Starting phenix.real_space_refine on Fri May 23 11:45:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f02_50092/05_2025/9f02_50092.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f02_50092/05_2025/9f02_50092.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9f02_50092/05_2025/9f02_50092.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f02_50092/05_2025/9f02_50092.map" model { file = "/net/cci-nas-00/data/ceres_data/9f02_50092/05_2025/9f02_50092.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f02_50092/05_2025/9f02_50092.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 sd= 0.023 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 141 5.16 5 C 15141 2.51 5 N 4083 2.21 5 O 4818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24183 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 882 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 110} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3470 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 419} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 3470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3470 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 419} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 882 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 110} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 882 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 110} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1711 Classifications: {'peptide': 230} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 217} Chain: "L" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1629 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 200} Chain: "I" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1711 Classifications: {'peptide': 230} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 217} Chain: "J" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1629 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 200} Chain: "K" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1711 Classifications: {'peptide': 230} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 217} Chain: "M" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1629 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 200} Chain: "N" Number of atoms: 3470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3470 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 419} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "e" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "h" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "G" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "N" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 14.46, per 1000 atoms: 0.60 Number of scatterers: 24183 At special positions: 0 Unit cell: (175.75, 171.95, 146.3, 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 141 16.00 O 4818 8.00 N 4083 7.00 C 15141 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS C 501 " 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=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 605 " - pdb=" SG CYS N 501 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS H 216 " - pdb=" SG CYS L 214 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 140 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 216 " - pdb=" SG CYS J 214 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 134 " - pdb=" SG CYS J 194 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 140 " - pdb=" SG CYS K 196 " distance=2.03 Simple disulfide: pdb=" SG CYS K 216 " - pdb=" SG CYS M 214 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 134 " - pdb=" SG CYS M 194 " distance=2.03 Simple disulfide: pdb=" SG CYS N 54 " - pdb=" SG CYS N 74 " distance=2.04 Simple disulfide: pdb=" SG CYS N 119 " - pdb=" SG CYS N 205 " distance=2.04 Simple disulfide: pdb=" SG CYS N 126 " - pdb=" SG CYS N 196 " distance=2.03 Simple disulfide: pdb=" SG CYS N 131 " - pdb=" SG CYS N 157 " distance=2.03 Simple disulfide: pdb=" SG CYS N 228 " - pdb=" SG CYS N 239 " distance=2.03 Simple disulfide: pdb=" SG CYS N 296 " - pdb=" SG CYS N 331 " distance=2.03 Simple disulfide: pdb=" SG CYS N 378 " - pdb=" SG CYS N 445 " distance=2.03 Simple disulfide: pdb=" SG CYS N 385 " - pdb=" SG CYS N 418 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 4 " " BMA g 3 " - " MAN g 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG D 1 " - " NAG D 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG u 1 " - " NAG u 2 " NAG-ASN " NAG B 1 " - " ASN C 386 " " NAG C 601 " - " ASN C 234 " " NAG C 602 " - " ASN C 392 " " NAG C 603 " - " ASN C 301 " " NAG C 604 " - " ASN C 355 " " NAG C 605 " - " ASN C 339 " " NAG C 606 " - " ASN C 197 " " NAG C 607 " - " ASN C 160 " " NAG C 608 " - " ASN C 448 " " NAG D 1 " - " ASN C 363 " " NAG G 601 " - " ASN G 234 " " NAG G 602 " - " ASN G 392 " " NAG G 603 " - " ASN G 301 " " NAG G 604 " - " ASN G 355 " " NAG G 605 " - " ASN G 339 " " NAG G 606 " - " ASN G 197 " " NAG G 607 " - " ASN G 160 " " NAG G 608 " - " ASN G 448 " " NAG N 601 " - " ASN N 234 " " NAG N 602 " - " ASN N 392 " " NAG N 603 " - " ASN N 301 " " NAG N 604 " - " ASN N 355 " " NAG N 605 " - " ASN N 339 " " NAG N 606 " - " ASN N 197 " " NAG N 607 " - " ASN N 160 " " NAG N 608 " - " ASN N 448 " " NAG O 1 " - " ASN C 332 " " NAG P 1 " - " ASN C 156 " " NAG Q 1 " - " ASN C 295 " " NAG R 1 " - " ASN G 276 " " NAG S 1 " - " ASN G 386 " " NAG T 1 " - " ASN G 363 " " NAG U 1 " - " ASN G 332 " " NAG V 1 " - " ASN G 156 " " NAG W 1 " - " ASN G 295 " " NAG X 1 " - " ASN N 276 " " NAG Y 1 " - " ASN N 386 " " NAG Z 1 " - " ASN N 363 " " NAG a 1 " - " ASN N 332 " " NAG b 1 " - " ASN N 156 " " NAG c 1 " - " ASN N 295 " " NAG d 1 " - " ASN G 262 " " NAG e 1 " - " ASN C 262 " " NAG f 1 " - " ASN G 88 " " NAG g 1 " - " ASN N 262 " " NAG h 1 " - " ASN N 88 " " NAG q 1 " - " ASN C 88 " " NAG u 1 " - " ASN C 276 " Time building additional restraints: 6.99 Conformation dependent library (CDL) restraints added in 2.9 seconds 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5514 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 63 sheets defined 15.5% alpha, 40.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.12 Creating SS restraints... Processing helix chain 'A' and resid 523 through 527 removed outlier: 3.505A pdb=" N ALA A 526 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLY A 527 " --> pdb=" O GLY A 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 523 through 527' Processing helix chain 'A' and resid 531 through 535 removed outlier: 3.590A pdb=" N MET A 535 " --> pdb=" O ALA A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 543 removed outlier: 4.042A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 596 Processing helix chain 'A' and resid 618 through 622 removed outlier: 3.570A pdb=" N ILE A 622 " --> pdb=" O LEU A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 636 removed outlier: 3.511A pdb=" N LYS A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 652 Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 99 through 115 removed outlier: 3.587A pdb=" N GLN C 103 " --> pdb=" O ASN C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 354 removed outlier: 4.184A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY C 354 " --> pdb=" O ARG C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 480 Processing helix chain 'G' and resid 70 through 74 Processing helix chain 'G' and resid 96 through 98 No H-bonds generated for 'chain 'G' and resid 96 through 98' Processing helix chain 'G' and resid 99 through 115 Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 335 through 350 Processing helix chain 'G' and resid 474 through 478 removed outlier: 3.586A pdb=" N ASP G 477 " --> pdb=" O ASP G 474 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 527 removed outlier: 4.592A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 4.063A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 596 removed outlier: 3.549A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 622 removed outlier: 3.541A pdb=" N ILE F 622 " --> pdb=" O LEU F 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 652 Processing helix chain 'E' and resid 531 through 535 removed outlier: 3.748A pdb=" N MET E 535 " --> pdb=" O ALA E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 536 through 543 removed outlier: 4.067A pdb=" N GLN E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 597 removed outlier: 3.522A pdb=" N ALA E 578 " --> pdb=" O LYS E 574 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 636 removed outlier: 3.518A pdb=" N LYS E 633 " --> pdb=" O LEU E 629 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 652 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 127 through 129 No H-bonds generated for 'chain 'H' and resid 127 through 129' Processing helix chain 'H' and resid 156 through 158 No H-bonds generated for 'chain 'H' and resid 156 through 158' Processing helix chain 'H' and resid 187 through 189 No H-bonds generated for 'chain 'H' and resid 187 through 189' Processing helix chain 'L' and resid 121 through 126 Processing helix chain 'L' and resid 183 through 189 removed outlier: 3.719A pdb=" N HIS L 189 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 127 through 129 No H-bonds generated for 'chain 'I' and resid 127 through 129' Processing helix chain 'I' and resid 156 through 158 No H-bonds generated for 'chain 'I' and resid 156 through 158' Processing helix chain 'I' and resid 187 through 189 No H-bonds generated for 'chain 'I' and resid 187 through 189' Processing helix chain 'J' and resid 121 through 126 Processing helix chain 'J' and resid 183 through 189 removed outlier: 3.652A pdb=" N HIS J 189 " --> pdb=" O ASP J 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 127 through 129 No H-bonds generated for 'chain 'K' and resid 127 through 129' Processing helix chain 'K' and resid 156 through 158 No H-bonds generated for 'chain 'K' and resid 156 through 158' Processing helix chain 'K' and resid 187 through 189 No H-bonds generated for 'chain 'K' and resid 187 through 189' Processing helix chain 'M' and resid 121 through 126 Processing helix chain 'M' and resid 183 through 189 removed outlier: 3.768A pdb=" N HIS M 189 " --> pdb=" O ASP M 185 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 74 Processing helix chain 'N' and resid 98 through 115 removed outlier: 4.295A pdb=" N GLU N 102 " --> pdb=" O ASN N 98 " (cutoff:3.500A) Processing helix chain 'N' and resid 122 through 126 Processing helix chain 'N' and resid 335 through 354 removed outlier: 4.203A pdb=" N LYS N 351 " --> pdb=" O LYS N 347 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N HIS N 352 " --> pdb=" O GLN N 348 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE N 353 " --> pdb=" O LEU N 349 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY N 354 " --> pdb=" O ARG N 350 " (cutoff:3.500A) Processing helix chain 'N' and resid 368 through 373 removed outlier: 3.507A pdb=" N THR N 373 " --> pdb=" O LEU N 369 " (cutoff:3.500A) Processing helix chain 'N' and resid 475 through 480 Processing sheet with id=AA1, first strand: chain 'A' and resid 603 through 609 removed outlier: 5.087A pdb=" N VAL C 36 