Starting phenix.real_space_refine on Sat Sep 28 12:04:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6olp_20118/09_2024/6olp_20118.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6olp_20118/09_2024/6olp_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6olp_20118/09_2024/6olp_20118.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6olp_20118/09_2024/6olp_20118.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6olp_20118/09_2024/6olp_20118.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6olp_20118/09_2024/6olp_20118.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 13.88, per 1000 atoms: 0.74 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: 6.69 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 2.47 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: 6.27 Time building geometry restraints manager: 6.94 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 505 or resid 603 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: 2.320 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: 0.830 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 47.490 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.180 ------------------------------------------------------------------------------- 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 19228 Z= 0.553 Angle : 1.131 12.307 26090 Z= 0.558 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 : 7.16 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.033 0.004 TRP F 614 HIS 0.012 0.002 HIS E 363 PHE 0.030 0.004 PHE I 49 TYR 0.036 0.003 TYR A 217 ARG 0.009 0.001 ARG B 585 *********************** 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 fitting. rotamer outliers: 9 poor density : 377 time to evaluate : 2.161 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: 0.7981 (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: 0.8163 (mp0) REVERT: A 434 MET cc_start: 0.8873 (tmm) cc_final: 0.8474 (tmm) REVERT: B 638 TYR cc_start: 0.8994 (m-80) cc_final: 0.8764 (m-10) REVERT: B 645 LEU cc_start: 0.9481 (mt) cc_final: 0.9030 (tp) REVERT: B 656 ASN cc_start: 0.8931 (t0) cc_final: 0.8727 (t0) REVERT: B 657 GLU cc_start: 0.9190 (mt-10) cc_final: 0.8823 (tm-30) REVERT: B 659 GLU cc_start: 0.9474 (tt0) cc_final: 0.9102 (tm-30) REVERT: C 42 VAL cc_start: 0.9409 (t) cc_final: 0.9149 (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: 0.8149 (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: 0.7253 (m-90) REVERT: E 104 MET cc_start: 0.8105 (mmm) cc_final: 0.7894 (tpp) REVERT: E 111 LEU cc_start: 0.9031 (mt) cc_final: 0.8797 (tp) REVERT: E 293 GLU cc_start: 0.8128 (tt0) cc_final: 0.7851 (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: 0.6747 (mmm) REVERT: E 427 TRP cc_start: 0.7660 (m-90) cc_final: 0.7252 (m-90) REVERT: F 539 VAL cc_start: 0.9689 (t) cc_final: 0.9452 (p) REVERT: F 629 MET cc_start: 0.8215 (mtp) cc_final: 0.7812 (mtm) REVERT: F 630 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8091 (mt-10) REVERT: F 640 SER cc_start: 0.9276 (m) cc_final: 0.9009 (p) REVERT: G 35 TYR cc_start: 0.8853 (m-80) cc_final: 0.8563 (m-10) REVERT: G 76 LYS cc_start: 0.9387 (mmtt) cc_final: 0.9187 (mmmm) 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: 0.7685 (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: 0.8572 (tp) REVERT: H 90 ASP cc_start: 0.9140 (m-30) cc_final: 0.8881 (m-30) REVERT: L 17 GLN cc_start: 0.8420 (tt0) cc_final: 0.8166 (tm-30) REVERT: L 21 ILE cc_start: 0.7749 (mt) cc_final: 0.7305 (pt) REVERT: L 92 LYS cc_start: 0.9203 (tptp) cc_final: 0.8455 (tppp) REVERT: L 103 LYS cc_start: 0.8453 (tttt) cc_final: 0.8183 (tmtt) outliers start: 9 outliers final: 1 residues processed: 384 average time/residue: 0.3635 time to fit residues: 200.8921 Evaluate side-chains 194 residues out of total 1923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 193 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 179 optimal weight: 3.9990 chunk 161 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 193 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 19228 Z= 0.227 Angle : 0.765 11.828 26090 Z= 0.378 Chirality : 0.053 0.456 3308 Planarity : 0.005 0.060 3132 Dihedral : 14.212 103.406 4898 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 0.16 % Allowed : 2.23 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.71 (0.16), residues: 2131 helix: -2.11 (0.23), residues: 343 sheet: -2.30 (0.20), residues: 545 loop : -2.72 (0.16), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 479 HIS 0.006 0.001 HIS C 374 PHE 0.022 0.002 PHE I 49 TYR 0.021 0.002 TYR A 217 ARG 0.007 0.001 ARG B 585 *********************** 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 298 residues out of total 1923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 297 time to evaluate : 2.