Starting phenix.real_space_refine on Fri Sep 19 07:23:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f02_50092/09_2025/9f02_50092.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f02_50092/09_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_50092/09_2025/9f02_50092.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f02_50092/09_2025/9f02_50092.map" model { file = "/net/cci-nas-00/data/ceres_data/9f02_50092/09_2025/9f02_50092.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f02_50092/09_2025/9f02_50092.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 5.77, per 1000 atoms: 0.24 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: 2.36 Conformation dependent library (CDL) restraints added in 904.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.11 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: 4.55 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 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: 3.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.250 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.590 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG E 585 TYR 0.011 0.001 TYR I 98 PHE 0.013 0.001 PHE N 383 TRP 0.010 0.001 TRP C 96 HIS 0.003 0.001 HIS K 200 Details of bonding type rmsd covalent geometry : bond 0.00225 (24687) covalent geometry : angle 0.50771 (33525) SS BOND : bond 0.00277 ( 45) SS BOND : angle 0.84689 ( 90) hydrogen bonds : bond 0.13969 ( 937) hydrogen bonds : angle 5.23969 ( 2616) link_ALPHA1-3 : bond 0.00607 ( 3) link_ALPHA1-3 : angle 1.26994 ( 9) link_BETA1-4 : bond 0.00693 ( 30) link_BETA1-4 : angle 1.98576 ( 90) link_NAG-ASN : bond 0.00219 ( 48) link_NAG-ASN : angle 1.80114 ( 144) *********************** 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 : 0.850 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: 0.1696 time to fit residues: 163.4860 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 : 0.836 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.0980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.4980 chunk 111 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3839 r_free = 0.3839 target = 0.142954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.106866 restraints weight = 37141.173| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.82 r_work: 0.3161 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24813 Z= 0.132 Angle : 0.597 10.354 33858 Z= 0.293 Chirality : 0.045 0.271 4008 Planarity : 0.004 0.046 4173 Dihedral : 5.729 57.076 4877 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.21 % Allowed : 10.13 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.16), residues: 2943 helix: 0.57 (0.26), residues: 444 sheet: 1.58 (0.16), residues: 1053 loop : -0.45 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 444 TYR 0.016 0.001 TYR I 98 PHE 0.021 0.002 PHE N 53 TRP 0.007 0.001 TRP G 112 HIS 0.005 0.001 HIS N 249 Details of bonding type rmsd covalent geometry : bond 0.00309 (24687) covalent geometry : angle 0.56948 (33525) SS BOND : bond 0.00329 ( 45) SS BOND : angle 1.71228 ( 90) hydrogen bonds : bond 0.04384 ( 937) hydrogen bonds : angle 4.78897 ( 2616) link_ALPHA1-3 : bond 0.00675 ( 3) link_ALPHA1-3 : angle 1.23689 ( 9) link_BETA1-4 : bond 0.00658 ( 30) link_BETA1-4 : angle 2.08365 ( 90) link_NAG-ASN : bond 0.00298 ( 48) link_NAG-ASN : angle 1.92603 ( 144) *********************** 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 643 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 586 time to evaluate : 0.847 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: 0.8721 (m-80) cc_final: 0.8344 (m-80) REVERT: C 46 LYS cc_start: 0.8126 (tppt) cc_final: 0.7768 (tppt) REVERT: C 83 GLU cc_start: 0.8106 (tt0) cc_final: 0.7805 (tt0) REVERT: C 99 ASN cc_start: 0.8496 (t0) cc_final: 0.8043 (t0) REVERT: C 153 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7712 (mm-30) REVERT: C 164 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7896 (mt-10) REVERT: C 178 ARG cc_start: 0.7795 (ttp-110) cc_final: 0.7434 (ttp-110) REVERT: C 318 TYR cc_start: 0.8731 (m-80) cc_final: 0.8526 (m-80) REVERT: C 444 ARG cc_start: 0.7792 (ttt90) cc_final: 0.7508 (ttt90) REVERT: C 446 VAL cc_start: 0.8823 (p) cc_final: 0.8572 (t) REVERT: C 500 ARG cc_start: 0.8245 (ptp-110) cc_final: 0.7903 (mtp85) REVERT: G 46 LYS cc_start: 0.8180 (tppt) cc_final: 0.7836 (tppt) REVERT: G 87 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7597 (mp0) REVERT: G 91 GLU cc_start: 0.8024 (tp30) cc_final: 0.7733 (mm-30) REVERT: G 153 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7828 (mm-30) REVERT: G 191 TYR cc_start: 0.8729 (m-80) cc_final: 0.8413 (m-80) REVERT: G 267 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7875 (mm-30) REVERT: G 350 ARG cc_start: 0.8365 (ttm-80) cc_final: 0.8144 (ttm110) REVERT: G 381 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7264 (mm-30) REVERT: G 492 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8292 (mt-10) REVERT: F 581 LEU cc_start: 0.8567 (tp) cc_final: 0.8318 (tt) REVERT: L 24 GLN cc_start: 0.7874 (tm-30) cc_final: 0.7368 (tp40) REVERT: L 33 LEU cc_start: 0.8483 (tp) cc_final: 0.8193 (tp) REVERT: L 47 LEU cc_start: 0.8772 (mt) cc_final: 0.8569 (mt) REVERT: L 65 SER cc_start: 0.8381 (t) cc_final: 0.7872 (p) REVERT: L 89 GLN cc_start: 0.8427 (tt0) cc_final: 0.7903 (tt0) REVERT: L 107 LYS cc_start: 0.7233 (tppt) cc_final: 0.6971 (tppt) REVERT: J 3 GLN cc_start: 0.8475 (mm-40) cc_final: 0.8176 (mm-40) REVERT: J 24 GLN cc_start: 0.7838 (tm-30) cc_final: 0.7435 (tp40) REVERT: J 39 LYS cc_start: 0.8225 (mttt) cc_final: 0.7910 (mttm) REVERT: J 65 SER cc_start: 0.8269 (t) cc_final: 0.7819 (p) REVERT: K 31 THR cc_start: 0.8597 (p) cc_final: 0.8237 (m) REVERT: K 115 SER cc_start: 0.8344 (m) cc_final: 0.7793 (t) REVERT: K 141 LEU cc_start: 0.5741 (OUTLIER) cc_final: 0.5344 (pp) REVERT: K 164 HIS cc_start: 0.8067 (m90) cc_final: 0.7760 (m90) REVERT: M 6 GLN cc_start: 0.7766 (tt0) cc_final: 0.7436 (tt0) REVERT: M 24 GLN cc_start: 0.7830 (tm-30) cc_final: 0.7435 (tp40) REVERT: M 65 SER cc_start: 0.8367 (t) cc_final: 0.7764 (p) REVERT: M 166 GLN cc_start: 0.8160 (tt0) cc_final: 0.7946 (tt0) REVERT: M 174 SER cc_start: 0.8009 (m) cc_final: 0.7635 (t) REVERT: N 102 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7665 (mm-30) REVERT: N 129 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7926 (mt) REVERT: N 138 ILE cc_start: 0.7817 (pp) cc_final: 0.7614 (pp) REVERT: N 140 ASP cc_start: 0.7747 (t0) cc_final: 0.7497 (t0) REVERT: N 305 LYS cc_start: 0.8165 (ptmt) cc_final: 0.7956 (ptpt) REVERT: N 335 LYS cc_start: 0.7928 (ttmm) cc_final: 0.7705 (tttm) REVERT: N 412 ASP cc_start: 0.7517 (m-30) cc_final: 0.7163 (m-30) REVERT: N 424 ILE cc_start: 0.8704 (mm) cc_final: 0.8438 (mp) REVERT: N 455 THR cc_start: 0.8456 (t) cc_final: 0.8217 (m) outliers start: 57 outliers final: 33 residues processed: 606 average time/residue: 0.1912 time to fit residues: 174.9937 Evaluate side-chains 604 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 568 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 194 ILE 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 G residue 87 GLU 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 120 SER 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 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 333 VAL Chi-restraints excluded: chain N residue 396 ILE Chi-restraints excluded: chain N residue 432 GLN 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 179 optimal weight: 0.9980 chunk 126 optimal weight: 0.0980 chunk 68 optimal weight: 1.9990 chunk 240 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 268 