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.647A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.101A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.366A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.531A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 12.118A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 11.885A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.096A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.100A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 271 through 273 removed outlier: 11.100A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 11.096A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.885A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 12.118A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.531A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.519A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 494 through 499 removed outlier: 5.041A pdb=" N VAL G 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 45 through 47 removed outlier: 4.638A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 75 through 76 Processing sheet with id=AB4, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'G' and resid 169 through 177 Processing sheet with id=AB6, first strand: chain 'G' and resid 200 through 203 removed outlier: 6.092A pdb=" N ALA G 200 " --> pdb=" O ALA G 433 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N TYR G 435 " --> pdb=" O ALA G 200 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.296A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.471A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 12.099A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 11.879A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 11.082A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 11.112A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS G 421 " --> pdb=" O PHE G 382 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU G 381 " --> pdb=" O CYS G 378 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 271 through 273 removed outlier: 11.112A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 11.082A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 11.879A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 12.099A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 10.471A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 304 through 312 removed outlier: 6.503A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 603 through 609 removed outlier: 5.109A pdb=" N VAL N 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.579A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AC5, first strand: chain 'H' and resid 97 through 100A removed outlier: 6.300A pdb=" N ARG H 100D" --> pdb=" O SER H 100 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 120 through 124 removed outlier: 3.581A pdb=" N ASP H 144 " --> pdb=" O TYR H 176 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 131 through 132 removed outlier: 3.581A pdb=" N ASP H 144 " --> pdb=" O TYR H 176 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 151 through 154 removed outlier: 4.325A pdb=" N TYR H 194 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD1, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.640A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N LYS L 107 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ALA L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU L 33 " --> pdb=" O THR L 49 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N THR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.640A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N LYS L 107 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ALA L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.812A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 153 through 155 removed outlier: 4.832A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AD6, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.553A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 10 through 12 Processing sheet with id=AD8, first strand: chain 'I' and resid 97 through 100A removed outlier: 6.279A pdb=" N ARG I 100D" --> pdb=" O SER I 100 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 120 through 124 removed outlier: 3.526A pdb=" N ASP I 144 " --> pdb=" O TYR I 176 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TYR I 176 " --> pdb=" O ASP I 144 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 131 through 132 removed outlier: 3.526A pdb=" N ASP I 144 " --> pdb=" O TYR I 176 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TYR I 176 " --> pdb=" O ASP I 144 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 151 through 154 removed outlier: 4.200A pdb=" N TYR I 194 " --> pdb=" O VAL I 211 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AE4, first strand: chain 'J' and resid 10 through 14 removed outlier: 7.027A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N LYS J 107 " --> pdb=" O LEU J 11 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ALA J 13 " --> pdb=" O LYS J 107 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU J 33 " --> pdb=" O THR J 49 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N THR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 10 through 14 removed outlier: 7.027A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N LYS J 107 " --> pdb=" O LEU J 11 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ALA J 13 " --> pdb=" O LYS J 107 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR J 97 " --> pdb=" O GLN J 90 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 114 through 118 removed outlier: 6.119A pdb=" N TYR J 173 " --> pdb=" O ASN J 138 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 153 through 154 Processing sheet with id=AE8, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AE9, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.561A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 10 through 12 Processing sheet with id=AF2, first strand: chain 'K' and resid 97 through 99 Processing sheet with id=AF3, first strand: chain 'K' and resid 120 through 124 removed outlier: 3.614A pdb=" N ASP K 144 " --> pdb=" O TYR K 176 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N TYR K 176 " --> pdb=" O ASP K 144 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 131 through 132 removed outlier: 3.614A pdb=" N ASP K 144 " --> pdb=" O TYR K 176 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N TYR K 176 " --> pdb=" O ASP K 144 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 151 through 154 removed outlier: 4.328A pdb=" N TYR K 194 " --> pdb=" O VAL K 211 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AF7, first strand: chain 'M' and resid 10 through 14 removed outlier: 6.655A pdb=" N LEU M 11 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LYS M 107 " --> pdb=" O LEU M 11 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ALA M 13 " --> pdb=" O LYS M 107 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU M 33 " --> pdb=" O THR M 49 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N THR M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 10 through 14 removed outlier: 6.655A pdb=" N LEU M 11 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LYS M 107 " --> pdb=" O LEU M 11 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ALA M 13 " --> pdb=" O LYS M 107 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR M 97 " --> pdb=" O GLN M 90 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 114 through 118 removed outlier: 5.853A pdb=" N TYR M 173 " --> pdb=" O ASN M 138 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 153 through 154 Processing sheet with id=AG2, first strand: chain 'N' and resid 45 through 47 removed outlier: 4.643A pdb=" N VAL N 242 " --> pdb=" O LEU N 86 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'N' and resid 75 through 76 Processing sheet with id=AG4, first strand: chain 'N' and resid 91 through 94 removed outlier: 3.576A pdb=" N GLU N 91 " --> pdb=" O CYS N 239 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 169 through 177 Processing sheet with id=AG6, first strand: chain 'N' and resid 200 through 203 removed outlier: 6.098A pdb=" N ALA N 200 " --> pdb=" O ALA N 433 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N TYR N 435 " --> pdb=" O ALA N 200 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR N 202 " --> pdb=" O TYR N 435 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'N' and resid 259 through 261 removed outlier: 6.435A pdb=" N LEU N 260 " --> pdb=" O THR N 450 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLY N 451 " --> pdb=" O THR N 290 " (cutoff:3.500A) removed outlier: 10.626A pdb=" N THR N 290 " --> pdb=" O GLY N 451 " (cutoff:3.500A) removed outlier: 12.102A pdb=" N ILE N 453 " --> pdb=" O PHE N 288 " (cutoff:3.500A) removed outlier: 11.868A pdb=" N PHE N 288 " --> pdb=" O ILE N 453 " (cutoff:3.500A) removed outlier: 11.086A pdb=" N THR N 455 " --> pdb=" O VAL N 286 " (cutoff:3.500A) removed outlier: 11.093A pdb=" N VAL N 286 " --> pdb=" O THR N 455 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N GLN N 293 " --> pdb=" O SER N 334 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER N 334 " --> pdb=" O GLN N 293 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS N 421 " --> pdb=" O PHE N 382 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N PHE N 382 " --> pdb=" O LYS N 421 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU N 381 " --> pdb=" O CYS N 378 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'N' and resid 271 through 273 removed outlier: 11.093A pdb=" N VAL N 286 " --> pdb=" O THR N 455 " (cutoff:3.500A) removed outlier: 11.086A pdb=" N THR N 455 " --> pdb=" O VAL N 286 " (cutoff:3.500A) removed outlier: 11.868A pdb=" N PHE N 288 " --> pdb=" O ILE N 453 " (cutoff:3.500A) removed outlier: 12.102A pdb=" N ILE N 453 " --> pdb=" O PHE N 288 " (cutoff:3.500A) removed outlier: 10.626A pdb=" N THR N 290 " --> pdb=" O GLY N 451 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLY N 451 " --> pdb=" O THR N 290 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 304 through 312 removed outlier: 6.509A pdb=" N GLN N 315 " --> pdb=" O ILE N 309 " (cutoff:3.500A) 1018 hydrogen bonds defined for protein. 