Starting phenix.real_space_refine on Thu Mar 5 04:29:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6olp_20118/03_2026/6olp_20118.cif Found real_map, /net/cci-nas-00/data/ceres_data/6olp_20118/03_2026/6olp_20118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6olp_20118/03_2026/6olp_20118.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6olp_20118/03_2026/6olp_20118.map" model { file = "/net/cci-nas-00/data/ceres_data/6olp_20118/03_2026/6olp_20118.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6olp_20118/03_2026/6olp_20118.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 116 5.16 5 C 11840 2.51 5 N 3064 2.21 5 O 3848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18868 Number of models: 1 Model: "" Number of chains: 40 Chain: "A" Number of atoms: 3392 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 430, 3386 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 22, 'TRANS': 407} Chain breaks: 5 Conformer: "B" Number of residues, atoms: 430, 3386 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 22, 'TRANS': 407} Chain breaks: 5 bond proxies already assigned to first conformer: 3449 Chain: "B" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1152 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 1, 'TRANS': 141} Chain: "C" Number of atoms: 3454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3454 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 22, 'TRANS': 415} Chain breaks: 3 Chain: "D" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1014 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "E" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3298 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 22, 'TRANS': 396} Chain breaks: 6 Chain: "F" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1063 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 1, 'TRANS': 132} Chain breaks: 2 Chain: "G" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1062 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 6, 'TRANS': 127} Chain: "I" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 838 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 102} Chain: "H" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1073 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "L" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 854 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 104} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" 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: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 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: 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: 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: "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: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 110 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 1, 'MAN': 2, 'NAG': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "W" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 96 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 1, 'MAN': 2, 'NAG': 3} 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: "X" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "c" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: "e" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 110 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 1, 'MAN': 2, 'NAG': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "f" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 121 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" 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: "A" 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: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} 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 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER A 393 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 393 " occ=0.50 Time building chain proxies: 4.70, per 1000 atoms: 0.25 Number of scatterers: 18868 At special positions: 0 Unit cell: (127.72, 133.9, 147.29, 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 116 16.00 O 3848 8.00 N 3064 7.00 C 11840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 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 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.02 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA P 3 " - " MAN P 4 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 7 " " BMA b 3 " - " MAN b 4 " " BMA e 3 " - " MAN e 4 " " BMA f 3 " - " MAN f 9 " ALPHA1-6 " BMA V 3 " - " MAN V 8 " " BMA W 3 " - " MAN W 4 " " BMA b 3 " - " MAN b 5 " " BMA e 3 " - " MAN e 7 " " BMA f 3 " - " MAN f 4 " BETA1-2 " MAN V 4 " - " NAG V 5 " " MAN e 4 " - " NAG e 5 " " MAN e 7 " - " NAG e 8 " " MAN f 4 " - " NAG f 5 " BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " MAN V 4 " - " NAG V 7 " " NAG V 5 " - " GAL V 6 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG W 5 " - " GAL W 6 " " 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 b 2 " - " BMA b 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG e 5 " - " GAL e 6 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG f 5 " - " GAL f 6 " " NAG f 7 " - " GAL f 8 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " BETA1-6 " NAG K 1 " - " NAG K 2 " " NAG V 1 " - " FUC V 9 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG W 1 " - " FUC W 8 " " MAN W 4 " - " NAG W 5 " " NAG X 1 " - " FUC X 2 " " NAG c 1 " - " FUC c 2 " " NAG e 1 " - " FUC e 9 " " NAG f 1 " - " FUC f 10 " " MAN f 4 " - " NAG f 7 " NAG-ASN " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 197 " " NAG A 605 " - " ASN A 234 " " NAG A 618 " - " ASN A 332 " " NAG A 619 " - " ASN A 392 " " NAG A 629 " - " ASN A 188 " " NAG A 632 " - " ASN A 356 " " NAG A 633 " - " ASN A 362 " " NAG C 603 " - " ASN C 130 " " NAG C 606 " - " ASN C 234 " " NAG C 614 " - " ASN C 448 " " NAG C 615 " - " ASN C 276 " " NAG C 616 " - " ASN C 156 " " NAG C 617 " - " ASN C 188 " " NAG C 620 " - " ASN C 295 " " NAG C 621 " - " ASN C 301 " " NAG C 622 " - " ASN C 332 " " NAG C 623 " - " ASN C 289 " " NAG C 624 " - " ASN C 392 " " NAG C 627 " - " ASN C 356 " " NAG C 628 " - " ASN C 362 " " NAG D 901 " - " ASN D 625 " " NAG E 608 " - " ASN E 160 " " NAG E 609 " - " ASN E 156 " " NAG E 610 " - " ASN E 276 " " NAG E 611 " - " ASN E 289 " " NAG E 612 " - " ASN E 332 " " NAG E 613 " - " ASN E 295 " " NAG E 614 " - " ASN E 301 " " NAG E 615 " - " ASN E 392 " " NAG E 616 " - " ASN E 362 " " NAG E 617 " - " ASN E 234 " " NAG E 618 " - " ASN E 356 " " NAG E 619 " - " ASN E 188 " " NAG E 620 " - " ASN E 197 " " NAG E 621 " - " ASN E 130 " " NAG E 622 " - " ASN E 448 " " NAG F 901 " - " ASN F 616 " " NAG F 902 " - " ASN F 625 " " NAG F 903 " - " ASN F 637 " " NAG F 904 " - " ASN F 611 " " NAG J 1 " - " ASN A 130 " " NAG K 1 " - " ASN A 241 " " NAG M 1 " - " ASN A 276 " " NAG N 1 " - " ASN A 386 " " NAG O 1 " - " ASN A 295 " " NAG P 1 " - " ASN A 262 " " NAG Q 1 " - " ASN A 301 " " NAG R 1 " - " ASN A 448 " " NAG S 1 " - " ASN A 88 " " NAG T 1 " - " ASN A 156 " " NAG U 1 " - " ASN A 289 " " NAG V 1 " - " ASN B 637 " " NAG W 1 " - " ASN B 611 " " NAG X 1 " - " ASN B 625 " " NAG Y 1 " - " ASN C 88 " " NAG Z 1 " - " ASN C 160 " " NAG a 1 " - " ASN C 241 " " NAG b 1 " - " ASN C 262 " " NAG c 1 " - " ASN C 197 " " NAG d 1 " - " ASN C 386 " " NAG e 1 " - " ASN D 637 " " NAG f 1 " - " ASN D 611 " " NAG g 1 " - " ASN E 88 " " NAG h 1 " - " ASN E 241 " " NAG i 1 " - " ASN E 262 " Time building additional restraints: 1.93 Conformation dependent library (CDL) restraints added in 853.2 milliseconds 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4062 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 39 sheets defined 19.2% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 98 through 106 removed outlier: 4.176A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET A 104 " --> pdb=" O MET A 100 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS A 105 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 115 Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.519A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 350 removed outlier: 3.704A pdb=" N ASN A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN A 344 " --> pdb=" O ASP A 340 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS A 348 " --> pdb=" O GLN A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 373 removed outlier: 3.815A pdb=" N MET A 373 " --> pdb=" O PRO A 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 369 through 373' Processing helix chain 'A' and resid 474 through 482 removed outlier: 3.524A pdb=" N TRP A 479 " --> pdb=" O ARG A 476 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A 480 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 537 removed outlier: 3.921A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N THR B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 556 removed outlier: 4.353A pdb=" N ASN B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 removed outlier: 4.091A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR B 586 " --> pdb=" O ALA B 582 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU B 592 " --> pdb=" O LYS B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 removed outlier: 3.806A pdb=" N ILE B 622 " --> pdb=" O SER B 618 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TRP B 623 " --> pdb=" O TYR B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 636 removed outlier: 3.519A pdb=" N ARG B 633 " --> pdb=" O MET B 629 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B 635 " --> pdb=" O TRP B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 648 removed outlier: 3.648A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 664 removed outlier: 3.947A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 117 removed outlier: 3.523A pdb=" N HIS C 105 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.730A pdb=" N LEU C 125 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 122 through 126' Processing helix chain 'C' and resid 334 through 349 removed outlier: 3.575A pdb=" N TRP C 338 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS C 343 " --> pdb=" O ASN C 339 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN C 344 " --> pdb=" O ASP C 340 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL C 347 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS C 348 " --> pdb=" O GLN C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 391 removed outlier: 3.531A pdb=" N LEU C 390 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE C 391 " --> pdb=" O THR C 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 387 through 391' Processing helix chain 'C' and resid 475 through 483 Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 543 removed outlier: 4.340A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 576 removed outlier: 4.185A pdb=" N GLN D 575 " --> pdb=" O GLY D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 596 removed outlier: 3.841A pdb=" N LEU D 581 " --> pdb=" O GLN D 577 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR D 586 " --> pdb=" O ALA D 582 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS D 588 " --> pdb=" O GLU D 584 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU D 593 " --> pdb=" O ASP D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.886A pdb=" N ARG D 633 " --> pdb=" O MET D 629 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU D 634 " --> pdb=" O GLU D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 648 removed outlier: 3.572A pdb=" N GLU D 647 " --> pdb=" O TYR D 643 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 660 removed outlier: 3.751A pdb=" N ASN D 656 " --> pdb=" O GLN D 652 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN D 658 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU D 660 " --> pdb=" O ASN D 656 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 106 removed outlier: 3.514A pdb=" N MET E 104 " --> pdb=" O MET E 100 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N HIS E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 115 removed outlier: 3.707A pdb=" N ASP E 113 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N SER E 115 " --> pdb=" O LEU E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 352 removed outlier: 3.729A pdb=" N TRP E 338 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASN E 339 " --> pdb=" O GLY E 335 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP E 340 " --> pdb=" O THR E 336 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS E 343 " --> pdb=" O ASN E 339 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE E 345 " --> pdb=" O THR E 341 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL E 347 " --> pdb=" O LYS E 343 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS E 348 " --> pdb=" O GLN E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 392 removed outlier: 4.099A pdb=" N ASN E 392 " --> pdb=" O THR E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 429 No H-bonds generated for 'chain 'E' and resid 427 through 429' Processing helix chain 'E' and resid 475 through 480 removed outlier: 3.978A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.575A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 535 removed outlier: 3.523A pdb=" N MET F 535 " --> pdb=" O ALA F 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 532 through 535' Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.618A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 574 No H-bonds generated for 'chain 'F' and resid 572 through 574' Processing helix chain 'F' and resid 577 through 596 removed outlier: 3.523A pdb=" N ALA F 582 " --> pdb=" O ALA F 578 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL F 583 " --> pdb=" O ARG F 579 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 623 removed outlier: 3.904A pdb=" N ILE F 622 " --> pdb=" O SER F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.692A pdb=" N TRP F 631 " --> pdb=" O THR F 627 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE F 635 " --> pdb=" O TRP F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 649 removed outlier: 3.514A pdb=" N THR F 644 " --> pdb=" O SER F 640 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU F 645 " --> pdb=" O LEU F 641 " (cutoff:3.500A) Processing helix chain 'F' and resid 653 through 658 removed outlier: 3.595A pdb=" N GLN F 658 " --> pdb=" O LYS F 655 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.551A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.545A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA A 224 " --> pdb=" O VAL A 489 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 131 through 132 Processing sheet with id=AA4, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA5, first strand: chain 'A' and resid 201 through 203 Processing sheet with id=AA6, first strand: chain 'A' and resid 256 through 257 removed outlier: 3.544A pdb=" N HIS A 330 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 10.706A pdb=" N VAL A 286 " --> pdb=" O ILE A 455 " (cutoff:3.500A) removed outlier: 10.525A pdb=" N ILE A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.727A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.939A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.783A pdb=" N LYS A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N GLY A 451 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.770A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N GLY A 451 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 11.783A pdb=" N LYS A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.939A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.727A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.525A pdb=" N ILE A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.706A pdb=" N VAL A 286 " --> pdb=" O ILE A 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 298 current: chain 'A' and resid 360 through 361 Processing sheet with id=AA8, first strand: chain 'A' and resid 303 through 312 removed outlier: 6.976A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 309 " --> pdb=" O ARG A 315 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ARG A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 495 through 499 removed outlier: 5.647A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.517A pdb=" N LYS C 46 " --> pdb=" O LYS C 490 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL C 489 " --> pdb=" O ALA C 224 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 66 through 67 removed outlier: 6.578A pdb=" N HIS C 66 " --> pdb=" O SER C 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 93 through 94 Processing sheet with id=AB4, first strand: chain 'C' and resid 132 through 133 removed outlier: 3.532A pdb=" N ASN C 156 " --> pdb=" O THR C 132 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AB6, first strand: chain 'C' and resid 271 through 273 Processing sheet with id=AB7, first strand: chain 'C' and resid 374 through 377 removed outlier: 8.309A pdb=" N CYS C 296 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N SER C 447 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N ARG C 298 " --> pdb=" O CYS C 445 " (cutoff:3.500A) removed outlier: 8.888A pdb=" N CYS C 445 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ASN C 300 " --> pdb=" O ILE C 443 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ILE C 443 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN C 302 " --> pdb=" O GLY C 441 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 307 through 312 removed outlier: 4.328A pdb=" N HIS C 308 " --> pdb=" O PHE C 317 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE C 317 " --> pdb=" O HIS C 308 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 517 through 521 removed outlier: 7.401A pdb=" N GLY G 113 " --> pdb=" O VAL D 518 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 84 through 85 removed outlier: 4.009A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS E 487 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N VAL E 489 " --> pdb=" O TRP E 45 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N TRP E 45 " --> pdb=" O VAL E 489 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N ILE E 491 " --> pdb=" O PRO E 43 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 53 through 56 removed outlier: 4.038A pdb=" N PHE E 53 " --> pdb=" O CYS E 218 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS E 218 " --> pdb=" O PHE E 53 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC4, first strand: chain 'E' and resid 130 through 