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 162 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 289 ASN L 92 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 = 0.3824 r_free = 0.3824 target = 0.141724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.104943 restraints weight = 37013.680| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.57 r_work: 0.3149 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24813 Z= 0.139 Angle : 0.586 10.530 33858 Z= 0.288 Chirality : 0.044 0.277 4008 Planarity : 0.004 0.045 4173 Dihedral : 5.656 57.137 4872 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.76 % Allowed : 12.38 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.16), residues: 2943 helix: 1.03 (0.27), residues: 423 sheet: 1.60 (0.17), residues: 1002 loop : -0.42 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 542 TYR 0.015 0.001 TYR I 98 PHE 0.017 0.002 PHE N 53 TRP 0.011 0.001 TRP G 112 HIS 0.005 0.001 HIS N 249 Details of bonding type rmsd covalent geometry : bond 0.00330 (24687) covalent geometry : angle 0.55776 (33525) SS BOND : bond 0.00396 ( 45) SS BOND : angle 1.50990 ( 90) hydrogen bonds : bond 0.04486 ( 937) hydrogen bonds : angle 4.73044 ( 2616) link_ALPHA1-3 : bond 0.00632 ( 3) link_ALPHA1-3 : angle 1.25370 ( 9) link_BETA1-4 : bond 0.00662 ( 30) link_BETA1-4 : angle 2.03557 ( 90) link_NAG-ASN : bond 0.00318 ( 48) link_NAG-ASN : angle 2.02976 ( 144) *********************** 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 654 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 583 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.8714 (m-80) cc_final: 0.8272 (m-80) REVERT: C 46 LYS cc_start: 0.8130 (tppt) cc_final: 0.7812 (tppt) REVERT: C 83 GLU cc_start: 0.8216 (tt0) cc_final: 0.7900 (tt0) REVERT: C 140 ASP cc_start: 0.7893 (t0) cc_final: 0.7681 (t0) REVERT: C 153 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7594 (mm-30) REVERT: C 208 VAL cc_start: 0.7989 (t) cc_final: 0.7738 (m) REVERT: C 444 ARG cc_start: 0.7849 (ttt90) cc_final: 0.7614 (ttt90) REVERT: C 446 VAL cc_start: 0.8853 (OUTLIER) cc_final: 0.8634 (t) REVERT: C 500 ARG cc_start: 0.8313 (ptp-110) cc_final: 0.7965 (mtp85) REVERT: G 46 LYS cc_start: 0.8184 (tppt) cc_final: 0.7861 (tppt) REVERT: G 91 GLU cc_start: 0.8029 (tp30) cc_final: 0.7732 (mm-30) REVERT: G 102 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7570 (mm-30) REVERT: G 153 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7784 (mm-30) REVERT: G 191 TYR cc_start: 0.8751 (m-80) cc_final: 0.8420 (m-80) REVERT: G 305 LYS cc_start: 0.8447 (ptmt) cc_final: 0.8241 (ptmt) REVERT: G 350 ARG cc_start: 0.8359 (ttm-80) cc_final: 0.8119 (ttm110) REVERT: G 381 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7295 (mm-30) REVERT: G 446 VAL cc_start: 0.8747 (p) cc_final: 0.8405 (t) REVERT: G 492 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8312 (mt-10) REVERT: F 581 LEU cc_start: 0.8569 (tp) cc_final: 0.8271 (tt) REVERT: E 646 LEU cc_start: 0.8095 (mt) cc_final: 0.7780 (mt) REVERT: H 141 LEU cc_start: 0.5771 (pp) cc_final: 0.5551 (pp) REVERT: L 24 GLN cc_start: 0.7917 (tm-30) cc_final: 0.7438 (tp40) REVERT: L 33 LEU cc_start: 0.8497 (tp) cc_final: 0.8287 (tp) REVERT: L 47 LEU cc_start: 0.8806 (mt) cc_final: 0.8597 (mt) REVERT: L 65 SER cc_start: 0.8346 (t) cc_final: 0.7871 (p) REVERT: L 79 GLN cc_start: 0.7218 (mm-40) cc_final: 0.6962 (mm-40) REVERT: L 89 GLN cc_start: 0.8461 (tm-30) cc_final: 0.7987 (tt0) REVERT: L 107 LYS cc_start: 0.7222 (tppt) cc_final: 0.6913 (tppt) REVERT: J 3 GLN cc_start: 0.8514 (mm-40) cc_final: 0.8222 (mm-40) REVERT: J 5 THR cc_start: 0.8403 (p) cc_final: 0.8089 (t) REVERT: J 24 GLN cc_start: 0.7893 (tm-30) cc_final: 0.7413 (tp40) REVERT: J 39 LYS cc_start: 0.8367 (mttt) cc_final: 0.8063 (mttm) REVERT: J 65 SER cc_start: 0.8286 (t) cc_final: 0.7813 (p) REVERT: J 79 GLN cc_start: 0.7422 (mm110) cc_final: 0.7120 (mm110) REVERT: K 2 VAL cc_start: 0.8012 (OUTLIER) cc_final: 0.7737 (t) REVERT: K 31 THR cc_start: 0.8552 (p) cc_final: 0.8268 (m) REVERT: K 115 SER cc_start: 0.8446 (m) cc_final: 0.7902 (t) REVERT: K 141 LEU cc_start: 0.5777 (OUTLIER) cc_final: 0.5370 (pp) REVERT: K 164 HIS cc_start: 0.8113 (m90) cc_final: 0.7801 (m90) REVERT: M 6 GLN cc_start: 0.7770 (tt0) cc_final: 0.7431 (tt0) REVERT: M 24 GLN cc_start: 0.7852 (tm-30) cc_final: 0.7510 (tp40) REVERT: M 65 SER cc_start: 0.8419 (t) cc_final: 0.7793 (p) REVERT: M 89 GLN cc_start: 0.8207 (tm-30) cc_final: 0.7646 (tt0) REVERT: M 166 GLN cc_start: 0.8222 (tt0) cc_final: 0.7733 (mt0) REVERT: M 174 SER cc_start: 0.7975 (m) cc_final: 0.7590 (t) REVERT: N 83 GLU cc_start: 0.8210 (tt0) cc_final: 0.7928 (tt0) REVERT: N 102 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7583 (mm-30) REVERT: N 129 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7948 (mt) REVERT: N 138 ILE cc_start: 0.7836 (pp) cc_final: 0.7632 (pp) REVERT: N 140 ASP cc_start: 0.7783 (t0) cc_final: 0.7542 (t0) REVERT: N 173 TYR cc_start: 0.8600 (p90) cc_final: 0.8256 (p90) REVERT: N 208 VAL cc_start: 0.7875 (t) cc_final: 0.7609 (m) REVERT: N 335 LYS cc_start: 0.8013 (ttmm) cc_final: 0.7678 (ttmm) REVERT: N 412 ASP cc_start: 0.7518 (m-30) cc_final: 0.7190 (m-30) outliers start: 71 outliers final: 50 residues processed: 618 average time/residue: 0.1906 time to fit residues: 179.0440 Evaluate side-chains 621 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 567 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 290 THR 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 396 ILE Chi-restraints excluded: chain C residue 446 VAL 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 G residue 422 GLN 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 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 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 97 THR 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 120 SER Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 49 THR 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 140 optimal weight: 5.9990 chunk 292 optimal weight: 0.6980 chunk 228 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 131 optimal weight: 0.0050 chunk 280 optimal weight: 3.9990 chunk 172 optimal weight: 0.4980 chunk 183 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 201 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 315 GLN F 637 ASN ** J 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 155 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.140958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.105085 restraints weight = 37125.419| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.83 r_work: 0.3131 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24813 Z= 0.157 Angle : 0.604 9.579 33858 Z= 0.298 Chirality : 0.045 0.281 4008 Planarity : 0.004 0.044 4173 Dihedral : 5.783 58.540 4871 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.26 % Allowed : 13.