 " --> pdb=" O ASN C 332 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 302 through 308 removed outlier: 6.222A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.556A pdb=" N SER G 21 " --> pdb=" O SER G 7 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.556A pdb=" N SER G 21 " --> pdb=" O SER G 7 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.711A pdb=" N TRP G 35 " --> pdb=" O ASP G 50 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP G 50 " --> pdb=" O TRP G 35 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.991A pdb=" N CYS G 92 " --> pdb=" O VAL G 102 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL G 102 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG G 94 " --> pdb=" O MET G 100M" (cutoff:3.500A) removed outlier: 4.439A pdb=" N MET G 100M" --> pdb=" O ARG G 94 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ALA G 96 " --> pdb=" O TYR G 100K" (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 4 through 5 Processing sheet with id=AD6, first strand: chain 'J' and resid 9 through 13 removed outlier: 6.199A pdb=" N VAL J 11 " --> pdb=" O THR J 105 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP J 85 " --> pdb=" O GLN J 38 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR J 87 " --> pdb=" O TYR J 36 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N TRP J 35 " --> pdb=" O ILE J 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 9 through 13 removed outlier: 6.199A pdb=" N VAL J 11 " --> pdb=" O THR J 105 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER J 90 " --> pdb=" O MET J 97 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 498 through 499 removed outlier: 6.159A pdb=" N VAL D 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR F 606 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL D 38 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS F 604 " --> pdb=" O VAL D 38 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 46 through 47 removed outlier: 4.060A pdb=" N LYS D 46 " --> pdb=" O LYS D 490 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA D 224 " --> pdb=" O VAL D 489 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL D 242 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.726A pdb=" N PHE D 53 " --> pdb=" O CYS D 218 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 91 through 93 removed outlier: 3.625A pdb=" N GLU D 91 " --> pdb=" O CYS D 239 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY D 237 " --> pdb=" O PHE D 93 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 130 through 133 removed outlier: 3.586A pdb=" N SER D 174 " --> pdb=" O CYS D 157 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AE5, first strand: chain 'D' and resid 200 through 203 removed outlier: 5.835A pdb=" N ALA D 200 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N TYR D 435 " --> pdb=" O ALA D 200 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET D 434 " --> pdb=" O ILE D 424 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 271 through 273 removed outlier: 3.585A pdb=" N ILE D 271 " --> pdb=" O GLN D 287 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 374 through 378 removed outlier: 3.518A pdb=" N CYS D 331 " --> pdb=" O LEU D 416 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN D 295 " --> pdb=" O ASN D 332 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 302 through 308 removed outlier: 6.222A pdb=" N LYS D 305 " --> pdb=" O THR D 320 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N THR D 320 " --> pdb=" O LYS D 305 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE D 307 " --> pdb=" O TYR D 318 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N TYR D 318 " --> pdb=" O ILE D 307 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.555A pdb=" N SER I 21 " --> pdb=" O SER I 7 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.555A pdb=" N SER I 21 " --> pdb=" O SER I 7 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.710A pdb=" N TRP I 35 " --> pdb=" O ASP I 50 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASP I 50 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.991A pdb=" N CYS I 92 " --> pdb=" O VAL I 102 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL I 102 " --> pdb=" O CYS I 92 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG I 94 " --> pdb=" O MET I 100M" (cutoff:3.500A) removed outlier: 4.438A pdb=" N MET I 100M" --> pdb=" O ARG I 94 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ALA I 96 " --> pdb=" O TYR I 100K" (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 4 through 5 Processing sheet with id=AF5, first strand: chain 'K' and resid 9 through 13 removed outlier: 6.198A pdb=" N VAL K 11 " --> pdb=" O THR K 105 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP K 85 " --> pdb=" O GLN K 38 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR K 87 " --> pdb=" O TYR K 36 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N TRP K 35 " --> pdb=" O ILE K 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 9 through 13 removed outlier: 6.198A pdb=" N VAL K 11 " --> pdb=" O THR K 105 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER K 90 " --> pdb=" O MET K 97 " (cutoff:3.500A) 577 hydrogen bonds defined for protein. 1461 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.10 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6156 1.34 - 1.46: 5223 1.46 - 1.58: 9033 1.58 - 1.70: 3 1.70 - 1.82: 168 Bond restraints: 20583 Sorted by residual: bond pdb=" C1 MAN S 10 " pdb=" O5 MAN S 10 " ideal model delta sigma weight residual 1.399 1.487 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C1 MAN m 10 " pdb=" O5 MAN m 10 " ideal model delta sigma weight residual 1.399 1.486 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" C1 MAN c 10 " pdb=" O5 MAN c 10 " ideal model delta sigma weight residual 1.399 1.486 -0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" C1 MAN c 10 " pdb=" C2 MAN c 10 " ideal model delta sigma weight residual 1.526 1.606 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C1 MAN m 10 " pdb=" C2 MAN m 10 " ideal model delta sigma weight residual 1.526 1.605 -0.079 2.00e-02 2.50e+03 1.58e+01 ... (remaining 20578 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 26327 2.26 - 4.51: 1337 4.51 - 6.77: 206 6.77 - 9.02: 60 9.02 - 11.28: 33 Bond angle restraints: 27963 Sorted by residual: angle pdb=" C ASN D 136 " pdb=" N ASN D 137 " pdb=" CA ASN D 137 " ideal model delta sigma weight residual 121.54 132.82 -11.28 1.91e+00 2.74e-01 3.49e+01 angle pdb=" C ASN A 136 " pdb=" N ASN A 137 " pdb=" CA ASN A 137 " ideal model delta sigma weight residual 121.54 132.78 -11.24 1.91e+00 2.74e-01 3.46e+01 angle pdb=" C ASN C 136 " pdb=" N ASN C 137 " pdb=" CA ASN C 137 " ideal model delta sigma weight residual 121.54 132.78 -11.24 1.91e+00 2.74e-01 3.46e+01 angle pdb=" C ASN C 137 " pdb=" N ILE C 138 " pdb=" CA ILE C 138 " ideal model delta sigma weight residual 121.97 131.25 -9.28 1.80e+00 3.09e-01 2.66e+01 angle pdb=" C ASN D 137 " pdb=" N ILE D 138 " pdb=" CA ILE D 138 " ideal model delta sigma weight residual 121.97 131.23 -9.26 1.80e+00 3.09e-01 2.64e+01 ... (remaining 27958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.37: 10640 16.37 - 32.74: 558 32.74 - 49.11: 119 49.11 - 65.49: 14 65.49 - 81.86: 15 Dihedral angle restraints: 11346 sinusoidal: 4557 harmonic: 6789 Sorted by residual: dihedral pdb=" CB CYS D 126 " pdb=" SG CYS D 126 " pdb=" SG CYS D 196 " pdb=" CB CYS D 196 " ideal model delta sinusoidal sigma weight residual 93.00 174.86 -81.86 1 1.00e+01 1.00e-02 8.24e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 174.86 -81.86 1 1.00e+01 1.00e-02 8.24e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 174.84 -81.84 1 1.00e+01 1.00e-02 8.24e+01 ... (remaining 11343 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 3140 0.099 - 0.198: 367 0.198 - 0.297: 30 0.297 - 0.396: 21 0.396 - 0.495: 3 Chirality restraints: 3561 Sorted by residual: chirality pdb=" C1 NAG Y 1 " pdb=" ND2 ASN C 197 " pdb=" C2 NAG Y 1 " pdb=" O5 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 6.12e+00 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN A 197 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.88e+00 chirality pdb=" C1 NAG i 1 " pdb=" ND2 ASN D 197 " pdb=" C2 NAG i 1 " pdb=" O5 NAG i 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.84e+00 ... (remaining 3558 not shown) Planarity restraints: 3393 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN H 26 " -0.035 2.00e-02 2.50e+03 3.62e-02 1.64e+01 pdb=" CG ASN H 26 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN H 26 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN H 26 " 0.053 2.00e-02 2.50e+03 pdb=" C1 NAG H 301 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 197 " 0.040 2.00e-02 2.50e+03 3.62e-02 1.64e+01 pdb=" CG ASN C 197 " -0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN C 197 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN C 197 " -0.039 2.00e-02 2.50e+03 pdb=" C1 NAG Y 1 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 197 " 0.040 2.00e-02 2.50e+03 3.55e-02 1.58e+01 pdb=" CG ASN A 197 " -0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN A 197 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 197 " -0.038 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " 0.040 2.00e-02 2.50e+03 ... (remaining 3390 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3928 2.77 - 3.30: 18011 3.30 - 3.84: 32493 3.84 - 4.37: 36517 4.37 - 4.90: 60722 Nonbonded interactions: 151671 Sorted by model distance: nonbonded pdb=" OD2 ASP H 50 " pdb=" O3 MAN U 6 " model vdw 2.240 3.040 nonbonded pdb=" NE2 HIS H 33 " pdb=" O2 MAN S 9 " model vdw 2.259 3.120 nonbonded pdb=" NH1 ARG H 29 " pdb=" O5 MAN S 7 " model vdw 2.263 3.120 nonbonded pdb=" O LEU F 646 " pdb=" ND2 ASN F 651 " model vdw 2.266 3.120 nonbonded pdb=" O LEU E 646 " pdb=" ND2 ASN E 651 " model vdw 2.267 3.120 ... (remaining 151666 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'W' selection = chain 'g' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'd' selection = chain 'f' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'n' selection = chain 'p' } ncs_group { reference = chain 'P' selection = chain 'U' selection = chain 'Z' selection = chain 'e' selection = chain 'j' selection = chain 'o' } ncs_group { reference = chain 'R' selection = chain 'b' selection = chain 'l' } ncs_group { reference = chain 'S' selection = chain 'c' 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: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.050 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.080 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: 24.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.113 20757 Z= 0.363 Angle : 1.247 11.579 28446 Z= 0.581 Chirality : 0.069 0.495 3561 Planarity : 0.007 0.060 3345 Dihedral : 10.339 80.424 6843 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 0.29 % Allowed : 3.90 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.24 (0.15), residues: 2295 helix: -4.06 (0.14), residues: 324 sheet: -1.95 (0.18), residues: 693 loop : -3.05 (0.15), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 29 TYR 0.031 0.004 TYR G 53 PHE 0.025 0.003 PHE I 78 TRP 0.034 0.004 TRP B 614 HIS 0.007 0.002 HIS B 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00760 / 0.36 (20583) covalent geometry : angle 1.18416 / 0.57 (27963) SS BOND : bond 0.02346 / 1.86 ( 39) SS BOND : angle 1.88219 / 1.30 ( 78) hydrogen bonds : bond 0.32048 / 21.29 ( 523) hydrogen bonds : angle 11.77462 / 8.09 ( 1461) link_ALPHA1-2 : bond 0.00640 / 0.41 ( 18) link_ALPHA1-2 : angle 3.13979 / 2.26 ( 54) link_ALPHA1-3 : bond 0.01104 / 0.68 ( 15) link_ALPHA1-3 : angle 2.44953 / 1.80 ( 45) link_ALPHA1-6 : bond 0.00587 / 0.30 ( 9) link_ALPHA1-6 : angle 1.96880 / 1.27 ( 27) link_BETA1-4 : bond 0.00637 / 0.42 ( 45) link_BETA1-4 : angle 3.65174 / 2.54 ( 135) link_NAG-ASN : bond 0.01653 / 1.12 ( 48) link_NAG-ASN : angle 3.73170 / 2.61 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 286 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8618 (ptm) cc_final: 0.7896 (ppp) REVERT: A 99 ASN cc_start: 0.8935 (m-40) cc_final: 0.8230 (t0) REVERT: A 195 ASN cc_start: 0.9061 (p0) cc_final: 0.8773 (p0) REVERT: B 606 THR cc_start: 0.8695 (p) cc_final: 0.8311 (t) REVERT: B 608 VAL cc_start: 0.9286 (p) cc_final: 0.9044 (p) REVERT: B 630 GLN cc_start: 0.9401 (mt0) cc_final: 0.9132 (mp10) REVERT: H 89 MET cc_start: 0.8724 (tpp) cc_final: 0.8369 (tpp) REVERT: L 97 MET cc_start: 0.8630 (pmm) cc_final: 0.8424 (pmm) REVERT: C 95 MET cc_start: 0.8539 (ptm) cc_final: 0.8022 (ppp) REVERT: C 195 ASN cc_start: 0.9091 (p0) cc_final: 0.8741 (p0) REVERT: E 574 LYS cc_start: 0.6969 (pttt) cc_final: 0.6613 (pttp) REVERT: E 606 THR cc_start: 0.8556 (p) cc_final: 0.8288 (t) REVERT: E 608 VAL cc_start: 0.9269 (p) cc_final: 0.9010 (p) REVERT: E 630 GLN cc_start: 0.9422 (mt0) cc_final: 0.9124 (mp10) REVERT: G 5 ARG cc_start: 0.8054 (ttt180) cc_final: 0.7814 (mtm-85) REVERT: G 32 ASP cc_start: 0.8282 (m-30) cc_final: 0.8067 (m-30) REVERT: G 89 MET cc_start: 0.8794 (tpp) cc_final: 0.8582 (tpp) REVERT: D 95 MET cc_start: 0.8695 (ptm) cc_final: 0.8131 (ppp) REVERT: D 99 ASN cc_start: 0.8838 (m-40) cc_final: 0.8228 (t0) REVERT: D 195 ASN cc_start: 0.9105 (p0) cc_final: 0.8623 (p0) REVERT: D 323 ILE cc_start: 0.9509 (OUTLIER) cc_final: 0.9244 (mp) REVERT: F 530 MET cc_start: 0.7685 (tpt) cc_final: 0.7285 (tpt) REVERT: F 542 ARG cc_start: 0.8449 (ptm-80) cc_final: 0.7757 (ttp80) REVERT: F 608 VAL cc_start: 0.9153 (p) cc_final: 0.8790 (p) REVERT: F 648 GLU cc_start: 0.8644 (tt0) cc_final: 0.8367 (pt0) outliers start: 6 outliers final: 0 residues processed: 292 average time/residue: 0.1837 time to fit residues: 77.9372 Evaluate side-chains 144 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 4.