133 removed outlier: 3.546A pdb=" N PHE E 176 " --> pdb=" O LYS E 155 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AC6, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.560A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.802A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 374 through 377 removed outlier: 3.861A pdb=" N HIS E 330 " --> pdb=" O THR E 297 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N CYS E 296 " --> pdb=" O SER E 447 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N SER E 447 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ARG E 298 " --> pdb=" O CYS E 445 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N CYS E 445 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN E 300 " --> pdb=" O ILE E 443 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ILE E 443 " --> pdb=" O ASN E 300 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 304 through 308 Processing sheet with id=AD1, first strand: chain 'G' and resid 4 through 5 removed outlier: 3.886A pdb=" N VAL G 5 " --> pdb=" O VAL G 23 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP G 73 " --> pdb=" O THR G 78 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.621A pdb=" N VAL G 131 " --> pdb=" O ALA G 92 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA G 92 " --> pdb=" O VAL G 131 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA G 97 " --> pdb=" O TYR G 35 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N MET G 34 " --> pdb=" O ALA G 50 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ALA G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.621A pdb=" N VAL G 131 " --> pdb=" O ALA G 92 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA G 92 " --> pdb=" O VAL G 131 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N CYS G 96 " --> pdb=" O TRP G 125 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N TRP G 125 " --> pdb=" O CYS G 96 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG G 98 " --> pdb=" O ASP G 123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.654A pdb=" N SER I 22 " --> pdb=" O THR I 7 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 10 through 12 Processing sheet with id=AD6, first strand: chain 'I' and resid 45 through 48 removed outlier: 7.461A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN I 38 " --> pdb=" O PHE I 85 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.606A pdb=" N VAL H 18 " --> pdb=" O MET H 83 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AD9, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.722A pdb=" N THR H 132 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL H 131 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA H 92 " --> pdb=" O VAL H 131 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL H 37 " --> pdb=" O ARG H 95 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA H 97 " --> pdb=" O TYR H 35 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.722A pdb=" N THR H 132 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL H 131 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA H 92 " --> pdb=" O VAL H 131 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL H 124 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 19 through 22 removed outlier: 3.579A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.856A pdb=" N GLU L 50 " --> pdb=" O ASN L 53 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LEU L 46 " --> pdb=" O ARG L 37 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ARG L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1122 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: 2.96 Time building geometry restraints manager: 2.44 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: 5740 1.34 - 1.46: 4898 1.46 - 1.59: 8425 1.59 - 1.71: 1 1.71 - 1.83: 164 Bond restraints: 19228 Sorted by residual: bond pdb=" C ASP I 93 " pdb=" N PHE I 94 " ideal model delta sigma weight residual 1.331 1.222 0.109 2.07e-02 2.33e+03 2.77e+01 bond pdb=" C1 NAG C 615 " pdb=" O5 NAG C 615 " ideal model delta sigma weight residual 1.406 1.507 -0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C1 MAN b 4 " pdb=" C2 MAN b 4 " ideal model delta sigma weight residual 1.526 1.597 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C1 NAG g 1 " pdb=" O5 NAG g 1 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C5 MAN f 4 " pdb=" O5 MAN f 4 " ideal model delta sigma weight residual 1.418 1.480 -0.062 2.00e-02 2.50e+03 9.48e+00 ... (remaining 19223 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 24970 2.46 - 4.92: 947 4.92 - 7.38: 137 7.38 - 9.85: 31 9.85 - 12.31: 5 Bond angle restraints: 26090 Sorted by residual: angle pdb=" C LEU B 565 " pdb=" N LEU B 566 " pdb=" CA LEU B 566 " ideal model delta sigma weight residual 121.54 132.80 -11.26 1.91e+00 2.74e-01 3.47e+01 angle pdb=" C GLY A 354 " pdb=" N ASN A 356 " pdb=" CA ASN A 356 " ideal model delta sigma weight residual 121.54 132.18 -10.64 1.91e+00 2.74e-01 3.11e+01 angle pdb=" C PHE C 353 " pdb=" N GLY C 354 " pdb=" CA GLY C 354 " ideal model delta sigma weight residual 121.41 131.10 -9.69 1.96e+00 2.60e-01 2.45e+01 angle pdb=" C PHE A 159 " pdb=" N ASN A 160 " pdb=" CA ASN A 160 " ideal model delta sigma weight residual 122.14 114.50 7.64 1.67e+00 3.59e-01 2.09e+01 angle pdb=" N ASN E 289 " pdb=" CA ASN E 289 " pdb=" C ASN E 289 " ideal model delta sigma weight residual 110.55 104.40 6.15 1.35e+00 5.49e-01 2.07e+01 ... (remaining 26085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.48: 12467 23.48 - 46.95: 452 46.95 - 70.43: 121 70.43 - 93.90: 54 93.90 - 117.38: 49 Dihedral angle restraints: 13143 sinusoidal: 6852 harmonic: 6291 Sorted by residual: dihedral pdb=" CB CYS C 378 " pdb=" SG CYS C 378 " pdb=" SG CYS C 445 " pdb=" CB CYS C 445 " ideal model delta sinusoidal sigma weight residual -86.00 -148.37 62.37 1 1.00e+01 1.00e-02 5.15e+01 dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual 93.00 152.37 -59.37 1 1.00e+01 1.00e-02 4.71e+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 -137.52 51.52 1 1.00e+01 1.00e-02 3.63e+01 ... (remaining 13140 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 3243 0.160 - 0.321: 52 0.321 - 0.481: 9 0.481 - 0.641: 2 0.641 - 0.801: 2 Chirality restraints: 3308 Sorted by residual: chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN B 625 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.60 -0.80 2.00e-01 2.50e+01 1.60e+01 chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN A 88 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.12e+01 chirality pdb=" C1 NAG C 623 " pdb=" ND2 ASN C 289 " pdb=" C2 NAG C 623 " pdb=" O5 NAG C 623 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.98e+00 ... (remaining 3305 not shown) Planarity restraints: 3198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 88 " -0.033 2.00e-02 2.50e+03 3.11e-02 1.21e+01 pdb=" CG ASN A 88 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN A 88 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 88 " 0.037 2.00e-02 2.50e+03 pdb=" C1 NAG S 1 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 625 " 0.014 2.00e-02 2.50e+03 2.91e-02 8.47e+00 pdb=" C ASN B 625 " -0.050 2.00e-02 2.50e+03 pdb=" O ASN B 625 " 0.019 2.00e-02 2.50e+03 pdb=" N MET B 626 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 651 " 0.015 2.00e-02 2.50e+03 2.90e-02 8.43e+00 pdb=" CG ASN B 651 " -0.050 2.00e-02 2.50e+03 pdb=" OD1 ASN B 651 " 0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN B 651 " 0.017 2.00e-02 2.50e+03 ... (remaining 3195 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3097 2.76 - 3.29: 17425 3.29 - 3.83: 30751 3.83 - 4.36: 34347 4.36 - 4.90: 57830 Nonbonded interactions: 143450 Sorted by model distance: nonbonded pdb=" OG SER A 209 " pdb=" OE1 GLU A 211 " model vdw 2.224 3.040 nonbonded pdb=" OG SER I 25 " pdb=" O GLU I 27 " model vdw 2.239 3.040 nonbonded pdb=" OG1 THR A 303 " pdb=" O GLU A 322 " model vdw 2.263 3.040 nonbonded pdb=" OG SER G 120 " pdb=" OH TYR I 34 " model vdw 2.268 3.040 nonbonded pdb=" O MET H 122 " pdb=" OH TYR L 36 " model vdw 2.286 3.040 ... (remaining 143445 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' and (resid 33 through 58 or resid 65 through 134 or resid 152 through \ 165 or resid 170 through 353 or resid 356 through 392 or resid 413 through 457 \ or resid 467 through 633)) selection = (chain 'C' and (resid 33 through 58 or resid 65 through 134 or resid 152 through \ 165 or resid 170 through 353 or resid 356 through 364 or resid 368 through 392 \ or resid 413 through 457 or resid 467 through 505 or resid 617 through 628)) selection = (chain 'E' and (resid 33 through 134 or resid 152 through 364 or resid 368 throu \ gh 392 or resid 413 through 505 or resid 615 through 622)) } ncs_group { reference = (chain 'B' and (resid 522 through 557 or resid 571 through 574 or resid 576 thro \ ugh 659)) selection = (chain 'F' and resid 522 through 659) } ncs_group { reference = chain 'G' selection = (chain 'H' and resid 2 through 135) } ncs_group { reference = chain 'I' selection = (chain 'L' and resid 2 through 105) } ncs_group { reference = (chain 'J' and resid 1) selection = (chain 'K' and resid 1) selection = (chain 'M' and resid 1) selection = (chain 'N' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'S' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'U' and