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.16), residues: 2943 helix: 1.02 (0.27), residues: 423 sheet: 1.55 (0.16), residues: 1041 loop : -0.47 (0.16), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 444 TYR 0.017 0.001 TYR I 98 PHE 0.022 0.002 PHE N 53 TRP 0.011 0.001 TRP G 112 HIS 0.005 0.001 HIS N 249 Details of bonding type rmsd covalent geometry : bond 0.00375 (24687) covalent geometry : angle 0.57608 (33525) SS BOND : bond 0.00465 ( 45) SS BOND : angle 1.49240 ( 90) hydrogen bonds : bond 0.04641 ( 937) hydrogen bonds : angle 4.74265 ( 2616) link_ALPHA1-3 : bond 0.00633 ( 3) link_ALPHA1-3 : angle 1.25461 ( 9) link_BETA1-4 : bond 0.00659 ( 30) link_BETA1-4 : angle 2.03421 ( 90) link_NAG-ASN : bond 0.00361 ( 48) link_NAG-ASN : angle 2.07556 ( 144) *********************** 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 667 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 583 time to evaluate : 0.946 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: C 39 TYR cc_start: 0.8723 (m-80) cc_final: 0.8224 (m-80) REVERT: C 46 LYS cc_start: 0.8145 (tppt) cc_final: 0.7808 (tppt) REVERT: C 83 GLU cc_start: 0.8303 (tt0) cc_final: 0.7953 (tt0) REVERT: C 140 ASP cc_start: 0.7990 (t0) cc_final: 0.7779 (t0) REVERT: C 153 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7587 (mm-30) REVERT: C 208 VAL cc_start: 0.8078 (t) cc_final: 0.7843 (m) REVERT: C 327 ARG cc_start: 0.7614 (mtm180) cc_final: 0.7382 (mpp80) REVERT: C 444 ARG cc_start: 0.7870 (ttt90) cc_final: 0.7659 (ttt90) REVERT: C 446 VAL cc_start: 0.8880 (p) cc_final: 0.8640 (t) REVERT: C 500 ARG cc_start: 0.8333 (ptp-110) cc_final: 0.8093 (mtp85) REVERT: G 87 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7596 (mp0) REVERT: G 91 GLU cc_start: 0.8073 (tp30) cc_final: 0.7773 (mm-30) REVERT: G 102 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7608 (mm-30) REVERT: G 153 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7732 (mm-30) REVERT: G 191 TYR cc_start: 0.8762 (m-80) cc_final: 0.8378 (m-80) REVERT: G 229 LYS cc_start: 0.8280 (mtmm) cc_final: 0.7980 (mtmm) REVERT: G 350 ARG cc_start: 0.8347 (ttm-80) cc_final: 0.8118 (ttm110) REVERT: G 381 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7314 (mm-30) REVERT: G 391 PHE cc_start: 0.8818 (m-80) cc_final: 0.8604 (m-80) REVERT: G 446 VAL cc_start: 0.8702 (p) cc_final: 0.8377 (t) REVERT: E 646 LEU cc_start: 0.8085 (mt) cc_final: 0.7789 (mt) REVERT: H 4 LEU cc_start: 0.8580 (mt) cc_final: 0.8363 (mp) REVERT: H 141 LEU cc_start: 0.6061 (pp) cc_final: 0.5781 (pp) REVERT: L 24 GLN cc_start: 0.7878 (tm-30) cc_final: 0.7413 (tp40) REVERT: L 33 LEU cc_start: 0.8493 (tp) cc_final: 0.8281 (tp) REVERT: L 47 LEU cc_start: 0.8804 (mt) cc_final: 0.8589 (mt) REVERT: L 65 SER cc_start: 0.8354 (t) cc_final: 0.7854 (p) REVERT: L 79 GLN cc_start: 0.7283 (mm-40) cc_final: 0.6877 (mm-40) REVERT: L 89 GLN cc_start: 0.8511 (tm-30) cc_final: 0.7986 (tt0) REVERT: L 107 LYS cc_start: 0.7249 (tppt) cc_final: 0.6944 (tppt) REVERT: L 169 LYS cc_start: 0.7452 (mtmm) cc_final: 0.7208 (mtmm) REVERT: J 3 GLN cc_start: 0.8532 (mm-40) cc_final: 0.8253 (mm-40) REVERT: J 24 GLN cc_start: 0.7899 (tm-30) cc_final: 0.7458 (tp40) REVERT: J 39 LYS cc_start: 0.8375 (mttt) cc_final: 0.8095 (mttm) REVERT: J 55 LYS cc_start: 0.8236 (tppt) cc_final: 0.8006 (mmmm) REVERT: J 65 SER cc_start: 0.8232 (t) cc_final: 0.7771 (p) REVERT: K 2 VAL cc_start: 0.8037 (OUTLIER) cc_final: 0.7805 (t) REVERT: K 31 THR cc_start: 0.8516 (p) cc_final: 0.8249 (m) REVERT: K 115 SER cc_start: 0.8489 (m) cc_final: 0.7954 (t) REVERT: K 141 LEU cc_start: 0.5852 (OUTLIER) cc_final: 0.5422 (pp) REVERT: K 200 HIS cc_start: 0.7865 (t-90) cc_final: 0.7390 (t-90) REVERT: M 6 GLN cc_start: 0.7861 (tt0) cc_final: 0.7476 (tt0) REVERT: M 24 GLN cc_start: 0.7856 (tm-30) cc_final: 0.7317 (tp40) REVERT: M 89 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7659 (tt0) REVERT: M 166 GLN cc_start: 0.8251 (tt0) cc_final: 0.7850 (mt0) REVERT: M 174 SER cc_start: 0.7957 (m) cc_final: 0.7491 (t) REVERT: N 83 GLU cc_start: 0.8266 (tt0) cc_final: 0.7984 (tt0) REVERT: N 102 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7649 (mm-30) REVERT: N 138 ILE cc_start: 0.7876 (pp) cc_final: 0.7660 (pp) REVERT: N 140 ASP cc_start: 0.7829 (t0) cc_final: 0.7605 (t0) REVERT: N 161 MET cc_start: 0.8313 (tpp) cc_final: 0.7883 (tpp) REVERT: N 173 TYR cc_start: 0.8616 (p90) cc_final: 0.8254 (p90) REVERT: N 208 VAL cc_start: 0.7861 (t) cc_final: 0.7623 (m) REVERT: N 335 LYS cc_start: 0.8110 (ttmm) cc_final: 0.7792 (ttmm) REVERT: N 412 ASP cc_start: 0.7555 (m-30) cc_final: 0.7220 (m-30) REVERT: N 432 GLN cc_start: 0.8268 (mt0) cc_final: 0.8059 (mt0) REVERT: N 446 VAL cc_start: 0.8784 (p) cc_final: 0.8508 (t) outliers start: 84 outliers final: 61 residues processed: 624 average time/residue: 0.1933 time to fit residues: 183.7544 Evaluate side-chains 622 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 558 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 CYS 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 290 THR 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 478 ASN 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 125 LEU Chi-restraints excluded: chain G residue 169 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 422 GLN 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 115 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain J residue 49 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 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 120 SER Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 78 LEU 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 199 SER 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 445 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 262 optimal weight: 0.4980 chunk 276 optimal weight: 0.5980 chunk 263 optimal weight: 0.0980 chunk 213 optimal weight: 2.9990 chunk 223 optimal weight: 0.2980 chunk 180 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 165 optimal weight: 3.9990 chunk 41 optimal weight: 0.3980 chunk 115 optimal weight: 1.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.142554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.106081 restraints weight = 36870.008| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.60 r_work: 0.3161 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24813 Z= 0.104 Angle : 0.568 13.971 33858 Z= 0.277 Chirality : 0.044 0.262 4008 Planarity : 0.004 0.044 4173 Dihedral : 5.654 56.878 4871 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.33 % Allowed : 15.25 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.16), residues: 2943 helix: 1.21 (0.27), residues: 426 sheet: 1.55 (0.16), residues: 1041 loop : -0.41 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 83 TYR 0.011 0.001 TYR I 98 PHE 0.027 0.001 PHE N 53 TRP 0.012 0.001 TRP N 35 HIS 0.003 0.001 HIS N 85 Details of bonding type rmsd covalent geometry : bond 0.00237 (24687) covalent geometry : angle 0.54256 (33525) SS BOND : bond 0.00336 ( 45) SS BOND : angle 1.28868 ( 90) hydrogen bonds : bond 0.03925 ( 937) hydrogen bonds : angle 4.59708 ( 2616) link_ALPHA1-3 : bond 0.00588 ( 3) link_ALPHA1-3 : angle 1.31473 ( 9) link_BETA1-4 : bond 0.00694 ( 30) link_BETA1-4 : angle 1.97213 ( 90) link_NAG-ASN : bond 0.00258 ( 48) link_NAG-ASN : angle 1.92627 ( 144) *********************** 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 628 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 568 time to evaluate : 0.972 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: 0.8216 (m-80) REVERT: C 46 LYS cc_start: 0.8096 (tppt) cc_final: 0.7783 (tppt) REVERT: C 83 GLU cc_start: 0.8249 (tt0) cc_final: 0.7906 (tt0) REVERT: C 102 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7455 (mm-30) REVERT: C 140 ASP cc_start: 0.7945 (t0) cc_final: 0.7741 (t0) REVERT: C 153 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7525 (mm-30) REVERT: C 208 VAL cc_start: 0.8089 (t) cc_final: 0.7866 (m) REVERT: C 290 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.8076 (p) REVERT: C 446 VAL cc_start: 0.8733 (OUTLIER) cc_final: 0.8487 (t) REVERT: C 500 ARG cc_start: 0.8183 (ptp-110) cc_final: 0.7946 (mtp85) REVERT: G 87 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7635 (mp0) REVERT: G 91 GLU cc_start: 0.8043 (tp30) cc_final: 0.7748 (mm-30) REVERT: G 102 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7511 (mm-30) REVERT: G 153 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7693 (mm-30) REVERT: G 191 TYR cc_start: 0.8749 (m-80) cc_final: 0.8369 (m-80) REVERT: G 229 LYS cc_start: 0.8301 (mtmm) cc_final: 0.8015 (mtmm) REVERT: G 381 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7243 (mm-30) REVERT: G 391 PHE cc_start: 0.8802 (m-80) cc_final: 0.8553 (m-80) REVERT: G 393 SER cc_start: 0.8198 (p) cc_final: 0.7926 (m) REVERT: G 446 VAL cc_start: 0.8658 (p) cc_final: 0.8354 (t) REVERT: F 581 LEU cc_start: 0.8501 (tp) cc_final: 0.8253 (tt) REVERT: E 646 LEU cc_start: 0.8132 (mt) cc_final: 0.7869 (mt) REVERT: H 5 VAL cc_start: 0.8113 (t) cc_final: 0.7885 (m) REVERT: H 141 LEU cc_start: 0.6069 (pp) cc_final: 0.5772 (pp) REVERT: L 24 GLN cc_start: 0.7842 (tm-30) cc_final: 0.7446 (tp40) REVERT: L 33 LEU cc_start: 0.8523 (tp) cc_final: 0.8314 (tp) REVERT: L 47 LEU cc_start: 0.8805 (mt) cc_final: 0.8600 (mt) REVERT: L 65 SER cc_start: 0.8351 (t) cc_final: 0.7859 (p) REVERT: L 79 GLN cc_start: 0.7276 (mm-40) cc_final: 0.6941 (mm-40) REVERT: L 89 GLN cc_start: 0.8469 (tm-30) cc_final: 0.7843 (tt0) REVERT: L 107 LYS cc_start: 0.7210 (tppt) cc_final: 0.6915 (tppt) REVERT: L 126 LYS cc_start: 0.6642 (mttp) cc_final: 0.6374 (ptpp) REVERT: L 169 LYS cc_start: 0.7429 (mtmm) cc_final: 0.7174 (mtmm) REVERT: L 174 SER cc_start: 0.7639 (m) cc_final: 0.7303 (t) REVERT: J 3 GLN cc_start: 0.8536 (mm-40) cc_final: 0.8273 (mm-40) REVERT: J 24 GLN cc_start: 0.7851 (tm-30) cc_final: 0.7371 (tp40) REVERT: J 39 LYS cc_start: 0.8400 (mttt) cc_final: 0.8108 (mttm) REVERT: J 55 LYS cc_start: 0.8200 (tppt) cc_final: 0.7830 (mmmm) REVERT: J 65 SER cc_start: 0.8252 (t) cc_final: 0.7791 (p) REVERT: J 79 GLN cc_start: 0.7578 (mm110) cc_final: 0.7129 (mm110) REVERT: J 188 LYS cc_start: 0.7150 (mtmm) cc_final: 0.6938 (mtmm) REVERT: K 5 VAL cc_start: 0.8334 (t) cc_final: 0.8123 (m) REVERT: K 115 SER cc_start: 0.8468 (m) cc_final: 0.7947 (t) REVERT: K 141 LEU cc_start: 0.5889 (OUTLIER) cc_final: 0.5477 (pp) REVERT: K 164 HIS cc_start: 0.8127 (m90) cc_final: 0.7869 (m90) REVERT: K 200 HIS cc_start: 0.7875 (t-90) cc_final: 0.7394 (t-90) REVERT: M 89 GLN cc_start: 0.8191 (tm-30) cc_final: 0.7651 (tt0) REVERT: M 107 LYS cc_start: 0.7260 (tppt) cc_final: 0.7016 (tppt) REVERT: M 166 GLN cc_start: 0.8249 (tt0) cc_final: 0.7876 (mt0) REVERT: M 174 SER cc_start: 0.7911 (m) cc_final: 0.7412 (t) REVERT: N 40 TYR cc_start: 0.8872 (t80) cc_final: 0.8628 (t80) REVERT: N 83 GLU cc_start: 0.8210 (tt0) cc_final: 0.7946 (tt0) REVERT: N 102 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7555 (mm-30) REVERT: N 129 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7914 (mt) REVERT: N 140 ASP cc_start: 0.7847 (t0) cc_final: 0.7615 (t0) REVERT: N 161 MET cc_start: 0.8276 (tpp) cc_final: 0.7991 (tpp) REVERT: N 173 TYR cc_start: 0.8608 (p90) cc_final: 0.8280 (p90) REVERT: N 191 TYR cc_start: 0.8875 (m-80) cc_final: 0.8643 (m-80) REVERT: N 208 VAL cc_start: 0.7865 (t) cc_final: 0.7631 (m) REVERT: N 412 ASP cc_start: 0.7529 (m-30) cc_final: 0.7161 (m-30) REVERT: N 432 GLN cc_start: 0.8238 (mt0) cc_final: 0.7995 (mt0) REVERT: N 446 VAL cc_start: 0.8559 (p) cc_final: 0.8264 (t) outliers start: 60 outliers final: 41 residues processed: 599 average time/residue: 0.1901 time to fit residues: 173.1389 Evaluate side-chains 614 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 568 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 290 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 446 VAL 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 201 ILE Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 377 ASN Chi-restraints excluded: chain G residue 422 GLN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain L residue 97 THR 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 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 78 THR 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 97 LYS 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 333 VAL Chi-restraints excluded: chain N residue 342 LEU Chi-restraints excluded: chain N residue 396 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 259 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 172 optimal weight: 0.7980 chunk 13 optimal weight: 0.4980 chunk 127 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 chunk 224 optimal weight: 0.8980 chunk 206 optimal weight: 0.6980 chunk 135 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.141295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.104948 restraints weight = 36833.446| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.58 r_work: 0.3147 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24813 Z= 0.148 Angle : 0.604 10.237 33858 Z= 0.296 Chirality : 0.045 0.274 4008 Planarity : 0.004 0.043 4173 Dihedral : 5.720 58.918 4871 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.95 % Allowed : 14.75 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.15), residues: 2943 helix: 1.12 (0.27), residues: 423 sheet: 1.49 (0.16), residues: 1056 loop : -0.43 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 83 TYR 0.018 0.001 TYR I 98 PHE 0.029 0.002 PHE N 53 TRP 0.011 0.001 TRP G 112 HIS 0.004 0.001 HIS N 249 Details of bonding type rmsd covalent geometry : bond 0.00354 (24687) covalent geometry : angle 0.57421 (33525) SS BOND : bond 0.00409 ( 45) SS BOND : angle 1.41441 ( 90) hydrogen bonds : bond 0.04484 ( 937) hydrogen bonds : angle 4.66789 ( 2616) link_ALPHA1-3 : bond 0.00619 ( 3) link_ALPHA1-3 : angle 1.28517 ( 9) link_BETA1-4 : bond 0.00632 ( 30) link_BETA1-4 : angle 2.00065 ( 90) link_NAG-ASN : bond 0.00386 ( 48) link_NAG-ASN : angle 2.25139 ( 144) *********************** 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 662 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 586 time to evaluate : 0.946 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: 0.8712 (m-80) cc_final: 0.8206 (m-80) REVERT: C 46 LYS cc_start: 0.8107 (tppt) cc_final: 0.7785 (tppt) REVERT: C 83 GLU cc_start: 0.8305 (tt0) cc_final: 0.7969 (tt0) REVERT: C 153 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7520 (mm-30) REVERT: C 208 VAL cc_start: 0.8126 (t) cc_final: 0.7897 (m) REVERT: C 290 THR cc_start: 0.8352 (OUTLIER) cc_final: 0.8136 (p) REVERT: C 444 ARG cc_start: 0.7936 (ttt90) cc_final: 0.7724 (ttt90) REVERT: C 446 VAL cc_start: 0.8868 (p) cc_final: 0.8607 (t) REVERT: C 467 THR cc_start: 0.8513 (t) cc_final: 0.8310 (p) REVERT: C 500 ARG cc_start: 0.8186 (ptp-110) cc_final: 0.7904 (mtp85) REVERT: G 87 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7630 (mp0) REVERT: G 91 GLU cc_start: 0.8065 (tp30) cc_final: 0.7727 (mm-30) REVERT: G 102 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7587 (mm-30) REVERT: G 153 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7673 (mm-30) REVERT: G 191 TYR cc_start: 0.8741 (m-80) cc_final: 0.8339 (m-80) REVERT: G 229 LYS cc_start: 0.8285 (mtmm) cc_final: 0.8015 (mtmm) REVERT: G 381 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7263 (mm-30) REVERT: G 391 PHE cc_start: 0.8808 (m-80) cc_final: 0.8589 (m-80) REVERT: G 393 SER cc_start: 0.8221 (p) cc_final: 0.7967 (m) REVERT: G 446 VAL cc_start: 0.8706 (p) cc_final: 0.8429 (t) REVERT: E 646 LEU cc_start: 0.8128 (mt) cc_final: 0.7834 (mt) REVERT: H 4 LEU cc_start: 0.8597 (mt) cc_final: 0.8386 (mp) REVERT: H 141 LEU cc_start: 0.6131 (pp) cc_final: 0.5828 (pp) REVERT: L 24 GLN cc_start: 0.7859 (tm-30) cc_final: 0.7478 (tp40) REVERT: L 33 LEU cc_start: 0.8558 (tp) cc_final: 0.8235 (tp) REVERT: L 65 SER cc_start: 0.8336 (t) cc_final: 0.7839 (p) REVERT: L 89 GLN cc_start: 0.8469 (tm-30) cc_final: 0.7928 (tt0) REVERT: L 107 LYS