2616 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: 9.95 Time building geometry restraints manager: 7.97 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: 7581 1.34 - 1.46: 6028 1.46 - 1.58: 10892 1.58 - 1.70: 0 1.70 - 1.82: 186 Bond restraints: 24687 Sorted by residual: bond pdb=" C PHE H 100H" pdb=" N GLY H 100I" ideal model delta sigma weight residual 1.334 1.324 0.010 1.12e-02 7.97e+03 8.10e-01 bond pdb=" C PHE K 100H" pdb=" N GLY K 100I" ideal model delta sigma weight residual 1.334 1.324 0.010 1.12e-02 7.97e+03 7.68e-01 bond pdb=" CA LYS C 117 " pdb=" C LYS C 117 " ideal model delta sigma weight residual 1.520 1.530 -0.010 1.23e-02 6.61e+03 6.64e-01 bond pdb=" C LYS C 117 " pdb=" N PRO C 118 " ideal model delta sigma weight residual 1.331 1.338 -0.006 7.90e-03 1.60e+04 6.10e-01 bond pdb=" C2 NAG N 607 " pdb=" N2 NAG N 607 " ideal model delta sigma weight residual 1.439 1.455 -0.016 2.00e-02 2.50e+03 6.05e-01 ... (remaining 24682 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 33168 1.90 - 3.80: 316 3.80 - 5.70: 36 5.70 - 7.60: 2 7.60 - 9.50: 3 Bond angle restraints: 33525 Sorted by residual: angle pdb=" N ILE F 622 " pdb=" CA ILE F 622 " pdb=" C ILE F 622 " ideal model delta sigma weight residual 111.56 108.83 2.73 8.60e-01 1.35e+00 1.01e+01 angle pdb=" C2 NAG G 607 " pdb=" N2 NAG G 607 " pdb=" C7 NAG G 607 " ideal model delta sigma weight residual 124.56 134.06 -9.50 3.00e+00 1.11e-01 1.00e+01 angle pdb=" C2 NAG C 607 " pdb=" N2 NAG C 607 " pdb=" C7 NAG C 607 " ideal model delta sigma weight residual 124.56 133.98 -9.42 3.00e+00 1.11e-01 9.87e+00 angle pdb=" C2 NAG N 607 " pdb=" N2 NAG N 607 " pdb=" C7 NAG N 607 " ideal model delta sigma weight residual 124.56 133.98 -9.42 3.00e+00 1.11e-01 9.87e+00 angle pdb=" C ASN N 136 " pdb=" N ASN N 137 " pdb=" CA ASN N 137 " ideal model delta sigma weight residual 121.54 125.71 -4.17 1.91e+00 2.74e-01 4.76e+00 ... (remaining 33520 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.37: 14987 16.37 - 32.75: 639 32.75 - 49.12: 157 49.12 - 65.50: 47 65.50 - 81.87: 13 Dihedral angle restraints: 15843 sinusoidal: 7266 harmonic: 8577 Sorted by residual: dihedral pdb=" CA CYS N 196 " pdb=" C CYS N 196 " pdb=" N ASN N 197 " pdb=" CA ASN N 197 " ideal model delta harmonic sigma weight residual 180.00 158.44 21.56 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -119.27 33.27 1 1.00e+01 1.00e-02 1.57e+01 dihedral pdb=" CB CYS N 119 " pdb=" SG CYS N 119 " pdb=" SG CYS N 205 " pdb=" CB CYS N 205 " ideal model delta sinusoidal sigma weight residual -86.00 -119.15 33.15 1 1.00e+01 1.00e-02 1.56e+01 ... (remaining 15840 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3287 0.050 - 0.100: 524 0.100 - 0.150: 192 0.150 - 0.200: 2 0.200 - 0.250: 3 Chirality restraints: 4008 Sorted by residual: chirality pdb=" C2 NAG N 607 " pdb=" C1 NAG N 607 " pdb=" C3 NAG N 607 " pdb=" N2 NAG N 607 " both_signs ideal model delta sigma weight residual False -2.49 -2.24 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" C2 NAG G 607 " pdb=" C1 NAG G 607 " pdb=" C3 NAG G 607 " pdb=" N2 NAG G 607 " both_signs ideal model delta sigma weight residual False -2.49 -2.24 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" C2 NAG C 607 " pdb=" C1 NAG C 607 " pdb=" C3 NAG C 607 " pdb=" N2 NAG C 607 " both_signs ideal model delta sigma weight residual False -2.49 -2.24 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 4005 not shown) Planarity restraints: 4221 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 148 " -0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO H 149 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO H 149 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO H 149 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU K 148 " 0.033 5.00e-02 4.00e+02 4.90e-02 3.84e+00 pdb=" N PRO K 149 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO K 149 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO K 149 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU I 148 " -0.032 5.00e-02 4.00e+02 4.79e-02 3.67e+00 pdb=" N PRO I 149 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO I 149 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO I 149 " -0.024 5.00e-02 4.00e+02 ... (remaining 4218 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1018 2.73 - 3.27: 21549 3.27 - 3.81: 37369 3.81 - 4.36: 46209 4.36 - 4.90: 81543 Nonbonded interactions: 187688 Sorted by model distance: nonbonded pdb=" OE2 GLU L 105 " pdb=" OH TYR L 173 " model vdw 2.183 3.040 nonbonded pdb=" OE2 GLU M 105 " pdb=" OH TYR M 173 " model vdw 2.191 3.040 nonbonded pdb=" OG1 THR G 37 " pdb=" OG1 THR G 499 " model vdw 2.195 3.040 nonbonded pdb=" OG1 THR N 37 " pdb=" OG1 THR N 499 " model vdw 2.198 3.040 nonbonded pdb=" OG1 THR C 37 " pdb=" OG1 THR C 499 " model vdw 2.202 3.040 ... (remaining 187683 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'u' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'N' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'd' selection = chain 'e' selection = chain 'g' } ncs_group { reference = chain 'f' selection = chain 'h' selection = chain 'q' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.060 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 56.650 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.200 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 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 : 0.002 0.026 24813 Z= 0.109 Angle : 0.531 9.499 33858 Z= 0.273 Chirality : 0.043 0.250 4008 Planarity : 0.004 0.050 4173 Dihedral : 9.922 81.871 10194 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.24 % Allowed : 5.55 % Favored : 93.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.16), residues: 2943 helix: 0.63 (0.27), residues: 423 sheet: 1.58 (0.16), residues: 1047 loop : -0.49 (0.16), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 96 HIS 0.003 0.001 HIS K 200 PHE 0.013 0.001 PHE N 383 TYR 0.011 0.001 TYR I 98 ARG 0.003 0.000 ARG E 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00219 ( 48) link_NAG-ASN : angle 1.80114 ( 144) link_BETA1-4 : bond 0.00693 ( 30) link_BETA1-4 : angle 1.98576 ( 90) link_ALPHA1-3 : bond 0.00607 ( 3) link_ALPHA1-3 : angle 1.26994 ( 9) hydrogen bonds : bond 0.13969 ( 937) hydrogen bonds : angle 5.23969 ( 2616) SS BOND : bond 0.00277 ( 45) SS BOND : angle 0.84689 ( 90) covalent geometry : bond 0.00225 (24687) covalent geometry : angle 0.50771 (33525) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 616 time to evaluate : 2.486 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: C 39 TYR cc_start: 0.8463 (m-80) cc_final: 0.8127 (m-80) REVERT: C 46 LYS cc_start: 0.7674 (tppt) cc_final: 0.7433 (tppt) REVERT: C 76 PRO cc_start: 0.7719 (Cg_exo) cc_final: 0.7444 (Cg_endo) REVERT: C 83 GLU cc_start: 0.7718 (tt0) cc_final: 0.7517 (tt0) REVERT: C 99 ASN cc_start: 0.8175 (t0) cc_final: 0.7690 (t0) REVERT: C 140 ASP cc_start: 0.7809 (t0) cc_final: 0.7514 (t0) REVERT: C 153 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7164 (mm-30) REVERT: C 161 MET cc_start: 0.7758 (tpp) cc_final: 0.7519 (tpp) REVERT: C 289 ASN cc_start: 0.8231 (t0) cc_final: 0.8019 (t160) REVERT: C 318 TYR cc_start: 0.8554 (m-80) cc_final: 0.8320 (m-80) REVERT: C 500 ARG cc_start: 0.8236 (ptp-110) cc_final: 0.7737 (mtp85) REVERT: G 46 LYS cc_start: 0.7699 (tppt) cc_final: 0.7493 (tppt) REVERT: G 76 PRO cc_start: 0.7879 (Cg_exo) cc_final: 0.7612 (Cg_endo) REVERT: G 111 LEU cc_start: 0.8861 (mt) cc_final: 0.8620 (mt) REVERT: G 153 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7209 (mm-30) REVERT: G 191 TYR cc_start: 0.8636 (m-80) cc_final: 0.8398 (m-80) REVERT: G 267 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7606 (mm-30) REVERT: G 358 ILE cc_start: 0.7808 (mm) cc_final: 0.7466 (mm) REVERT: G 381 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7219 (mm-30) REVERT: G 492 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7867 (mt-10) REVERT: F 540 GLN cc_start: 0.8590 (mp-120) cc_final: 0.7848 (mp10) REVERT: F 613 SER cc_start: 0.8373 (p) cc_final: 0.8163 (p) REVERT: L 24 GLN cc_start: 0.7815 (tm-30) cc_final: 0.7469 (tp40) REVERT: L 65 SER cc_start: 0.8570 (t) cc_final: 0.8214 (p) REVERT: L 89 GLN cc_start: 0.7900 (tt0) cc_final: 0.7560 (tt0) REVERT: L 107 LYS cc_start: 0.7321 (tppt) cc_final: 0.7005 (tppt) REVERT: J 3 GLN cc_start: 0.8593 (mm-40) cc_final: 0.8357 (mm-40) REVERT: J 24 GLN cc_start: 0.7700 (tm-30) cc_final: 0.7302 (tp40) REVERT: J 39 LYS cc_start: 0.8397 (mttt) cc_final: 0.8138 (mttm) REVERT: J 65 SER cc_start: 0.8459 (t) cc_final: 0.8177 (p) REVERT: K 4 LEU cc_start: 0.8609 (mt) cc_final: 0.8385 (mt) REVERT: K 115 SER cc_start: 0.8096 (m) cc_final: 0.7524 (t) REVERT: K 141 LEU cc_start: 0.5578 (OUTLIER) cc_final: 0.5153 (pp) REVERT: K 164 HIS cc_start: 0.8009 (m90) cc_final: 0.7608 (m90) REVERT: M 4 LEU cc_start: 0.8228 (mt) cc_final: 0.8023 (mp) REVERT: M 24 GLN cc_start: 0.7705 (tm-30) cc_final: 0.7388 (tp40) REVERT: M 65 SER cc_start: 0.8458 (t) cc_final: 0.8117 (p) REVERT: N 138 ILE cc_start: 0.7866 (pp) cc_final: 0.7602 (pp) REVERT: N 140 ASP cc_start: 0.7775 (t0) cc_final: 0.7542 (t0) REVERT: N 178 ARG cc_start: 0.7431 (ttp-110) cc_final: 0.7119 (ttp-110) REVERT: N 231 LYS cc_start: 0.8578 (mttm) cc_final: 0.8378 (mtpp) REVERT: N 412 ASP cc_start: 0.7113 (m-30) cc_final: 0.6857 (m-30) REVERT: N 426 MET cc_start: 0.8171 (mmm) cc_final: 0.7901 (mmm) REVERT: N 455 THR cc_start: 0.8436 (t) cc_final: 0.8233 (p) REVERT: N 466 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7487 (mm-30) outliers start: 32 outliers final: 6 residues processed: 634 average time/residue: 0.3849 time to fit residues: 368.9524 Evaluate side-chains 552 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 545 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 178 THR Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain N residue 323 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 2.9990 chunk 225 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 76 optimal weight: 0.4980 chunk 151 optimal weight: 0.0070 chunk 120 optimal weight: 0.9980 chunk 232 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 141 optimal weight: 9.9990 chunk 173 optimal weight: 4.9990 chunk 269 optimal weight: 2.9990 overall best weight: 0.9002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 ASN C 356 ASN G 289 ASN F 637 ASN H 155 ASN ** H 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 ASN ** J 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN M 198 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.141534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.104709 restraints weight = 37103.693| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.59 r_work: 0.3138 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24813 Z= 0.173 Angle : 0.632 10.041 33858 Z= 0.311 Chirality : 0.046 0.284 4008 Planarity : 0.004 0.046 4173 Dihedral : 5.825 57.261 4877 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.29 % Allowed : 10.21 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.16), residues: 2943 helix: 0.49 (0.26), residues: 444 sheet: 1.61 (0.17), residues: 1005 loop : -0.46 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 112 HIS 0.007 0.001 HIS N 249 PHE 0.022 0.002 PHE N 53 TYR 0.019 0.001 TYR I 98 ARG 0.006 0.001 ARG I 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00395 ( 48) link_NAG-ASN : angle 2.06633 ( 144) link_BETA1-4 : bond 0.00658 ( 30) link_BETA1-4 : angle 2.13689 ( 90) link_ALPHA1-3 : bond 0.00694 ( 3) link_ALPHA1-3 : angle 1.22401 ( 9) hydrogen bonds : bond 0.04920 ( 937) hydrogen bonds : angle 4.88016 ( 2616) SS BOND : bond 0.00447 ( 45) SS BOND : angle 1.74214 ( 90) covalent geometry : bond 0.00415 (24687) covalent geometry : angle 0.60385 (33525) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 588 time to evaluate : 2.758 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: C 39 TYR cc_start: 0.8710 (m-80) cc_final: 0.8282 (m-80) REVERT: C 46 LYS cc_start: 0.8178 (tppt) cc_final: 0.7880 (tppt) REVERT: C 83 GLU cc_start: 0.8193 (tt0) cc_final: 0.7863 (tt0) REVERT: C 99 ASN cc_start: 0.8512 (t0) cc_final: 0.8056 (t0) REVERT: C 153 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7675 (mm-30) REVERT: C 178 ARG cc_start: 0.7746 (ttp-110) cc_final: 0.7362 (ttp-110) REVERT: C 444 ARG cc_start: 0.7772 (ttt90) cc_final: 0.7484 (ttt90) REVERT: C 446 VAL cc_start: 0.8843 (p) cc_final: 0.8591 (t) REVERT: C 500 ARG cc_start: 