resid 1) selection = (chain 'X' and resid 1) selection = (chain 'Y' and resid 1) selection = (chain 'Z' and resid 1) selection = (chain 'a' and resid 1) selection = (chain 'c' and resid 1) selection = (chain 'd' and resid 1) selection = (chain 'g' and resid 1) selection = (chain 'h' and resid 1) } ncs_group { reference = chain 'R' selection = chain 'i' } ncs_group { reference = (chain 'V' and resid 9) selection = (chain 'W' and resid 8) selection = (chain 'e' and resid 9) selection = (chain 'f' and resid 10) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 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: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.150 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 : 0.009 0.109 19388 Z= 0.414 Angle : 1.223 18.235 26536 Z= 0.577 Chirality : 0.070 0.801 3308 Planarity : 0.007 0.059 3132 Dihedral : 15.438 117.378 8979 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.75 % Favored : 88.25 % Rotamer: Outliers : 0.57 % Allowed : 3.22 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.54 (0.15), residues: 2131 helix: -3.53 (0.18), residues: 342 sheet: -2.65 (0.19), residues: 537 loop : -3.12 (0.15), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 585 TYR 0.036 0.003 TYR A 217 PHE 0.030 0.004 PHE I 49 TRP 0.033 0.004 TRP F 614 HIS 0.012 0.002 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00888 (19228) covalent geometry : angle 1.13074 (26090) SS BOND : bond 0.00557 ( 34) SS BOND : angle 1.53555 ( 68) hydrogen bonds : bond 0.30925 ( 418) hydrogen bonds : angle 10.98581 ( 1122) link_ALPHA1-3 : bond 0.00722 ( 6) link_ALPHA1-3 : angle 1.88907 ( 18) link_ALPHA1-6 : bond 0.00505 ( 5) link_ALPHA1-6 : angle 1.98480 ( 15) link_BETA1-2 : bond 0.01175 ( 4) link_BETA1-2 : angle 2.15059 ( 12) link_BETA1-4 : bond 0.01061 ( 36) link_BETA1-4 : angle 3.48835 ( 108) link_BETA1-6 : bond 0.00807 ( 9) link_BETA1-6 : angle 2.67492 ( 27) link_NAG-ASN : bond 0.00942 ( 66) link_NAG-ASN : angle 4.77478 ( 198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 377 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8308 (m-90) cc_final: 0.7987 (m-90) REVERT: A 106 GLU cc_start: 0.8410 (mm-30) cc_final: 0.7836 (pt0) REVERT: A 211 GLU cc_start: 0.8395 (mp0) cc_final: 0.8162 (mp0) REVERT: A 434 MET cc_start: 0.8873 (tmm) cc_final: 0.8473 (tmm) REVERT: B 638 TYR cc_start: 0.8994 (m-80) cc_final: 0.8763 (m-10) REVERT: B 645 LEU cc_start: 0.9481 (mt) cc_final: 0.9029 (tp) REVERT: B 656 ASN cc_start: 0.8931 (t0) cc_final: 0.8724 (t0) REVERT: B 657 GLU cc_start: 0.9191 (mt-10) cc_final: 0.8822 (tm-30) REVERT: B 659 GLU cc_start: 0.9474 (tt0) cc_final: 0.9103 (tm-30) REVERT: C 42 VAL cc_start: 0.9409 (t) cc_final: 0.9150 (p) REVERT: C 260 LEU cc_start: 0.8864 (pp) cc_final: 0.8583 (pp) REVERT: C 304 ARG cc_start: 0.8363 (tpm170) cc_final: 0.8152 (mmm160) REVERT: D 626 MET cc_start: 0.8925 (mtp) cc_final: 0.8543 (ttm) REVERT: D 632 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8213 (tm-30) REVERT: D 651 ASN cc_start: 0.8850 (m-40) cc_final: 0.8618 (t0) REVERT: E 69 TRP cc_start: 0.7950 (m-90) cc_final: 0.7259 (m-90) REVERT: E 104 MET cc_start: 0.8105 (mmm) cc_final: 0.7898 (tpp) REVERT: E 111 LEU cc_start: 0.9031 (mt) cc_final: 0.8798 (tp) REVERT: E 293 GLU cc_start: 0.8128 (tt0) cc_final: 0.7856 (tm-30) REVERT: E 373 MET cc_start: 0.9044 (mmp) cc_final: 0.8598 (mmt) REVERT: E 426 MET cc_start: 0.6995 (mmm) cc_final: 0.6748 (mmm) REVERT: E 427 TRP cc_start: 0.7661 (m-90) cc_final: 0.7252 (m-90) REVERT: F 539 VAL cc_start: 0.9689 (t) cc_final: 0.9452 (p) REVERT: F 640 SER cc_start: 0.9276 (m) cc_final: 0.9012 (p) REVERT: G 35 TYR cc_start: 0.8853 (m-80) cc_final: 0.8564 (m-10) REVERT: I 27 GLU cc_start: 0.8645 (tp30) cc_final: 0.8431 (tp30) REVERT: I 89 MET cc_start: 0.8562 (ttt) cc_final: 0.7691 (ttt) REVERT: H 1 ARG cc_start: 0.7130 (ttp80) cc_final: 0.5677 (ttm-80) REVERT: H 45 LEU cc_start: 0.8797 (tp) cc_final: 0.8574 (tp) REVERT: H 90 ASP cc_start: 0.9140 (m-30) cc_final: 0.8879 (m-30) REVERT: L 17 GLN cc_start: 0.8420 (tt0) cc_final: 0.8164 (tm-30) REVERT: L 92 LYS cc_start: 0.9203 (tptp) cc_final: 0.8459 (tppp) REVERT: L 103 LYS cc_start: 0.8453 (tttt) cc_final: 0.8181 (tmtt) outliers start: 9 outliers final: 1 residues processed: 384 average time/residue: 0.1511 time to fit residues: 84.7517 Evaluate side-chains 191 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 0.9980 chunk 212 optimal weight: 8.9990 chunk 77 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 105 HIS A 216 HIS A 300 ASN C 82 GLN C 229 ASN C 287 GLN C 300 ASN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 HIS E 344 GLN ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 GLN H 115 ASN L 53 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.061256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.050143 restraints weight = 95866.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.051619 restraints weight = 53974.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.052631 restraints weight = 36724.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.053319 restraints weight = 28157.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.053755 restraints weight = 23423.619| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19388 Z= 0.152 Angle : 0.849 13.875 26536 Z= 0.396 Chirality : 0.053 0.444 3308 Planarity : 0.005 0.063 3132 Dihedral : 14.205 103.805 4898 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 0.10 % Allowed : 2.23 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.74 (0.16), residues: 2131 helix: -2.17 (0.23), residues: 346 sheet: -2.33 (0.20), residues: 535 loop : -2.72 (0.16), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 585 TYR 0.020 0.002 TYR A 217 PHE 0.021 0.002 PHE I 49 TRP 0.019 0.002 TRP C 479 HIS 0.007 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00319 (19228) covalent geometry : angle 0.77213 (26090) SS BOND : bond 0.00332 ( 34) SS BOND : angle 1.03264 ( 68) hydrogen bonds : bond 0.05799 ( 418) hydrogen bonds : angle 7.41698 ( 1122) link_ALPHA1-3 : bond 0.01510 ( 6) link_ALPHA1-3 : angle 2.21947 ( 18) link_ALPHA1-6 : bond 0.00745 ( 5) link_ALPHA1-6 : angle 1.80088 ( 15) link_BETA1-2 : bond 0.00547 ( 4) link_BETA1-2 : angle 1.68862 ( 12) link_BETA1-4 : bond 0.00771 ( 36) link_BETA1-4 : angle 2.46533 ( 108) link_BETA1-6 : bond 0.00690 ( 9) link_BETA1-6 : angle 1.52752 ( 27) link_NAG-ASN : bond 0.00747 ( 66) link_NAG-ASN : angle 3.62379 ( 198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8149 (m90) cc_final: 0.7701 (m90) REVERT: A 69 TRP cc_start: 0.8245 (m-90) cc_final: 0.7879 (m-90) REVERT: A 106 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7819 (pt0) REVERT: A 211 GLU cc_start: 0.8426 (mp0) cc_final: 0.8004 (mp0) REVERT: A 434 MET cc_start: 0.8890 (tmm) cc_final: 0.8584 (tmm) REVERT: A 477 ASP cc_start: 0.8898 (m-30) cc_final: 0.8630 (m-30) REVERT: B 638 TYR cc_start: 0.9157 (m-80) cc_final: 0.8909 (m-10) REVERT: B 651 ASN cc_start: 0.8704 (m110) cc_final: 0.8434 (t0) REVERT: C 42 VAL cc_start: 0.9515 (t) cc_final: 0.9275 (p) REVERT: C 304 ARG cc_start: 0.8103 (tpm170) cc_final: 0.7764 (mmm160) REVERT: D 584 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7742 (tm-30) REVERT: D 620 ASN cc_start: 0.8874 (m-40) cc_final: 0.8553 (t0) REVERT: D 632 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8041 (tm-30) REVERT: D 640 SER cc_start: 0.9110 (p) cc_final: 0.8898 (p) REVERT: D 650 GLN cc_start: 0.7931 (tt0) cc_final: 0.7699 (tt0) REVERT: E 69 TRP cc_start: 0.7948 (m-90) cc_final: 0.7281 (m-90) REVERT: E 95 MET cc_start: 0.9345 (ptm) cc_final: 0.9004 (ptm) REVERT: E 210 PHE cc_start: 0.8684 (m-80) cc_final: 0.8447 (m-10) REVERT: E 373 MET cc_start: 0.8997 (mmp) cc_final: 0.8590 (mmt) REVERT: E 427 TRP cc_start: 0.7772 (m-90) cc_final: 0.7438 (m-90) REVERT: F 586 TYR cc_start: 0.8919 (t80) cc_final: 0.8288 (t80) REVERT: F 646 ILE cc_start: 0.9653 (mm) cc_final: 0.9380 (tp) REVERT: G 87 LYS cc_start: 0.8846 (mppt) cc_final: 0.8562 (mtmm) REVERT: I 27 ARG cc_start: 0.7877 (tpt90) cc_final: 0.7574 (mmm160) REVERT: I 89 MET cc_start: 0.8418 (ttt) cc_final: 0.6685 (ttt) REVERT: H 108 LEU cc_start: 0.9150 (tp) cc_final: 0.8908 (tt) REVERT: L 17 GLN cc_start: 0.8834 (tt0) cc_final: 0.8398 (tm-30) REVERT: L 27 GLU cc_start: 0.8036 (tp30) cc_final: 0.7699 (tm-30) REVERT: L 74 ARG cc_start: 0.8142 (tpp80) cc_final: 0.7742 (mmm-85) REVERT: L 92 LYS cc_start: 0.9150 (tptp) cc_final: 0.8734 (tppp) REVERT: L 103 LYS cc_start: 0.8479 (tttt) cc_final: 0.7985 (tmtt) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.1324 time to fit residues: 59.4031 Evaluate side-chains 198 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 197 optimal weight: 10.0000 chunk 50 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 67 optimal weight: 30.0000 chunk 212 optimal weight: 9.9990 chunk 187 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 84 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 chunk 117 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** B 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 590 GLN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.061801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.050554 restraints weight = 98648.