cc_start: 0.7197 (tppt) cc_final: 0.6901 (tppt) REVERT: L 125 LEU cc_start: 0.5323 (pp) cc_final: 0.4790 (mp) REVERT: L 169 LYS cc_start: 0.7443 (mtmm) cc_final: 0.7143 (mtmm) REVERT: J 3 GLN cc_start: 0.8546 (mm-40) cc_final: 0.8282 (mm-40) REVERT: J 24 GLN cc_start: 0.7883 (tm-30) cc_final: 0.7397 (tp40) REVERT: J 39 LYS cc_start: 0.8393 (mttt) cc_final: 0.8111 (mttm) REVERT: J 55 LYS cc_start: 0.8296 (tppt) cc_final: 0.8087 (mmmm) REVERT: J 65 SER cc_start: 0.8283 (t) cc_final: 0.7851 (p) REVERT: J 79 GLN cc_start: 0.7696 (mm110) cc_final: 0.7296 (mm110) REVERT: J 155 GLN cc_start: 0.8023 (mm110) cc_final: 0.7814 (mp10) REVERT: K 5 VAL cc_start: 0.8345 (t) cc_final: 0.8133 (m) REVERT: K 115 SER cc_start: 0.8420 (m) cc_final: 0.7891 (t) REVERT: K 116 THR cc_start: 0.8203 (p) cc_final: 0.7993 (t) REVERT: K 141 LEU cc_start: 0.6025 (OUTLIER) cc_final: 0.5596 (pp) REVERT: K 200 HIS cc_start: 0.7879 (t-90) cc_final: 0.7572 (t-90) REVERT: M 6 GLN cc_start: 0.7872 (tt0) cc_final: 0.7591 (tt0) REVERT: M 89 GLN cc_start: 0.8201 (tm-30) cc_final: 0.7662 (tt0) REVERT: M 107 LYS cc_start: 0.7225 (tppt) cc_final: 0.6981 (tppt) REVERT: M 166 GLN cc_start: 0.8255 (tt0) cc_final: 0.7902 (mt0) REVERT: M 174 SER cc_start: 0.7974 (m) cc_final: 0.7653 (t) REVERT: N 40 TYR cc_start: 0.8891 (t80) cc_final: 0.8592 (t80) REVERT: N 83 GLU cc_start: 0.8194 (tt0) cc_final: 0.7920 (tt0) REVERT: N 102 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7624 (mm-30) REVERT: N 150 MET cc_start: 0.8050 (tpt) cc_final: 0.7835 (tpt) REVERT: N 166 ARG cc_start: 0.7672 (ttp80) cc_final: 0.7395 (tmm160) REVERT: N 173 TYR cc_start: 0.8603 (p90) cc_final: 0.8256 (p90) REVERT: N 208 VAL cc_start: 0.7843 (t) cc_final: 0.7624 (m) REVERT: N 335 LYS cc_start: 0.8153 (ttmm) cc_final: 0.7847 (ttmm) REVERT: N 381 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7220 (mt-10) REVERT: N 412 ASP cc_start: 0.7551 (m-30) cc_final: 0.7204 (m-30) REVERT: N 432 GLN cc_start: 0.8272 (mt0) cc_final: 0.8041 (mt0) REVERT: N 446 VAL cc_start: 0.8621 (p) cc_final: 0.8344 (t) outliers start: 76 outliers final: 57 residues processed: 621 average time/residue: 0.1850 time to fit residues: 175.4709 Evaluate side-chains 645 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 585 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 290 THR 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 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 201 ILE Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain G residue 348 GLN Chi-restraints excluded: chain G residue 358 ILE Chi-restraints excluded: chain G residue 377 ASN Chi-restraints excluded: chain G residue 422 GLN 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 87 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 L residue 133 VAL 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 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 68 THR 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 135 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 199 SER 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 443 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 119 optimal weight: 0.0020 chunk 25 optimal weight: 0.9980 chunk 255 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 76 optimal weight: 0.4980 chunk 133 optimal weight: 7.9990 chunk 217 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 138 optimal weight: 0.0870 chunk 213 optimal weight: 3.9990 overall best weight: 0.3566 ------------------------------------------------------------------------------- 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 J 166 GLN J 198 HIS M 189 HIS N 85 HIS N 440 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.142158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.106023 restraints weight = 36818.204| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.59 r_work: 0.3166 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24813 Z= 0.103 Angle : 0.563 9.944 33858 Z= 0.276 Chirality : 0.044 0.261 4008 Planarity : 0.004 0.044 4173 Dihedral : 5.570 59.913 4871 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.17 % Allowed : 15.95 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.15), residues: 2943 helix: 1.27 (0.27), residues: 423 sheet: 1.45 (0.16), residues: 1065 loop : -0.36 (0.16), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 83 TYR 0.011 0.001 TYR I 98 PHE 0.026 0.001 PHE N 53 TRP 0.007 0.001 TRP N 69 HIS 0.006 0.001 HIS M 189 Details of bonding type rmsd covalent geometry : bond 0.00233 (24687) covalent geometry : angle 0.53818 (33525) SS BOND : bond 0.00312 ( 45) SS BOND : angle 1.18574 ( 90) hydrogen bonds : bond 0.03807 ( 937) hydrogen bonds : angle 4.52931 ( 2616) link_ALPHA1-3 : bond 0.00590 ( 3) link_ALPHA1-3 : angle 1.34268 ( 9) link_BETA1-4 : bond 0.00689 ( 30) link_BETA1-4 : angle 1.94901 ( 90) link_NAG-ASN : bond 0.00255 ( 48) link_NAG-ASN : angle 1.96429 ( 144) *********************** 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 655 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 599 time to evaluate : 0.948 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: 0.8703 (m-80) cc_final: 0.8220 (m-80) REVERT: C 46 LYS cc_start: 0.8107 (tppt) cc_final: 0.7804 (tppt) REVERT: C 83 GLU cc_start: 0.8281 (tt0) cc_final: 0.7999 (tt0) REVERT: C 102 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7456 (mm-30) REVERT: C 153 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7495 (mm-30) REVERT: C 208 VAL cc_start: 0.8100 (t) cc_final: 0.7882 (m) REVERT: C 290 THR cc_start: 0.8361 (OUTLIER) cc_final: 0.8155 (p) REVERT: C 444 ARG cc_start: 0.7927 (ttt90) cc_final: 0.7689 (ttt90) REVERT: C 446 VAL cc_start: 0.8773 (p) cc_final: 0.8504 (t) REVERT: C 500 ARG cc_start: 0.8075 (ptp-110) cc_final: 0.7834 (mtp85) REVERT: G 87 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7646 (mp0) REVERT: G 102 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7489 (mm-30) REVERT: G 153 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7649 (mm-30) REVERT: G 191 TYR cc_start: 0.8743 (m-80) cc_final: 0.8334 (m-80) REVERT: G 229 LYS cc_start: 0.8275 (mtmm) cc_final: 0.8014 (mtmm) REVERT: G 381 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7236 (mm-30) REVERT: G 391 PHE cc_start: 0.8770 (m-80) cc_final: 0.8529 (m-80) REVERT: G 393 SER cc_start: 0.8197 (p) cc_final: 0.7929 (m) REVERT: G 446 VAL cc_start: 0.8667 (p) cc_final: 0.8382 (t) REVERT: H 141 LEU cc_start: 0.6123 (pp) cc_final: 0.5818 (pp) REVERT: L 24 GLN cc_start: 0.7831 (tm-30) cc_final: 0.7505 (tp40) REVERT: L 33 LEU cc_start: 0.8540 (tp) cc_final: 0.8336 (tp) REVERT: L 65 SER cc_start: 0.8304 (t) cc_final: 0.7805 (p) REVERT: L 79 GLN cc_start: 0.7333 (mm-40) cc_final: 0.6741 (mm110) REVERT: L 89 GLN cc_start: 0.8441 (tm-30) cc_final: 0.7888 (tt0) REVERT: L 107 LYS cc_start: 0.7167 (tppt) cc_final: 0.6874 (tppt) REVERT: L 125 LEU cc_start: 0.5284 (pp) cc_final: 0.4783 (mp) REVERT: L 169 LYS cc_start: 0.7432 (mtmm) cc_final: 0.7101 (mtmm) REVERT: J 3 GLN cc_start: 0.8565 (mm-40) cc_final: 0.8296 (mm-40) REVERT: J 24 GLN cc_start: 0.7835 (tm-30) cc_final: 0.7363 (tp40) REVERT: J 39 LYS cc_start: 0.8400 (mttt) cc_final: 0.8116 (mttm) REVERT: J 55 LYS cc_start: 0.8274 (tppt) cc_final: 0.8070 (mmmm) REVERT: J 65 SER cc_start: 0.8243 (t) cc_final: 0.7796 (p) REVERT: J 79 GLN cc_start: 0.7643 (mm110) cc_final: 0.7208 (mm-40) REVERT: K 5 VAL cc_start: 0.8331 (t) cc_final: 0.8129 (m) REVERT: K 115 SER cc_start: 0.8411 (m) cc_final: 0.7888 (t) REVERT: K 141 LEU cc_start: 0.6049 (OUTLIER) cc_final: 0.5636 (pp) REVERT: M 24 GLN cc_start: 0.7798 (tm-30) cc_final: 0.7260 (tp40) REVERT: M 89 GLN cc_start: 