0.8299 (ptp-110) cc_final: 0.7944 (mtp85) REVERT: G 46 LYS cc_start: 0.8210 (tppt) cc_final: 0.7860 (tppt) REVERT: G 91 GLU cc_start: 0.8045 (tp30) cc_final: 0.7769 (mm-30) REVERT: G 111 LEU cc_start: 0.8665 (mt) cc_final: 0.8462 (mt) REVERT: G 153 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7798 (mm-30) REVERT: G 166 ARG cc_start: 0.7488 (ttp80) cc_final: 0.7285 (ttp-170) REVERT: G 191 TYR cc_start: 0.8752 (m-80) cc_final: 0.8428 (m-80) REVERT: G 327 ARG cc_start: 0.7875 (mtm180) cc_final: 0.7658 (mtm180) REVERT: G 350 ARG cc_start: 0.8400 (ttm-80) cc_final: 0.8183 (ttm110) REVERT: G 358 ILE cc_start: 0.7927 (mm) cc_final: 0.7727 (mm) REVERT: G 381 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7316 (mm-30) REVERT: G 391 PHE cc_start: 0.8801 (m-80) cc_final: 0.8483 (m-80) REVERT: G 492 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8311 (mt-10) REVERT: L 24 GLN cc_start: 0.7909 (tm-30) cc_final: 0.7389 (tp40) REVERT: L 33 LEU cc_start: 0.8487 (tp) cc_final: 0.8206 (tp) REVERT: L 47 LEU cc_start: 0.8802 (mt) cc_final: 0.8600 (mt) REVERT: L 65 SER cc_start: 0.8427 (t) cc_final: 0.7914 (p) REVERT: L 89 GLN cc_start: 0.8489 (tt0) cc_final: 0.7988 (tt0) REVERT: L 107 LYS cc_start: 0.7235 (tppt) cc_final: 0.6978 (tppt) REVERT: J 3 GLN cc_start: 0.8485 (mm-40) cc_final: 0.8186 (mm-40) REVERT: J 24 GLN cc_start: 0.7857 (tm-30) cc_final: 0.7471 (tp40) REVERT: J 37 GLN cc_start: 0.8287 (tt0) cc_final: 0.8062 (tt0) REVERT: J 39 LYS cc_start: 0.8250 (mttt) cc_final: 0.7950 (mttm) REVERT: J 65 SER cc_start: 0.8301 (t) cc_final: 0.7855 (p) REVERT: K 115 SER cc_start: 0.8364 (m) cc_final: 0.7817 (t) REVERT: K 141 LEU cc_start: 0.5836 (OUTLIER) cc_final: 0.5438 (pp) REVERT: K 164 HIS cc_start: 0.8115 (m90) cc_final: 0.7812 (m90) REVERT: M 24 GLN cc_start: 0.7831 (tm-30) cc_final: 0.7485 (tp40) REVERT: M 65 SER cc_start: 0.8382 (t) cc_final: 0.7785 (p) REVERT: M 166 GLN cc_start: 0.8157 (tt0) cc_final: 0.7682 (mt0) REVERT: M 174 SER cc_start: 0.8054 (m) cc_final: 0.7669 (t) REVERT: N 102 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7691 (mm-30) REVERT: N 136 ASN cc_start: 0.7514 (m-40) cc_final: 0.7234 (p0) REVERT: N 138 ILE cc_start: 0.7885 (pp) cc_final: 0.7681 (pp) REVERT: N 140 ASP cc_start: 0.7790 (t0) cc_final: 0.7543 (t0) REVERT: N 335 LYS cc_start: 0.8029 (ttmm) cc_final: 0.7802 (tttm) REVERT: N 412 ASP cc_start: 0.7543 (m-30) cc_final: 0.7204 (m-30) REVERT: N 455 THR cc_start: 0.8460 (t) cc_final: 0.8226 (m) outliers start: 59 outliers final: 36 residues processed: 609 average time/residue: 0.3811 time to fit residues: 348.9284 Evaluate side-chains 603 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 566 time to evaluate : 2.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 117 LYS Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 445 CYS Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain M residue 209 PHE Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain N residue 201 ILE Chi-restraints excluded: chain N residue 308 ARG Chi-restraints excluded: chain N residue 323 ILE Chi-restraints excluded: chain N residue 333 VAL Chi-restraints excluded: chain N residue 342 LEU Chi-restraints excluded: chain N residue 396 ILE Chi-restraints excluded: chain N residue 445 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 160 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 193 optimal weight: 0.0010 chunk 268 optimal weight: 1.9990 chunk 277 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 281 optimal weight: 0.8980 chunk 92 optimal weight: 0.0670 chunk 94 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 overall best weight: 0.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 289 ASN G 195 ASN L 92 ASN ** J 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 155 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.141881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.105215 restraints weight = 36678.645| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.55 r_work: 0.3158 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24813 Z= 0.127 Angle : 0.585 10.182 33858 Z= 0.288 Chirality : 0.044 0.276 4008 Planarity : 0.004 0.044 4173 Dihedral : 5.738 57.193 4874 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.64 % Allowed : 12.88 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.16), residues: 2943 helix: 0.98 (0.27), residues: 423 sheet: 1.58 (0.16), residues: 1044 loop : -0.48 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 35 HIS 0.004 0.001 HIS N 249 PHE 0.018 0.001 PHE N 53 TYR 0.014 0.001 TYR I 98 ARG 0.004 0.000 ARG F 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 48) link_NAG-ASN : angle 2.02065 ( 144) link_BETA1-4 : bond 0.00672 ( 30) link_BETA1-4 : angle 2.02843 ( 90) link_ALPHA1-3 : bond 0.00635 ( 3) link_ALPHA1-3 : angle 1.25691 ( 9) hydrogen bonds : bond 0.04387 ( 937) hydrogen bonds : angle 4.75029 ( 2616) SS BOND : bond 0.00423 ( 45) SS BOND : angle 1.68811 ( 90) covalent geometry : bond 0.00299 (24687) covalent geometry : angle 0.55598 (33525) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 583 time to evaluate : 2.704 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: C 39 TYR cc_start: 0.8710 (m-80) cc_final: 0.8247 (m-80) REVERT: C 46 LYS cc_start: 0.8110 (tppt) cc_final: 0.7810 (tppt) REVERT: C 83 GLU cc_start: 0.8211 (tt0) cc_final: 0.7876 (tt0) REVERT: C 99 ASN cc_start: 0.8458 (t0) cc_final: 0.8187 (t0) REVERT: C 140 ASP cc_start: 0.7916 (t0) cc_final: 0.7694 (t0) REVERT: C 153 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7579 (mm-30) REVERT: C 164 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7623 (mt-10) REVERT: C 208 VAL cc_start: 0.7982 (t) cc_final: 0.7733 (m) REVERT: C 444 ARG cc_start: 0.7828 (ttt90) cc_final: 0.7600 (ttt90) REVERT: C 446 VAL cc_start: 0.8830 (OUTLIER) cc_final: 0.8615 (t) REVERT: G 46 LYS cc_start: 0.8179 (tppt) cc_final: 0.7852 (tppt) REVERT: G 87 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7537 (mp0) REVERT: G 91 GLU cc_start: 0.8015 (tp30) cc_final: 0.7730 (mm-30) REVERT: G 102 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7536 (mm-30) REVERT: G 111 LEU cc_start: 0.8658 (mt) cc_final: 0.8449 (mt) REVERT: G 153 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7771 (mm-30) REVERT: G 166 ARG cc_start: 0.7536 (ttp80) cc_final: 0.7311 (ttp-170) REVERT: G 191 TYR cc_start: 0.8738 (m-80) cc_final: 0.8405 (m-80) REVERT: G 327 ARG cc_start: 0.7877 (mtm180) cc_final: 0.7645 (mtm180) REVERT: G 350 ARG cc_start: 0.8358 (ttm-80) cc_final: 0.8119 (ttm110) REVERT: G 381 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7278 (mm-30) REVERT: G 446 VAL cc_start: 0.8768 (p) cc_final: 0.8422 (t) REVERT: G 492 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8306 (mt-10) REVERT: F 581 LEU cc_start: 0.8525 (tp) cc_final: 0.8249 (tt) REVERT: E 646 LEU cc_start: 0.8085 (mt) cc_final: 0.7772 (mt) REVERT: H 141 LEU cc_start: 0.5752 (pp) cc_final: 0.5538 (pp) REVERT: L 24 GLN cc_start: 0.7905 (tm-30) cc_final: 0.7420 (tp40) REVERT: L 33 LEU cc_start: 0.8506 (tp) cc_final: 0.8292 (tp) REVERT: L 37 GLN cc_start: 0.8169 (tt0) cc_final: 0.7886 (tt0) REVERT: L 47 LEU cc_start: 0.8801 (mt) cc_final: 0.8596 (mt) REVERT: L 65 SER cc_start: 0.8374 (t) cc_final: 0.7904 (p) REVERT: L 79 GLN cc_start: 0.7230 (mm-40) cc_final: 0.6990 (mm-40) REVERT: L 89 GLN cc_start: 0.8463 (tm-30) cc_final: 0.7988 (tt0) REVERT: L 107 LYS cc_start: 0.7210 (tppt) cc_final: 0.6898 (tppt) REVERT: J 3 GLN cc_start: 0.8504 (mm-40) cc_final: 0.8206 (mm-40) REVERT: J 5 THR cc_start: 0.8405 (p) cc_final: 0.8092 (t) REVERT: J 24 GLN cc_start: 0.7887 (tm-30) cc_final: 0.7410 (tp40) REVERT: J 39 LYS cc_start: 0.8358 (mttt) cc_final: 0.8076 (mttm) REVERT: J 65 SER cc_start: 0.8286 (t) cc_final: 0.7812 (p) REVERT: J 79 GLN cc_start: 0.7435 (mm110) cc_final: 0.7147 (mm110) REVERT: K 2 VAL cc_start: 0.8005 (OUTLIER) cc_final: 0.7730 (t) REVERT: K 31 THR cc_start: 0.8509 (p) cc_final: 0.8257 (m) REVERT: K 115 SER cc_start: 0.8448 (m) cc_final: 0.7909 (t) REVERT: K 141 LEU cc_start: 0.5848 (OUTLIER) cc_final: 0.5450 (pp) REVERT: K 164 HIS cc_start: 0.8113 (m90) cc_final: 0.7792 (m90) REVERT: M 65 SER cc_start: 0.8422 (t) cc_final: 0.7796 (p) REVERT: M 89 GLN cc_start: 0.8204 (tm-30) cc_final: 0.7643 (tt0) REVERT: M 166 GLN cc_start: 0.8219 (tt0) cc_final: 0.7729 (mt0) REVERT: M 174 SER cc_start: 0.8020 (m) cc_final: 0.7624 (t) REVERT: N 40 TYR cc_start: 0.8900 (t80) cc_final: 0.8591 (t80) REVERT: N 83 GLU cc_start: 0.8210 (tt0) cc_final: 0.7936 (tt0) REVERT: N 102 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7585 (mm-30) REVERT: N 129 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.7938 (mt) REVERT: N 138 ILE cc_start: 0.7846 (pp) cc_final: 0.7642 (pp) REVERT: N 140 ASP cc_start: 0.7783 (t0) cc_final: 0.7548 (t0) REVERT: N 173 TYR cc_start: 0.8588 (p90) cc_final: 0.8245 (p90) REVERT: N 208 VAL cc_start: 0.7873 (t) cc_final: 0.7607 (m) REVERT: N 335 LYS cc_start: 0.8006 (ttmm) cc_final: 0.7684 (ttmm) REVERT: N 412 ASP cc_start: 0.7517 (m-30) cc_final: 0.7186 (m-30) REVERT: N 455 THR cc_start: 0.8441 (t) cc_final: 0.8236 (m) outliers start: 68 outliers final: 43 residues processed: 613 average time/residue: 0.3755 time to fit residues: 351.7925 Evaluate side-chains 612 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 564 time to evaluate : 2.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 117 LYS Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 178 THR Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 162 SER Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain N residue 129 LEU Chi-restraints excluded: chain N residue 201 ILE Chi-restraints excluded: chain N residue 308 ARG Chi-restraints excluded: chain N residue 323 ILE Chi-restraints excluded: chain N residue 325 ASP Chi-restraints excluded: chain N residue 333 VAL Chi-restraints excluded: chain N residue 342 LEU Chi-restraints excluded: chain N residue 396 ILE Chi-restraints excluded: chain N residue 445 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 17 optimal weight: 1.9990 chunk 289 optimal weight: 0.0070 chunk 19 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 96 optimal weight: 0.0010 chunk 211 optimal weight: 2.9990 chunk 199 optimal weight: 7.9990 chunk 114 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 132 optimal weight: 0.1980 chunk 128 optimal weight: 0.6980 overall best weight: 0.