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.052046 restraints weight = 55264.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.053058 restraints weight = 37529.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.053750 restraints weight = 28858.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.054203 restraints weight = 24042.765| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19388 Z= 0.132 Angle : 0.762 13.006 26536 Z= 0.353 Chirality : 0.051 0.398 3308 Planarity : 0.004 0.050 3132 Dihedral : 12.360 96.129 4898 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 0.10 % Allowed : 2.44 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.30 (0.16), residues: 2131 helix: -1.46 (0.25), residues: 353 sheet: -2.05 (0.20), residues: 536 loop : -2.55 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 585 TYR 0.023 0.001 TYR A 217 PHE 0.016 0.001 PHE I 49 TRP 0.025 0.001 TRP E 338 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00277 (19228) covalent geometry : angle 0.69737 (26090) SS BOND : bond 0.00305 ( 34) SS BOND : angle 0.93259 ( 68) hydrogen bonds : bond 0.04412 ( 418) hydrogen bonds : angle 6.54190 ( 1122) link_ALPHA1-3 : bond 0.01631 ( 6) link_ALPHA1-3 : angle 2.01002 ( 18) link_ALPHA1-6 : bond 0.00904 ( 5) link_ALPHA1-6 : angle 1.74453 ( 15) link_BETA1-2 : bond 0.00419 ( 4) link_BETA1-2 : angle 1.52784 ( 12) link_BETA1-4 : bond 0.00703 ( 36) link_BETA1-4 : angle 2.20755 ( 108) link_BETA1-6 : bond 0.00738 ( 9) link_BETA1-6 : angle 1.33908 ( 27) link_NAG-ASN : bond 0.00801 ( 66) link_NAG-ASN : angle 3.13024 ( 198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.652 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: A 66 HIS cc_start: 0.8015 (m90) cc_final: 0.7474 (m90) REVERT: A 69 TRP cc_start: 0.8183 (m-90) cc_final: 0.7786 (m-90) REVERT: A 106 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7827 (pt0) REVERT: A 176 PHE cc_start: 0.8749 (m-10) cc_final: 0.8424 (m-10) REVERT: A 211 GLU cc_start: 0.8310 (mp0) cc_final: 0.7946 (mp0) REVERT: A 434 MET cc_start: 0.8883 (tmm) cc_final: 0.8576 (tmm) REVERT: A 477 ASP cc_start: 0.8812 (m-30) cc_final: 0.8566 (m-30) REVERT: B 595 ILE cc_start: 0.9616 (mt) cc_final: 0.9371 (mt) REVERT: B 657 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8600 (mp0) REVERT: C 42 VAL cc_start: 0.9438 (t) cc_final: 0.9210 (p) REVERT: C 304 ARG cc_start: 0.8125 (tpm170) cc_final: 0.7638 (mmm160) REVERT: C 427 TRP cc_start: 0.4110 (t60) cc_final: 0.3712 (t60) REVERT: D 584 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7760 (tm-30) REVERT: D 632 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8148 (tm-30) REVERT: D 655 LYS cc_start: 0.9140 (mmtm) cc_final: 0.8919 (mmmt) REVERT: E 42 VAL cc_start: 0.9266 (t) cc_final: 0.8913 (p) REVERT: E 69 TRP cc_start: 0.7772 (m-90) cc_final: 0.7247 (m-90) REVERT: E 95 MET cc_start: 0.9313 (ptm) cc_final: 0.9073 (ptm) REVERT: E 104 MET cc_start: 0.8818 (mtm) cc_final: 0.8586 (mtp) REVERT: E 210 PHE cc_start: 0.8612 (m-80) cc_final: 0.8367 (m-10) REVERT: E 293 GLU cc_start: 0.8385 (tt0) cc_final: 0.7938 (tm-30) REVERT: E 373 MET cc_start: 0.9086 (mmp) cc_final: 0.8658 (mmt) REVERT: F 586 TYR cc_start: 0.8892 (t80) cc_final: 0.8476 (t80) REVERT: G 87 LYS cc_start: 0.8796 (mppt) cc_final: 0.8514 (mtmm) REVERT: I 4 MET cc_start: 0.6700 (tmm) cc_final: 0.6481 (tmm) REVERT: I 89 MET cc_start: 0.8529 (ttt) cc_final: 0.6996 (ttt) REVERT: H 99 MET cc_start: 0.7789 (mtp) cc_final: 0.7438 (mtp) REVERT: L 27 GLU cc_start: 0.7868 (tp30) cc_final: 0.7543 (tm-30) REVERT: L 89 MET cc_start: 0.8631 (ttt) cc_final: 0.8356 (ttt) REVERT: L 92 LYS cc_start: 0.9223 (tptp) cc_final: 0.8598 (tppp) REVERT: L 103 LYS cc_start: 0.8488 (tttt) cc_final: 0.7996 (tmtt) outliers start: 0 outliers final: 0 residues processed: 274 average time/residue: 0.1326 time to fit residues: 55.9471 Evaluate side-chains 196 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 64 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 166 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 190 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 160 optimal weight: 0.5980 chunk 194 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 GLN C 66 HIS ** F 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 GLN ** 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 = 0.3261 r_free = 0.3261 target = 0.060682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.049592 restraints weight = 100110.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.050996 restraints weight = 56964.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.051958 restraints weight = 39278.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.052590 restraints weight = 30541.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.053034 restraints weight = 25824.995| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19388 Z= 0.159 Angle : 0.769 13.189 26536 Z= 0.355 Chirality : 0.051 0.391 3308 Planarity : 0.004 0.048 3132 Dihedral : 11.329 91.206 4898 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 0.16 % Allowed : 2.70 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.95 (0.17), residues: 2131 helix: -0.77 (0.28), residues: 351 sheet: -1.97 (0.20), residues: 522 loop : -2.38 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 77 TYR 0.020 0.001 TYR B 638 PHE 0.014 0.002 PHE A 277 TRP 0.018 0.002 TRP E 338 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00349 (19228) covalent geometry : angle 0.70895 (26090) SS BOND : bond 0.00288 ( 34) SS BOND : angle 0.84965 ( 68) hydrogen bonds : bond 0.03956 ( 418) hydrogen bonds : angle 6.21165 ( 1122) link_ALPHA1-3 : bond 0.01406 ( 6) link_ALPHA1-3 : angle 1.88716 ( 18) link_ALPHA1-6 : bond 0.00932 ( 5) link_ALPHA1-6 : angle 1.84813 ( 15) link_BETA1-2 : bond 0.00568 ( 4) link_BETA1-2 : angle 1.47539 ( 12) link_BETA1-4 : bond 0.00623 ( 36) link_BETA1-4 : angle 2.21204 ( 108) link_BETA1-6 : bond 0.00582 ( 9) link_BETA1-6 : angle 1.49045 ( 27) link_NAG-ASN : bond 0.00547 ( 66) link_NAG-ASN : angle 3.02682 ( 198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 235 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8056 (m90) cc_final: 0.7623 (m90) REVERT: A 69 TRP cc_start: 0.8119 (m-90) cc_final: 0.7621 (m-90) REVERT: A 106 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7826 (pt0) REVERT: A 165 MET cc_start: 0.8223 (mtm) cc_final: 0.7950 (mtp) REVERT: A 211 GLU cc_start: 0.8332 (mp0) cc_final: 0.7980 (mp0) REVERT: A 434 MET cc_start: 0.8788 (tmm) cc_final: 0.8538 (tmm) REVERT: A 477 ASP cc_start: 0.8725 (m-30) cc_final: 0.8482 (m-30) REVERT: B 657 GLU cc_start: 0.9124 (mm-30) cc_final: 0.8897 (mm-30) REVERT: C 42 VAL cc_start: 0.9390 (t) cc_final: 0.9183 (p) REVERT: C 304 ARG cc_start: 0.8206 (tpm170) cc_final: 0.7726 (mmm160) REVERT: D 584 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7861 (tm-30) REVERT: D 591 GLN cc_start: 0.8555 (tt0) cc_final: 0.8010 (tt0) REVERT: D 601 LYS cc_start: 0.8171 (mttp) cc_final: 0.7938 (mttp) REVERT: D 632 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8254 (tm-30) REVERT: E 42 VAL cc_start: 0.9377 (t) cc_final: 0.9057 (p) REVERT: E 69 TRP cc_start: 0.7676 (m-90) cc_final: 0.7115 (m-90) REVERT: E 104 MET cc_start: 0.8789 (mtm) cc_final: 0.8547 (mtp) REVERT: E 210 PHE cc_start: 0.8558 (m-80) cc_final: 0.8306 (m-10) REVERT: E 277 PHE cc_start: 0.7992 (p90) cc_final: 0.7766 (p90) REVERT: E 293 GLU cc_start: 0.8346 (tt0) cc_final: 0.7964 (tm-30) REVERT: E 373 MET cc_start: 0.9074 (mmp) cc_final: 0.8640 (mmt) REVERT: F 586 TYR cc_start: 0.8987 (t80) cc_final: 0.8542 (t80) REVERT: G 35 TYR cc_start: 0.8180 (m-80) cc_final: 0.7692 (m-10) REVERT: G 99 MET cc_start: 0.8214 (tpp) cc_final: 0.7248 (tpt) REVERT: I 4 MET cc_start: 0.6844 (tmm) cc_final: 0.6524 (ppp) REVERT: I 89 MET cc_start: 0.8562 (ttt) cc_final: 0.8005 (ppp) REVERT: L 17 GLN cc_start: 0.8833 (tt0) cc_final: 0.8330 (tm-30) REVERT: L 27 GLU cc_start: 0.7876 (tp30) cc_final: 0.7544 (tm-30) REVERT: L 74 ARG cc_start: 0.7973 (tpp80) cc_final: 0.7676 (mmm160) REVERT: L 92 LYS cc_start: 0.9236 (tptp) cc_final: 0.8621 (tppp) REVERT: L 103 LYS cc_start: 0.8417 (tttt) cc_final: 0.7926 (tmtt) outliers start: 1 outliers final: 1 residues processed: 236 average time/residue: 0.1340 time to fit residues: 48.9433 Evaluate side-chains 188 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 99 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 113 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 116 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 153 optimal weight: 0.4980 chunk 151 optimal weight: 3.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.060548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.049327 restraints weight = 98716.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.050775 restraints weight = 55607.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.051766 restraints weight = 38032.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.052434 restraints weight = 29351.