0.8179 (tm-30) cc_final: 0.7656 (tt0) REVERT: M 166 GLN cc_start: 0.8253 (tt0) cc_final: 0.7899 (mt0) REVERT: M 174 SER cc_start: 0.7945 (m) cc_final: 0.7491 (t) REVERT: N 40 TYR cc_start: 0.8877 (t80) cc_final: 0.8615 (t80) REVERT: N 83 GLU cc_start: 0.8168 (tt0) cc_final: 0.7901 (tt0) REVERT: N 102 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7537 (mm-30) REVERT: N 150 MET cc_start: 0.7956 (tpt) cc_final: 0.7723 (tpt) REVERT: N 173 TYR cc_start: 0.8602 (p90) cc_final: 0.8266 (p90) REVERT: N 208 VAL cc_start: 0.7828 (t) cc_final: 0.7617 (m) REVERT: N 412 ASP cc_start: 0.7542 (m-30) cc_final: 0.7179 (m-30) REVERT: N 432 GLN cc_start: 0.8233 (mt0) cc_final: 0.7982 (mt0) REVERT: N 446 VAL cc_start: 0.8586 (p) cc_final: 0.8313 (t) outliers start: 56 outliers final: 47 residues processed: 624 average time/residue: 0.1845 time to fit residues: 176.1765 Evaluate side-chains 643 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 593 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 290 THR 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 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 G residue 422 GLN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 87 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 133 VAL Chi-restraints excluded: chain L residue 176 SER 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 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 141 LEU Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain M residue 209 PHE Chi-restraints excluded: chain N residue 92 GLU Chi-restraints excluded: chain N residue 97 LYS 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 159 optimal weight: 8.9990 chunk 58 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 266 optimal weight: 0.0170 chunk 67 optimal weight: 1.9990 chunk 178 optimal weight: 0.6980 chunk 122 optimal weight: 10.0000 chunk 16 optimal weight: 0.6980 chunk 281 optimal weight: 0.7980 chunk 166 optimal weight: 8.9990 overall best weight: 0.6420 ------------------------------------------------------------------------------- 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 N 85 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.141112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.105242 restraints weight = 36599.289| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.54 r_work: 0.3156 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24813 Z= 0.132 Angle : 0.591 10.069 33858 Z= 0.290 Chirality : 0.044 0.269 4008 Planarity : 0.004 0.044 4173 Dihedral : 5.513 56.726 4871 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.52 % Allowed : 15.99 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.15), residues: 2943 helix: 1.20 (0.27), residues: 423 sheet: 1.43 (0.16), residues: 1065 loop : -0.40 (0.16), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 83 TYR 0.016 0.001 TYR I 98 PHE 0.026 0.001 PHE N 53 TRP 0.009 0.001 TRP G 112 HIS 0.003 0.001 HIS N 105 Details of bonding type rmsd covalent geometry : bond 0.00314 (24687) covalent geometry : angle 0.56635 (33525) SS BOND : bond 0.00382 ( 45) SS BOND : angle 1.29562 ( 90) hydrogen bonds : bond 0.04228 ( 937) hydrogen bonds : angle 4.59497 ( 2616) link_ALPHA1-3 : bond 0.00598 ( 3) link_ALPHA1-3 : angle 1.31412 ( 9) link_BETA1-4 : bond 0.00656 ( 30) link_BETA1-4 : angle 1.98080 ( 90) link_NAG-ASN : bond 0.00312 ( 48) link_NAG-ASN : angle 1.98213 ( 144) *********************** 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 658 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 593 time to evaluate : 0.826 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: 0.8704 (m-80) cc_final: 0.8182 (m-80) REVERT: C 46 LYS cc_start: 0.8089 (tppt) cc_final: 0.7766 (tppt) REVERT: C 83 GLU cc_start: 0.8309 (tt0) cc_final: 0.8018 (tt0) REVERT: C 102 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7506 (mm-30) REVERT: C 153 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7495 (mm-30) REVERT: C 208 VAL cc_start: 0.8098 (t) cc_final: 0.7875 (m) REVERT: C 290 THR cc_start: 0.8366 (OUTLIER) cc_final: 0.8148 (p) REVERT: C 444 ARG cc_start: 0.7946 (ttt90) cc_final: 0.7681 (ttt90) REVERT: C 446 VAL cc_start: 0.8856 (p) cc_final: 0.8581 (t) REVERT: C 500 ARG cc_start: 0.8072 (ptp-110) cc_final: 0.7788 (mtp85) REVERT: G 87 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7615 (mp0) REVERT: G 91 GLU cc_start: 0.8045 (tp30) cc_final: 0.7726 (mm-30) REVERT: G 102 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7527 (mm-30) REVERT: G 153 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7644 (mm-30) REVERT: G 167 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.7329 (t0) REVERT: G 191 TYR cc_start: 0.8741 (m-80) cc_final: 0.8298 (m-80) REVERT: G 229 LYS cc_start: 0.8272 (mtmm) cc_final: 0.8007 (mtmm) REVERT: G 356 ASN cc_start: 0.8106 (p0) cc_final: 0.7790 (p0) REVERT: G 381 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7214 (mm-30) REVERT: G 391 PHE cc_start: 0.8799 (m-80) cc_final: 0.8572 (m-80) REVERT: G 393 SER cc_start: 0.8196 (p) cc_final: 0.7970 (m) REVERT: G 446 VAL cc_start: 0.8701 (p) cc_final: 0.8414 (t) REVERT: H 141 LEU cc_start: 0.6092 (pp) cc_final: 0.5811 (pp) REVERT: L 24 GLN cc_start: 0.7804 (tm-30) cc_final: 0.7463 (tp40) REVERT: L 33 LEU cc_start: 0.8542 (tp) cc_final: 0.8212 (tp) REVERT: L 65 SER cc_start: 0.8285 (t) cc_final: 0.7775 (p) REVERT: L 79 GLN cc_start: 0.7357 (mm-40) cc_final: 0.6862 (mm110) REVERT: L 89 GLN cc_start: 0.8354 (tm-30) cc_final: 0.7704 (tt0) REVERT: L 125 LEU cc_start: 0.5349 (pp) cc_final: 0.4895 (mp) REVERT: L 139 PHE cc_start: 0.7518 (p90) cc_final: 0.7052 (p90) REVERT: L 169 LYS cc_start: 0.7450 (mtmm) cc_final: 0.7082 (mtmm) REVERT: J 3 GLN cc_start: 0.8559 (mm-40) cc_final: 0.8293 (mm-40) REVERT: J 24 GLN cc_start: 0.7848 (tm-30) cc_final: 0.7360 (tp40) REVERT: J 39 LYS cc_start: 0.8379 (mttt) cc_final: 0.8092 (mttm) REVERT: J 65 SER cc_start: 0.8239 (t) cc_final: 0.7793 (p) REVERT: J 79 GLN cc_start: 0.7653 (mm110) cc_final: 0.7182 (mm110) REVERT: J 188 LYS cc_start: 0.7091 (mtmm) cc_final: 0.6858 (mtmm) REVERT: K 5 VAL cc_start: 0.8309 (t) cc_final: 0.8102 (m) REVERT: K 82 SER cc_start: 0.6873 (m) cc_final: 0.6512 (p) REVERT: K 115 SER cc_start: 0.8416 (m) cc_final: 0.7893 (t) REVERT: K 116 THR cc_start: 0.8215 (p) cc_final: 0.8007 (t) REVERT: K 141 LEU cc_start: 0.6087 (OUTLIER) cc_final: 0.5662 (pp) REVERT: M 6 GLN cc_start: 0.7869 (tt0) cc_final: 0.7600 (tt0) REVERT: M 24 GLN cc_start: 0.7787 (tm-30) cc_final: 0.7216 (tp40) REVERT: M 50 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7617 (mm-30) REVERT: M 89 GLN cc_start: 0.8206 (tm-30) cc_final: 0.7667 (tt0) REVERT: M 166 GLN cc_start: 0.8249 (tt0) cc_final: 0.7874 (mt0) REVERT: M 174 SER cc_start: 0.7988 (m) cc_final: 0.7508 (t) REVERT: N 40 TYR cc_start: 0.8885 (t80) cc_final: 0.8586 (t80) REVERT: N 83 GLU cc_start: 0.8164 (tt0) cc_final: 0.7881 (tt0) REVERT: N 102 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7565 (mm-30) REVERT: N 150 MET cc_start: 0.7916 (tpt) cc_final: 0.7709 (tpt) REVERT: N 173 TYR cc_start: 0.8589 (p90) cc_final: 0.8284 (p90) REVERT: N 191 TYR cc_start: 0.8879 (m-80) cc_final: 0.8613 (m-80) REVERT: N 208 VAL cc_start: 0.7818 (t) cc_final: 0.7611 (m) REVERT: N 335 LYS cc_start: 0.8117 (ttmm) cc_final: 0.7801 (ttmm) REVERT: N 381 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7142 (mt-10) REVERT: N 412 ASP cc_start: 0.7531 (m-30) cc_final: 0.7186 (m-30) REVERT: N 432 GLN cc_start: 0.8242 (mt0) cc_final: 0.7995 (mt0) REVERT: N 446 VAL cc_start: 0.8636 (p) cc_final: 0.8388 (t) outliers start: 65 outliers final: 52 residues processed: 621 average time/residue: 