Starting phenix.real_space_refine on Tue May 27 21:53:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jn5_36433/05_2025/8jn5_36433.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jn5_36433/05_2025/8jn5_36433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jn5_36433/05_2025/8jn5_36433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jn5_36433/05_2025/8jn5_36433.map" model { file = "/net/cci-nas-00/data/ceres_data/8jn5_36433/05_2025/8jn5_36433.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jn5_36433/05_2025/8jn5_36433.cif" } resolution = 3.6 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= 1.000 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 202 5.16 5 C 19172 2.51 5 N 5062 2.21 5 O 5768 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 240 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 30204 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3757 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 16, 'TRANS': 476} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 585 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 3757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3757 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 16, 'TRANS': 476} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 585 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 3757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3757 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 16, 'TRANS': 476} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 585 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 950 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 870 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 2, 'MAN': 1, '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: "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: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 2, 'MAN': 1, '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: "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: 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: "O" Number of atoms: 3757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3757 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 16, 'TRANS': 476} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "P" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 585 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Q" Number of atoms: 3757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3757 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 16, 'TRANS': 476} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "R" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 585 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "S" Number of atoms: 3757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3757 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 16, 'TRANS': 476} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "T" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 585 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "U" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 950 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "V" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 870 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 2, 'MAN': 1, '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: "X" 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: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 2, 'MAN': 1, '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: "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: "0" 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: "1" 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 Time building chain proxies: 17.81, per 1000 atoms: 0.59 Number of scatterers: 30204 At special positions: 0 Unit cell: (165.87, 241.11, 117.99, 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 202 16.00 O 5768 8.00 N 5062 7.00 C 19172 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 30 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 105 " distance=2.03 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 116 " distance=2.04 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 283 " distance=2.04 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS C 30 " distance=2.02 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 121 " distance=2.03 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS C 105 " distance=2.03 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 116 " distance=2.03 Simple disulfide: pdb=" SG CYS C 300 " - pdb=" SG CYS C 331 " distance=2.02 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 121 " distance=2.04 Simple disulfide: pdb=" SG CYS E 92 " - pdb=" SG CYS E 116 " distance=2.04 Simple disulfide: pdb=" SG CYS E 300 " - pdb=" SG CYS E 331 " distance=2.03 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 94 " distance=2.04 Simple disulfide: pdb=" SG CYS O 3 " - pdb=" SG CYS O 30 " distance=2.03 Simple disulfide: pdb=" SG CYS