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.052884 restraints weight = 24577.492| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19388 Z= 0.154 Angle : 0.750 13.191 26536 Z= 0.345 Chirality : 0.050 0.377 3308 Planarity : 0.004 0.047 3132 Dihedral : 10.595 82.292 4898 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 0.10 % Allowed : 1.87 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.79 (0.17), residues: 2131 helix: -0.54 (0.28), residues: 362 sheet: -1.89 (0.20), residues: 550 loop : -2.30 (0.17), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 585 TYR 0.034 0.001 TYR G 94 PHE 0.012 0.001 PHE I 49 TRP 0.012 0.001 TRP A 395 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00337 (19228) covalent geometry : angle 0.69331 (26090) SS BOND : bond 0.00271 ( 34) SS BOND : angle 0.84365 ( 68) hydrogen bonds : bond 0.03731 ( 418) hydrogen bonds : angle 5.97576 ( 1122) link_ALPHA1-3 : bond 0.01381 ( 6) link_ALPHA1-3 : angle 1.84152 ( 18) link_ALPHA1-6 : bond 0.01075 ( 5) link_ALPHA1-6 : angle 1.95338 ( 15) link_BETA1-2 : bond 0.00458 ( 4) link_BETA1-2 : angle 1.44748 ( 12) link_BETA1-4 : bond 0.00608 ( 36) link_BETA1-4 : angle 2.08369 ( 108) link_BETA1-6 : bond 0.00594 ( 9) link_BETA1-6 : angle 1.48292 ( 27) link_NAG-ASN : bond 0.00514 ( 66) link_NAG-ASN : angle 2.90494 ( 198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.729 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: A 69 TRP cc_start: 0.8162 (m-90) cc_final: 0.7630 (m-90) REVERT: A 106 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7854 (pt0) REVERT: A 165 MET cc_start: 0.8242 (mtm) cc_final: 0.7969 (mtp) REVERT: A 211 GLU cc_start: 0.8395 (mp0) cc_final: 0.8048 (mp0) REVERT: A 434 MET cc_start: 0.8774 (tmm) cc_final: 0.8497 (tmm) REVERT: A 477 ASP cc_start: 0.8644 (m-30) cc_final: 0.8441 (m-30) REVERT: B 650 GLN cc_start: 0.7483 (pp30) cc_final: 0.7042 (tm-30) REVERT: B 657 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8845 (mm-30) REVERT: C 42 VAL cc_start: 0.9449 (t) cc_final: 0.9229 (p) REVERT: C 304 ARG cc_start: 0.8090 (tpm170) cc_final: 0.7614 (mmm160) REVERT: D 584 GLU cc_start: 0.8302 (tm-30) cc_final: 0.8010 (tm-30) REVERT: D 591 GLN cc_start: 0.8678 (tt0) cc_final: 0.8177 (tt0) REVERT: D 601 LYS cc_start: 0.8136 (mttp) cc_final: 0.7798 (mttp) REVERT: D 632 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8237 (tm-30) REVERT: E 42 VAL cc_start: 0.9370 (t) cc_final: 0.9079 (p) REVERT: E 69 TRP cc_start: 0.7499 (m-90) cc_final: 0.6907 (m-90) REVERT: E 95 MET cc_start: 0.9312 (ptm) cc_final: 0.9040 (ptm) REVERT: E 277 PHE cc_start: 0.7962 (p90) cc_final: 0.7652 (p90) REVERT: E 293 GLU cc_start: 0.8278 (tt0) cc_final: 0.7948 (tm-30) REVERT: E 373 MET cc_start: 0.9064 (mmp) cc_final: 0.8648 (mmt) REVERT: F 586 TYR cc_start: 0.9068 (t80) cc_final: 0.8669 (t80) REVERT: G 35 TYR cc_start: 0.8199 (m-80) cc_final: 0.7711 (m-80) REVERT: G 99 MET cc_start: 0.8070 (tpp) cc_final: 0.6947 (tpt) REVERT: I 89 MET cc_start: 0.8620 (ttt) cc_final: 0.6301 (ttt) REVERT: I 98 PHE cc_start: 0.8649 (m-80) cc_final: 0.7738 (m-80) REVERT: L 27 GLU cc_start: 0.7958 (tp30) cc_final: 0.7566 (tm-30) REVERT: L 74 ARG cc_start: 0.8041 (tpp80) cc_final: 0.7701 (mmm160) REVERT: L 92 LYS cc_start: 0.9197 (tptp) cc_final: 0.8542 (tppp) REVERT: L 103 LYS cc_start: 0.8335 (tttt) cc_final: 0.7801 (tmtt) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.1244 time to fit residues: 47.2136 Evaluate side-chains 188 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 205 optimal weight: 0.9990 chunk 187 optimal weight: 0.0050 chunk 104 optimal weight: 0.0050 chunk 24 optimal weight: 6.9990 chunk 199 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 178 optimal weight: 0.1980 chunk 172 optimal weight: 10.0000 overall best weight: 1.0412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 550 GLN ** F 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.061423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.050287 restraints weight = 97751.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.051689 restraints weight = 55932.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.052646 restraints weight = 38731.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.053306 restraints weight = 30221.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.053749 restraints weight = 25440.499| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19388 Z= 0.119 Angle : 0.716 13.141 26536 Z= 0.328 Chirality : 0.050 0.316 3308 Planarity : 0.004 0.047 3132 Dihedral : 9.893 78.926 4898 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 0.10 % Allowed : 1.19 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.18), residues: 2131 helix: -0.34 (0.29), residues: 358 sheet: -1.74 (0.21), residues: 540 loop : -2.19 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 72 TYR 0.017 0.001 TYR I 34 PHE 0.011 0.001 PHE I 49 TRP 0.014 0.001 TRP B 614 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00259 (19228) covalent geometry : angle 0.66078 (26090) SS BOND : bond 0.00243 ( 34) SS BOND : angle 0.78146 ( 68) hydrogen bonds : bond 0.03493 ( 418) hydrogen bonds : angle 5.78886 ( 1122) link_ALPHA1-3 : bond 0.01393 ( 6) link_ALPHA1-3 : angle 1.74852 ( 18) link_ALPHA1-6 : bond 0.01030 ( 5) link_ALPHA1-6 : angle 1.82681 ( 15) link_BETA1-2 : bond 0.00423 ( 4) link_BETA1-2 : angle 1.43998 ( 12) link_BETA1-4 : bond 0.00619 ( 36) link_BETA1-4 : angle 1.99015 ( 108) link_BETA1-6 : bond 0.00636 ( 9) link_BETA1-6 : angle 1.41336 ( 27) link_NAG-ASN : bond 0.00555 ( 66) link_NAG-ASN : angle 2.81040 ( 198) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8042 (m-90) cc_final: 0.7530 (m-90) REVERT: A 104 MET cc_start: 0.9054 (ttm) cc_final: 0.8831 (ttm) REVERT: A 106 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7839 (pt0) REVERT: A 107 ASP cc_start: 0.8526 (m-30) cc_final: 0.8203 (m-30) REVERT: A 176 PHE cc_start: 0.8745 (m-10) cc_final: 0.8496 (m-10) REVERT: A 211 GLU cc_start: 0.8307 (mp0) cc_final: 0.7997 (mp0) REVERT: A 434 MET cc_start: 0.8808 (tmm) cc_final: 0.8533 (tmm) REVERT: A 477 ASP cc_start: 0.8658 (m-30) cc_final: 0.8433 (m-30) REVERT: B 574 LYS cc_start: 0.9380 (mmmm) cc_final: 0.9140 (mmtp) REVERT: B 657 GLU cc_start: 0.9217 (mm-30) cc_final: 0.8957 (mm-30) REVERT: B 660 LEU cc_start: 0.9548 (mt) cc_final: 0.9340 (mm) REVERT: C 42 VAL cc_start: 0.9442 (t) cc_final: 0.9216 (p) REVERT: C 304 ARG cc_start: 0.8085 (tpm170) cc_final: 0.7537 (mmm160) REVERT: D 584 GLU cc_start: 0.8277 (tm-30) cc_final: 0.8005 (tm-30) REVERT: D 601 LYS cc_start: 0.7972 (mttp) cc_final: 0.7737 (mttp) REVERT: D 629 MET cc_start: 0.8378 (tpp) cc_final: 0.8120 (tpp) REVERT: D 632 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8244 (tm-30) REVERT: D 652 GLN cc_start: 0.9225 (tp40) cc_final: 0.8998 (tp40) REVERT: E 42 VAL cc_start: 0.9414 (t) cc_final: 0.9073 (p) REVERT: E 69 TRP cc_start: 0.7422 (m-90) cc_final: 0.6860 (m-90) REVERT: E 210 PHE cc_start: 0.8517 (m-10) cc_final: 0.8223 (m-10) REVERT: E 277 PHE cc_start: 0.7752 (p90) cc_final: 0.7442 (p90) REVERT: E 293 GLU cc_start: 0.8235 (tt0) cc_final: 0.7917 (tm-30) REVERT: E 373 MET cc_start: 0.9032 (mmp) cc_final: 0.8615 (mmt) REVERT: E 434 MET cc_start: 0.7703 (tmm) cc_final: 0.7385 (tmm) REVERT: F 586 TYR cc_start: 0.9048 (t80) cc_final: 0.8586 (t80) REVERT: I 4 MET cc_start: 0.7660 (ppp) cc_final: 0.7080 (ppp) REVERT: I 98 PHE cc_start: 0.8598 (m-80) cc_final: 0.8095 (m-10) REVERT: H 99 MET cc_start: 0.7558 (mtp) cc_final: 0.7203 (mtp) REVERT: L 17 GLN cc_start: 0.8600 (tt0) cc_final: 0.8126 (tm-30) REVERT: L 27 GLU cc_start: 0.7832 (tp30) cc_final: 0.7506 (tm-30) REVERT: L 74 ARG cc_start: 0.8056 (tpp80) cc_final: 0.7678 (mmm160) REVERT: L 92 LYS cc_start: 0.9207 (tptp) cc_final: 0.8558 (tppp) REVERT: L 103 LYS cc_start: 0.8317 (tttt) cc_final: 0.7807 (tmtt) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.1299 time to fit residues: 50.0045 Evaluate side-chains 195 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 76 optimal weight: 8.9990 chunk 134 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 125 optimal weight: 9.9990 chunk 155 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 170 optimal weight: 0.0670 chunk 150 optimal weight: 0.0980 chunk 52 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** F 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.061431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.050078 restraints weight = 97306.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.051584 restraints weight = 53508.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.052631 restraints weight = 36077.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.053332 restraints weight = 27467.