0.1777 time to fit residues: 169.0544 Evaluate side-chains 643 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 587 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 290 THR 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 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 125 LEU Chi-restraints excluded: chain G residue 167 ASP 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 348 GLN Chi-restraints excluded: chain G residue 377 ASN Chi-restraints excluded: chain G residue 422 GLN Chi-restraints excluded: chain F residue 634 GLU Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 115 SER 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 87 THR Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 93 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 110 VAL 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 261 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 227 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 254 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 139 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 267 optimal weight: 0.7980 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 L 160 GLN J 38 GLN N 85 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.141333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.105408 restraints weight = 36768.972| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.56 r_work: 0.3159 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24813 Z= 0.133 Angle : 0.591 9.942 33858 Z= 0.290 Chirality : 0.045 0.268 4008 Planarity : 0.004 0.043 4173 Dihedral : 5.409 56.851 4869 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.33 % Allowed : 16.26 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.15), residues: 2943 helix: 1.20 (0.27), residues: 423 sheet: 1.43 (0.16), residues: 1065 loop : -0.41 (0.16), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 83 TYR 0.015 0.001 TYR I 98 PHE 0.027 0.001 PHE N 53 TRP 0.009 0.001 TRP N 69 HIS 0.003 0.001 HIS N 105 Details of bonding type rmsd covalent geometry : bond 0.00316 (24687) covalent geometry : angle 0.56637 (33525) SS BOND : bond 0.00378 ( 45) SS BOND : angle 1.27895 ( 90) hydrogen bonds : bond 0.04201 ( 937) hydrogen bonds : angle 4.60819 ( 2616) link_ALPHA1-3 : bond 0.00608 ( 3) link_ALPHA1-3 : angle 1.31214 ( 9) link_BETA1-4 : bond 0.00654 ( 30) link_BETA1-4 : angle 1.98323 ( 90) link_NAG-ASN : bond 0.00300 ( 48) link_NAG-ASN : angle 1.99879 ( 144) *********************** 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 644 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 584 time to evaluate : 1.063 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: 0.8702 (m-80) cc_final: 0.8181 (m-80) REVERT: C 46 LYS cc_start: 0.8101 (tppt) cc_final: 0.7773 (tppt) REVERT: C 83 GLU cc_start: 0.8311 (tt0) cc_final: 0.7964 (tt0) REVERT: C 102 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7505 (mm-30) REVERT: C 153 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7481 (mm-30) REVERT: C 208 VAL cc_start: 0.8108 (t) cc_final: 0.7887 (m) REVERT: C 290 THR cc_start: 0.8376 (OUTLIER) cc_final: 0.8175 (p) REVERT: C 381 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7132 (mm-30) REVERT: C 444 ARG cc_start: 0.7937 (ttt90) cc_final: 0.7668 (ttt180) REVERT: C 446 VAL cc_start: 0.8846 (p) cc_final: 0.8593 (t) REVERT: C 500 ARG cc_start: 0.8067 (ptp-110) cc_final: 0.7777 (mtp85) REVERT: G 87 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7620 (mp0) REVERT: G 91 GLU cc_start: 0.8040 (tp30) cc_final: 0.7626 (mm-30) REVERT: G 102 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7520 (mm-30) REVERT: G 153 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7627 (mm-30) REVERT: G 191 TYR cc_start: 0.8742 (m-80) cc_final: 0.8275 (m-80) REVERT: G 229 LYS cc_start: 0.8267 (mtmm) cc_final: 0.8001 (mtmm) REVERT: G 356 ASN cc_start: 0.8108 (p0) cc_final: 0.7770 (p0) REVERT: G 381 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7223 (mm-30) REVERT: G 391 PHE cc_start: 0.8823 (m-80) cc_final: 0.8584 (m-80) REVERT: G 393 SER cc_start: 0.8203 (p) cc_final: 0.7963 (m) REVERT: G 446 VAL cc_start: 0.8711 (p) cc_final: 0.8417 (t) REVERT: H 141 LEU cc_start: 0.6161 (pp) cc_final: 0.5873 (pp) REVERT: L 24 GLN cc_start: 0.7783 (tm-30) cc_final: 0.7452 (tp40) REVERT: L 33 LEU cc_start: 0.8541 (tp) cc_final: 0.8216 (tp) REVERT: L 65 SER cc_start: 0.8279 (t) cc_final: 0.7715 (p) REVERT: L 79 GLN cc_start: 0.7379 (mm-40) cc_final: 0.6903 (mm110) REVERT: L 89 GLN cc_start: 0.8388 (tm-30) cc_final: 0.7773 (tt0) REVERT: L 107 LYS cc_start: 0.7095 (tppt) cc_final: 0.6804 (tppt) REVERT: L 139 PHE cc_start: 0.7571 (p90) cc_final: 0.7015 (p90) REVERT: L 169 LYS cc_start: 0.7460 (mtmm) cc_final: 0.7127 (mtmm) REVERT: J 3 GLN cc_start: 0.8584 (mm-40) cc_final: 0.8324 (mm-40) REVERT: J 24 GLN cc_start: 0.7848 (tm-30) cc_final: 0.7347 (tp40) REVERT: J 39 LYS cc_start: 0.8387 (mttt) cc_final: 0.8103 (mttm) REVERT: J 65 SER cc_start: 0.8231 (t) cc_final: 0.7778 (p) REVERT: J 79 GLN cc_start: 0.7668 (mm110) cc_final: 0.7199 (mm110) REVERT: K 5 VAL cc_start: 0.8315 (t) cc_final: 0.8105 (m) REVERT: K 82 SER cc_start: 0.6910 (m) cc_final: 0.6587 (p) REVERT: K 115 SER cc_start: 0.8405 (m) cc_final: 0.7884 (t) REVERT: K 141 LEU cc_start: 0.6139 (OUTLIER) cc_final: 0.5706 (pp) REVERT: M 24 GLN cc_start: 0.7768 (tm-30) cc_final: 0.7231 (tp40) REVERT: M 50 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7595 (mm-30) REVERT: M 89 GLN cc_start: 0.8211 (tm-30) cc_final: 0.7659 (tt0) REVERT: M 166 GLN cc_start: 0.8255 (tt0) cc_final: 0.7868 (mt0) REVERT: M 174 SER cc_start: 0.7869 (m) cc_final: 0.7380 (t) REVERT: N 40 TYR cc_start: 0.8894 (t80) cc_final: 0.8591 (t80) REVERT: N 83 GLU cc_start: 0.8157 (tt0) cc_final: 0.7865 (tt0) REVERT: N 102 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7550 (mm-30) REVERT: N 173 TYR cc_start: 0.8577 (p90) cc_final: 0.8262 (p90) REVERT: N 335 LYS cc_start: 0.8111 (ttmm) cc_final: 0.7795 (ttmm) REVERT: N 412 ASP cc_start: 0.7526 (m-30) cc_final: 0.7179 (m-30) REVERT: N 432 GLN cc_start: 0.8259 (mt0) cc_final: 0.8014 (mt0) REVERT: N 446 VAL cc_start: 0.8633 (p) cc_final: 0.8380 (t) outliers start: 60 outliers final: 50 residues processed: 610 average time/residue: 0.1822 time to fit residues: 169.7976 Evaluate side-chains 635 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 582 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 290 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 478 ASN 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 125 LEU 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 368 ASP Chi-restraints excluded: chain G residue 377 ASN Chi-restraints excluded: chain G residue 422 GLN Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 115 SER 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 87 THR Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain J residue 78 LEU 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 110 VAL 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 467 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 291 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 260 optimal weight: 0.0270 chunk 57 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 246 optimal weight: 1.9990 chunk 203 optimal weight: 0.4980 chunk 110 optimal weight: 0.9990 chunk 275 optimal weight: 1.9990 chunk 204 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- 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 540 GLN F 637 ASN ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN N 85 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.141083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.105295 