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 GLN A 105 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 GLN C 103 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 658 GLN G 100JHIS D 103 GLN D 105 HIS ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 658 GLN I 73 GLN I 100JHIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.041142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.034004 restraints weight = 176370.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.034956 restraints weight = 104195.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.035605 restraints weight = 72423.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.036046 restraints weight = 56050.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.036337 restraints weight = 46841.248| |-----------------------------------------------------------------------------| r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 20757 Z= 0.279 Angle : 0.961 10.593 28446 Z= 0.455 Chirality : 0.051 0.319 3561 Planarity : 0.006 0.060 3345 Dihedral : 6.808 28.047 2517 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.68 % Favored : 89.19 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.64 (0.16), residues: 2295 helix: -3.04 (0.20), residues: 363 sheet: -1.76 (0.19), residues: 642 loop : -2.63 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 64 TYR 0.019 0.002 TYR H 53 PHE 0.018 0.002 PHE G 78 TRP 0.035 0.003 TRP F 596 HIS 0.008 0.002 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.28 (20583) covalent geometry : angle 0.92174 / 0.45 (27963) SS BOND : bond 0.00408 / 0.28 ( 39) SS BOND : angle 1.08632 / 0.71 ( 78) hydrogen bonds : bond 0.05733 / 3.86 ( 523) hydrogen bonds : angle 7.97076 / 5.45 ( 1461) link_ALPHA1-2 : bond 0.00331 / 0.19 ( 18) link_ALPHA1-2 : angle 2.33272 / 1.70 ( 54) link_ALPHA1-3 : bond 0.01129 / 0.69 ( 15) link_ALPHA1-3 : angle 2.49419 / 1.80 ( 45) link_ALPHA1-6 : bond 0.00590 / 0.34 ( 9) link_ALPHA1-6 : angle 1.82257 / 1.21 ( 27) link_BETA1-4 : bond 0.00406 / 0.24 ( 45) link_BETA1-4 : angle 2.37706 / 1.60 ( 135) link_NAG-ASN : bond 0.00439 / 0.28 ( 48) link_NAG-ASN : angle 2.65097 / 1.93 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.795 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8702 (ptm) cc_final: 0.8274 (ppp) REVERT: A 99 ASN cc_start: 0.8898 (m-40) cc_final: 0.8275 (t0) REVERT: A 104 MET cc_start: 0.8870 (tpt) cc_final: 0.8668 (tpt) REVERT: A 195 ASN cc_start: 0.9119 (p0) cc_final: 0.8781 (p0) REVERT: A 426 MET cc_start: 0.8255 (ttm) cc_final: 0.8043 (ttm) REVERT: B 606 THR cc_start: 0.8585 (p) cc_final: 0.8212 (t) REVERT: B 651 ASN cc_start: 0.8254 (m-40) cc_final: 0.8041 (m-40) REVERT: L 4 LEU cc_start: 0.8521 (mt) cc_final: 0.8198 (mt) REVERT: C 95 MET cc_start: 0.8659 (ptm) cc_final: 0.8338 (ppp) REVERT: C 426 MET cc_start: 0.8395 (ttm) cc_final: 0.8098 (ttm) REVERT: E 574 LYS cc_start: 0.6610 (pttt) cc_final: 0.6350 (pttp) REVERT: E 606 THR cc_start: 0.8525 (p) cc_final: 0.8251 (t) REVERT: E 607 ASN cc_start: 0.8553 (p0) cc_final: 0.8084 (m-40) REVERT: E 630 GLN cc_start: 0.9320 (mt0) cc_final: 0.8761 (tm-30) REVERT: E 647 GLU cc_start: 0.8712 (pm20) cc_final: 0.8297 (pm20) REVERT: G 13 LYS cc_start: 0.8041 (mmtt) cc_final: 0.7482 (tppt) REVERT: G 86 ASP cc_start: 0.8204 (m-30) cc_final: 0.7868 (m-30) REVERT: G 100 GLU cc_start: 0.8582 (mm-30) cc_final: 0.7683 (mp0) REVERT: D 95 MET cc_start: 0.8772 (ptm) cc_final: 0.8374 (ppp) REVERT: D 99 ASN cc_start: 0.8854 (m-40) cc_final: 0.8208 (t0) REVERT: D 195 ASN cc_start: 0.9084 (p0) cc_final: 0.8731 (p0) REVERT: F 542 ARG cc_start: 0.8614 (ptm-80) cc_final: 0.8050 (ttp80) REVERT: F 590 GLN cc_start: 0.8616 (tm-30) cc_final: 0.8399 (tm-30) REVERT: F 648 GLU cc_start: 0.9014 (tt0) cc_final: 0.8653 (pt0) REVERT: F 650 GLN cc_start: 0.7916 (tt0) cc_final: 0.7690 (mm110) REVERT: F 651 ASN cc_start: 0.8509 (m-40) cc_final: 0.8282 (m-40) REVERT: F 652 GLN cc_start: 0.7696 (mp10) cc_final: 0.7391 (mp10) REVERT: F 660 LEU cc_start: 0.8690 (mm) cc_final: 0.8484 (pp) REVERT: K 4 LEU cc_start: 0.8586 (mt) cc_final: 0.8311 (mt) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1665 time to fit residues: 44.4743 Evaluate side-chains 120 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 183 optimal weight: 8.9990 chunk 186 optimal weight: 9.9990 chunk 218 optimal weight: 0.0270 chunk 100 optimal weight: 7.9990 chunk 115 optimal weight: 30.0000 chunk 211 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 77 optimal weight: 0.3980 chunk 126 optimal weight: 0.9990 overall best weight: 1.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN L 89 GLN C 136 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN E 651 ASN J 89 GLN D 136 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.042484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.035147 restraints weight = 171965.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.036167 restraints weight = 99609.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.036861 restraints weight = 68309.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.037343 restraints weight = 52297.