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.053828 restraints weight = 22792.335| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19388 Z= 0.118 Angle : 0.711 13.226 26536 Z= 0.328 Chirality : 0.049 0.312 3308 Planarity : 0.004 0.046 3132 Dihedral : 9.370 72.150 4898 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 0.10 % Allowed : 0.73 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.18), residues: 2131 helix: -0.33 (0.29), residues: 362 sheet: -1.45 (0.21), residues: 527 loop : -2.15 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 585 TYR 0.020 0.001 TYR I 34 PHE 0.017 0.001 PHE H 27 TRP 0.018 0.001 TRP E 479 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00256 (19228) covalent geometry : angle 0.65593 (26090) SS BOND : bond 0.00313 ( 34) SS BOND : angle 1.47678 ( 68) hydrogen bonds : bond 0.03399 ( 418) hydrogen bonds : angle 5.70871 ( 1122) link_ALPHA1-3 : bond 0.01381 ( 6) link_ALPHA1-3 : angle 1.68044 ( 18) link_ALPHA1-6 : bond 0.01057 ( 5) link_ALPHA1-6 : angle 1.84231 ( 15) link_BETA1-2 : bond 0.00400 ( 4) link_BETA1-2 : angle 1.44899 ( 12) link_BETA1-4 : bond 0.00622 ( 36) link_BETA1-4 : angle 1.93487 ( 108) link_BETA1-6 : bond 0.00684 ( 9) link_BETA1-6 : angle 1.41721 ( 27) link_NAG-ASN : bond 0.00551 ( 66) link_NAG-ASN : angle 2.70193 ( 198) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.703 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: A 69 TRP cc_start: 0.8016 (m-90) cc_final: 0.7487 (m-90) REVERT: A 106 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7837 (pt0) REVERT: A 107 ASP cc_start: 0.8510 (m-30) cc_final: 0.8119 (m-30) REVERT: A 165 MET cc_start: 0.8127 (mtm) cc_final: 0.7868 (mtp) REVERT: A 176 PHE cc_start: 0.8723 (m-10) cc_final: 0.8516 (m-10) REVERT: A 211 GLU cc_start: 0.8235 (mp0) cc_final: 0.7941 (mp0) REVERT: A 434 MET cc_start: 0.8773 (tmm) cc_final: 0.8480 (tmm) REVERT: A 477 ASP cc_start: 0.8622 (m-30) cc_final: 0.8402 (m-30) REVERT: B 574 LYS cc_start: 0.9359 (mmmm) cc_final: 0.9096 (mmtp) REVERT: B 657 GLU cc_start: 0.9217 (mm-30) cc_final: 0.8938 (mm-30) REVERT: C 42 VAL cc_start: 0.9436 (t) cc_final: 0.9215 (p) REVERT: D 584 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7977 (tm-30) REVERT: D 601 LYS cc_start: 0.7947 (mttp) cc_final: 0.7721 (mttp) REVERT: D 629 MET cc_start: 0.8319 (tpp) cc_final: 0.8019 (tpp) REVERT: D 632 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8274 (tm-30) REVERT: D 655 LYS cc_start: 0.9020 (mptt) cc_final: 0.8816 (mmtt) REVERT: E 42 VAL cc_start: 0.9404 (t) cc_final: 0.9110 (p) REVERT: E 69 TRP cc_start: 0.7429 (m-90) cc_final: 0.6855 (m-90) REVERT: E 95 MET cc_start: 0.9148 (ptm) cc_final: 0.8852 (ptm) REVERT: E 104 MET cc_start: 0.8534 (ttm) cc_final: 0.8277 (ttm) REVERT: E 210 PHE cc_start: 0.8480 (m-10) cc_final: 0.8157 (m-10) REVERT: E 293 GLU cc_start: 0.8256 (tt0) cc_final: 0.7940 (tm-30) REVERT: E 373 MET cc_start: 0.8986 (mmp) cc_final: 0.8534 (mmt) REVERT: F 586 TYR cc_start: 0.9057 (t80) cc_final: 0.8671 (t80) REVERT: I 4 MET cc_start: 0.7672 (ppp) cc_final: 0.7132 (ppp) REVERT: I 89 MET cc_start: 0.7716 (ppp) cc_final: 0.6675 (ttp) REVERT: I 98 PHE cc_start: 0.8501 (m-80) cc_final: 0.6555 (m-80) REVERT: L 17 GLN cc_start: 0.8544 (tt0) cc_final: 0.8103 (tm-30) REVERT: L 27 GLU cc_start: 0.7724 (tp30) cc_final: 0.7454 (tm-30) REVERT: L 73 LEU cc_start: 0.8132 (tp) cc_final: 0.7835 (tp) REVERT: L 74 ARG cc_start: 0.8049 (tpp80) cc_final: 0.7704 (mmm160) REVERT: L 77 ARG cc_start: 0.8359 (tpp-160) cc_final: 0.8019 (tpp-160) REVERT: L 92 LYS cc_start: 0.9198 (tptp) cc_final: 0.8576 (tppp) REVERT: L 103 LYS cc_start: 0.8206 (tttt) cc_final: 0.7690 (tmtt) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.1245 time to fit residues: 47.5772 Evaluate side-chains 192 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 203 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 3 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 205 optimal weight: 9.9990 chunk 201 optimal weight: 8.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.060011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.048778 restraints weight = 101896.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.050163 restraints weight = 58987.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.051090 restraints weight = 41010.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.051745 restraints weight = 32179.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.052099 restraints weight = 27235.155| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 19388 Z= 0.189 Angle : 0.762 13.445 26536 Z= 0.352 Chirality : 0.051 0.518 3308 Planarity : 0.004 0.046 3132 Dihedral : 9.446 64.380 4898 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 0.10 % Allowed : 1.04 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.18), residues: 2131 helix: -0.03 (0.30), residues: 355 sheet: -1.53 (0.21), residues: 541 loop : -2.14 (0.17), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 504 TYR 0.017 0.001 TYR I 34 PHE 0.018 0.002 PHE E 277 TRP 0.014 0.002 TRP A 395 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00417 (19228) covalent geometry : angle 0.70827 (26090) SS BOND : bond 0.00304 ( 34) SS BOND : angle 1.21128 ( 68) hydrogen bonds : bond 0.03687 ( 418) hydrogen bonds : angle 5.74729 ( 1122) link_ALPHA1-3 : bond 0.01384 ( 6) link_ALPHA1-3 : angle 1.80143 ( 18) link_ALPHA1-6 : bond 0.00943 ( 5) link_ALPHA1-6 : angle 1.87591 ( 15) link_BETA1-2 : bond 0.00456 ( 4) link_BETA1-2 : angle 1.45294 ( 12) link_BETA1-4 : bond 0.00626 ( 36) link_BETA1-4 : angle 2.02357 ( 108) link_BETA1-6 : bond 0.00738 ( 9) link_BETA1-6 : angle 1.61993 ( 27) link_NAG-ASN : bond 0.00509 ( 66) link_NAG-ASN : angle 2.80724 ( 198) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.681 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: A 69 TRP cc_start: 0.8097 (m-90) cc_final: 0.7599 (m-90) REVERT: A 106 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7862 (pt0) REVERT: A 211 GLU cc_start: 0.8340 (mp0) cc_final: 0.8030 (mp0) REVERT: A 434 MET cc_start: 0.8776 (tmm) cc_final: 0.8061 (tmm) REVERT: B 657 GLU cc_start: 0.9285 (mm-30) cc_final: 0.9080 (mm-30) REVERT: C 42 VAL cc_start: 0.9467 (t) cc_final: 0.9229 (p) REVERT: D 584 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8164 (tm-30) REVERT: D 591 GLN cc_start: 0.8659 (tt0) cc_final: 0.7961 (tt0) REVERT: D 601 LYS cc_start: 0.8087 (mttp) cc_final: 0.7818 (mttp) REVERT: D 629 MET cc_start: 0.8397 (tpp) cc_final: 0.8015 (tpp) REVERT: D 632 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8279 (tm-30) REVERT: E 42 VAL cc_start: 0.9406 (t) cc_final: 0.9034 (p) REVERT: E 69 TRP cc_start: 0.7387 (m-90) cc_final: 0.6799 (m-90) REVERT: E 104 MET cc_start: 0.8635 (ttm) cc_final: 0.8346 (ttm) REVERT: E 210 PHE cc_start: 0.8564 (m-10) cc_final: 0.8293 (m-10) REVERT: E 293 GLU cc_start: 0.8280 (tt0) cc_final: 0.7994 (tm-30) REVERT: E 373 MET cc_start: 0.8968 (mmp) cc_final: 0.8473 (mmt) REVERT: F 586 TYR cc_start: 0.9144 (t80) cc_final: 0.8571 (t80) REVERT: G 35 TYR cc_start: 0.8326 (m-80) cc_final: 0.8105 (m-80) REVERT: G 99 MET cc_start: 0.8292 (tpp) cc_final: 0.7987 (tpt) REVERT: I 4 MET cc_start: 0.7763 (ppp) cc_final: 0.7222 (ppp) REVERT: I 89 MET cc_start: 0.7842 (ppp) cc_final: 0.7477 (tmm) REVERT: I 98 PHE cc_start: 0.8567 (m-80) cc_final: 0.8221 (m-10) REVERT: H 45 LEU cc_start: 0.9077 (tp) cc_final: 0.8796 (tp) REVERT: H 46 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8071 (mm-30) REVERT: L 17 GLN cc_start: 0.8677 (tt0) cc_final: 0.8280 (tm-30) REVERT: L 27 GLU cc_start: 0.7899 (tp30) cc_final: 0.7523 (tm-30) REVERT: L 73 LEU cc_start: 0.8190 (tp) cc_final: 0.7879 (tp) REVERT: L 74 ARG cc_start: 0.8096 (tpp80) cc_final: 0.7787 (mmm160) REVERT: L 77 ARG cc_start: 0.8384 (tpp-160) cc_final: 0.8087 (tpp-160) REVERT: L 92 LYS cc_start: 0.9167 (tptp) cc_final: 0.8540 (tppp) REVERT: L 103 LYS cc_start: 0.8222 (tttt) cc_final: 0.7664 (tmtt) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.1354 time to fit residues: 47.9655 Evaluate side-chains 184 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 14 optimal weight: 4.9990 chunk 169 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 195 optimal weight: 6.9990 chunk 181 optimal weight: 20.0000 chunk 93 optimal weight: 8.9990 chunk 121 optimal weight: 20.0000 chunk 192 optimal weight: 8.9990 chunk 100 optimal weight: 0.0570 chunk 145 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 overall best weight: 3.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 442 GLN ** F 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.059694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.048623 restraints weight = 100589.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.049965 restraints weight = 59410.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.050874 restraints weight = 41790.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.051504 restraints weight = 32916.