restraints weight = 36675.249| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.55 r_work: 0.3155 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24813 Z= 0.135 Angle : 0.597 9.863 33858 Z= 0.294 Chirality : 0.045 0.269 4008 Planarity : 0.004 0.043 4173 Dihedral : 5.392 56.765 4869 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.21 % Allowed : 16.69 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.15), residues: 2943 helix: 1.24 (0.27), residues: 423 sheet: 1.38 (0.16), residues: 1083 loop : -0.44 (0.16), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 83 TYR 0.016 0.001 TYR I 98 PHE 0.027 0.001 PHE N 53 TRP 0.009 0.001 TRP N 69 HIS 0.003 0.001 HIS N 105 Details of bonding type rmsd covalent geometry : bond 0.00321 (24687) covalent geometry : angle 0.57284 (33525) SS BOND : bond 0.00382 ( 45) SS BOND : angle 1.27732 ( 90) hydrogen bonds : bond 0.04261 ( 937) hydrogen bonds : angle 4.63209 ( 2616) link_ALPHA1-3 : bond 0.00604 ( 3) link_ALPHA1-3 : angle 1.31845 ( 9) link_BETA1-4 : bond 0.00660 ( 30) link_BETA1-4 : angle 1.98051 ( 90) link_NAG-ASN : bond 0.00312 ( 48) link_NAG-ASN : angle 1.97666 ( 144) ********************** 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 642 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 585 time to evaluate : 0.944 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: 0.8695 (m-80) cc_final: 0.8181 (m-80) REVERT: C 46 LYS cc_start: 0.8096 (tppt) cc_final: 0.7767 (tppt) REVERT: C 83 GLU cc_start: 0.8289 (tt0) cc_final: 0.7971 (tt0) REVERT: C 102 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7491 (mm-30) REVERT: C 153 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7488 (mm-30) REVERT: C 208 VAL cc_start: 0.8115 (t) cc_final: 0.7889 (m) REVERT: C 290 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.8189 (p) REVERT: C 381 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7111 (mm-30) REVERT: C 444 ARG cc_start: 0.7916 (ttt90) cc_final: 0.7653 (ttt180) REVERT: C 446 VAL cc_start: 0.8854 (p) cc_final: 0.8596 (t) REVERT: C 500 ARG cc_start: 0.8084 (ptp-110) cc_final: 0.7765 (mtp85) REVERT: G 87 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7632 (mp0) REVERT: G 91 GLU cc_start: 0.8041 (tp30) cc_final: 0.7625 (mm-30) REVERT: G 102 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7518 (mm-30) REVERT: G 153 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7612 (mm-30) REVERT: G 167 ASP cc_start: 0.7654 (t0) cc_final: 0.7315 (t0) REVERT: G 229 LYS cc_start: 0.8266 (mtmm) cc_final: 0.8004 (mtmm) REVERT: G 381 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7216 (mm-30) REVERT: G 393 SER cc_start: 0.8203 (p) cc_final: 0.7971 (m) REVERT: G 446 VAL cc_start: 0.8720 (p) cc_final: 0.8422 (t) REVERT: H 141 LEU cc_start: 0.6188 (pp) cc_final: 0.5905 (pp) REVERT: L 24 GLN cc_start: 0.7783 (tm-30) cc_final: 0.7476 (tp40) REVERT: L 33 LEU cc_start: 0.8547 (tp) cc_final: 0.8225 (tp) REVERT: L 65 SER cc_start: 0.8283 (t) cc_final: 0.7723 (p) REVERT: L 79 GLN cc_start: 0.7355 (mm-40) cc_final: 0.6873 (mm110) REVERT: L 89 GLN cc_start: 0.8389 (tm-30) cc_final: 0.7764 (tt0) REVERT: L 107 LYS cc_start: 0.6888 (tppt) cc_final: 0.6618 (tppt) REVERT: L 139 PHE cc_start: 0.7650 (p90) cc_final: 0.7090 (p90) REVERT: J 3 GLN cc_start: 0.8550 (mm-40) cc_final: 0.8278 (mm-40) REVERT: J 24 GLN cc_start: 0.7861 (tm-30) cc_final: 0.7331 (tp40) REVERT: J 39 LYS cc_start: 0.8386 (mttt) cc_final: 0.8122 (mttm) REVERT: J 65 SER cc_start: 0.8226 (t) cc_final: 0.7795 (p) REVERT: J 79 GLN cc_start: 0.7695 (mm110) cc_final: 0.7282 (mm110) REVERT: J 188 LYS cc_start: 0.7247 (mtmm) cc_final: 0.6968 (mtmm) REVERT: K 82 SER cc_start: 0.6963 (m) cc_final: 0.6650 (p) REVERT: K 115 SER cc_start: 0.8362 (m) cc_final: 0.7869 (t) REVERT: K 141 LEU cc_start: 0.6219 (OUTLIER) cc_final: 0.5785 (pp) REVERT: M 24 GLN cc_start: 0.7765 (tm-30) cc_final: 0.7238 (tp40) REVERT: M 50 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7569 (mm-30) REVERT: M 89 GLN cc_start: 0.8218 (tm-30) cc_final: 0.7667 (tt0) REVERT: M 166 GLN cc_start: 0.8260 (tt0) cc_final: 0.7853 (mt0) REVERT: M 174 SER cc_start: 0.7830 (m) cc_final: 0.7342 (t) REVERT: N 40 TYR cc_start: 0.8903 (t80) cc_final: 0.8595 (t80) REVERT: N 83 GLU cc_start: 0.8163 (tt0) cc_final: 0.7879 (tt0) REVERT: N 102 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7566 (mm-30) REVERT: N 173 TYR cc_start: 0.8569 (p90) cc_final: 0.8302 (p90) REVERT: N 335 LYS cc_start: 0.8116 (ttmm) cc_final: 0.7804 (ttmm) REVERT: N 412 ASP cc_start: 0.7515 (m-30) cc_final: 0.7172 (m-30) REVERT: N 432 GLN cc_start: 0.8253 (mt0) cc_final: 0.8008 (mt0) REVERT: N 446 VAL cc_start: 0.8647 (p) cc_final: 0.8388 (t) outliers start: 57 outliers final: 51 residues processed: 610 average time/residue: 0.1829 time to fit residues: 170.2199 Evaluate side-chains 634 residues out of total 2586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 580 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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 290 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 377 ASN Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 478 ASN 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 125 LEU 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 377 ASN Chi-restraints excluded: chain G residue 422 GLN Chi-restraints excluded: chain G residue 445 CYS Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 87 THR 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 L residue 176 SER 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 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 82 LEU 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 443 ILE Chi-restraints excluded: chain N residue 445 CYS Chi-restraints excluded: chain N residue 467 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 163 optimal weight: 9.9990 chunk 80 optimal weight: 0.0670 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 chunk 180 optimal weight: 4.9990 chunk 231 optimal weight: 10.0000 chunk 171 optimal weight: 1.9990 chunk 264 optimal weight: 0.4980 chunk 179 optimal weight: 0.4980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 ASN G 289 ASN F 637 ASN ** J 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 160 GLN N 85 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 = 0.141420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.105825 restraints weight = 36591.687| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.54 r_work: 0.3164 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24813 Z= 0.118 Angle : 0.590 13.754 33858 Z= 0.289 Chirality : 0.044 0.263 4008 Planarity : 0.004 0.043 4173 Dihedral : 5.340 57.079 4869 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.33 % Allowed : 16.72 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.15), residues: 2943 helix: 1.22 (0.27), residues: 423 sheet: 1.47 (0.16), residues: 1065 loop : -0.43 (0.16), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 83 TYR 0.013 0.001 TYR I 98 PHE 0.026 0.001 PHE N 53 TRP 0.009 0.001 TRP N 69 HIS 0.003 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00275 (24687) covalent geometry : angle 0.56641 (33525) SS BOND : bond 0.00345 ( 45) SS BOND : angle 1.21929 ( 90) hydrogen bonds : bond 0.04046 ( 937) hydrogen bonds : angle 4.60004 ( 2616) link_ALPHA1-3 : bond 0.00597 ( 3) link_ALPHA1-3 : angle 1.31744 ( 9) link_BETA1-4 : bond 0.00662 ( 30) link_BETA1-4 : angle 1.96066 ( 90) link_NAG-ASN : bond 0.00275 ( 48) link_NAG-ASN : angle 1.93611 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9603.36 seconds wall clock time: 164 minutes 10.65 seconds (9850.65 seconds total)