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8107 (m90) cc_final: 0.7689 (m90) REVERT: A 69 TRP cc_start: 0.8272 (m-90) cc_final: 0.7919 (m-90) REVERT: A 106 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7815 (pt0) REVERT: A 211 GLU cc_start: 0.8452 (mp0) cc_final: 0.8118 (mp0) REVERT: A 434 MET cc_start: 0.8842 (tmm) cc_final: 0.8515 (tmm) REVERT: A 477 ASP cc_start: 0.8931 (m-30) cc_final: 0.8650 (m-30) REVERT: B 638 TYR cc_start: 0.9159 (m-80) cc_final: 0.8865 (m-10) REVERT: B 657 GLU cc_start: 0.9107 (mt-10) cc_final: 0.8859 (mm-30) REVERT: B 659 GLU cc_start: 0.9469 (tt0) cc_final: 0.9154 (tm-30) REVERT: C 304 ARG cc_start: 0.8030 (tpm170) cc_final: 0.7763 (mmm160) REVERT: D 584 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7977 (tm-30) REVERT: D 620 ASN cc_start: 0.9101 (m-40) cc_final: 0.8692 (t0) REVERT: D 632 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8137 (tm-30) REVERT: D 645 LEU cc_start: 0.9674 (tp) cc_final: 0.9429 (tp) REVERT: D 650 GLN cc_start: 0.8568 (tt0) cc_final: 0.8296 (tt0) REVERT: D 657 GLU cc_start: 0.8746 (tm-30) cc_final: 0.8342 (tm-30) REVERT: D 661 LEU cc_start: 0.9229 (tp) cc_final: 0.8928 (pp) REVERT: E 69 TRP cc_start: 0.8017 (m-90) cc_final: 0.7391 (m-90) REVERT: E 95 MET cc_start: 0.9249 (ptm) cc_final: 0.8900 (ptm) REVERT: E 104 MET cc_start: 0.8475 (mmm) cc_final: 0.8156 (tpt) REVERT: E 373 MET cc_start: 0.9085 (mmp) cc_final: 0.8677 (mmt) REVERT: E 427 TRP cc_start: 0.7863 (m-90) cc_final: 0.7414 (m-90) REVERT: F 586 TYR cc_start: 0.8945 (t80) cc_final: 0.8297 (t80) REVERT: F 601 LYS cc_start: 0.8957 (mtmm) cc_final: 0.8537 (mtmm) REVERT: F 640 SER cc_start: 0.9293 (m) cc_final: 0.9033 (p) REVERT: G 87 LYS cc_start: 0.8841 (mppt) cc_final: 0.8550 (mtmm) REVERT: G 122 MET cc_start: 0.7329 (mtm) cc_final: 0.6818 (mtt) REVERT: I 4 MET cc_start: 0.6834 (tmm) cc_final: 0.6432 (ppp) REVERT: I 27 ARG cc_start: 0.7970 (tpt90) cc_final: 0.7686 (mmm160) REVERT: I 89 MET cc_start: 0.8331 (ttt) cc_final: 0.7211 (ttt) REVERT: H 90 ASP cc_start: 0.9067 (m-30) cc_final: 0.8847 (m-30) REVERT: H 108 LEU cc_start: 0.9204 (tp) cc_final: 0.8866 (tt) REVERT: L 17 GLN cc_start: 0.8649 (tt0) cc_final: 0.8272 (tm-30) REVERT: L 21 ILE cc_start: 0.7739 (mt) cc_final: 0.7288 (pt) REVERT: L 74 ARG cc_start: 0.8034 (tpp80) cc_final: 0.7646 (mmm-85) REVERT: L 75 ILE cc_start: 0.7651 (mm) cc_final: 0.7023 (tt) REVERT: L 92 LYS cc_start: 0.9190 (tptp) cc_final: 0.8893 (tppp) REVERT: L 103 LYS cc_start: 0.8473 (tttt) cc_final: 0.8102 (tmtt) outliers start: 1 outliers final: 0 residues processed: 297 average time/residue: 0.3204 time to fit residues: 142.6659 Evaluate side-chains 202 residues out of total 1923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 2.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 107 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 chunk 53 optimal weight: 0.5980 chunk 193 optimal weight: 9.9990 chunk 209 optimal weight: 10.0000 chunk 172 optimal weight: 7.9990 chunk 192 optimal weight: 4.9990 chunk 66 optimal weight: 0.3980 chunk 155 optimal weight: 3.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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** A 478 ASN C 66 HIS D 590 GLN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 621 GLN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19228 Z= 0.265 Angle : 0.740 10.320 26090 Z= 0.362 Chirality : 0.052 0.430 3308 Planarity : 0.005 0.047 3132 Dihedral : 12.765 94.111 4898 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 0.10 % Allowed : 2.91 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.17), residues: 2131 helix: -1.25 (0.26), residues: 353 sheet: -2.20 (0.20), residues: 545 loop : -2.56 (0.16), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 125 HIS 0.004 0.001 HIS A 249 PHE 0.016 0.002 PHE A 277 TYR 0.030 0.002 TYR A 217 ARG 0.005 0.001 ARG B 585 *********************** 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 251 residues out of total 1923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 2.473 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: A 66 HIS cc_start: 0.8161 (m90) cc_final: 0.7741 (m90) REVERT: A 69 TRP cc_start: 0.8267 (m-90) cc_final: 0.7831 (m-90) REVERT: A 106 GLU cc_start: 0.8441 (mm-30) cc_final: 0.7814 (pt0) REVERT: A 107 ASP cc_start: 0.8689 (m-30) cc_final: 0.8443 (m-30) REVERT: A 211 GLU cc_start: 0.8491 (mp0) cc_final: 0.8178 (mp0) REVERT: A 434 MET cc_start: 0.8816 (tmm) cc_final: 0.8497 (tmm) REVERT: A 477 ASP cc_start: 0.8875 (m-30) cc_final: 0.8673 (m-30) REVERT: B 638 TYR cc_start: 0.9158 (m-80) cc_final: 