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.037676 restraints weight = 43238.184| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20757 Z= 0.129 Angle : 0.783 10.931 28446 Z= 0.367 Chirality : 0.048 0.319 3561 Planarity : 0.004 0.049 3345 Dihedral : 6.047 27.395 2517 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.10 % Favored : 91.76 % Rotamer: Outliers : 0.14 % Allowed : 3.52 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.10 (0.16), residues: 2295 helix: -2.22 (0.25), residues: 336 sheet: -1.22 (0.20), residues: 636 loop : -2.52 (0.15), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 94 TYR 0.012 0.001 TYR G 53 PHE 0.015 0.001 PHE A 382 TRP 0.040 0.002 TRP B 596 HIS 0.004 0.001 HIS C 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (20583) covalent geometry : angle 0.75074 / 0.36 (27963) SS BOND : bond 0.00207 / 0.12 ( 39) SS BOND : angle 0.73485 / 0.48 ( 78) hydrogen bonds : bond 0.04309 / 2.91 ( 523) hydrogen bonds : angle 6.91346 / 4.71 ( 1461) link_ALPHA1-2 : bond 0.00376 / 0.26 ( 18) link_ALPHA1-2 : angle 1.80309 / 1.28 ( 54) link_ALPHA1-3 : bond 0.01071 / 0.72 ( 15) link_ALPHA1-3 : angle 1.99538 / 1.42 ( 45) link_ALPHA1-6 : bond 0.00527 / 0.29 ( 9) link_ALPHA1-6 : angle 1.55434 / 0.99 ( 27) link_BETA1-4 : bond 0.00377 / 0.24 ( 45) link_BETA1-4 : angle 1.89118 / 1.32 ( 135) link_NAG-ASN : bond 0.00326 / 0.22 ( 48) link_NAG-ASN : angle 2.25902 / 1.60 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 194 time to evaluate : 0.845 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8492 (ptm) cc_final: 0.8267 (ppp) REVERT: A 99 ASN cc_start: 0.8883 (m-40) cc_final: 0.8254 (t0) REVERT: A 136 ASN cc_start: 0.5435 (OUTLIER) cc_final: 0.5197 (p0) REVERT: A 195 ASN cc_start: 0.8929 (p0) cc_final: 0.8705 (p0) REVERT: B 630 GLN cc_start: 0.8655 (pp30) cc_final: 0.7991 (pp30) REVERT: H 13 LYS cc_start: 0.7628 (mmtt) cc_final: 0.7336 (mmtm) REVERT: H 86 ASP cc_start: 0.7846 (m-30) cc_final: 0.7627 (m-30) REVERT: H 89 MET cc_start: 0.8429 (tpt) cc_final: 0.7880 (tpp) REVERT: L 4 LEU cc_start: 0.8265 (mt) cc_final: 0.8001 (mt) REVERT: C 95 MET cc_start: 0.8384 (ptm) cc_final: 0.8013 (ppp) REVERT: E 606 THR cc_start: 0.8579 (p) cc_final: 0.8177 (t) REVERT: E 651 ASN cc_start: 0.7652 (m110) cc_final: 0.7300 (m-40) REVERT: G 82 MET cc_start: 0.6987 (mmp) cc_final: 0.6687 (mmm) REVERT: G 100 GLU cc_start: 0.8480 (mm-30) cc_final: 0.7497 (mp0) REVERT: G 103 TRP cc_start: 0.8520 (m100) cc_final: 0.8214 (m100) REVERT: J 4 LEU cc_start: 0.8592 (mt) cc_final: 0.8264 (mt) REVERT: J 17 GLN cc_start: 0.8731 (mp10) cc_final: 0.8527 (mp10) REVERT: D 99 ASN cc_start: 0.8850 (m-40) cc_final: 0.8245 (t0) REVERT: D 136 ASN cc_start: 0.5192 (OUTLIER) cc_final: 0.4872 (p0) REVERT: D 195 ASN cc_start: 0.8917 (p0) cc_final: 0.8543 (p0) REVERT: F 651 ASN cc_start: 0.8376 (m-40) cc_final: 0.7244 (m-40) REVERT: I 64 ARG cc_start: 0.9023 (mtp-110) cc_final: 0.8747 (mtp85) REVERT: K 4 LEU cc_start: 0.8698 (mt) cc_final: 0.8489 (mt) outliers start: 3 outliers final: 0 residues processed: 197 average time/residue: 0.1569 time to fit residues: 47.3263 Evaluate side-chains 127 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 16 optimal weight: 20.0000 chunk 85 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 184 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 56 optimal weight: 30.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 591 GLN ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 ASN ** D 374 HIS ** 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 = 0.3035 r_free = 0.3035 target = 0.040772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.033517 restraints weight = 177863.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.034492 restraints weight = 105119.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.035163 restraints weight = 72926.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.035631 restraints weight = 56362.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.035949 restraints weight = 46780.556| |-----------------------------------------------------------------------------| r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 20757 Z= 0.213 Angle : 0.861 9.692 28446 Z= 0.400 Chirality : 0.048 0.285 3561 Planarity : 0.005 0.053 3345 Dihedral : 5.990 24.807 2517 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.11 % Favored : 89.76 % Rotamer: Outliers : 0.05 % Allowed : 2.94 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.16), residues: 2295 helix: -1.90 (0.25), residues: 330 sheet: -1.05 (0.20), residues: 657 loop : -2.50 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 29 TYR 0.019 0.002 TYR F 586 PHE 0.017 0.002 PHE C 382 TRP 0.032 0.002 TRP C 112 HIS 0.005 0.001 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.21 (20583) covalent geometry : angle 0.82697 / 0.39 (27963) SS BOND : bond 0.00587 / 0.37 ( 39) SS BOND : angle 1.09531 / 0.72 ( 78) hydrogen bonds : bond 0.04030 / 2.67 ( 523) hydrogen bonds : angle 6.69480 / 4.56 ( 1461) link_ALPHA1-2 : bond 0.00300 / 0.17 ( 18) link_ALPHA1-2 : angle 2.17959 / 1.57 ( 54) link_ALPHA1-3 : bond 0.00736 / 0.48 ( 15) link_ALPHA1-3 : angle 2.18198 / 1.54 ( 45) link_ALPHA1-6 : bond 0.00549 / 0.32 ( 9) link_ALPHA1-6 : angle 2.20520 / 1.48 ( 27) link_BETA1-4 : bond 0.00326 / 0.20 ( 45) link_BETA1-4 : angle 2.04159 / 1.39 ( 135) link_NAG-ASN : bond 0.00424 / 0.28 ( 48) link_NAG-ASN : angle 2.21369 / 1.62 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 0.785 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: symmetry clash REVERT: A 95 MET cc_start: 0.8664 (ptm) cc_final: 0.8296 (ppp) REVERT: A 99 ASN cc_start: 0.8895 (m-40) cc_final: 0.8239 (t0) REVERT: A 104 MET cc_start: 0.8779 (tpt) cc_final: 0.8533 (tpt) REVERT: B 651 ASN cc_start: 0.8192 (m-40) cc_final: 0.7915 (m-40) REVERT: H 86 ASP cc_start: 0.8187 (m-30) cc_final: 0.7956 (m-30) REVERT: H 89 MET cc_start: 0.8394 (tpt) cc_final: 0.7929 (tpp) REVERT: H 100 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8485 (mm-30) REVERT: C 95 MET cc_start: 0.8630 (ptm) cc_final: 0.8293 (ppp) REVERT: E 606 THR cc_start: 0.8389 (p) cc_final: 0.8168 (t) REVERT: E 607 ASN cc_start: 0.9075 (p0) cc_final: 0.8242 (m-40) REVERT: E 626 MET cc_start: 0.7763 (tmm) cc_final: 0.6061 (tmm) REVERT: E 630 GLN cc_start: 0.9373 (mt0) cc_final: 0.8994 (tm-30) REVERT: G 82 MET cc_start: 0.7002 (mmp) cc_final: 0.6612 (mmm) REVERT: G 100 GLU cc_start: 0.8805 (mm-30) cc_final: 0.7947 (mp0) REVERT: J 17 GLN cc_start: 0.8785 (mp10) cc_final: 0.8505 (mp10) REVERT: D 95 MET cc_start: 0.8571 (ppp) cc_final: 0.8047 (ppp) REVERT: D 99 ASN cc_start: 0.8877 (m-40) cc_final: 0.8242 (t0) REVERT: D 195 ASN cc_start: 0.9054 (p0) cc_final: 0.8766 (p0) REVERT: F 530 MET cc_start: 0.6790 (tpt) cc_final: 0.6122 (tpt) REVERT: I 43 LYS cc_start: 0.8579 (mmtt) cc_final: 0.8374 (mmtp) REVERT: I 63 LEU cc_start: 0.9209 (mt) cc_final: 0.8984 (mt) REVERT: I 100 GLU cc_start: 0.8185 (mp0) cc_final: 0.7774 (mp0) outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.1466 time to fit residues: 37.3676 Evaluate side-chains 110 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 210 optimal weight: 0.0040 chunk 29 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 124 optimal weight: 0.4980 chunk 84 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 157 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 150 optimal weight: 5.9990 overall best weight: 3.