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 637 ASN ** J 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 198 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 = 0.3835 r_free = 0.3835 target = 0.142747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.106517 restraints weight = 37013.104| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.70 r_work: 0.3157 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24813 Z= 0.105 Angle : 0.564 12.315 33858 Z= 0.276 Chirality : 0.044 0.264 4008 Planarity : 0.004 0.044 4173 Dihedral : 5.678 59.927 4872 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.68 % Allowed : 13.93 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.16), residues: 2943 helix: 1.22 (0.27), residues: 423 sheet: 1.56 (0.16), residues: 1050 loop : -0.44 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 35 HIS 0.003 0.001 HIS N 85 PHE 0.025 0.001 PHE N 53 TYR 0.013 0.001 TYR I 98 ARG 0.003 0.000 ARG I 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 48) link_NAG-ASN : angle 1.89260 ( 144) link_BETA1-4 : bond 0.00687 ( 30) link_BETA1-4 : angle 1.97454 ( 90) link_ALPHA1-3 : bond 0.00602 ( 3) link_ALPHA1-3 : angle 1.27872 ( 9) hydrogen bonds : bond 0.03923 ( 937) hydrogen bonds : angle 4.62202 ( 2616) SS BOND : bond 0.00337 ( 45) SS BOND : angle 1.36744 ( 90) covalent geometry : bond 0.00240 (24687) covalent geometry : angle 0.53819 (33525) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 564 time to evaluate : 2.559 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: C 39 TYR cc_start: 0.8730 (m-80) cc_final: 0.8271 (m-80) REVERT: C 46 LYS cc_start: 0.8142 (tppt) cc_final: 0.7780 (tppt) REVERT: C 83 GLU cc_start: 0.8229 (tt0) cc_final: 0.7887 (tt0) REVERT: C 140 ASP cc_start: 0.7946 (t0) cc_final: 0.7731 (t0) REVERT: C 153 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7583 (mm-30) REVERT: C 164 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7578 (mt-10) REVERT: C 208 VAL cc_start: 0.8041 (t) cc_final: 0.7793 (m) REVERT: C 327 ARG cc_start: 0.7562 (mtm180) cc_final: 0.7357 (mpp80) REVERT: C 446 VAL cc_start: 0.8819 (OUTLIER) cc_final: 0.8604 (t) REVERT: C 492 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8533 (mt-10) REVERT: G 87 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7603 (mp0) REVERT: G 91 GLU cc_start: 0.8048 (tp30) cc_final: 0.7760 (mm-30) REVERT: G 102 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7543 (mm-30) REVERT: G 153 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7759 (mm-30) REVERT: G 166 ARG cc_start: 0.7451 (ttp80) cc_final: 0.7245 (ttp80) REVERT: G 191 TYR cc_start: 0.8745 (m-80) cc_final: 0.8406 (m-80) REVERT: G 229 LYS cc_start: 0.8326 (mtmm) cc_final: 0.8025 (mtmm) REVERT: G 267 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7866 (mm-30) REVERT: G 350 ARG cc_start: 0.8376 (ttm-80) cc_final: 0.8132 (ttm110) REVERT: G 381 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7316 (mm-30) REVERT: G 446 VAL cc_start: 0.8696 (p) cc_final: 0.8359 (t) REVERT: F 581 LEU cc_start: 0.8553 (tp) cc_final: 0.8291 (tt) REVERT: E 646 LEU cc_start: 0.8132 (mt) cc_final: 0.7794 (mt) REVERT: H 141 LEU cc_start: 0.5865 (pp) cc_final: 0.5606 (pp) REVERT: L 33 LEU cc_start: 0.8521 (tp) cc_final: 0.8306 (tp) REVERT: L 47 LEU cc_start: 0.8808 (mt) cc_final: 0.8604 (mt) REVERT: L 65 SER cc_start: 0.8393 (t) cc_final: 0.7905 (p) REVERT: L 79 GLN cc_start: 0.7248 (mm-40) cc_final: 0.6868 (mm-40) REVERT: L 89 GLN cc_start: 0.8472 (tm-30) cc_final: 0.7932 (tt0) REVERT: L 107 LYS cc_start: 0.7203 (tppt) cc_final: 0.6903 (tppt) REVERT: L 169 LYS cc_start: 0.7505 (mtmm) cc_final: 0.7264 (mtmm) REVERT: I 56 LYS cc_start: 0.7624 (OUTLIER) cc_final: 0.7314 (ttmm) REVERT: I 164 HIS cc_start: 0.8163 (m90) cc_final: 0.7667 (m90) REVERT: J 3 GLN cc_start: 0.8523 (mm-40) cc_final: 0.8251 (mm-40) REVERT: J 24 GLN cc_start: 0.7878 (tm-30) cc_final: 0.7427 (tp40) REVERT: J 39 LYS cc_start: 0.8385 (mttt) cc_final: 0.8107 (mttm) REVERT: J 55 LYS cc_start: 0.8290 (tppt) cc_final: 0.8004 (mmmm) REVERT: J 65 SER cc_start: 0.8297 (t) cc_final: 0.7842 (p) REVERT: J 79 GLN cc_start: 0.7483 (mm110) cc_final: 0.7189 (mm110) REVERT: K 115 SER cc_start: 0.8401 (m) cc_final: 0.7857 (t) REVERT: K 141 LEU cc_start: 0.5832 (OUTLIER) cc_final: 0.5433 (pp) REVERT: K 164 HIS cc_start: 0.8110 (m90) cc_final: 0.7776 (m90) REVERT: K 200 HIS cc_start: 0.7823 (t-90) cc_final: 0.7325 (t-90) REVERT: M 89 GLN cc_start: 0.8195 (tm-30) cc_final: 0.7684 (tt0) REVERT: M 166 GLN cc_start: 0.8234 (tt0) cc_final: 0.7794 (mt0) REVERT: M 174 SER cc_start: 0.7973 (m) cc_final: 0.7571 (t) REVERT: N 40 TYR cc_start: 0.8894 (t80) cc_final: 0.8623 (t80) REVERT: N 76 PRO cc_start: 0.7629 (Cg_exo) cc_final: 0.7411 (Cg_endo) REVERT: N 83 GLU cc_start: 0.8210 (tt0) cc_final: 0.7947 (tt0) REVERT: N 102 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7610 (mm-30) REVERT: N 129 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.7944 (mt) REVERT: N 140 ASP cc_start: 0.7791 (t0) cc_final: 0.7557 (t0) REVERT: N 161 MET cc_start: 0.8302 (tpp) cc_final: 0.8089 (tpp) REVERT: N 173 TYR cc_start: 0.8627 (p90) cc_final: 0.8337 (p90) REVERT: N 191 TYR cc_start: 0.8889 (m-80) cc_final: 0.8481 (m-80) REVERT: N 208 VAL cc_start: 0.7893 (t) cc_final: 0.7642 (m) REVERT: N 232 LYS cc_start: 0.8791 (mttm) cc_final: 0.8584 (mttm) REVERT: N 412 ASP cc_start: 0.7546 (m-30) cc_final: 0.7199 (m-30) REVERT: N 446 VAL cc_start: 0.8773 (p) cc_final: 0.8490 (t) outliers start: 69 outliers final: 45 residues processed: 601 average time/residue: 0.3724 time to fit residues: 339.7532 Evaluate side-chains 608 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 558 time to evaluate : 2.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 117 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain I residue 56 LYS Chi-restraints excluded: chain I residue 80 MET Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain J residue 178 THR Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 209 PHE Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain N residue 129 LEU Chi-restraints excluded: chain N residue 201 ILE Chi-restraints excluded: chain N residue 308 ARG Chi-restraints excluded: chain N residue 323 ILE Chi-restraints excluded: chain N residue 325 ASP Chi-restraints excluded: chain N residue 333 VAL Chi-restraints excluded: chain N residue 396 ILE Chi-restraints excluded: chain N residue 445 CYS Chi-restraints excluded: chain N residue 501 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 179 optimal weight: 4.9990 chunk 245 optimal weight: 0.9980 chunk 217 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 196 optimal weight: 0.8980 chunk 235 optimal weight: 0.2980 chunk 63 optimal weight: 2.9990 chunk 290 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 115 optimal weight: 0.2980 chunk 86 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 ASN F 637 ASN ** J 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 440 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.141719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.105651 restraints weight = 36936.982| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.66 r_work: 0.3148 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24813 Z= 0.134 Angle : 0.589 11.822 33858 Z= 0.289 Chirality : 0.045 0.273 4008 Planarity : 0.004 0.044 4173 Dihedral : 5.686 56.814 4871 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.07 % Allowed : 14.28 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.16), residues: 2943 helix: 1.22 (0.27), residues: 423 sheet: 1.52 (0.16), residues: 1047 loop : -0.45 (0.16), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 112 HIS 0.004 0.001 HIS N 249 PHE 0.027 0.001 PHE N 53 TYR 0.016 0.001 TYR I 98 ARG 0.006 0.000 ARG K 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 48) link_NAG-ASN : angle 1.98343 ( 144) link_BETA1-4 : bond 0.00653 ( 30) link_BETA1-4 : angle 1.99085 ( 90) link_ALPHA1-3 : bond 0.00607 ( 3) link_ALPHA1-3 : angle 1.28253 ( 9) hydrogen bonds : bond 0.04333 ( 937) hydrogen bonds : angle 4.64453 ( 2616) SS BOND : bond 0.00402 ( 45) SS BOND : angle 1.42167 ( 90) covalent geometry : bond 0.00317 (24687) covalent geometry : angle 0.56255 (33525) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 571 time to evaluate : 2.748 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: C 39 TYR cc_start: 0.8723 (m-80) cc_final: 0.8201 (m-80) REVERT: C 46 LYS cc_start: 0.8125 (tppt) cc_final: 0.7766 (tppt) REVERT: C 83 GLU cc_start: 0.8300 (tt0) cc_final: 0.7937 (tt0) REVERT: C 140 ASP cc_start: 0.7962 (t0) cc_final: 0.7762 (t0) REVERT: C 153 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7535 (mm-30) REVERT: C 208 VAL cc_start: 0.8037 (t) cc_final: 0.7800 (m) REVERT: C 446 VAL cc_start: 0.8839 (OUTLIER) cc_final: 0.8569 (t) REVERT: C 492 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8525 (mt-10) REVERT: G 87 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7576 (mp0) REVERT: G 91 GLU cc_start: 0.8070 (tp30) cc_final: 0.7782 (mm-30) REVERT: G 102 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7584 (mm-30) REVERT: G 153 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7725 (mm-30) REVERT: G 191 TYR cc_start: 0.8744 (m-80) cc_final: 0.8363 (m-80) REVERT: G 229 LYS cc_start: 0.8293 (mtmm) cc_final: 0.8011 (mtmm) REVERT: G 267 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7836 (mm-30) REVERT: G 350 ARG cc_start: 0.8325 (ttm-80) cc_final: 0.8093 (ttm110) REVERT: G 381 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7295 (mm-30) REVERT: G 391 PHE cc_start: 0.8819 (m-80) cc_final: 0.8543 (m-80) REVERT: G 446 VAL cc_start: 0.8719 (p) cc_final: 0.8409 (t) REVERT: F 581 LEU cc_start: 0.8521 (tp) cc_final: 0.8259 (tt) REVERT: E 646 LEU cc_start: 0.8087 (mt) cc_final: 0.7813 (mt) REVERT: H 141 LEU cc_start: 0.6067 (pp) cc_final: 0.5771 (pp) REVERT: L 33 LEU cc_start: 0.8496 (tp) cc_final: 0.8291 (tp) REVERT: L 47 LEU cc_start: 0.8797 (mt) cc_final: 0.8585 (mt) REVERT: L 65 SER cc_start: 0.8350 (t) cc_final: 0.7849 (p) REVERT: L 89 GLN cc_start: 0.8415 (tm-30) cc_final: 0.7942 (tt0) REVERT: L 107 LYS cc_start: 0.7240 (tppt) cc_final: 0.6926 (tppt) REVERT: L 125 LEU cc_start: 0.5242 (pp) cc_final: 0.4684 (mp) REVERT: L 169 LYS cc_start: 0.7457 (mtmm) cc_final: 0.7213 (mtmm) REVERT: L 174 SER cc_start: 0.7669 (m) cc_final: 0.7323 (t) REVERT: I 56 LYS cc_start: 0.7633 (OUTLIER) cc_final: 0.7308 (ttmm) REVERT: J 3 GLN cc_start: 0.8538 (mm-40) cc_final: 0.8269 (mm-40) REVERT: J 24 GLN cc_start: 0.7870 (tm-30) cc_final: 0.7412 (tp40) REVERT: J 39 LYS cc_start: 0.8399 (mttt) cc_final: 0.8119 (mttm) REVERT: J 55 LYS cc_start: 0.8217 (tppt) cc_final: 0.7870 (mmmm) REVERT: J 65 SER cc_start: 0.8235 (t) cc_final: 0.7778 (p) REVERT: K 115 SER cc_start: 0.8443 (m) cc_final: 0.7912 (t) REVERT: K 141 LEU cc_start: 0.5864 (OUTLIER) cc_final: 0.5441 (pp) REVERT: M 89 GLN cc_start: 0.8206 (tm-30) cc_final: 0.7668 (tt0) REVERT: M 107 LYS cc_start: 0.7295 (tppt) cc_final: 0.7031 (tppt) REVERT: M 166 GLN cc_start: 0.8250 (tt0) cc_final: 0.7866 (mt0) REVERT: M 174 SER cc_start: 0.7924 (m) cc_final: 0.7453 (t) REVERT: N 40 TYR cc_start: 0.8908 (t80) cc_final: 0.8579 (t80) REVERT: N 83 GLU cc_start: 0.8245 (tt0) cc_final: 0.7972 (tt0) REVERT: N 102 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7602 (mm-30) REVERT: N 129 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7934 (mt) REVERT: N 140 ASP cc_start: 0.7800 (t0) cc_final: 0.7578 (t0) REVERT: N 173 TYR cc_start: 0.8613 (p90) cc_final: 0.8282 (p90) REVERT: N 191 TYR cc_start: 0.8891 (m-80) cc_final: 0.8598 (m-80) REVERT: N 208 VAL cc_start: 0.7829 (t) cc_final: 0.7610 (m) REVERT: N 335 LYS cc_start: 0.8034 (ttmm) cc_final: 0.7718 (ttmm) REVERT: N 381 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7259 (mt-10) REVERT: N 412 ASP cc_start: 0.7530 (m-30) cc_final: 0.7188 (m-30) REVERT: N 446 VAL cc_start: 0.8581 (p) cc_final: 0.8293 (t) outliers start: 79 outliers final: 58 residues processed: 611 average time/residue: 0.3831 time to fit residues: 355.9297 Evaluate side-chains 629 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 566 time to evaluate : 2.