0.8922 (m-10) REVERT: B 659 GLU cc_start: 0.9475 (tt0) cc_final: 0.9153 (tm-30) REVERT: C 304 ARG cc_start: 0.8239 (tpm170) cc_final: 0.7793 (mmm160) REVERT: D 584 GLU cc_start: 0.8400 (tm-30) cc_final: 0.8092 (tm-30) REVERT: D 620 ASN cc_start: 0.9109 (m-40) cc_final: 0.8784 (t0) REVERT: D 629 MET cc_start: 0.8533 (tpp) cc_final: 0.8221 (tpp) REVERT: D 632 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8166 (tm-30) REVERT: D 645 LEU cc_start: 0.9702 (tp) cc_final: 0.9432 (tp) REVERT: D 650 GLN cc_start: 0.8388 (tt0) cc_final: 0.8167 (tt0) REVERT: D 654 GLU cc_start: 0.9278 (mm-30) cc_final: 0.8880 (tp30) REVERT: D 657 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8232 (tm-30) REVERT: D 661 LEU cc_start: 0.9267 (tp) cc_final: 0.8960 (pp) REVERT: E 42 VAL cc_start: 0.9345 (t) cc_final: 0.9040 (p) REVERT: E 69 TRP cc_start: 0.7928 (m-90) cc_final: 0.7355 (m-90) REVERT: E 104 MET cc_start: 0.8579 (mmm) cc_final: 0.8186 (tpt) REVERT: E 293 GLU cc_start: 0.8138 (tt0) cc_final: 0.7931 (tm-30) REVERT: E 373 MET cc_start: 0.9130 (mmp) cc_final: 0.8650 (mmt) REVERT: F 586 TYR cc_start: 0.9048 (t80) cc_final: 0.8543 (t80) REVERT: F 640 SER cc_start: 0.9345 (m) cc_final: 0.9111 (p) REVERT: I 89 MET cc_start: 0.8396 (ttt) cc_final: 0.6171 (ttt) REVERT: H 90 ASP cc_start: 0.9095 (m-30) cc_final: 0.8846 (m-30) REVERT: H 108 LEU cc_start: 0.9320 (tp) cc_final: 0.9047 (tt) REVERT: L 17 GLN cc_start: 0.8690 (tt0) cc_final: 0.8336 (tm-30) REVERT: L 75 ILE cc_start: 0.7632 (mm) cc_final: 0.7144 (tt) REVERT: L 92 LYS cc_start: 0.9254 (tptp) cc_final: 0.8809 (tppp) REVERT: L 103 LYS cc_start: 0.8438 (tttt) cc_final: 0.8130 (tmtt) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.3012 time to fit residues: 115.6897 Evaluate side-chains 181 residues out of total 1923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 191 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 21 optimal weight: 0.0010 chunk 92 optimal weight: 0.5980 chunk 130 optimal weight: 7.9990 chunk 194 optimal weight: 5.9990 chunk 205 optimal weight: 9.9990 chunk 101 optimal weight: 0.5980 chunk 184 optimal weight: 9.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN B 651 ASN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19228 Z= 0.165 Angle : 0.682 11.138 26090 Z= 0.330 Chirality : 0.051 0.383 3308 Planarity : 0.004 0.048 3132 Dihedral : 11.347 94.250 4898 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 0.16 % Allowed : 1.97 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.17), residues: 2131 helix: -0.82 (0.27), residues: 352 sheet: -1.99 (0.20), residues: 526 loop : -2.42 (0.16), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 427 HIS 0.005 0.001 HIS E 105 PHE 0.014 0.001 PHE I 49 TYR 0.032 0.001 TYR H 80 ARG 0.005 0.000 ARG L 77 *********************** 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 258 residues out of total 1923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 257 time to evaluate : 2.531 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: A 69 TRP cc_start: 0.8281 (m-90) cc_final: 0.7645 (m-90) REVERT: A 106 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7806 (pt0) REVERT: A 176 PHE cc_start: 0.8795 (m-10) cc_final: 0.8509 (m-80) REVERT: A 211 GLU cc_start: 0.8396 (mp0) cc_final: 0.8076 (mp0) REVERT: A 434 MET cc_start: 0.8801 (tmm) cc_final: 0.8426 (tmm) REVERT: A 477 ASP cc_start: 0.8702 (m-30) cc_final: 0.8427 (m-30) REVERT: B 659 GLU cc_start: 0.9429 (tt0) cc_final: 0.9122 (tm-30) REVERT: C 304 ARG cc_start: 0.7923 (tpm170) cc_final: 0.7533 (mmm160) REVERT: D 584 GLU cc_start: 0.8409 (tm-30) cc_final: 0.8096 (tm-30) REVERT: D 620 ASN cc_start: 0.9115 (m-40) cc_final: 0.8811 (t0) REVERT: D 632 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8309 (tm-30) REVERT: D 642 ILE cc_start: 0.9726 (mt) cc_final: 0.9439 (tp) REVERT: D 645 LEU cc_start: 0.9711 (tp) cc_final: 0.9478 (tp) REVERT: D 654 GLU cc_start: 0.9218 (mm-30) cc_final: 0.8620 (tp30) REVERT: D 655 LYS cc_start: 0.9439 (mmmt) cc_final: 0.9039 (mmmt) REVERT: D 657 GLU cc_start: 0.8653 (tm-30) cc_final: 0.7965 (tm-30) REVERT: D 661 LEU cc_start: 0.9092 (tp) cc_final: 0.8865 (pp) REVERT: E 42 VAL cc_start: 0.9317 (t) cc_final: 0.9070 (p) REVERT: E 69 TRP cc_start: 0.7768 (m-90) cc_final: 0.7170 (m-90) REVERT: E 95 MET cc_start: 0.9210 (ptm) cc_final: 0.8928 (ptm) REVERT: E 210 PHE cc_start: 0.8698 (m-80) cc_final: 0.8471 (m-10) REVERT: E 373 MET cc_start: 0.9066 (mmp) cc_final: 0.8641 (mmt) REVERT: F 586 TYR cc_start: 0.8943 (t80) cc_final: 0.8602 (t80) REVERT: F 640 SER cc_start: 0.9330 (m) cc_final: 0.9103 (p) REVERT: G 35 TYR cc_start: 0.8291 (m-80) cc_final: 0.7994 (m-80) REVERT: G 83 MET cc_start: 