O 60 " - pdb=" SG CYS O 121 " distance=2.03 Simple disulfide: pdb=" SG CYS O 74 " - pdb=" SG CYS O 105 " distance=2.03 Simple disulfide: pdb=" SG CYS O 92 " - pdb=" SG CYS O 116 " distance=2.04 Simple disulfide: pdb=" SG CYS O 183 " - pdb=" SG CYS O 283 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 3 " - pdb=" SG CYS Q 30 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 60 " - pdb=" SG CYS Q 121 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 74 " - pdb=" SG CYS Q 105 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 92 " - pdb=" SG CYS Q 116 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 300 " - pdb=" SG CYS Q 331 " distance=2.02 Simple disulfide: pdb=" SG CYS S 60 " - pdb=" SG CYS S 121 " distance=2.04 Simple disulfide: pdb=" SG CYS S 92 " - pdb=" SG CYS S 116 " distance=2.04 Simple disulfide: pdb=" SG CYS S 300 " - pdb=" SG CYS S 331 " distance=2.03 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 96 " distance=2.03 Simple disulfide: pdb=" SG CYS V 23 " - pdb=" SG CYS V 94 " 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 G 3 " - " MAN G 4 " " BMA J 3 " - " MAN J 4 " " BMA W 3 " - " MAN W 4 " " BMA Y 3 " - " MAN Y 4 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " BETA1-6 " BMA G 3 " - " BMA G 5 " " BMA J 3 " - " BMA J 5 " " BMA W 3 " - " BMA W 5 " " BMA Y 3 " - " BMA Y 5 " NAG-ASN " NAG 0 1 " - " ASN S 67 " " NAG 1 1 " - " ASN S 153 " " NAG G 1 " - " ASN A 67 " " NAG I 1 " - " ASN A 153 " " NAG J 1 " - " ASN C 67 " " NAG K 1 " - " ASN C 153 " " NAG M 1 " - " ASN E 67 " " NAG N 1 " - " ASN E 153 " " NAG W 1 " - " ASN O 67 " " NAG X 1 " - " ASN O 153 " " NAG Y 1 " - " ASN Q 67 " " NAG Z 1 " - " ASN Q 153 " Time building additional restraints: 7.51 Conformation dependent library (CDL) restraints added in 3.5 seconds 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6984 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 74 sheets defined 25.8% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.89 Creating SS restraints... Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 190 through 192 No H-bonds generated for 'chain 'A' and resid 190 through 192' Processing helix chain 'A' and resid 208 through 212 Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.921A pdb=" N LEU A 234 " --> pdb=" O ARG A 231 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 235 " --> pdb=" O LYS A 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 231 through 235' Processing helix chain 'A' and resid 242 through 244 No H-bonds generated for 'chain 'A' and resid 242 through 244' Processing helix chain 'A' and resid 254 through 262 Processing helix chain 'A' and resid 394 through 414 Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 425 through 447 removed outlier: 3.805A pdb=" N SER A 429 " --> pdb=" O GLY A 425 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 430 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 468 Processing helix chain 'A' and resid 470 through 490 Processing helix chain 'B' and resid 26 through 39 removed outlier: 4.183A pdb=" N VAL B 32 " --> pdb=" O GLN B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 removed outlier: 3.985A pdb=" N ILE B 44 " --> pdb=" O PRO B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 75 Proline residue: B 72 - end of helix Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'C' and resid 208 through 214 Processing helix chain 'C' and resid 231 through 235 removed outlier: 3.766A pdb=" N LEU C 234 " --> pdb=" O ARG C 231 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 235 " --> pdb=" O LYS C 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 231 through 235' Processing helix chain 'C' and resid 254 through 262 Processing helix chain 'C' and resid 394 through 414 Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.760A pdb=" N TRP C 418 " --> pdb=" O ASP C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 447 removed outlier: 3.527A pdb=" N SER C 429 " --> pdb=" O GLY C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 467 removed outlier: 3.742A pdb=" N ILE C 455 " --> pdb=" O TRP C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 490 removed outlier: 4.140A pdb=" N ILE C 478 " --> pdb=" O SER C 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 26 removed outlier: 4.637A pdb=" N TRP D 26 " --> pdb=" O ALA D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 39 Processing helix chain 'D' and resid 40 through 54 removed outlier: 3.884A pdb=" N ILE D 44 " --> pdb=" O PRO D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 75 removed outlier: 3.578A pdb=" N LYS D 60 " --> pdb=" O SER D 56 " (cutoff:3.500A) Proline residue: D 72 - end of helix Processing helix chain 'E' and resid 82 through 86 Processing helix chain 'E' and resid 131 through 133 No H-bonds generated for 'chain 'E' and resid 131 through 133' Processing helix chain 'E' and resid 208 through 213 Processing helix chain 'E' and resid 231 through 236 removed outlier: 3.539A