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 117 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 377 ASN Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain I residue 56 LYS Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain I residue 80 MET Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain J residue 178 THR Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 135 LEU Chi-restraints excluded: chain M residue 136 LEU Chi-restraints excluded: chain M residue 162 SER Chi-restraints excluded: chain M residue 209 PHE Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain N residue 129 LEU Chi-restraints excluded: chain N residue 201 ILE Chi-restraints excluded: chain N residue 308 ARG Chi-restraints excluded: chain N residue 323 ILE Chi-restraints excluded: chain N residue 325 ASP Chi-restraints excluded: chain N residue 333 VAL Chi-restraints excluded: chain N residue 342 LEU Chi-restraints excluded: chain N residue 501 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 161 optimal weight: 9.9990 chunk 142 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 246 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 294 optimal weight: 0.0070 chunk 234 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 187 optimal weight: 20.0000 overall best weight: 0.9804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 ASN F 637 ASN ** J 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.140249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.104580 restraints weight = 36589.042| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.70 r_work: 0.3136 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 24813 Z= 0.175 Angle : 0.637 11.379 33858 Z= 0.312 Chirality : 0.046 0.280 4008 Planarity : 0.004 0.058 4173 Dihedral : 5.818 58.939 4871 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.95 % Allowed : 14.82 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.15), residues: 2943 helix: 1.05 (0.27), residues: 423 sheet: 1.42 (0.16), residues: 1062 loop : -0.50 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 112 HIS 0.005 0.001 HIS N 249 PHE 0.028 0.002 PHE N 53 TYR 0.020 0.002 TYR I 98 ARG 0.007 0.000 ARG G 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00428 ( 48) link_NAG-ASN : angle 2.41121 ( 144) link_BETA1-4 : bond 0.00610 ( 30) link_BETA1-4 : angle 2.04647 ( 90) link_ALPHA1-3 : bond 0.00622 ( 3) link_ALPHA1-3 : angle 1.27172 ( 9) hydrogen bonds : bond 0.04850 ( 937) hydrogen bonds : angle 4.77956 ( 2616) SS BOND : bond 0.00516 ( 45) SS BOND : angle 1.60251 ( 90) covalent geometry : bond 0.00419 (24687) covalent geometry : angle 0.60516 (33525) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 581 time to evaluate : 2.600 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: C 39 TYR cc_start: 0.8713 (m-80) cc_final: 0.8202 (m-80) REVERT: C 46 LYS cc_start: 0.8129 (tppt) cc_final: 0.7832 (tppt) REVERT: C 83 GLU cc_start: 0.8297 (tt0) cc_final: 0.7980 (tt0) REVERT: C 140 ASP cc_start: 0.7917 (t0) cc_final: 0.7711 (t0) REVERT: C 153 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7519 (mm-30) REVERT: C 208 VAL cc_start: 0.8109 (t) cc_final: 0.7876 (m) REVERT: C 444 ARG cc_start: 0.7890 (ttt90) cc_final: 0.7680 (ttt90) REVERT: G 87 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: G 91 GLU cc_start: 0.8055 (tp30) cc_final: 0.7757 (mm-30) REVERT: G 102 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7580 (mm-30) REVERT: G 153 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7662 (mm-30) REVERT: G 191 TYR cc_start: 0.8746 (m-80) cc_final: 0.8329 (m-80) REVERT: G 229 LYS cc_start: 0.8268 (mtmm) cc_final: 0.7991 (mtmm) REVERT: G 335 LYS cc_start: 0.7920 (ttmm) cc_final: 0.7598 (ttmm) REVERT: G 350 ARG cc_start: 0.8344 (ttm-80) cc_final: 0.8130 (ttm110) REVERT: G 381 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7304 (mm-30) REVERT: G 393 SER cc_start: 0.8224 (p) cc_final: 0.7957 (m) REVERT: G 446 VAL cc_start: 0.8771 (p) cc_final: 0.8477 (t) REVERT: G 466 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7784 (mm-30) REVERT: E 646 LEU cc_start: 0.8062 (mt) cc_final: 0.7787 (mt) REVERT: H 5 VAL cc_start: 0.8118 (t) cc_final: 0.7886 (m) REVERT: H 141 LEU cc_start: 0.6127 (pp) cc_final: 0.5842 (pp) REVERT: L 33 LEU cc_start: 0.8504 (tp) cc_final: 0.8193 (tp) REVERT: L 47 LEU cc_start: 0.8787 (mt) cc_final: 0.8581 (mt) REVERT: L 65 SER cc_start: 0.8333 (t) cc_final: 0.7822 (p) REVERT: L 79 GLN cc_start: 0.7358 (mm-40) cc_final: 0.6860 (mm110) REVERT: L 89 GLN cc_start: 0.8462 (tm-30) cc_final: 0.7909 (tt0) REVERT: L 125 LEU cc_start: 0.5451 (pp) cc_final: 0.4939 (mp) REVERT: L 139 PHE cc_start: 0.7743 (p90) cc_final: 0.7501 (p90) REVERT: L 169 LYS cc_start: 0.7463 (mtmm) cc_final: 0.7146 (mtmm) REVERT: I 56 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7301 (ttmm) REVERT: J 3 GLN cc_start: 0.8545 (mm-40) cc_final: 0.8270 (mm-40) REVERT: J 24 GLN cc_start: 0.7852 (tm-30) cc_final: 0.7371 (tp40) REVERT: J 39 LYS cc_start: 0.8378 (mttt) cc_final: 0.8088 (mttm) REVERT: J 55 LYS cc_start: 0.8160 (tppt) cc_final: 0.7908 (mmmm) REVERT: J 65 SER cc_start: 0.8221 (t) cc_final: 0.7777 (p) REVERT: J 155 GLN cc_start: 0.8095 (mm110) cc_final: 0.7850 (mp10) REVERT: J 188 LYS cc_start: 0.7319 (mtmm) cc_final: 0.6619 (pttm) REVERT: K 5 VAL cc_start: 0.8324 (t) cc_final: 0.8106 (m) REVERT: K 31 THR cc_start: 0.8456 (p) cc_final: 0.8221 (m) REVERT: K 115 SER cc_start: 0.8412 (m) cc_final: 0.7861 (t) REVERT: K 141 LEU cc_start: 0.6091 (OUTLIER) cc_final: 0.5659 (pp) REVERT: M 6 GLN cc_start: 0.7934 (tt0) cc_final: 0.7660 (tt0) REVERT: M 24 GLN cc_start: 0.7854 (tm-30) cc_final: 0.7310 (tp40) REVERT: M 89 GLN cc_start: 0.8221 (tm-30) cc_final: 0.7654 (tt0) REVERT: M 174 SER cc_start: 0.7914 (m) cc_final: 0.7605 (t) REVERT: N 40 TYR cc_start: 0.8897 (t80) cc_final: 0.8561 (t80) REVERT: N 83 GLU cc_start: 0.8245 (tt0) cc_final: 0.7970 (tt0) REVERT: N 102 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7609 (mm-30) REVERT: N 173 TYR cc_start: 0.8608 (p90) cc_final: 0.8240 (p90) REVERT: N 191 TYR cc_start: 0.8885 (m-80) cc_final: 0.8640 (m-80) REVERT: N 208 VAL cc_start: 0.7833 (t) cc_final: 0.7619 (m) REVERT: N 232 LYS cc_start: 0.8736 (mttm) cc_final: 0.8510 (mttm) REVERT: N 335 LYS cc_start: 0.8146 (ttmm) cc_final: 0.7838 (ttmm) REVERT: N 412 ASP cc_start: 0.7534 (m-30) cc_final: 0.7188 (m-30) REVERT: N 446 VAL cc_start: 0.8670 (p) cc_final: 0.8421 (t) outliers start: 76 outliers final: 58 residues processed: 618 average time/residue: 0.3734 time to fit residues: 352.1644 Evaluate side-chains 640 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 579 time to evaluate : 2.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 117 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 377 ASN Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain I residue 56 LYS Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain I residue 80 MET Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 150 VAL Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 209 PHE Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain N residue 201 ILE Chi-restraints excluded: chain N residue 308 ARG Chi-restraints excluded: chain N residue 325 ASP Chi-restraints excluded: chain N residue 333 VAL Chi-restraints excluded: chain N residue 342 LEU Chi-restraints excluded: chain N residue 443 ILE Chi-restraints excluded: chain N residue 445 CYS Chi-restraints excluded: chain N residue 501 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 92 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 80 optimal weight: 0.2980 chunk 33 optimal weight: 0.8980 chunk 106 optimal weight: 0.4980 chunk 158 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 chunk 193 optimal weight: 3.9990 chunk 105 optimal weight: 0.0870 chunk 275 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 ASN F 637 ASN J 166 GLN J 198 HIS M 189 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.140988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.104945 restraints weight = 36838.194| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.53 r_work: 0.3164 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24813 Z= 0.111 Angle : 0.578 9.679 33858 Z= 0.283 Chirality : 0.044 0.267 4008 Planarity : 0.004 0.044 4173 Dihedral : 5.601 56.959 4869 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.25 % Allowed : 16.18 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.15), residues: 2943 helix: 1.22 (0.27), residues: 423 sheet: 1.45 (0.16), residues: 1062 loop : -0.44 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 69 HIS 0.010 0.001 HIS M 189 PHE 0.024 0.001 PHE N 53 TYR 0.012 0.001 TYR C 173 ARG 0.006 0.000 ARG K 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00273 ( 48) link_NAG-ASN : angle 2.02060 ( 144) link_BETA1-4 : bond 0.00675 ( 30) link_BETA1-4 : angle 1.97377 ( 90) link_ALPHA1-3 : bond 0.00600 ( 3) link_ALPHA1-3 : angle 1.32989 ( 9) hydrogen bonds : bond 0.03998 ( 937) hydrogen bonds : angle 4.61916 ( 2616) SS BOND : bond 0.00341 ( 45) SS BOND : angle 1.23914 ( 90) covalent geometry : bond 0.00256 (24687) covalent geometry : angle 0.55166 (33525) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 585 time to evaluate : 2.549 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: C 39 TYR cc_start: 0.8717 (m-80) cc_final: 0.8192 (m-80) REVERT: C 46 LYS cc_start: 0.8115 (tppt) cc_final: 0.7821 (tppt) REVERT: C 83 GLU cc_start: 0.8287 (tt0) cc_final: 0.8037 (tt0) REVERT: C 102 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7419 (mm-30) REVERT: C 153 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7429 (mm-30) REVERT: C 208 VAL cc_start: 0.8096 (t) cc_final: 0.7881 (m) REVERT: C 444 ARG cc_start: 0.7893 (ttt90) cc_final: 0.7634 (ttt90) REVERT: C 446 VAL cc_start: 0.8821 (p) cc_final: 0.8552 (t) REVERT: G 87 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7587 (mp0) REVERT: G 91 GLU cc_start: 0.8027 (tp30) cc_final: 0.7689 (mm-30) REVERT: G 102 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7448 (mm-30) REVERT: G 153 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7616 (mm-30) REVERT: G 191 TYR cc_start: 0.8744 (m-80) cc_final: 0.8322 (m-80) REVERT: G 229 LYS cc_start: 0.8251 (mtmm) cc_final: 0.7995 (mtmm) REVERT: G 381 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7224 (mm-30) REVERT: G 393 SER cc_start: 0.8201 (p) cc_final: 0.7934 (m) REVERT: G 446 VAL cc_start: 0.8692 (p) cc_final: 0.8387 (t) REVERT: E 646 LEU cc_start: 0.8076 (mt) cc_final: 0.7806 (mt) REVERT: H 141 LEU cc_start: 0.6108 (pp) cc_final: 0.5828 (pp) REVERT: L 24 GLN cc_start: 0.7809 (tm-30) cc_final: 0.7471 (tp40) REVERT: L 33 LEU cc_start: 0.8528 (tp) cc_final: 0.8201 (tp) REVERT: L 47 LEU cc_start: 0.8786 (mt) cc_final: 0.8580 (mt) REVERT: L 65 SER cc_start: 0.8313 (t) cc_final: 0.7745 (p) REVERT: L 79 GLN cc_start: 0.7383 (mm-40) cc_final: 0.6890 (mm110) REVERT: L 89 GLN cc_start: 0.8365 (tm-30) cc_final: 0.7752 (tt0) REVERT: L 125 LEU cc_start: 0.5404 (pp) cc_final: 0.4923 (mp) REVERT: L 169 LYS cc_start: 0.7445 (mtmm) cc_final: 0.7108 (mtmm) REVERT: I 56 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7308 (ttmm) REVERT: J 3 GLN cc_start: 0.8542 (mm-40) cc_final: 0.8281 (mm-40) REVERT: J 24 GLN cc_start: 0.7806 (tm-30) cc_final: 0.7355 (tp40) REVERT: J 39 LYS cc_start: 0.8363 (mttt) cc_final: 