0.8229 (mpp) cc_final: 0.7936 (mpp) REVERT: G 99 MET cc_start: 0.8090 (tpp) cc_final: 0.7758 (tpp) REVERT: I 4 MET cc_start: 0.7104 (tmm) cc_final: 0.6818 (tmm) REVERT: I 89 MET cc_start: 0.8548 (ttt) cc_final: 0.7483 (ttp) REVERT: H 90 ASP cc_start: 0.9061 (m-30) cc_final: 0.8594 (m-30) REVERT: L 17 GLN cc_start: 0.8595 (tt0) cc_final: 0.8260 (tm-30) REVERT: L 75 ILE cc_start: 0.7758 (mm) cc_final: 0.7483 (tt) REVERT: L 92 LYS cc_start: 0.9240 (tptp) cc_final: 0.8689 (tppp) REVERT: L 103 LYS cc_start: 0.8431 (tttt) cc_final: 0.8015 (tmtt) outliers start: 1 outliers final: 0 residues processed: 258 average time/residue: 0.3220 time to fit residues: 127.4103 Evaluate side-chains 189 residues out of total 1923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 171 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 153 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 175 optimal weight: 9.9990 chunk 142 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 184 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 442 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 19228 Z= 0.462 Angle : 0.870 11.168 26090 Z= 0.419 Chirality : 0.054 0.436 3308 Planarity : 0.005 0.047 3132 Dihedral : 11.512 83.380 4898 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.09 % Favored : 88.91 % Rotamer: Outliers : 0.10 % Allowed : 2.91 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.17), residues: 2131 helix: -0.97 (0.26), residues: 371 sheet: -2.12 (0.20), residues: 566 loop : -2.46 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 427 HIS 0.007 0.002 HIS A 66 PHE 0.023 0.002 PHE A 277 TYR 0.026 0.002 TYR A 217 ARG 0.005 0.001 ARG A 504 *********************** 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 214 residues out of total 1923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 2.230 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: A 69 TRP cc_start: 0.8248 (m-90) cc_final: 0.7783 (m-90) REVERT: A 106 GLU cc_start: 0.8481 (mm-30) cc_final: 0.7872 (pt0) REVERT: A 211 GLU cc_start: 0.8573 (mp0) cc_final: 0.8227 (mp0) REVERT: A 426 MET cc_start: 0.7892 (ttp) cc_final: 0.7599 (ttp) REVERT: A 434 MET cc_start: 0.8699 (tmm) cc_final: 0.7889 (tmm) REVERT: A 477 ASP cc_start: 0.8760 (m-30) cc_final: 0.8557 (m-30) REVERT: B 659 GLU cc_start: 0.9518 (tt0) cc_final: 0.9170 (tm-30) REVERT: C 304 ARG cc_start: 0.8488 (tpm170) cc_final: 0.8031 (mmm160) REVERT: D 591 GLN cc_start: 0.9013 (tt0) cc_final: 0.8112 (tt0) REVERT: D 601 LYS cc_start: 0.8146 (mttp) cc_final: 0.7890 (mttp) REVERT: D 620 ASN cc_start: 0.9191 (m-40) cc_final: 0.8853 (t0) REVERT: D 629 MET cc_start: 0.8777 (tpp) cc_final: 0.8163 (tpp) REVERT: D 632 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8281 (tm-30) REVERT: D 645 LEU cc_start: 0.9727 (tp) cc_final: 0.9294 (tp) REVERT: D 654 GLU cc_start: 0.9397 (mm-30) cc_final: 0.9120 (tp30) REVERT: D 655 LYS cc_start: 0.9495 (mmmt) cc_final: 0.9091 (mmmm) REVERT: D 657 GLU cc_start: 0.8838 (tm-30) cc_final: 0.8409 (tm-30) REVERT: E 69 TRP cc_start: 0.7702 (m-90) cc_final: 0.7018 (m-90) REVERT: E 104 MET cc_start: 0.9287 (mtp) cc_final: 0.8934 (mtp) REVERT: E 373 MET cc_start: 0.9042 (mmp) cc_final: 0.8588 (mmt) REVERT: E 426 MET cc_start: 0.7486 (tpp) cc_final: 0.6824 (tpp) REVERT: F 530 MET cc_start: 0.8780 (mtm) cc_final: 0.8451 (mmm) REVERT: F 586 TYR cc_start: 0.9238 (t80) cc_final: 0.8578 (t80) REVERT: F 640 SER cc_start: 0.9447 (m) cc_final: 0.9224 (p) REVERT: I 89 MET cc_start: 0.8575 (ttt) cc_final: 0.8023 (ppp) REVERT: H 90 ASP cc_start: 0.9095 (m-30) cc_final: 0.8799 (m-30) REVERT: L 17 GLN cc_start: 0.8729 (tt0) cc_final: 0.8269 (tm-30) REVERT: L 73 LEU cc_start: 0.8322 (tp) cc_final: 0.8055 (tt) REVERT: L 74 ARG cc_start: 0.8052 (tpp80) cc_final: 0.7682 (mmm160) REVERT: L 92 LYS cc_start: 0.9212 (tptp) cc_final: 0.8736 (tppp) REVERT: L 103 LYS cc_start: 0.8360 (tttt) cc_final: 0.7982 (tmtt) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.3180 time to fit residues: 103.9153 Evaluate side-chains 177 residues out of total 1923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 69 optimal weight: 10.0000 chunk 185 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 206 optimal weight: 10.0000 chunk 171 optimal weight: 0.0670 chunk 95 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- 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 550 GLN ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 478 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19228 Z= 0.223 Angle : 0.710 11.617 26090 Z= 0.342 Chirality : 0.051 0.336 3308 Planarity : 0.004 0.046 3132 Dihedral : 10.680 83.955 4898 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 