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 591 GLN ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.040632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.033366 restraints weight = 173052.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.034331 restraints weight = 102744.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.035003 restraints weight = 71421.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.035470 restraints weight = 55172.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.035790 restraints weight = 45701.385| |-----------------------------------------------------------------------------| r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20757 Z= 0.171 Angle : 0.796 9.428 28446 Z= 0.372 Chirality : 0.046 0.303 3561 Planarity : 0.005 0.080 3345 Dihedral : 5.831 24.066 2517 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.67 % Favored : 91.24 % Rotamer: Outliers : 0.05 % Allowed : 2.07 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.77 (0.16), residues: 2295 helix: -1.64 (0.26), residues: 330 sheet: -0.89 (0.21), residues: 654 loop : -2.48 (0.16), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 64 TYR 0.013 0.001 TYR F 586 PHE 0.016 0.002 PHE C 382 TRP 0.038 0.002 TRP B 596 HIS 0.007 0.001 HIS D 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (20583) covalent geometry : angle 0.76527 / 0.37 (27963) SS BOND : bond 0.00226 / 0.14 ( 39) SS BOND : angle 0.93225 / 0.62 ( 78) hydrogen bonds : bond 0.03681 / 2.42 ( 523) hydrogen bonds : angle 6.37062 / 4.34 ( 1461) link_ALPHA1-2 : bond 0.00248 / 0.17 ( 18) link_ALPHA1-2 : angle 1.89079 / 1.35 ( 54) link_ALPHA1-3 : bond 0.00622 / 0.39 ( 15) link_ALPHA1-3 : angle 1.82874 / 1.29 ( 45) link_ALPHA1-6 : bond 0.00606 / 0.36 ( 9) link_ALPHA1-6 : angle 1.75029 / 1.16 ( 27) link_BETA1-4 : bond 0.00309 / 0.19 ( 45) link_BETA1-4 : angle 1.86741 / 1.27 ( 135) link_NAG-ASN : bond 0.00283 / 0.19 ( 48) link_NAG-ASN : angle 2.16052 / 1.55 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 0.795 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8904 (m-40) cc_final: 0.8262 (t0) REVERT: B 591 GLN cc_start: 0.8872 (tp-100) cc_final: 0.8614 (tt0) REVERT: B 626 MET cc_start: 0.8483 (mmp) cc_final: 0.8179 (mmm) REVERT: H 82 MET cc_start: 0.8978 (tmm) cc_final: 0.8706 (tmm) REVERT: H 89 MET cc_start: 0.8426 (tpt) cc_final: 0.8004 (tpp) REVERT: H 100 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8374 (mm-30) REVERT: L 4 LEU cc_start: 0.8401 (mt) cc_final: 0.8043 (mt) REVERT: C 95 MET cc_start: 0.8485 (ptm) cc_final: 0.8097 (ppp) REVERT: E 606 THR cc_start: 0.8446 (p) cc_final: 0.8194 (t) REVERT: E 607 ASN cc_start: 0.9047 (p0) cc_final: 0.8168 (m-40) REVERT: E 626 MET cc_start: 0.7558 (tmm) cc_final: 0.6738 (tmm) REVERT: E 630 GLN cc_start: 0.9350 (mt0) cc_final: 0.8920 (tm-30) REVERT: E 634 GLU cc_start: 0.8623 (tt0) cc_final: 0.8415 (tt0) REVERT: E 660 LEU cc_start: 0.8573 (mm) cc_final: 0.8358 (pp) REVERT: G 82 MET cc_start: 0.7002 (mmp) cc_final: 0.6595 (mmm) REVERT: G 100 GLU cc_start: 0.8768 (mm-30) cc_final: 0.7913 (mp0) REVERT: J 17 GLN cc_start: 0.8722 (mp10) cc_final: 0.8421 (mp10) REVERT: D 95 MET cc_start: 0.8361 (ppp) cc_final: 0.7982 (ppp) REVERT: D 99 ASN cc_start: 0.8882 (m-40) cc_final: 0.8270 (t0) REVERT: D 195 ASN cc_start: 0.8991 (p0) cc_final: 0.8671 (p0) REVERT: F 530 MET cc_start: 0.6571 (tpt) cc_final: 0.6315 (tpt) REVERT: F 651 ASN cc_start: 0.7994 (m-40) cc_final: 0.7786 (m110) REVERT: I 43 LYS cc_start: 0.8566 (mmtt) cc_final: 0.8357 (mmtp) REVERT: I 63 LEU cc_start: 0.9212 (mt) cc_final: 0.8994 (mt) REVERT: I 64 ARG cc_start: 0.9130 (mtp-110) cc_final: 0.8882 (mtp85) outliers start: 1 outliers final: 0 residues processed: 150 average time/residue: 0.1413 time to fit residues: 33.6215 Evaluate side-chains 114 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 174 optimal weight: 10.0000 chunk 167 optimal weight: 8.9990 chunk 207 optimal weight: 30.0000 chunk 39 optimal weight: 30.0000 chunk 188 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 137 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 151 optimal weight: 8.9990 chunk 181 optimal weight: 3.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 591 GLN ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.040670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.033425 restraints weight = 172343.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.034386 restraints weight = 102429.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.035046 restraints weight = 71431.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.035505 restraints weight = 55284.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.035825 restraints weight = 46080.179| |-----------------------------------------------------------------------------| r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20757 Z= 0.154 Angle : 0.767 9.511 28446 Z= 0.359 Chirality : 0.046 0.297 3561 Planarity : 0.004 0.044 3345 Dihedral : 5.637 23.370 2517 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.70 (0.17), residues: 2295 helix: -1.58 (0.26), residues: 345 sheet: -0.77 (0.20), residues: 681 loop : -2.52 (0.16), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 29 TYR 0.015 0.001 TYR C 40 PHE 0.017 0.002 PHE K 62 TRP 0.026 0.002 TRP A 112 HIS 0.003 0.001 HIS G 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (20583) covalent geometry : angle 0.73746 / 0.35 (27963) SS BOND : bond 0.00227 / 0.14 ( 39) SS BOND : angle 0.94950 / 0.62 ( 78) hydrogen bonds : bond 0.03520 / 2.36 ( 523) hydrogen bonds : angle 6.17566 / 4.21 ( 1461) link_ALPHA1-2 : bond 0.00248 / 0.17 ( 18) link_ALPHA1-2 : angle 1.87799 / 1.34 ( 54) link_ALPHA1-3 : bond 0.00439 / 0.26 ( 15) link_ALPHA1-3 : angle 1.57405 / 1.10 ( 45) link_ALPHA1-6 : bond 0.00586 / 0.35 ( 9) link_ALPHA1-6 : angle 1.74049 / 1.17 ( 27) link_BETA1-4 : bond 0.00286 / 0.17 ( 45) link_BETA1-4 : angle 1.81303 / 1.24 ( 135) link_NAG-ASN : bond 0.00305 / 0.21 ( 48) link_NAG-ASN : angle 2.06303 / 1.50 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.490 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8446 (ppp) cc_final: 0.7906 (ppp) REVERT: A 99 ASN cc_start: 0.8883 (m-40) cc_final: 0.8270 (t0) REVERT: A 323 ILE cc_start: 0.9367 (pt) cc_final: 0.9167 (tp) REVERT: B 591 GLN cc_start: 0.8950 (tp-100) cc_final: 0.8654 (tt0) REVERT: H 82 MET cc_start: 0.8879 (tmm) cc_final: 0.8594 (tmm) REVERT: H 89 MET cc_start: 0.8370 (tpt) cc_final: 0.8014 (tpp) REVERT: H 100 LEU cc_start: 0.9353 (tp) cc_final: 0.8766 (tp) REVERT: H 100 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8144 (mp0) REVERT: L 4 LEU cc_start: 0.8577 (mt) cc_final: 0.7976 (mt) REVERT: C 95 MET cc_start: 0.8553 (ptm) cc_final: 0.8192 (ppp) REVERT: E 606 THR cc_start: 0.8452 (p) cc_final: 0.8226 (t) REVERT: E 607 ASN cc_start: 0.9146 (p0) cc_final: 0.8233 (m-40) REVERT: E 626 MET cc_start: 0.7971 (tmm) cc_final: 0.6256 (tmm) REVERT: E 630 GLN cc_start: 0.9319 (mt0) cc_final: 0.8951 (tm-30) REVERT: G 82 MET cc_start: 0.7009 (mmp) cc_final: 0.6587 (mmm) REVERT: G 100 GLU cc_start: 0.8724 (mm-30) cc_final: 0.7974 (mp0) REVERT: J 17 GLN cc_start: 0.8836 (mp10) cc_final: 0.8538 (mp10) REVERT: J 28 LEU cc_start: 0.9102 (mm) cc_final: 0.8599 (tt) REVERT: D 95 MET cc_start: 0.8490 (ppp) cc_final: 0.8078 (ppp) REVERT: D 99 ASN cc_start: 0.8853 (m-40) cc_final: 0.8271 (t0) REVERT: D 195 ASN cc_start: 0.8944 (p0) cc_final: 0.8584 (p0) REVERT: F 530 MET cc_start: 0.6705 (tpt) cc_final: 0.6305 (tpt) REVERT: I 63 LEU cc_start: 0.9152 (mt) cc_final: 0.8933 (mt) REVERT: I 82 MET cc_start: 0.7239 (mmp) cc_final: 0.6979 (mmt) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1370 time to fit residues: 34.2278 Evaluate side-chains 121 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 210 optimal weight: 0.0980 chunk 190 optimal weight: 4.9990 chunk 226 optimal weight: 5.9990 chunk 193 optimal weight: 6.9990 chunk 224 optimal weight: 20.0000 chunk 75 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 17 optimal weight: 7.9990 chunk 169 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 591 GLN ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.041077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.033611 restraints weight = 170119.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.034630 restraints weight = 97306.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.035358 restraints weight = 66606.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.035866 restraints weight = 50485.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.036206 restraints weight = 41362.906| |-----------------------------------------------------------------------------| r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20757 Z= 0.125 Angle : 0.727 9.586 28446 Z= 0.341 Chirality : 0.046 0.320 3561 Planarity : 0.004 0.044 3345 Dihedral : 5.457 22.831 2517 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.17), residues: 2295 helix: -0.82 (0.29), residues: 309 sheet: -0.61 (0.20), residues: 675 loop : -2.47 (0.16), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 64 TYR 0.013 0.001 TYR A 217 PHE 0.016 0.001 PHE A 382 TRP 0.020 0.001 TRP B 596 HIS 0.006 0.001 HIS E 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (20583) covalent geometry : angle 0.69982 / 0.34 (27963) SS BOND : bond 0.00176 / 0.11 ( 39) SS BOND : angle 0.79511 / 0.52 ( 78) hydrogen bonds : bond 0.03267 / 2.17 ( 523) hydrogen bonds : angle 5.95136 / 4.06 ( 1461) link_ALPHA1-2 : bond 0.00303 / 0.21 ( 18) link_ALPHA1-2 : angle 1.77854 / 1.26 ( 54) link_ALPHA1-3 : bond 0.00506 / 0.31 ( 15) link_ALPHA1-3 : angle 1.42633 / 0.98 ( 45) link_ALPHA1-6 : bond 0.00532 / 0.32 ( 9) link_ALPHA1-6 : angle 1.57659 / 1.04 ( 27) link_BETA1-4 : bond 0.00313 / 0.20 ( 45) link_BETA1-4 : angle 1.70950 / 1.17 ( 135) link_NAG-ASN : bond 0.00253 / 0.17 ( 48) link_NAG-ASN : angle 2.00983 / 1.44 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.705 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: symmetry clash REVERT: A 95 MET cc_start: 0.8239 (ppp) cc_final: 0.7865 (ppp) REVERT: A 99 ASN cc_start: 0.8820 (m-40) cc_final: 0.8292 (t0) REVERT: A 195 ASN cc_start: 0.8904 (p0) cc_final: 0.8694 (p0) REVERT: B 591 GLN cc_start: 0.8952 (tp-100) cc_final: 0.8614 (tt0) REVERT: H 89 MET cc_start: 0.8449 (tpt) cc_final: 0.8098 (tpp) REVERT: H 100 LEU cc_start: 0.9344 (tp) cc_final: 0.8687 (tp) REVERT: H 100 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8105 (mp0) REVERT: L 4 LEU cc_start: 0.8501 (mt) cc_final: 0.8149 (mt) REVERT: C 95 MET cc_start: 0.8466 (ptm) cc_final: 0.8114 (ppp) REVERT: E 607 ASN cc_start: 0.9147 (p0) cc_final: 0.8290 (m-40) REVERT: E 626 MET cc_start: 0.7941 (tmm) cc_final: 0.6318 (tmm) REVERT: E 630 GLN cc_start: 0.9273 (mt0) cc_final: 0.8839 (tm-30) REVERT: G 63 LEU cc_start: 0.9044 (mt) cc_final: 0.8842 (mt) REVERT: G 82 MET cc_start: 0.6805 (mmp) cc_final: 0.6404 (mmm) REVERT: G 100 GLU cc_start: 0.8729 (mm-30) cc_final: 0.7946 (mp0) REVERT: G 103 TRP cc_start: 0.8711 (m100) cc_final: 0.8289 (m100) REVERT: J 17 GLN cc_start: 0.8777 (mp10) cc_final: 0.8495 (mp10) REVERT: J 28 LEU cc_start: 0.9173 (mm) cc_final: 0.8638 (tt) REVERT: D 95 MET cc_start: 0.8231 (ppp) cc_final: 0.7748 (ppp) REVERT: D 99 ASN cc_start: 0.8845 (m-40) cc_final: 0.8275 (t0) REVERT: D 195 ASN cc_start: 0.8970 (p0) cc_final: 0.8674 (p0) REVERT: D 323 ILE cc_start: 0.9200 (pt) cc_final: 0.8980 (mm) REVERT: F 530 MET cc_start: 0.6601 (tpt) cc_final: 0.6273 (tpt) REVERT: I 63 LEU cc_start: 0.9134 (mt) cc_final: 0.8903 (mt) REVERT: I 100 GLU cc_start: 0.8156 (mp0) cc_final: 0.7790 (mp0) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.1409 time to fit residues: 36.3036 Evaluate side-chains 118 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 78 optimal weight: 8.9990 chunk 205 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 119 optimal weight: 9.9990 chunk 166 optimal weight: 20.0000 chunk 114 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 58 optimal weight: 0.0970 chunk 173 optimal weight: 0.5980 chunk 155 optimal weight: 20.0000 chunk 82 optimal weight: 5.9990 overall best weight: 2.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 ASN E 591 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.040982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.033534 restraints weight = 170751.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.034576 restraints weight = 98012.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.035278 restraints weight = 66689.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.035784 restraints weight = 50899.