pdb=" N LEU E 234 " --> pdb=" O ARG E 231 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL E 236 " --> pdb=" O GLU E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 414 Processing helix chain 'E' and resid 415 through 420 Processing helix chain 'E' and resid 425 through 447 Processing helix chain 'E' and resid 450 through 467 removed outlier: 4.222A pdb=" N ILE E 455 " --> pdb=" O TRP E 451 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY E 456 " --> pdb=" O VAL E 452 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN E 467 " --> pdb=" O TRP E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 471 through 491 Processing helix chain 'F' and resid 26 through 39 Processing helix chain 'F' and resid 41 through 53 removed outlier: 4.103A pdb=" N LEU F 45 " --> pdb=" O GLY F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 75 Proline residue: F 72 - end of helix Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.786A pdb=" N ASN H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'L' and resid 85 through 89 removed outlier: 3.846A pdb=" N VAL L 89 " --> pdb=" O ALA L 86 " (cutoff:3.500A) Processing helix chain 'O' and resid 131 through 133 No H-bonds generated for 'chain 'O' and resid 131 through 133' Processing helix chain 'O' and resid 190 through 192 No H-bonds generated for 'chain 'O' and resid 190 through 192' Processing helix chain 'O' and resid 208 through 212 Processing helix chain 'O' and resid 231 through 235 removed outlier: 3.921A pdb=" N LEU O 234 " --> pdb=" O ARG O 231 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU O 235 " --> pdb=" O LYS O 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 231 through 235' Processing helix chain 'O' and resid 242 through 244 No H-bonds generated for 'chain 'O' and resid 242 through 244' Processing helix chain 'O' and resid 254 through 262 Processing helix chain 'O' and resid 394 through 414 Processing helix chain 'O' and resid 415 through 420 Processing helix chain 'O' and resid 425 through 447 removed outlier: 3.805A pdb=" N SER O 429 " --> pdb=" O GLY O 425 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU O 430 " --> pdb=" O VAL O 426 " (cutoff:3.500A) Processing helix chain 'O' and resid 450 through 468 Processing helix chain 'O' and resid 470 through 490 Processing helix chain 'P' and resid 26 through 39 removed outlier: 4.183A pdb=" N VAL P 32 " --> pdb=" O GLN P 28 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 53 removed outlier: 3.985A pdb=" N ILE P 44 " --> pdb=" O PRO P 40 " (cutoff:3.500A) Processing helix chain 'P' and resid 56 through 75 Proline residue: P 72 - end of helix Processing helix chain 'Q' and resid 100 through 104 Processing helix chain 'Q' and resid 208 through 214 Processing helix chain 'Q' and resid 231 through 235 removed outlier: 3.766A pdb=" N LEU Q 234 " --> pdb=" O ARG Q 231 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU Q 235 " --> pdb=" O LYS Q 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 231 through 235' Processing helix chain 'Q' and resid 254 through 262 Processing helix chain 'Q' and resid 394 through 414 Processing helix chain 'Q' and resid 415 through 420 removed outlier: 3.760A pdb=" N TRP Q 418 " --> pdb=" O ASP Q 415 " (cutoff:3.500A) Processing helix chain 'Q' and resid 425 through 447 removed outlier: 3.527A pdb=" N SER Q 429 " --> pdb=" O GLY Q 425 " (cutoff:3.500A) Processing helix chain 'Q' and resid 450 through 467 removed outlier: 3.742A pdb=" N ILE Q 455 " --> pdb=" O TRP Q 451 " (cutoff:3.500A) Processing helix chain 'Q' and resid 472 through 490 removed outlier: 4.140A pdb=" N ILE Q 478 " --> pdb=" O SER Q 474 " (cutoff:3.500A) Processing helix chain 'R' and resid 20 through 26 removed outlier: 4.637A pdb=" N TRP R 26 " --> pdb=" O ALA R 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 39 Processing helix chain 'R' and resid 40 through 54 removed outlier: 3.884A pdb=" N ILE R 44 " --> pdb=" O PRO R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 75 removed outlier: 3.578A pdb=" N LYS R 60 " --> pdb=" O SER R 56 " (cutoff:3.500A) Proline residue: R 72 - end of helix Processing helix chain 'S' and resid 82 through 86 Processing helix chain 'S' and resid 131 through 133 No H-bonds generated for 'chain 'S' and resid 131 through 133' Processing helix chain 'S' and resid 208 through 213 Processing helix chain 'S' and resid 231 through 236 removed outlier: 3.539A pdb=" N LEU S 234 " --> pdb=" O ARG S 231 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL S 236 " --> pdb=" O GLU S 233 " (cutoff:3.500A) Processing helix chain 'S' and resid 394 through 414 Processing helix chain 'S' and resid 415 through 420 Processing helix chain 'S' and resid 425 through 447 Processing helix chain 'S' and resid 450 through 467 removed outlier: 4.222A pdb=" N ILE S 455 " --> pdb=" O TRP S 451 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY S 456 " --> pdb=" O VAL S 452 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN S 467 " --> pdb=" O TRP S 463 " (cutoff:3.500A) Processing helix chain 'S' and resid 471 through 491 Processing helix chain 'T' and resid 26 through 39 Processing helix chain 'T' and resid 41 through 53 removed outlier: 4.103A pdb=" N LEU T 45 " --> pdb=" O GLY T 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 57 through 75 Proline residue: T 72 - end of helix Processing helix chain 'U' and resid 28 through 32 removed outlier: 3.786A pdb=" N ASN U 31 " --> pdb=" O THR U 28 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR U 32 " --> pdb=" O PHE U 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 28 through 32' Processing helix chain 'V' and resid 85 through 89 removed outlier: 3.846A pdb=" N VAL V 89 " --> pdb=" O ALA V 86 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 23 through 26 Processing sheet with id=2, first strand: chain 'A' and resid 31 through 35 removed outlier: 3.852A pdb=" N LEU A 41 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ALA A 35 " --> pdb=" O PRO A 39 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 31 through 35 removed outlier: 3.852A pdb=" N LEU A 41 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ALA A 35 " --> pdb=" O PRO A 39 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=5, first strand: chain 'A' and resid 63 through 72 removed outlier: 4.728A pdb=" N ILE A 68 " --> pdb=" O CYS A 116 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N CYS A 116 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N THR A 70 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL A 114 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER A 72 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N SER A 112 " --> pdb=" O SER A 72 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'A' and resid 63 through 72 removed outlier: 4.728A pdb=" N ILE A 68 " --> pdb=" O CYS A 116 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N CYS A 116 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N THR A 70 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL A 114 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER A 72 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N SER A 112 " --> pdb=" O SER A 72 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 171 through 173 removed outlier: 3.635A pdb=" N ALA A 171 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 179 " --> pdb=" O ALA A 171 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'A' and resid 194 through 195 Processing sheet with id=9, first strand: chain 'A' and resid 237 through 240 removed outlier: 3.705A pdb=" N GLU A 247 " --> pdb=" O LYS A 239 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'A' and resid 298 through 299 removed outlier: 6.706A pdb=" N ALA A 298 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N CYS A 331 " --> pdb=" O VAL A 356 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'A' and resid 304 through 306 Processing sheet with id=12, first strand: chain 'A' and resid 311 through 312 removed outlier: 4.204A pdb=" N SER A 311 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A 368 " --> pdb=" O ARG A 348 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG A 348 " --> pdb=" O GLU A 368 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'A' and resid 335 through 339 removed outlier: 3.657A pdb=" N TRP A 389 " --> pdb=" O SER A 374 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'C' and resid 21 through 26 Processing sheet with id=15, first strand: chain 'C' and resid 41 through 45 removed outlier: 3.501A pdb=" N ILE C 141 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C 158 " --> pdb=" O ILE C 141 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'C' and resid 49 through 50 Processing sheet with id=17, first strand: chain 'C' and resid 54 through 60 removed outlier: 5.495A pdb=" N THR C 55 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N VAL C 129 " --> pdb=" O THR C 55 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA C 203 " --> pdb=" O ILE C 268 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR C 266 " --> pdb=" O MET C 205 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'C' and resid 63 through 73 removed outlier: 5.493A pdb=" N ILE C 65 " --> pdb=" O GLN C 120 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N GLN C 120 " --> pdb=" O ILE C 65 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASN C 67 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS C 118 " --> pdb=" O ASN C 67 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER C 112 " --> pdb=" O ARG C 73 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR C 115 " --> pdb=" O LYS C 93 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS C 93 " --> pdb=" O THR C 115 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'C' and resid 169 through 172 removed outlier: 3.766A pdb=" N THR C 178 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS C 289 " --> pdb=" O THR C 178 