0.8071 (mttm) REVERT: J 65 SER cc_start: 0.8228 (t) cc_final: 0.7787 (p) REVERT: K 115 SER cc_start: 0.8411 (m) cc_final: 0.7881 (t) REVERT: K 141 LEU cc_start: 0.6136 (OUTLIER) cc_final: 0.5724 (pp) REVERT: M 89 GLN cc_start: 0.8191 (tm-30) cc_final: 0.7643 (tt0) REVERT: M 174 SER cc_start: 0.7938 (m) cc_final: 0.7473 (t) REVERT: N 40 TYR cc_start: 0.8873 (t80) cc_final: 0.8601 (t80) REVERT: N 83 GLU cc_start: 0.8189 (tt0) cc_final: 0.7921 (tt0) REVERT: N 102 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7520 (mm-30) REVERT: N 150 MET cc_start: 0.7930 (tpt) cc_final: 0.7725 (tpt) REVERT: N 173 TYR cc_start: 0.8598 (p90) cc_final: 0.8252 (p90) REVERT: N 191 TYR cc_start: 0.8868 (m-80) cc_final: 0.8618 (m-80) REVERT: N 208 VAL cc_start: 0.7818 (t) cc_final: 0.7614 (m) REVERT: N 232 LYS cc_start: 0.8739 (mttm) cc_final: 0.8533 (mttm) REVERT: N 412 ASP cc_start: 0.7533 (m-30) cc_final: 0.7173 (m-30) REVERT: N 446 VAL cc_start: 0.8616 (p) cc_final: 0.8362 (t) outliers start: 58 outliers final: 49 residues processed: 613 average time/residue: 0.3701 time to fit residues: 346.2423 Evaluate side-chains 629 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 577 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 229 LYS Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 117 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 184 ILE Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 377 ASN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain I residue 56 LYS Chi-restraints excluded: chain I residue 80 MET Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 209 PHE Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain N residue 199 SER Chi-restraints excluded: chain N residue 201 ILE Chi-restraints excluded: chain N residue 308 ARG Chi-restraints excluded: chain N residue 325 ASP Chi-restraints excluded: chain N residue 333 VAL Chi-restraints excluded: chain N residue 342 LEU Chi-restraints excluded: chain N residue 445 CYS Chi-restraints excluded: chain N residue 501 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 147 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 250 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 223 optimal weight: 8.9990 chunk 113 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 220 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 ASN C 289 ASN F 637 ASN L 160 GLN ** J 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN N 440 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.139146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.103221 restraints weight = 36664.330| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.54 r_work: 0.3117 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 24813 Z= 0.227 Angle : 0.678 9.803 33858 Z= 0.334 Chirality : 0.047 0.296 4008 Planarity : 0.004 0.046 4173 Dihedral : 5.889 59.629 4869 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.72 % Allowed : 16.03 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.15), residues: 2943 helix: 0.87 (0.26), residues: 423 sheet: 1.40 (0.17), residues: 1008 loop : -0.56 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 112 HIS 0.004 0.001 HIS N 249 PHE 0.032 0.002 PHE N 53 TYR 0.023 0.002 TYR I 98 ARG 0.007 0.001 ARG H 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00506 ( 48) link_NAG-ASN : angle 2.33063 ( 144) link_BETA1-4 : bond 0.00621 ( 30) link_BETA1-4 : angle 2.08320 ( 90) link_ALPHA1-3 : bond 0.00650 ( 3) link_ALPHA1-3 : angle 1.26401 ( 9) hydrogen bonds : bond 0.05297 ( 937) hydrogen bonds : angle 4.88359 ( 2616) SS BOND : bond 0.00547 ( 45) SS BOND : angle 1.72365 ( 90) covalent geometry : bond 0.00556 (24687) covalent geometry : angle 0.64844 (33525) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 584 time to evaluate : 2.445 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: C 39 TYR cc_start: 0.8707 (m-80) cc_final: 0.8200 (m-80) REVERT: C 46 LYS cc_start: 0.8140 (tppt) cc_final: 0.7840 (tppt) REVERT: C 83 GLU cc_start: 0.8315 (tt0) cc_final: 0.7995 (tt0) REVERT: C 99 ASN cc_start: 0.8445 (t0) cc_final: 0.8148 (t0) REVERT: C 153 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7505 (mm-30) REVERT: C 208 VAL cc_start: 0.8145 (t) cc_final: 0.7918 (m) REVERT: C 444 ARG cc_start: 0.7927 (ttt90) cc_final: 0.7693 (ttt180) REVERT: G 87 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7587 (mp0) REVERT: G 91 GLU cc_start: 0.8047 (tp30) cc_final: 0.7746 (mm-30) REVERT: G 102 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7587 (mm-30) REVERT: G 153 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7643 (mm-30) REVERT: G 161 MET cc_start: 0.8386 (tpp) cc_final: 0.8172 (tpp) REVERT: G 167 ASP cc_start: 0.7933 (t0) cc_final: 0.7618 (t0) REVERT: G 229 LYS cc_start: 0.8234 (mtmm) cc_final: 0.7987 (mtmm) REVERT: G 335 LYS cc_start: 0.7968 (ttmm) cc_final: 0.7642 (ttmm) REVERT: G 381 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7312 (mm-30) REVERT: G 393 SER cc_start: 0.8210 (p) cc_final: 0.7981 (m) REVERT: G 446 VAL cc_start: 0.8784 (p) cc_final: 0.8480 (t) REVERT: G 466 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7753 (mm-30) REVERT: F 645 LEU cc_start: 0.8363 (mt) cc_final: 0.8086 (mp) REVERT: E 646 LEU cc_start: 0.8105 (mt) cc_final: 0.7815 (mt) REVERT: H 141 LEU cc_start: 0.6359 (pp) cc_final: 0.6080 (pp) REVERT: L 24 GLN cc_start: 0.7834 (tm-30) cc_final: 0.7483 (tp40) REVERT: L 33 LEU cc_start: 0.8525 (tp) cc_final: 0.8226 (tp) REVERT: L 65 SER cc_start: 0.8320 (t) cc_final: 0.7811 (p) REVERT: L 79 GLN cc_start: 0.7453 (mm-40) cc_final: 0.7032 (mm-40) REVERT: L 89 GLN cc_start: 0.8437 (tm-30) cc_final: 0.7901 (tt0) REVERT: L 107 LYS cc_start: 0.7122 (tppt) cc_final: 0.6842 (tppt) REVERT: L 125 LEU cc_start: 0.5543 (pp) cc_final: 0.5129 (mp) REVERT: L 169 LYS cc_start: 0.7480 (mtmm) cc_final: 0.7155 (mtmm) REVERT: I 56 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7308 (ttmm) REVERT: J 3 GLN cc_start: 0.8542 (mm-40) cc_final: 0.8261 (mm-40) REVERT: J 24 GLN cc_start: 0.7894 (tm-30) cc_final: 0.7412 (tp40) REVERT: J 39 LYS cc_start: 0.8427 (mttt) cc_final: 0.8149 (mttm) REVERT: J 65 SER cc_start: 0.8247 (t) cc_final: 0.7810 (p) REVERT: J 188 LYS cc_start: 0.6931 (mtmm) cc_final: 0.6552 (mtmm) REVERT: K 67 LEU cc_start: 0.7990 (tp) cc_final: 0.7648 (mp) REVERT: K 115 SER cc_start: 0.8370 (m) cc_final: 0.7834 (t) REVERT: K 116 THR cc_start: 0.8239 (p) cc_final: 0.8005 (t) REVERT: K 141 LEU cc_start: 0.6280 (OUTLIER) cc_final: 0.5845 (pp) REVERT: M 24 GLN cc_start: 0.7830 (tm-30) cc_final: 0.7325 (tp40) REVERT: M 50 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7587 (mm-30) REVERT: M 89 GLN cc_start: 0.8238 (tm-30) cc_final: 0.7642 (tt0) REVERT: M 174 SER cc_start: 0.7879 (m) cc_final: 0.7431 (t) REVERT: N 83 GLU cc_start: 0.8229 (tt0) cc_final: 0.7960 (tt0) REVERT: N 102 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7687 (mm-30) REVERT: N 150 MET cc_start: 0.7958 (tpt) cc_final: 0.7754 (tpt) REVERT: N 161 MET cc_start: 0.8299 (tpp) cc_final: 0.7837 (tpp) REVERT: N 173 TYR cc_start: 0.8589 (p90) cc_final: 0.8296 (p90) REVERT: N 191 TYR cc_start: 0.8889 (m-80) cc_final: 0.8675 (m-80) REVERT: N 335 LYS cc_start: 0.8204 (ttmm) cc_final: 0.7894 (ttmm) REVERT: N 412 ASP cc_start: 0.7533 (m-30) cc_final: 0.7197 (m-30) REVERT: N 446 VAL cc_start: 0.8739 (p) cc_final: 0.8492 (t) outliers start: 70 outliers final: 55 residues processed: 613 average time/residue: 0.3706 time to fit residues: 346.4077 Evaluate side-chains 639 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 581 time to evaluate : 2.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 229 LYS Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 117 LYS Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 368 ASP Chi-restraints excluded: chain G residue 445 CYS Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain I residue 56 LYS Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 136 LEU Chi-restraints excluded: chain M residue 209 PHE Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain N residue 132 THR Chi-restraints excluded: chain N residue 182 VAL Chi-restraints excluded: chain N residue 201 ILE Chi-restraints excluded: chain N residue 308 ARG Chi-restraints excluded: chain N residue 325 ASP Chi-restraints excluded: chain N residue 333 VAL Chi-restraints excluded: chain N residue 342 LEU Chi-restraints excluded: chain N residue 443 ILE Chi-restraints excluded: chain N residue 445 CYS Chi-restraints excluded: chain N residue 501 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 113 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 187 optimal weight: 8.9990 chunk 190 optimal weight: 3.9990 chunk 155 optimal weight: 0.3980 chunk 41 optimal weight: 1.9990 chunk 235 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 219 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN A 637 ASN C 289 ASN F 540 GLN F 637 ASN E 637 ASN ** J 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.140422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.104605 restraints weight = 36677.565| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.53 r_work: 0.3145 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24813 Z= 0.136 Angle : 0.615 9.864 33858 Z= 0.302 Chirality : 0.045 0.275 4008 Planarity : 0.004 0.043 4173 Dihedral : 5.720 57.086 4869 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.13 % Allowed : 16.65 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.15), residues: 2943 helix: 1.00 (0.27), residues: 426 sheet: 1.46 (0.16), residues: 1059 loop : -0.59 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 69 HIS 0.003 0.001 HIS L 198 PHE 0.031 0.001 PHE N 53 TYR 0.015 0.001 TYR I 98 ARG 0.007 0.000 ARG K 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00330 ( 48) link_NAG-ASN : angle 2.12606 ( 144) link_BETA1-4 : bond 0.00645 ( 30) link_BETA1-4 : angle 2.00252 ( 90) link_ALPHA1-3 : bond 0.00624 ( 3) link_ALPHA1-3 : angle 1.30193 ( 9) hydrogen bonds : bond 0.04452 ( 937) hydrogen bonds : angle 4.74336 ( 2616) SS BOND : bond 0.00388 ( 45) SS BOND : angle 1.40390 ( 90) covalent geometry : bond 0.00323 (24687) covalent geometry : angle 0.58849 (33525) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 581 time to evaluate : 2.591 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: C 39 TYR cc_start: 0.8693 (m-80) cc_final: 0.8189 (m-80) REVERT: C 46 LYS cc_start: 0.8109 (tppt) cc_final: 0.7807 (tppt) REVERT: C 83 GLU cc_start: 0.8286 (tt0) cc_final: 0.7967 (tt0) REVERT: C 102 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7487 (mm-30) REVERT: C 153 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7496 (mm-30) REVERT: C 208 VAL cc_start: 0.8122 (t) cc_final: 0.7906 (m) REVERT: C 444 ARG cc_start: 0.7914 (ttt90) cc_final: 0.7646 (ttt180) REVERT: C 446 VAL cc_start: 0.8858 (p) cc_final: 0.8598 (t) REVERT: G 87 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7578 (mp0) REVERT: G 91 GLU cc_start: 0.8029 (tp30) cc_final: 0.7719 (mm-30) REVERT: G 102 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7490 (mm-30) REVERT: G 153 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7619 (mm-30) REVERT: G 161 MET cc_start: 0.8337 (tpp) cc_final: 0.8131 (tpp) REVERT: G 167 ASP cc_start: 0.7888 (t0) cc_final: 0.7508 (t0) REVERT: G 229 LYS cc_start: 0.8243 (mtmm) cc_final: 0.7997 (mtmm) REVERT: G 381 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7252 (mm-30) REVERT: G 393 SER cc_start: 0.8196 (p) cc_final: 0.7960 (m) REVERT: G 446 VAL cc_start: 0.8750 (p) cc_final: 0.8436 (t) REVERT: G 466 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7751 (mm-30) REVERT: F 645 LEU cc_start: 0.8375 (mt) cc_final: 0.8073 (mp) REVERT: E 646 LEU cc_start: 0.8076 (mt) cc_final: 0.7802 (mt) REVERT: H 141 LEU cc_start: 0.6334 (pp) cc_final: 0.6050 (pp) REVERT: L 24 GLN cc_start: 0.7796 (tm-30) cc_final: 0.7485 (tp40) REVERT: L 33 LEU cc_start: 0.8526 (tp) cc_final: 0.8218 (tp) REVERT: L 65 SER cc_start: 0.8278 (t) cc_final: 0.7701 (p) REVERT: L 79 GLN cc_start: 0.7420 (mm-40) cc_final: 0.6995 (mm-40) REVERT: L 89 GLN cc_start: 0.8399 (tm-30) cc_final: 0.7821 (tt0) REVERT: L 107 LYS cc_start: 0.7083 (tppt) cc_final: 0.6792 (tppt) REVERT: L 125 LEU cc_start: 0.5569 (pp) cc_final: 0.5163 (mp) REVERT: L 169 LYS cc_start: 0.7492 (mtmm) cc_final: 0.7199 (mtmm) REVERT: I 13 LYS cc_start: 0.6015 (mmtt) cc_final: 0.5637 (mmmt) REVERT: I 56 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7340 (ttmm) REVERT: J 3 GLN cc_start: 0.8592 (mm-40) cc_final: 0.8316 (mm-40) REVERT: J 24 GLN cc_start: 0.7840 (tm-30) cc_final: 0.7372 (tp40) REVERT: J 39 LYS cc_start: 0.8415 (mttt) cc_final: 0.8152 (mttm) REVERT: J 65 SER cc_start: 0.8229 (t) cc_final: 0.7790 (p) REVERT: K 115 SER cc_start: 0.8365 (m) cc_final: 0.7850 (t) REVERT: K 116 THR cc_start: 0.8239 (p) cc_final: 0.8006 (t) REVERT: K 141 LEU cc_start: 0.6195 (OUTLIER) cc_final: 0.5772 (pp) REVERT: M 50 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7566 (mm-30) REVERT: M 89 GLN cc_start: 0.8225 (tm-30) cc_final: 0.7647 (tt0) REVERT: M 107 LYS cc_start: 0.6945 (tppt) cc_final: 0.6728 (tppt) REVERT: M 174 SER cc_start: 0.7831 (m) cc_final: 0.7372 (t) REVERT: N 40 TYR cc_start: 0.8885 (t80) cc_final: 0.8564 (t80) REVERT: N 83 GLU cc_start: 0.8217 (tt0) cc_final: 0.7946 (tt0) REVERT: N 102 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7569 (mm-30) REVERT: N 173 TYR cc_start: 0.8582 (p90) cc_final: 0.8272 (p90) REVERT: N 191 TYR cc_start: 0.8856 (m-80) cc_final: 0.8650 (m-80) REVERT: N 321 ASP cc_start: 0.8001 (m-30) cc_final: 0.7722 (m-30) REVERT: N 335 LYS cc_start: 0.8107 (ttmm) cc_final: 0.7793 (ttmm) REVERT: N 412 ASP cc_start: 0.7524 (m-30) cc_final: 0.7190 (m-30) REVERT: N 446 VAL cc_start: 0.8664 (p) cc_final: 0.8415 (t) outliers start: 55 outliers final: 45 residues processed: 606 average time/residue: 0.3736 time to fit residues: 345.3850 Evaluate side-chains 628 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 580 time to evaluate : 2.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 229 LYS Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 117 LYS Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 445 CYS Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain I residue 56 LYS Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 209 PHE Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain N residue 182 VAL Chi-restraints excluded: chain N residue 201 ILE Chi-restraints excluded: chain N residue 308 ARG Chi-restraints excluded: chain N residue 325 ASP Chi-restraints excluded: chain N residue 333 VAL Chi-restraints excluded: chain N residue 342 LEU Chi-restraints excluded: chain N residue 445 CYS Chi-restraints excluded: chain N residue 501 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 92 optimal weight: 1.9990 chunk 288 optimal weight: 0.0670 chunk 154 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 2 optimal weight: 0.0000 chunk 232 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 279 optimal weight: 0.0870 chunk 250 optimal weight: 0.2980 chunk 16 optimal weight: 0.7980 chunk 186 optimal weight: 5.9990 overall best weight: 0.2500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 ASN F 637 ASN E 637 ASN ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 166 GLN M 189 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.142250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.106999 restraints weight = 36540.599| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.76 r_work: 0.3163 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 24813 Z= 0.100 Angle : 0.574 10.052 33858 Z= 0.282 Chirality : 0.044 0.257 4008 Planarity : 0.004 0.044 4173 Dihedral : 5.436 56.967 4869 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.82 % Allowed : 17.00 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.16), residues: 2943 helix: 1.55 (0.28), residues: 405 sheet: 1.50 (0.16), residues: 1062 loop : -0.58 (0.15), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 69 HIS 0.003 0.001 HIS L 189 PHE 0.026 0.001 PHE N 53 TYR 0.011 0.001 TYR C 173 ARG 0.007 0.000 ARG K 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00248 ( 48) link_NAG-ASN : angle 1.87351 ( 144) link_BETA1-4 : bond 0.00719 ( 30) link_BETA1-4 : angle 1.95102 ( 90) link_ALPHA1-3 : bond 0.00583 ( 3) link_ALPHA1-3 : angle 1.33619 ( 9) hydrogen bonds : bond 0.03633 ( 937) hydrogen bonds : angle 4.53834 ( 2616) SS BOND : bond 0.00277 ( 45) SS BOND : angle 1.16978 ( 90) covalent geometry : bond 0.00227 (24687) covalent geometry : angle 0.55096 (33525) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 589 time to evaluate : 2.586 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: C 39 TYR cc_start: 0.8723 (m-80) cc_final: 0.8205 (m-80) REVERT: C 46 LYS cc_start: 0.8126 (tppt) cc_final: 0.7719 (tppt) REVERT: C 83 GLU cc_start: 0.8323 (tt0) cc_final: 0.8048 (tt0) REVERT: C 102 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7407 (mm-30) REVERT: C 153 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7452 (mm-30) REVERT: C 208 VAL cc_start: 0.8119 (t) cc_final: 0.7904 (m) REVERT: C 444 ARG cc_start: 0.7881 (ttt90) cc_final: 0.7634 (ttt180) REVERT: C 446 VAL cc_start: 0.8785 (p) cc_final: 0.8523 (t) REVERT: C 492 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8343 (mt-10) REVERT: G 87 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7679 (mp0) REVERT: G 102 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7506 (mm-30) REVERT: G 167 ASP cc_start: 0.7705 (t0) cc_final: 0.7365 (t0) REVERT: G 191 TYR cc_start: 0.8778 (m-80) cc_final: 0.8331 (m-80) REVERT: G 229 LYS cc_start: 0.8263 (mtmm) cc_final: 0.8031 (mtmm) REVERT: G 356 ASN cc_start: 0.8055 (p0) cc_final: 0.7756 (p0) REVERT: G 381 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7265 (mm-30) REVERT: G 393 SER cc_start: 0.8202 (p) cc_final: 0.7982 (m) REVERT: G 446 VAL cc_start: 0.8675 (p) cc_final: 0.8364 (t) REVERT: E 646 LEU cc_start: 0.8098 (mt) cc_final: 0.7831 (mt) REVERT: H 141 LEU cc_start: 0.6177 (pp) cc_final: 0.5889 (pp) REVERT: L 24 GLN cc_start: 0.7785 (tm-30) cc_final: 0.7528 (tp40) REVERT: L 33 LEU cc_start: 0.8561 (tp) cc_final: 0.8240 (tp) REVERT: L 65 SER cc_start: 0.8297 (t) cc_final: 0.7730 (p) REVERT: L 79 GLN cc_start: 0.7407 (mm-40) cc_final: 0.6998 (mm-40) REVERT: L 107 LYS cc_start: 0.6858 (tppt) cc_final: 0.6592 (tppt) REVERT: L 125 LEU cc_start: 0.5555 (pp) cc_final: 0.5185 (mp) REVERT: I 13 LYS cc_start: 0.5892 (mmtt) cc_final: 0.5529 (mmmt) REVERT: I 56 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.7353 (ttmm) REVERT: J 3 GLN cc_start: 0.8576 (mm-40) cc_final: 0.8322 (mm-40) REVERT: J 24 GLN cc_start: 0.7841 (tm-30) cc_final: 0.7386 (tp40) REVERT: J 39 LYS cc_start: 0.8416 (mttt) cc_final: 0.8162 (mttm) REVERT: J 65 SER cc_start: 0.8241 (t) cc_final: 0.7804 (p) REVERT: K 115 SER cc_start: 0.8382 (m) cc_final: 0.7899 (t) REVERT: K 141 LEU cc_start: 0.6250 (OUTLIER) cc_final: 0.5820 (pp) REVERT: M 24 GLN cc_start: 0.7780 (tm-30) cc_final: 0.7286 (tp40) REVERT: M 50 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7583 (mm-30) REVERT: M 89 GLN cc_start: 0.8187 (tm-30) cc_final: 0.7675 (tt0) REVERT: M 107 LYS cc_start: 0.6940 (tppt) cc_final: 0.6714 (tppt) REVERT: M 174 SER cc_start: 0.7914 (m) cc_final: 0.7403 (t) REVERT: N 40 TYR cc_start: 0.8892 (t80) cc_final: 0.8620 (t80) REVERT: N 83 GLU cc_start: 0.8236 (tt0) cc_final: 0.7992 (tt0) REVERT: N 102 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7535 (mm-30) REVERT: N 161 MET cc_start: 0.8233 (tpp) cc_final: 0.7987 (tpp) REVERT: N 173 TYR cc_start: 0.8601 (p90) cc_final: 0.8294 (p90) REVERT: N 412 ASP cc_start: 0.7539 (m-30) cc_final: 0.7185 (m-30) REVERT: N 446 VAL cc_start: 0.8614 (p) cc_final: 0.8358 (t) outliers start: 47 outliers final: 41 residues processed: 610 average time/residue: 0.3708 time to fit residues: 345.1387 Evaluate side-chains 629 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 585 time to evaluate : 2.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 229 LYS Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 117 LYS Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 634 GLU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain I residue 56 LYS Chi-restraints excluded: chain I residue 80 MET Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 175 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 209 PHE Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain N residue 182 VAL Chi-restraints excluded: chain N residue 201 ILE Chi-restraints excluded: chain N residue 308 ARG Chi-restraints excluded: chain N residue 325 ASP Chi-restraints excluded: chain N residue 333 VAL Chi-restraints excluded: chain N residue 445 CYS Chi-restraints excluded: chain N residue 501 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 68 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 263 optimal weight: 0.5980 chunk 231 optimal weight: 20.0000 chunk 1 optimal weight: 0.0040 chunk 189 optimal weight: 4.9990 chunk 293 optimal weight: 0.2980 chunk 276 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 238 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 ASN F 540 GLN F 637 ASN E 637 ASN ** J 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 160 GLN M 189 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.141558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.105910 restraints weight = 36607.673| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.54 r_work: 0.3167 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24813 Z= 0.120 Angle : 0.592 9.685 33858 Z= 0.291 Chirality : 0.044 0.264 4008 Planarity : 0.004 0.051 4173 Dihedral : 5.388 56.757 4868 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.86 % Allowed : 17.35 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.16), residues: 2943 helix: 1.26 (0.27), residues: 423 sheet: 1.50 (0.16), residues: 1065 loop : -0.48 (0.16), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 103 HIS 0.003 0.001 HIS N 216 PHE 0.027 0.001 PHE N 53 TYR 0.015 0.001 TYR I 98 ARG 0.008 0.000 ARG K 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 48) link_NAG-ASN : angle 1.92522 ( 144) link_BETA1-4 : bond 0.00667 ( 30) link_BETA1-4 : angle 1.94781 ( 90) link_ALPHA1-3 : bond 0.00596 ( 3) link_ALPHA1-3 : angle 1.32272 ( 9) hydrogen bonds : bond 0.03977 ( 937) hydrogen bonds : angle 4.56467 ( 2616) SS BOND : bond 0.00338 ( 45) SS BOND : angle 1.31863 ( 90) covalent geometry : bond 0.00284 (24687) covalent geometry : angle 0.56842 (33525) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17475.60 seconds wall clock time: 302 minutes 17.32 seconds (18137.32 seconds total)