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.036106 restraints weight = 41878.512| |-----------------------------------------------------------------------------| r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20757 Z= 0.136 Angle : 0.748 12.061 28446 Z= 0.349 Chirality : 0.047 0.419 3561 Planarity : 0.004 0.044 3345 Dihedral : 5.371 22.041 2517 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.11 % Favored : 90.76 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.17), residues: 2295 helix: -0.77 (0.29), residues: 309 sheet: -0.55 (0.20), residues: 705 loop : -2.47 (0.16), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 20 TYR 0.023 0.001 TYR I 53 PHE 0.015 0.001 PHE A 382 TRP 0.017 0.001 TRP B 596 HIS 0.003 0.001 HIS I 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (20583) covalent geometry : angle 0.71076 / 0.34 (27963) SS BOND : bond 0.00213 / 0.13 ( 39) SS BOND : angle 1.12048 / 0.72 ( 78) hydrogen bonds : bond 0.03232 / 2.15 ( 523) hydrogen bonds : angle 5.91700 / 4.04 ( 1461) link_ALPHA1-2 : bond 0.00265 / 0.19 ( 18) link_ALPHA1-2 : angle 1.82221 / 1.30 ( 54) link_ALPHA1-3 : bond 0.00479 / 0.30 ( 15) link_ALPHA1-3 : angle 1.43912 / 1.00 ( 45) link_ALPHA1-6 : bond 0.00529 / 0.32 ( 9) link_ALPHA1-6 : angle 1.52355 / 1.02 ( 27) link_BETA1-4 : bond 0.00289 / 0.18 ( 45) link_BETA1-4 : angle 1.70835 / 1.17 ( 135) link_NAG-ASN : bond 0.00256 / 0.17 ( 48) link_NAG-ASN : angle 2.58606 / 2.12 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.805 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8248 (ppp) cc_final: 0.7910 (ppp) REVERT: A 99 ASN cc_start: 0.8820 (m-40) cc_final: 0.8244 (t0) REVERT: A 195 ASN cc_start: 0.8895 (p0) cc_final: 0.8672 (p0) REVERT: B 530 MET cc_start: 0.6486 (mmm) cc_final: 0.6185 (mmm) REVERT: B 591 GLN cc_start: 0.9041 (tp-100) cc_final: 0.8613 (tt0) REVERT: H 82 MET cc_start: 0.8939 (tmm) cc_final: 0.8606 (tmm) REVERT: H 89 MET cc_start: 0.8549 (tpt) cc_final: 0.8202 (tpp) REVERT: H 100 LEU cc_start: 0.9406 (tp) cc_final: 0.8716 (tp) REVERT: H 100 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8198 (mp0) REVERT: L 4 LEU cc_start: 0.8667 (mt) cc_final: 0.8216 (mt) REVERT: C 95 MET cc_start: 0.8473 (ptm) cc_final: 0.8074 (ppp) REVERT: E 607 ASN cc_start: 0.8996 (p0) cc_final: 0.8275 (m-40) REVERT: E 626 MET cc_start: 0.7901 (tmm) cc_final: 0.6008 (tmm) REVERT: E 630 GLN cc_start: 0.9351 (mt0) cc_final: 0.8918 (tm-30) REVERT: G 63 LEU cc_start: 0.9082 (mt) cc_final: 0.8877 (mt) REVERT: G 100 MET cc_start: 0.7536 (tpp) cc_final: 0.7251 (tpp) REVERT: J 17 GLN cc_start: 0.8775 (mp10) cc_final: 0.8468 (mp10) REVERT: J 28 LEU cc_start: 0.9215 (mm) cc_final: 0.8722 (tt) REVERT: D 95 MET cc_start: 0.8235 (ppp) cc_final: 0.7740 (ppp) REVERT: D 99 ASN cc_start: 0.8856 (m-40) cc_final: 0.8219 (t0) REVERT: D 195 ASN cc_start: 0.9038 (p0) cc_final: 0.8729 (p0) REVERT: D 323 ILE cc_start: 0.9154 (pt) cc_final: 0.8935 (mm) REVERT: F 530 MET cc_start: 0.6721 (tpt) cc_final: 0.6335 (tpt) REVERT: I 63 LEU cc_start: 0.9137 (mt) cc_final: 0.8893 (mt) REVERT: I 100 GLU cc_start: 0.8271 (mp0) cc_final: 0.7865 (mp0) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.1407 time to fit residues: 34.2682 Evaluate side-chains 118 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 79 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 145 optimal weight: 9.9990 chunk 204 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 183 optimal weight: 20.0000 chunk 104 optimal weight: 0.9980 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN L 6 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 ASN E 591 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN F 656 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.039666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.032475 restraints weight = 177368.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.033416 restraints weight = 105074.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.034060 restraints weight = 73332.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.034499 restraints weight = 57044.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.034816 restraints weight = 47772.261| |-----------------------------------------------------------------------------| r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 20757 Z= 0.217 Angle : 0.840 10.536 28446 Z= 0.391 Chirality : 0.048 0.378 3561 Planarity : 0.004 0.043 3345 Dihedral : 5.681 26.590 2517 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.59 % Favored : 89.28 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.17), residues: 2295 helix: -0.90 (0.29), residues: 312 sheet: -0.71 (0.20), residues: 705 loop : -2.42 (0.16), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 94 TYR 0.027 0.002 TYR C 217 PHE 0.020 0.002 PHE A 382 TRP 0.020 0.002 TRP A 35 HIS 0.005 0.001 HIS E 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.22 (20583) covalent geometry : angle 0.80294 / 0.38 (27963) SS BOND : bond 0.00350 / 0.21 ( 39) SS BOND : angle 1.25788 / 0.82 ( 78) hydrogen bonds : bond 0.03677 / 2.41 ( 523) hydrogen bonds : angle 6.17939 / 4.24 ( 1461) link_ALPHA1-2 : bond 0.00271 / 0.16 ( 18) link_ALPHA1-2 : angle 2.09817 / 1.51 ( 54) link_ALPHA1-3 : bond 0.00423 / 0.26 ( 15) link_ALPHA1-3 : angle 1.59997 / 1.12 ( 45) link_ALPHA1-6 : bond 0.00571 / 0.35 ( 9) link_ALPHA1-6 : angle 1.55054 / 1.07 ( 27) link_BETA1-4 : bond 0.00340 / 0.21 ( 45) link_BETA1-4 : angle 1.92124 / 1.30 ( 135) link_NAG-ASN : bond 0.00493 / 0.33 ( 48) link_NAG-ASN : angle 2.62546 / 2.11 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.771 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8371 (ppp) cc_final: 0.8062 (ppp) REVERT: A 99 ASN cc_start: 0.8911 (m-40) cc_final: 0.8235 (t0) REVERT: A 195 ASN cc_start: 0.9007 (p0) cc_final: 0.8779 (p0) REVERT: A 434 MET cc_start: 0.8541 (tmm) cc_final: 0.8329 (tmm) REVERT: B 530 MET cc_start: 0.6213 (mmm) cc_final: 0.5906 (mmm) REVERT: B 591 GLN cc_start: 0.9116 (tp-100) cc_final: 0.8664 (tt0) REVERT: B 626 MET cc_start: 0.8642 (mmp) cc_final: 0.8412 (mmm) REVERT: B 652 GLN cc_start: 0.7895 (mt0) cc_final: 0.7659 (mt0) REVERT: H 63 LEU cc_start: 0.8839 (mt) cc_final: 0.8616 (mt) REVERT: H 82 MET cc_start: 0.8949 (tmm) cc_final: 0.8545 (tmm) REVERT: H 89 MET cc_start: 0.8758 (tpt) cc_final: 0.8338 (tpp) REVERT: C 95 MET cc_start: 0.8561 (ptm) cc_final: 0.8143 (ppp) REVERT: C 104 MET cc_start: 0.8723 (tpt) cc_final: 0.8466 (tpt) REVERT: E 542 ARG cc_start: 0.8526 (ptm-80) cc_final: 0.8230 (ttp80) REVERT: E 607 ASN cc_start: 0.9021 (p0) cc_final: 0.8039 (m-40) REVERT: E 626 MET cc_start: 0.7921 (tmm) cc_final: 0.5843 (tmm) REVERT: E 630 GLN cc_start: 0.9394 (mt0) cc_final: 0.8900 (tm-30) REVERT: G 63 LEU cc_start: 0.9169 (mt) cc_final: 0.8968 (mt) REVERT: J 17 GLN cc_start: 0.8814 (mp10) cc_final: 0.8490 (mp10) REVERT: J 28 LEU cc_start: 0.9274 (mm) cc_final: 0.8835 (tt) REVERT: D 95 MET cc_start: 0.8266 (ppp) cc_final: 0.7970 (ppp) REVERT: D 99 ASN cc_start: 0.8875 (m-40) cc_final: 0.8188 (t0) REVERT: D 161 MET cc_start: 0.8840 (tpt) cc_final: 0.8600 (tpt) REVERT: D 195 ASN cc_start: 0.9125 (p0) cc_final: 0.8852 (p0) REVERT: F 530 MET cc_start: 0.6834 (tpt) cc_final: 0.6359 (tpt) REVERT: I 63 LEU cc_start: 0.9171 (mt) cc_final: 0.8951 (mt) REVERT: I 82 MET cc_start: 0.7416 (mmp) cc_final: 0.7195 (mmm) REVERT: I 89 MET cc_start: 0.8461 (tpt) cc_final: 0.8214 (tpp) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1432 time to fit residues: 33.5548 Evaluate side-chains 110 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 48 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 136 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 208 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 170 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN K 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.039850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.032727 restraints weight = 174385.