0.10 % Allowed : 1.09 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.17), residues: 2131 helix: -0.69 (0.27), residues: 366 sheet: -1.97 (0.20), residues: 547 loop : -2.33 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 427 HIS 0.005 0.001 HIS C 105 PHE 0.013 0.001 PHE I 49 TYR 0.030 0.001 TYR A 217 ARG 0.006 0.000 ARG F 585 *********************** 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 223 residues out of total 1923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 2.246 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: 0.8210 (m-90) cc_final: 0.7679 (m-90) REVERT: A 106 GLU cc_start: 0.8450 (mm-30) cc_final: 0.7845 (pt0) REVERT: A 107 ASP cc_start: 0.8706 (m-30) cc_final: 0.8474 (m-30) REVERT: A 211 GLU cc_start: 0.8467 (mp0) cc_final: 0.8171 (mp0) REVERT: A 426 MET cc_start: 0.7824 (ttp) cc_final: 0.7560 (ttp) REVERT: A 434 MET cc_start: 0.8709 (tmm) cc_final: 0.8436 (tmm) REVERT: A 477 ASP cc_start: 0.8649 (m-30) cc_final: 0.8435 (m-30) REVERT: B 659 GLU cc_start: 0.9489 (tt0) cc_final: 0.9105 (tm-30) REVERT: D 591 GLN cc_start: 0.8988 (tt0) cc_final: 0.8323 (tt0) REVERT: D 601 LYS cc_start: 0.7919 (mttp) cc_final: 0.7652 (mttp) REVERT: D 620 ASN cc_start: 0.9165 (m-40) cc_final: 0.8843 (t0) REVERT: D 629 MET cc_start: 0.8640 (tpp) cc_final: 0.8268 (tpp) REVERT: D 632 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8293 (tm-30) REVERT: D 654 GLU cc_start: 0.9289 (mm-30) cc_final: 0.8942 (tp30) REVERT: D 655 LYS cc_start: 0.9445 (mmmt) cc_final: 0.8998 (mmtt) REVERT: D 657 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8331 (tm-30) REVERT: E 42 VAL cc_start: 0.9440 (t) cc_final: 0.9195 (p) REVERT: E 69 TRP cc_start: 0.7613 (m-90) cc_final: 0.6904 (m-90) REVERT: E 104 MET cc_start: 0.9240 (mtp) cc_final: 0.8956 (mtm) REVERT: E 210 PHE cc_start: 0.8685 (m-80) cc_final: 0.8366 (m-10) REVERT: E 277 PHE cc_start: 0.7769 (p90) cc_final: 0.7568 (p90) REVERT: E 373 MET cc_start: 0.9002 (mmp) cc_final: 0.8550 (mmt) REVERT: F 586 TYR cc_start: 0.9126 (t80) cc_final: 0.8613 (t80) REVERT: F 633 ARG cc_start: 0.8967 (mtm180) cc_final: 0.8746 (mtm180) REVERT: F 640 SER cc_start: 0.9409 (m) cc_final: 0.9175 (p) REVERT: G 35 TYR cc_start: 0.8560 (m-80) cc_final: 0.8293 (m-80) REVERT: I 4 MET cc_start: 0.7156 (tmm) cc_final: 0.6916 (tmm) REVERT: H 90 ASP cc_start: 0.9070 (m-30) cc_final: 0.8758 (m-30) REVERT: H 122 MET cc_start: 0.7862 (pmm) cc_final: 0.7581 (pmm) REVERT: L 92 LYS cc_start: 0.9154 (tptp) cc_final: 0.8709 (tppp) REVERT: L 103 LYS cc_start: 0.8277 (tttt) cc_final: 0.7822 (tmtt) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.3160 time to fit residues: 107.0791 Evaluate side-chains 174 residues out of total 1923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 2.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 198 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 chunk 150 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 173 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 205 optimal weight: 0.6980 chunk 128 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 478 ASN ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19228 Z= 0.217 Angle : 0.694 11.288 26090 Z= 0.335 Chirality : 0.050 0.367 3308 Planarity : 0.004 0.045 3132 Dihedral : 10.144 80.489 4898 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 0.10 % Allowed : 1.30 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.17), residues: 2131 helix: -0.51 (0.28), residues: 363 sheet: -1.84 (0.21), residues: 546 loop : -2.29 (0.17), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 427 HIS 0.006 0.001 HIS C 105 PHE 0.013 0.001 PHE I 49 TYR 0.026 0.001 TYR A 217 ARG 0.003 0.000 ARG G 67 *********************** 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 234 residues out of total 1923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 2.158 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: 0.8230 (m-90) cc_final: 0.7690 (m-90) REVERT: A 106 GLU cc_start: 0.8427 (mm-30) cc_final: 0.7832 (pt0) REVERT: A 211 GLU cc_start: 0.8482 (mp0) cc_final: 0.8190 (mp0) REVERT: A 434 MET cc_start: 0.8703 (tmm) cc_final: 0.8381 (tmm) REVERT: A 477 ASP cc_start: 0.8630 (m-30) cc_final: 0.8414 (m-30) REVERT: B 659 GLU cc_start: 0.9442 (tt0) cc_final: 0.9056 (tm-30) REVERT: D 591 GLN cc_start: 0.9005 (tt0) cc_final: 0.8396 (tt0) REVERT: D 601 LYS cc_start: 0.7882 (mttp) cc_final: 0.7617 (mttp) REVERT: D 620 ASN cc_start: 0.9227 (m-40) cc_final: 0.8887 (t0) REVERT: D 632 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8342 (tm-30) REVERT: D 654 GLU cc_start: 0.9257 (mm-30) cc_final: 0.8885 (tp30) REVERT: D 655 LYS cc_start: 0.9452 (mmmt) cc_final: 0.9049 (mmtt) REVERT: D 657 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8287 (tm-30) REVERT: E 42 VAL cc_start: 0.9382 (t) cc_final: 0.9149 (p) REVERT: E 69 TRP cc_start: 0.7515 (m-90) cc_final: 0.6851 (m-90) REVERT: E 210 PHE cc_start: 0.8689 (m-80) cc_final: 0.8347 (m-10) REVERT: E 277 PHE cc_start: 0.7725 (p90) cc_final: 0.7505 (p90) REVERT: E 373 MET cc_start: 0.8989 (mmp) cc_final: 0.8558 (mmt) REVERT: F 586 TYR cc_start: 0.9143 (t80) cc_final: 0.8648 (t80) REVERT: F 640 SER cc_start: 0.9427 (m) cc_final: 0.9203 (p) REVERT: G 34 MET cc_start: 0.9131 (tpp) cc_final: 0.8739 (mmm) REVERT: G 35 TYR cc_start: 0.8560 (m-80) cc_final: 0.7513 (m-80) REVERT: I 4 MET cc_start: 0.7195 (tmm) cc_final: 0.6925 (tmm) REVERT: I 98 PHE cc_start: 0.8574 (m-80) cc_final: 0.8194 (m-10) REVERT: H 90 ASP cc_start: 0.9057 (m-30) cc_final: 0.8733 (m-30) REVERT: L 17 GLN cc_start: 0.8311 (tt0) cc_final: 0.8014 (tm-30) REVERT: L 18 PRO cc_start: 0.8641 (Cg_endo) cc_final: 0.8076 (Cg_exo) REVERT: L 27 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7456 (tm-30) REVERT: L 77 ARG cc_start: 0.8233 (tpp-160) cc_final: 0.7939 (tpp-160) REVERT: L 92 LYS cc_start: 0.9217 (tptp) cc_final: 0.8768 (tppp) REVERT: L 103 LYS cc_start: 0.8252 (tttt) cc_final: 0.7747 (tmtt) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.3222 time to fit residues: 113.1862 Evaluate side-chains 185 residues out of total 1923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 127 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 61 optimal weight: 0.0770 chunk 40 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 130 optimal weight: 7.9990 chunk 139 optimal weight: 20.0000 chunk 101 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 GLN ** C 478 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 19228 Z= 0.182 Angle : 0.688 11.575 26090 Z= 0.330 Chirality : 0.051 0.525 3308 Planarity : 0.004 0.046 3132 Dihedral : 9.579 75.245 4898 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 0.10 % Allowed : 0.52 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.17), residues: 2131 helix: -0.48 (0.28), residues: 369 sheet: -1.75 (0.20), residues: 565 loop : -2.27 (0.17), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 112 HIS 0.005 0.001 HIS C 374 PHE 0.014 0.001 PHE I 49 TYR 0.021 0.001 TYR A 217 ARG 0.010 0.000 ARG G 98 *********************** 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 243 residues out of total 1923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 2.328 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: A 69 TRP cc_start: 0.8175 (m-90) cc_final: 0.7664 (m-90) REVERT: A 106 GLU cc_start: 0.8401 (mm-30) cc_final: 0.7883 (pt0) REVERT: A 176 PHE cc_start: 0.8756 (m-10) cc_final: 0.8434 (m-80) REVERT: A 211 GLU cc_start: 0.8426 (mp0) cc_final: 0.8144 (mp0) REVERT: A 434 MET cc_start: 0.8686 (tmm) cc_final: 0.8350 (tmm) REVERT: A 477 ASP cc_start: 0.8646 (m-30) cc_final: 0.8399 (m-30) REVERT: B 659 GLU cc_start: 0.9460 (tt0) cc_final: 0.9091 (tm-30) REVERT: C 427 TRP cc_start: 0.4702 (t60) cc_final: 0.3669 (t60) REVERT: D 591 GLN cc_start: 0.8986 (tt0) cc_final: 0.8368 (tt0) REVERT: D 601 LYS cc_start: 0.7847 (mttp) cc_final: 0.7587 (mttp) REVERT: D 620 ASN cc_start: 0.9226 (m-40) cc_final: 0.8862 (t0) REVERT: D 629 MET cc_start: 0.8914 (tpp) cc_final: 0.8394 (tpp) REVERT: D 632 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8347 (tm-30) REVERT: D 642 ILE cc_start: 0.9727 (mt) cc_final: 0.9486 (tp) REVERT: D 654 GLU cc_start: 0.9181 (mm-30) cc_final: 0.8727 (tp30) REVERT: D 655 LYS cc_start: 0.9422 (mmmt) cc_final: 0.9002 (mmtt) REVERT: D 657 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8250 (tm-30) REVERT: E 42 VAL cc_start: 0.9348 (t) cc_final: 0.9131 (p) REVERT: E 69 TRP cc_start: 0.7511 (m-90) cc_final: 0.6850 (m-90) REVERT: E 104 MET cc_start: 0.9069 (mtp) cc_final: 0.8765 (ttm) REVERT: E 210 PHE cc_start: 0.8658 (m-80) cc_final: 0.8329 (m-10) REVERT: E 277 PHE cc_start: 0.7686 (p90) cc_final: 0.7436 (p90) REVERT: E 373 MET cc_start: 0.8946 (mmp) cc_final: 0.8515 (mmt) REVERT: F 586 TYR cc_start: 0.9134 (t80) cc_final: 0.8641 (t80) REVERT: F 640 SER cc_start: 0.9414 (m) cc_final: 0.9172 (p) REVERT: G 35 TYR cc_start: 0.8258 (m-80) cc_final: 0.7985 (m-80) REVERT: I 4 MET cc_start: 0.7187 (tmm) cc_final: 0.6954 (tmm) REVERT: I 89 MET cc_start: 0.7725 (ppp) cc_final: 0.7445 (tmm) REVERT: I 98 PHE cc_start: 0.8315 (m-80) cc_final: 0.7984 (m-10) REVERT: H 90 ASP cc_start: 0.9023 (m-30) cc_final: 0.8559 (m-30) REVERT: L 17 GLN cc_start: 0.8420 (tt0) cc_final: 0.8091 (tm-30) REVERT: L 18 PRO cc_start: 0.8644 (Cg_endo) cc_final: 0.8075 (Cg_exo) REVERT: L 27 