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'C' and resid 237 through 240 Processing sheet with id=21, first strand: chain 'C' and resid 304 through 306 removed outlier: 3.503A pdb=" N VAL C 322 " --> pdb=" O VAL C 363 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'C' and resid 336 through 338 removed outlier: 3.531A pdb=" N TRP C 389 " --> pdb=" O SER C 374 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.833A pdb=" N ASP E 10 " --> pdb=" O CYS E 30 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU E 41 " --> pdb=" O THR E 33 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR E 138 " --> pdb=" O GLN E 46 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N THR E 48 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LYS E 136 " --> pdb=" O THR E 48 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'E' and resid 20 through 26 removed outlier: 3.947A pdb=" N ARG E 284 " --> pdb=" O GLU E 182 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY E 180 " --> pdb=" O LYS E 286 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU E 181 " --> pdb=" O THR E 169 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR E 169 " --> pdb=" O LEU E 181 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'E' and resid 54 through 55 removed outlier: 3.668A pdb=" N LEU E 197 " --> pdb=" O TRP E 204 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TRP E 204 " --> pdb=" O LEU E 197 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ALA E 203 " --> pdb=" O ILE E 268 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THR E 266 " --> pdb=" O MET E 205 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'E' and resid 59 through 72 removed outlier: 3.598A pdb=" N ILE E 61 " --> pdb=" O GLU E 123 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N GLU E 123 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLY E 63 " --> pdb=" O CYS E 121 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N CYS E 121 " --> pdb=" O GLY E 63 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ILE E 65 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE E 119 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ASN E 67 " --> pdb=" O ALA E 117 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ALA E 117 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N THR E 69 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR E 115 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASP E 71 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU E 113 " --> pdb=" O ASP E 71 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'E' and resid 59 through 72 removed outlier: 3.598A pdb=" N ILE E 61 " --> pdb=" O GLU E 123 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N GLU E 123 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLY E 63 " --> pdb=" O CYS E 121 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N CYS E 121 " --> pdb=" O GLY E 63 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ILE E 65 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE E 119 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ASN E 67 " --> pdb=" O ALA E 117 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ALA E 117 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N THR E 69 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR E 115 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASP E 71 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU E 113 " --> pdb=" O ASP E 71 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR E 95 " --> pdb=" O LEU E 113 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'E' and resid 172 through 173 removed outlier: 3.979A pdb=" N GLY E 177 " --> pdb=" O LEU E 173 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'E' and resid 239 through 241 removed outlier: 3.853A pdb=" N ALA E 241 " --> pdb=" O LYS E 245 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LYS E 245 " --> pdb=" O ALA E 241 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'E' and resid 304 through 306 removed outlier: 3.650A pdb=" N VAL E 305 " --> pdb=" O GLU E 323 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'E' and resid 336 through 338 Processing sheet with id=32, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.530A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.557A pdb=" N ALA H 97 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=35, first strand: chain 'L' and resid 11 through 13 removed outlier: 5.833A pdb=" N LEU L 11 " --> pdb=" O GLU L 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=35 Processing sheet with id=36, first strand: chain 'L' and resid 30 through 31 removed outlier: 3.693A pdb=" N LYS L 36 " --> pdb=" O TRP L 31 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'L' and resid 51 through 55 removed outlier: 6.745A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN L 44 " --> pdb=" O LEU L 91 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'O' and resid 23 through 26 Processing sheet with