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.033680 restraints weight = 103142.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.034344 restraints weight = 71529.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.034793 restraints weight = 55241.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.035121 restraints weight = 46060.756| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20757 Z= 0.171 Angle : 0.792 10.371 28446 Z= 0.369 Chirality : 0.047 0.373 3561 Planarity : 0.004 0.045 3345 Dihedral : 5.613 23.304 2517 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.63 % Favored : 90.24 % Rotamer: Outliers : 0.05 % Allowed : 0.48 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.17), residues: 2295 helix: -0.88 (0.29), residues: 312 sheet: -0.65 (0.20), residues: 729 loop : -2.43 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 54 TYR 0.023 0.002 TYR A 217 PHE 0.018 0.002 PHE A 382 TRP 0.020 0.002 TRP D 427 HIS 0.003 0.001 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (20583) covalent geometry : angle 0.75749 / 0.36 (27963) SS BOND : bond 0.00277 / 0.16 ( 39) SS BOND : angle 1.13348 / 0.75 ( 78) hydrogen bonds : bond 0.03497 / 2.32 ( 523) hydrogen bonds : angle 6.05871 / 4.14 ( 1461) link_ALPHA1-2 : bond 0.00269 / 0.18 ( 18) link_ALPHA1-2 : angle 1.92754 / 1.37 ( 54) link_ALPHA1-3 : bond 0.00477 / 0.30 ( 15) link_ALPHA1-3 : angle 1.52227 / 1.07 ( 45) link_ALPHA1-6 : bond 0.00488 / 0.28 ( 9) link_ALPHA1-6 : angle 1.51695 / 1.01 ( 27) link_BETA1-4 : bond 0.00291 / 0.18 ( 45) link_BETA1-4 : angle 1.76263 / 1.20 ( 135) link_NAG-ASN : bond 0.00346 / 0.23 ( 48) link_NAG-ASN : angle 2.52182 / 1.99 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.811 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: symmetry clash REVERT: A 95 MET cc_start: 0.8438 (ppp) cc_final: 0.8108 (ppp) REVERT: A 99 ASN cc_start: 0.8839 (m-40) cc_final: 0.8259 (t0) REVERT: A 195 ASN cc_start: 0.8871 (p0) cc_final: 0.8643 (p0) REVERT: B 591 GLN cc_start: 0.8982 (tp-100) cc_final: 0.8607 (tt0) REVERT: B 648 GLU cc_start: 0.8509 (pt0) cc_final: 0.8171 (pt0) REVERT: B 652 GLN cc_start: 0.7832 (mt0) cc_final: 0.7533 (mt0) REVERT: H 63 LEU cc_start: 0.8788 (mt) cc_final: 0.8578 (mt) REVERT: H 82 MET cc_start: 0.8827 (tmm) cc_final: 0.8345 (tmm) REVERT: H 89 MET cc_start: 0.8559 (tpt) cc_final: 0.8225 (tpp) REVERT: C 95 MET cc_start: 0.8561 (ptm) cc_final: 0.8143 (ppp) REVERT: E 591 GLN cc_start: 0.9105 (tp40) cc_final: 0.8769 (tt0) REVERT: E 607 ASN cc_start: 0.9040 (p0) cc_final: 0.8131 (m-40) REVERT: E 630 GLN cc_start: 0.9317 (mt0) cc_final: 0.8897 (mp10) REVERT: J 17 GLN cc_start: 0.8746 (mp10) cc_final: 0.8453 (mp10) REVERT: J 28 LEU cc_start: 0.9265 (mm) cc_final: 0.8847 (tt) REVERT: D 95 MET cc_start: 0.8356 (ppp) cc_final: 0.8038 (ppp) REVERT: D 99 ASN cc_start: 0.8860 (m-40) cc_final: 0.8275 (t0) REVERT: D 195 ASN cc_start: 0.8966 (p0) cc_final: 0.8761 (p0) REVERT: F 530 MET cc_start: 0.6988 (tpt) cc_final: 0.6587 (tpt) REVERT: I 63 LEU cc_start: 0.9088 (mt) cc_final: 0.8886 (mt) REVERT: I 82 MET cc_start: 0.7419 (mmp) cc_final: 0.7140 (mmm) REVERT: I 89 MET cc_start: 0.8352 (tpt) cc_final: 0.8090 (tpp) REVERT: I 100 GLU cc_start: 0.8224 (mp0) cc_final: 0.7886 (mp0) outliers start: 1 outliers final: 0 residues processed: 143 average time/residue: 0.1336 time to fit residues: 31.4249 Evaluate side-chains 110 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 182 optimal weight: 20.0000 chunk 107 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 chunk 150 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 170 optimal weight: 8.9990 chunk 2 optimal weight: 20.0000 chunk 111 optimal weight: 4.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 ASN ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.039436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.032318 restraints weight = 178667.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.033259 restraints weight = 104955.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.033912 restraints weight = 72922.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.034347 restraints weight = 56368.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.034668 restraints weight = 47166.592| |-----------------------------------------------------------------------------| r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20757 Z= 0.200 Angle : 0.832 10.428 28446 Z= 0.386 Chirality : 0.047 0.341 3561 Planarity : 0.004 0.041 3345 Dihedral : 5.689 22.900 2517 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.89 % Favored : 88.98 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.17), residues: 2295 helix: -0.74 (0.29), residues: 312 sheet: -0.66 (0.19), residues: 729 loop : -2.42 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 54 TYR 0.038 0.002 TYR A 217 PHE 0.020 0.002 PHE A 382 TRP 0.022 0.002 TRP D 35 HIS 0.004 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.20 (20583) covalent geometry : angle 0.79740 / 0.38 (27963) SS BOND : bond 0.00302 / 0.18 ( 39) SS BOND : angle 1.16621 / 0.77 ( 78) hydrogen bonds : bond 0.03608 / 2.39 ( 523) hydrogen bonds : angle 6.18649 / 4.21 ( 1461) link_ALPHA1-2 : bond 0.00280 / 0.17 ( 18) link_ALPHA1-2 : angle 2.05581 / 1.48 ( 54) link_ALPHA1-3 : bond 0.00441 / 0.28 ( 15) link_ALPHA1-3 : angle 1.57697 / 1.11 ( 45) link_ALPHA1-6 : bond 0.00529 / 0.30 ( 9) link_ALPHA1-6 : angle 1.53098 / 1.03 ( 27) link_BETA1-4 : bond 0.00327 / 0.20 ( 45) link_BETA1-4 : angle 1.85717 / 1.26 ( 135) link_NAG-ASN : bond 0.00455 / 0.30 ( 48) link_NAG-ASN : angle 2.55374 / 2.03 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2620.17 seconds wall clock time: 46 minutes 59.95 seconds (2819.95 seconds total)