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7415 (tm-30) REVERT: L 77 ARG cc_start: 0.8224 (tpp-160) cc_final: 0.7948 (tpp-160) REVERT: L 89 MET cc_start: 0.8536 (tpp) cc_final: 0.8297 (tpp) REVERT: L 92 LYS cc_start: 0.9222 (tptp) cc_final: 0.8785 (tppp) REVERT: L 103 LYS cc_start: 0.8168 (tttt) cc_final: 0.7666 (tmtt) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.3214 time to fit residues: 117.7407 Evaluate side-chains 189 residues out of total 1923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 186 optimal weight: 20.0000 chunk 196 optimal weight: 4.9990 chunk 179 optimal weight: 10.0000 chunk 191 optimal weight: 0.8980 chunk 115 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 150 optimal weight: 0.4980 chunk 58 optimal weight: 2.9990 chunk 172 optimal weight: 0.7980 chunk 180 optimal weight: 0.0470 chunk 190 optimal weight: 7.9990 overall best weight: 1.0480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN C 428 GLN ** C 478 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 19228 Z= 0.169 Angle : 0.666 11.945 26090 Z= 0.321 Chirality : 0.050 0.473 3308 Planarity : 0.004 0.045 3132 Dihedral : 9.079 64.202 4898 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 0.10 % Allowed : 0.21 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.18), residues: 2131 helix: -0.34 (0.29), residues: 368 sheet: -1.60 (0.20), residues: 586 loop : -2.22 (0.17), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 69 HIS 0.003 0.001 HIS C 374 PHE 0.013 0.001 PHE I 49 TYR 0.021 0.001 TYR A 217 ARG 0.006 0.000 ARG L 74 *********************** 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 242 residues out of total 1923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 2.366 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 46 LYS cc_start: 0.8857 (mtmm) cc_final: 0.8654 (mttt) REVERT: A 66 HIS cc_start: 0.8201 (m90) cc_final: 0.7917 (m90) REVERT: A 69 TRP cc_start: 0.8200 (m-90) cc_final: 0.7676 (m-90) REVERT: A 106 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7885 (pt0) REVERT: A 165 MET cc_start: 0.8366 (mtm) cc_final: 0.8099 (mtp) REVERT: A 176 PHE cc_start: 0.8768 (m-10) cc_final: 0.8478 (m-80) REVERT: A 211 GLU cc_start: 0.8381 (mp0) cc_final: 0.8130 (mp0) REVERT: A 434 MET cc_start: 0.8676 (tmm) cc_final: 0.8334 (tmm) REVERT: A 477 ASP cc_start: 0.8620 (m-30) cc_final: 0.8370 (m-30) REVERT: B 659 GLU cc_start: 0.9482 (tt0) cc_final: 0.9123 (tm-30) REVERT: C 427 TRP cc_start: 0.4482 (t60) cc_final: 0.3815 (t60) REVERT: D 620 ASN cc_start: 0.9185 (m-40) cc_final: 0.8884 (t0) REVERT: D 629 MET cc_start: 0.8866 (tpp) cc_final: 0.8264 (tpp) REVERT: D 632 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8324 (tm-30) REVERT: D 642 ILE cc_start: 0.9713 (mt) cc_final: 0.9498 (tp) REVERT: D 654 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8453 (tp30) REVERT: D 657 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8198 (tm-30) REVERT: E 42 VAL cc_start: 0.9305 (t) cc_final: 0.9079 (p) REVERT: E 69 TRP cc_start: 0.7507 (m-90) cc_final: 0.6880 (m-90) REVERT: E 104 MET cc_start: 0.9071 (mtp) cc_final: 0.8766 (ttm) REVERT: E 210 PHE cc_start: 0.8669 (m-80) cc_final: 0.8324 (m-10) REVERT: E 373 MET cc_start: 0.8938 (mmp) cc_final: 0.8510 (mmt) REVERT: F 586 TYR cc_start: 0.9124 (t80) cc_final: 0.8665 (t80) REVERT: I 4 MET cc_start: 0.7183 (tmm) cc_final: 0.6801 (tmm) REVERT: I 89 MET cc_start: 0.7757 (ppp) cc_final: 0.7413 (ttp) REVERT: H 90 ASP cc_start: 0.8991 (m-30) cc_final: 0.8525 (m-30) REVERT: L 18 PRO cc_start: 0.8608 (Cg_endo) cc_final: 0.8200 (Cg_exo) REVERT: L 27 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7397 (tm-30) REVERT: L 77 ARG cc_start: 0.8173 (tpp-160) cc_final: 0.7921 (tpp-160) REVERT: L 89 MET cc_start: 0.8548 (tpp) cc_final: 0.8244 (tpp) REVERT: L 92 LYS cc_start: 0.9205 (tptp) cc_final: 0.8777 (tppp) REVERT: L 103 LYS cc_start: 0.8196 (tttt) cc_final: 0.7666 (tmtt) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.3195 time to fit residues: 117.3246 Evaluate side-chains 193 residues out of total 1923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 2.