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.051882 restraints weight = 27977.533| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19388 Z= 0.193 Angle : 0.780 13.510 26536 Z= 0.360 Chirality : 0.051 0.456 3308 Planarity : 0.004 0.046 3132 Dihedral : 9.438 59.643 4898 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 0.10 % Allowed : 0.57 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.18), residues: 2131 helix: -0.20 (0.29), residues: 364 sheet: -1.62 (0.21), residues: 568 loop : -2.16 (0.18), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 585 TYR 0.030 0.002 TYR A 217 PHE 0.019 0.002 PHE E 277 TRP 0.014 0.002 TRP A 427 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00426 (19228) covalent geometry : angle 0.72466 (26090) SS BOND : bond 0.00348 ( 34) SS BOND : angle 1.11652 ( 68) hydrogen bonds : bond 0.03685 ( 418) hydrogen bonds : angle 5.77697 ( 1122) link_ALPHA1-3 : bond 0.01365 ( 6) link_ALPHA1-3 : angle 1.75274 ( 18) link_ALPHA1-6 : bond 0.00892 ( 5) link_ALPHA1-6 : angle 1.77133 ( 15) link_BETA1-2 : bond 0.00486 ( 4) link_BETA1-2 : angle 1.40461 ( 12) link_BETA1-4 : bond 0.00628 ( 36) link_BETA1-4 : angle 1.99662 ( 108) link_BETA1-6 : bond 0.00769 ( 9) link_BETA1-6 : angle 1.64423 ( 27) link_NAG-ASN : bond 0.00582 ( 66) link_NAG-ASN : angle 2.95005 ( 198) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.879 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: A 69 TRP cc_start: 0.8146 (m-90) cc_final: 0.7697 (m-90) REVERT: A 106 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7882 (pt0) REVERT: A 165 MET cc_start: 0.8304 (mtm) cc_final: 0.8022 (mtp) REVERT: A 211 GLU cc_start: 0.8388 (mp0) cc_final: 0.8062 (mp0) REVERT: A 434 MET cc_start: 0.8749 (tmm) cc_final: 0.8026 (tmm) REVERT: A 477 ASP cc_start: 0.8600 (m-30) cc_final: 0.8380 (m-30) REVERT: B 626 MET cc_start: 0.6779 (tpp) cc_final: 0.6464 (tpp) REVERT: B 657 GLU cc_start: 0.9313 (mm-30) cc_final: 0.9102 (mm-30) REVERT: C 434 MET cc_start: 0.8746 (ptp) cc_final: 0.8486 (ptm) REVERT: D 584 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8213 (tm-30) REVERT: D 591 GLN cc_start: 0.8746 (tt0) cc_final: 0.8019 (tt0) REVERT: D 601 LYS cc_start: 0.8086 (mttp) cc_final: 0.7744 (mttp) REVERT: D 629 MET cc_start: 0.8450 (tpp) cc_final: 0.8216 (tpp) REVERT: D 632 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8278 (tm-30) REVERT: E 42 VAL cc_start: 0.9429 (t) cc_final: 0.9106 (p) REVERT: E 69 TRP cc_start: 0.7428 (m-90) cc_final: 0.6851 (m-90) REVERT: E 104 MET cc_start: 0.8703 (ttm) cc_final: 0.8367 (ttm) REVERT: E 210 PHE cc_start: 0.8603 (m-10) cc_final: 0.8323 (m-10) REVERT: E 373 MET cc_start: 0.8998 (mmp) cc_final: 0.8522 (mmt) REVERT: F 586 TYR cc_start: 0.9167 (t80) cc_final: 0.8565 (t80) REVERT: F 626 MET cc_start: 0.7450 (tmm) cc_final: 0.6968 (tmm) REVERT: F 629 MET cc_start: 0.8416 (mmp) cc_final: 0.8197 (mmm) REVERT: G 35 TYR cc_start: 0.8377 (m-80) cc_final: 0.8087 (m-80) REVERT: I 4 MET cc_start: 0.7772 (ppp) cc_final: 0.7204 (ppp) REVERT: I 98 PHE cc_start: 0.8513 (m-80) cc_final: 0.8207 (m-80) REVERT: H 45 LEU cc_start: 0.9050 (tp) cc_final: 0.8813 (tp) REVERT: H 46 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8150 (mm-30) REVERT: L 17 GLN cc_start: 0.8685 (tt0) cc_final: 0.8293 (tm-30) REVERT: L 27 GLU cc_start: 0.7963 (tp30) cc_final: 0.7547 (tm-30) REVERT: L 73 LEU cc_start: 0.8171 (tp) cc_final: 0.7851 (tp) REVERT: L 74 ARG cc_start: 0.8110 (tpp80) cc_final: 0.7781 (mmm160) REVERT: L 92 LYS cc_start: 0.9156 (tptp) cc_final: 0.8519 (tppp) REVERT: L 103 LYS cc_start: 0.8152 (tttt) cc_final: 0.7593 (tmtt) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.1288 time to fit residues: 45.6863 Evaluate side-chains 178 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 207 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 184 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 60 optimal weight: 0.3980 chunk 189 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 177 optimal weight: 7.9990 chunk 194 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 HIS ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 ASN ** I 6 GLN ** 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 = 0.3237 r_free = 0.3237 target = 0.059884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.048724 restraints weight = 99985.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.050125 restraints weight = 58127.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.051052 restraints weight = 40561.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.051653 restraints weight = 31774.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.052115 restraints weight = 27081.287| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19388 Z= 0.181 Angle : 0.773 13.467 26536 Z= 0.358 Chirality : 0.051 0.419 3308 Planarity : 0.004 0.046 3132 Dihedral : 9.250 59.233 4898 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 0.10 % Allowed : 0.26 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.18), residues: 2131 helix: -0.19 (0.29), residues: 361 sheet: -1.57 (0.21), residues: 554 loop : -2.18 (0.17), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 585 TYR 0.021 0.002 TYR C 217 PHE 0.019 0.002 PHE E 277 TRP 0.016 0.002 TRP B 631 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00402 (19228) covalent geometry : angle 0.71897 (26090) SS BOND : bond 0.00307 ( 34) SS BOND : angle 1.11299 ( 68) hydrogen bonds : bond 0.03739 ( 418) hydrogen bonds : angle 5.76419 ( 1122) link_ALPHA1-3 : bond 0.01365 ( 6) link_ALPHA1-3 : angle 1.69160 ( 18) link_ALPHA1-6 : bond 0.00819 ( 5) link_ALPHA1-6 : angle 1.69618 ( 15) link_BETA1-2 : bond 0.00487 ( 4) link_BETA1-2 : angle 1.41303 ( 12) link_BETA1-4 : bond 0.00626 ( 36) link_BETA1-4 : angle 1.97320 ( 108) link_BETA1-6 : bond 0.00739 ( 9) link_BETA1-6 : angle 1.57172 ( 27) link_NAG-ASN : bond 0.00560 ( 66) link_NAG-ASN : angle 2.91551 ( 198) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.729 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: A 69 TRP cc_start: 0.8123 (m-90) cc_final: 0.7723 (m-90) REVERT: A 106 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7854 (pt0) REVERT: A 211 GLU cc_start: 0.8393 (mp0) cc_final: 0.8079 (mp0) REVERT: A 434 MET cc_start: 0.8740 (tmm) cc_final: 0.8020 (tmm) REVERT: A 477 ASP cc_start: 0.8602 (m-30) cc_final: 0.8377 (m-30) REVERT: B 619 TYR cc_start: 0.7410 (t80) cc_final: 0.7110 (t80) REVERT: B 657 GLU cc_start: 0.9296 (mm-30) cc_final: 0.9089 (mm-30) REVERT: C 434 MET cc_start: 0.8750 (ptp) cc_final: 0.8516 (ptm) REVERT: D 584 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8198 (tm-30) REVERT: D 591 GLN cc_start: 0.8724 (tt0) cc_final: 0.7975 (tt0) REVERT: D 601 LYS cc_start: 0.8077 (mttp) cc_final: 0.7769 (mttp) REVERT: D 629 MET cc_start: 0.8431 (tpp) cc_final: 0.8151 (tpp) REVERT: D 632 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8298 (tm-30) REVERT: E 42 VAL cc_start: 0.9436 (t) cc_final: 0.9077 (p) REVERT: E 69 TRP cc_start: 0.7402 (m-90) cc_final: 0.6834 (m-90) REVERT: E 104 MET cc_start: 0.8590 (ttm) cc_final: 0.8358 (ttm) REVERT: E 210 PHE cc_start: 0.8597 (m-10) cc_final: 0.8295 (m-10) REVERT: E 373 MET cc_start: 0.8997 (mmp) cc_final: 0.8526 (mmt) REVERT: F 586 TYR cc_start: 0.9157 (t80) cc_final: 0.8554 (t80) REVERT: F 626 MET cc_start: 0.7402 (tmm) cc_final: 0.7034 (tmm) REVERT: F 629 MET cc_start: 0.8424 (mmp) cc_final: 0.8205 (mmm) REVERT: I 4 MET cc_start: 0.7809 (ppp) cc_final: 0.7188 (ppp) REVERT: I 98 PHE cc_start: 0.8653 (m-80) cc_final: 0.8207 (m-10) REVERT: H 45 LEU cc_start: 0.9035 (tp) cc_final: 0.8803 (tp) REVERT: H 46 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8098 (mm-30) REVERT: L 17 GLN cc_start: 0.8697 (tt0) cc_final: 0.8227 (tm-30) REVERT: L 27 GLU cc_start: 0.7957 (tp30) cc_final: 0.7567 (tm-30) REVERT: L 73 LEU cc_start: 0.8217 (tp) cc_final: 0.7892 (tp) REVERT: L 74 ARG cc_start: 0.8086 (tpp80) cc_final: 0.7743 (mmm160) REVERT: L 92 LYS cc_start: 0.9140 (tptp) cc_final: 0.8526 (tppp) REVERT: L 103 LYS cc_start: 0.8157 (tttt) cc_final: 0.7582 (tmtt) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.1274 time to fit residues: 44.0723 Evaluate side-chains 174 residues out of total 1923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 151 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 171 optimal weight: 7.9990 chunk 144 optimal weight: 3.9990 chunk 184 optimal weight: 7.9990 chunk 123 optimal weight: 6.9990 chunk 158 optimal weight: 4.9990 chunk 195 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN ** F 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** 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 = 0.3196 r_free = 0.3196 target = 0.058175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.047190 restraints weight = 101362.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.048505 restraints weight = 59619.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.049408 restraints weight = 41823.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.050021 restraints weight = 33009.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.050420 restraints weight = 27943.997| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 19388 Z= 0.291 Angle : 0.901 13.637 26536 Z= 0.419 Chirality : 0.053 0.372 3308 Planarity : 0.005 0.047 3132 Dihedral : 9.818 59.816 4898 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.56 % Favored : 88.44 % Rotamer: Outliers : 0.10 % Allowed : 0.31 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.17), residues: 2131 helix: -0.51 (0.27), residues: 359 sheet: -1.71 (0.21), residues: 553 loop : -2.31 (0.17), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 585 TYR 0.023 0.002 TYR E 217 PHE 0.020 0.002 PHE A 277 TRP 0.025 0.002 TRP B 631 HIS 0.007 0.002 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00640 (19228) covalent geometry : angle 0.84769 (26090) SS BOND : bond 0.00476 ( 34) SS BOND : angle 1.25374 ( 68) hydrogen bonds : bond 0.04164 ( 418) hydrogen bonds : angle 6.11045 ( 1122) link_ALPHA1-3 : bond 0.01394 ( 6) link_ALPHA1-3 : angle 1.80298 ( 18) link_ALPHA1-6 : bond 0.00626 ( 5) link_ALPHA1-6 : angle 1.89447 ( 15) link_BETA1-2 : bond 0.00721 ( 4) link_BETA1-2 : angle 1.57385 ( 12) link_BETA1-4 : bond 0.00668 ( 36) link_BETA1-4 : angle 2.17995 ( 108) link_BETA1-6 : bond 0.00866 ( 9) link_BETA1-6 : angle 1.86281 ( 27) link_NAG-ASN : bond 0.00610 ( 66) link_NAG-ASN : angle 3.11641 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2855.38 seconds wall clock time: 51 minutes 21.43 seconds (3081.43 seconds total)