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 125 optimal weight: 0.8980 chunk 202 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 140 optimal weight: 4.9990 chunk 212 optimal weight: 5.9990 chunk 195 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 130 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 GLN ** C 478 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 19228 Z= 0.282 Angle : 0.720 11.433 26090 Z= 0.348 Chirality : 0.051 0.408 3308 Planarity : 0.004 0.053 3132 Dihedral : 9.220 59.978 4898 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % 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 : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.18), residues: 2131 helix: -0.28 (0.29), residues: 368 sheet: -1.63 (0.21), residues: 574 loop : -2.27 (0.17), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 631 HIS 0.005 0.001 HIS C 105 PHE 0.019 0.002 PHE E 277 TYR 0.025 0.002 TYR A 217 ARG 0.008 0.001 ARG L 74 ********************** 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 225 residues out of total 1923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 2.330 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 46 LYS cc_start: 0.8864 (mtmm) cc_final: 0.8626 (mttt) REVERT: A 69 TRP cc_start: 0.8252 (m-90) cc_final: 0.7784 (m-90) REVERT: A 106 GLU cc_start: 0.8420 (mm-30) cc_final: 0.7915 (pt0) REVERT: A 165 MET cc_start: 0.8348 (mtm) cc_final: 0.8030 (mtp) REVERT: A 211 GLU cc_start: 0.8492 (mp0) cc_final: 0.8183 (mp0) REVERT: A 434 MET cc_start: 0.8670 (tmm) cc_final: 0.7838 (tmm) REVERT: A 477 ASP cc_start: 0.8678 (m-30) cc_final: 0.8444 (m-30) REVERT: B 619 TYR cc_start: 0.7798 (t80) cc_final: 0.7589 (t80) REVERT: B 659 GLU cc_start: 0.9531 (tt0) cc_final: 0.9192 (tm-30) REVERT: D 530 MET cc_start: 0.8470 (ppp) cc_final: 0.8225 (ppp) REVERT: D 591 GLN cc_start: 0.9018 (tt0) cc_final: 0.8300 (tt0) REVERT: D 601 LYS cc_start: 0.7782 (mttp) cc_final: 0.7449 (mttp) REVERT: D 620 ASN cc_start: 0.9244 (m-40) cc_final: 0.8895 (t0) REVERT: D 629 MET cc_start: 0.8953 (tpp) cc_final: 0.8257 (tpp) REVERT: D 632 GLU cc_start: 0.9090 (mm-30) cc_final: 0.8342 (tm-30) REVERT: D 642 ILE cc_start: 0.9740 (mt) cc_final: 0.9515 (tp) REVERT: D 654 GLU cc_start: 0.9160 (mm-30) cc_final: 0.8801 (tp30) REVERT: D 655 LYS cc_start: 0.9408 (mmmt) cc_final: 0.9166 (mmtt) REVERT: D 657 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8291 (tm-30) REVERT: E 42 VAL cc_start: 0.9370 (t) cc_final: 0.9150 (p) REVERT: E 69 TRP cc_start: 0.7483 (m-90) cc_final: 0.6842 (m-90) REVERT: E 104 MET cc_start: 0.9176 (mtp) cc_final: 0.8798 (ttm) REVERT: E 210 PHE cc_start: 0.8693 (m-80) cc_final: 0.8307 (m-10) REVERT: E 373 MET cc_start: 0.9006 (mmp) cc_final: 0.8578 (mmt) REVERT: F 586 TYR cc_start: 0.9195 (t80) cc_final: 0.8610 (t80) REVERT: I 4 MET cc_start: 0.7141 (tmm) cc_final: 0.6923 (tmm) REVERT: I 89 MET cc_start: 0.7872 (ppp) cc_final: 0.7626 (tmm) REVERT: I 98 PHE cc_start: 0.8294 (m-80) cc_final: 0.8016 (m-80) REVERT: H 34 MET cc_start: 0.8652 (mmm) cc_final: 0.8392 (tpp) REVERT: H 45 LEU cc_start: 0.8955 (tp) cc_final: 0.8722 (tp) REVERT: H 90 ASP cc_start: 0.9016 (m-30) cc_final: 0.8566 (m-30) REVERT: L 27 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7390 (tm-30) REVERT: L 92 LYS cc_start: 0.9233 (tptp) cc_final: 0.8810 (tppp) REVERT: L 103 LYS cc_start: 0.8066 (tttt) cc_final: 0.7586 (tmtt) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.3167 time to fit residues: 107.9572 Evaluate side-chains 181 residues out of total 1923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 2.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 134 optimal weight: 3.9990 chunk 180 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 155 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 chunk 46 optimal weight: 0.0070 chunk 169 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 chunk 173 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 overall best weight: 2.5802 ------------------------------------------------------------------------------- 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 651 ASN ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.059795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.048795 restraints weight = 97819.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.050188 restraints weight = 56209.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.051116 restraints weight = 38780.262| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 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 = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 19228 Z= 0.249 Angle : 0.704 11.503 26090 Z= 0.340 Chirality : 0.050 0.389 3308 Planarity : 0.004 0.062 3132 Dihedral : 9.017 59.968 4898 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 0.10 % Allowed : 0.36 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.18), residues: 2131 helix: -0.06 (0.29), residues: 358 sheet: -1.58 (0.21), residues: 560 loop : -2.18 (0.17), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 427 HIS 0.004 0.001 HIS C 374 PHE 0.020 0.001 PHE E 277 TYR 0.024 0.001 TYR A 217 ARG 0.007 0.000 ARG L 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3545.26 seconds wall clock time: 67 minutes 53.70 seconds (4073.70 seconds total)