id=39, first strand: chain 'O' and resid 31 through 35 removed outlier: 3.852A pdb=" N LEU O 41 " --> pdb=" O THR O 33 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ALA O 35 " --> pdb=" O PRO O 39 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'O' and resid 31 through 35 removed outlier: 3.852A pdb=" N LEU O 41 " --> pdb=" O THR O 33 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ALA O 35 " --> pdb=" O PRO O 39 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'O' and resid 59 through 60 Processing sheet with id=42, first strand: chain 'O' and resid 63 through 72 removed outlier: 4.728A pdb=" N ILE O 68 " --> pdb=" O CYS O 116 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N CYS O 116 " --> pdb=" O ILE O 68 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N THR O 70 " --> pdb=" O VAL O 114 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL O 114 " --> pdb=" O THR O 70 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER O 72 " --> pdb=" O SER O 112 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N SER O 112 " --> pdb=" O SER O 72 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'O' and resid 63 through 72 removed outlier: 4.728A pdb=" N ILE O 68 " --> pdb=" O CYS O 116 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N CYS O 116 " --> pdb=" O ILE O 68 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N THR O 70 " --> pdb=" O VAL O 114 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL O 114 " --> pdb=" O THR O 70 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER O 72 " --> pdb=" O SER O 112 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N SER O 112 " --> pdb=" O SER O 72 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'O' and resid 171 through 173 removed outlier: 3.635A pdb=" N ALA O 171 " --> pdb=" O LEU O 179 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU O 179 " --> pdb=" O ALA O 171 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'O' and resid 194 through 195 Processing sheet with id=46, first strand: chain 'O' and resid 237 through 240 removed outlier: 3.705A pdb=" N GLU O 247 " --> pdb=" O LYS O 239 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'O' and resid 298 through 299 removed outlier: 6.706A pdb=" N ALA O 298 " --> pdb=" O LYS O 332 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N CYS O 331 " --> pdb=" O VAL O 356 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'O' and resid 304 through 306 Processing sheet with id=49, first strand: chain 'O' and resid 311 through 312 removed outlier: 4.204A pdb=" N SER O 311 " --> pdb=" O LEU O 319 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU O 368 " --> pdb=" O ARG O 348 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG O 348 " --> pdb=" O GLU O 368 " (cutoff:3.500A) Processing sheet with id=50, first strand: chain 'O' and resid 335 through 339 removed outlier: 3.657A pdb=" N TRP O 389 " --> pdb=" O SER O 374 " (cutoff:3.500A) Processing sheet with id=51, first strand: chain 'Q' and resid 21 through 26 Processing sheet with id=52, first strand: chain 'Q' and resid 41 through 45 removed outlier: 3.501A pdb=" N ILE Q 141 " --> pdb=" O VAL Q 158 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL Q 158 " --> pdb=" O ILE Q 141 " (cutoff:3.500A) Processing sheet with id=53, first strand: chain 'Q' and resid 49 through 50 Processing sheet with id=54, first strand: chain 'Q' and resid 54 through 60 removed outlier: 5.495A pdb=" N THR Q 55 " --> pdb=" O VAL Q 129 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N VAL Q 129 " --> pdb=" O THR Q 55 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA Q 203 " --> pdb=" O ILE Q 268 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR Q 266 " --> pdb=" O MET Q 205 " (cutoff:3.500A) Processing sheet with id=55, first strand: chain 'Q' and resid 63 through 73 removed outlier: 5.493A pdb=" N ILE Q 65 " --> pdb=" O GLN Q 120 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N GLN Q 120 " --> pdb=" O ILE Q 65 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASN Q 67 " --> pdb=" O LYS Q 118 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS Q 118 " --> pdb=" O ASN Q 67 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER Q 112 " --> pdb=" O ARG Q 73 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR Q 115 " --> pdb=" O LYS Q 93 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS Q 93 " --> pdb=" O THR Q 115 " (cutoff:3.500A) Processing sheet with id=56, first strand: chain 'Q' and resid 169 through 172 removed outlier: 3.766A pdb=" N THR Q 178 " --> pdb=" O LYS Q 289 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS Q 289 " --> pdb=" O THR Q 178 " (cutoff:3.500A) Processing sheet with id=57, first strand: chain 'Q' and resid 237 through 240 Processing sheet with id=58, first strand: chain 'Q' and resid 304 through 306 removed outlier: 3.503A pdb=" N VAL Q 322 " --> pdb=" O VAL Q 363 " (cutoff:3.500A) Processing sheet with id=59, first strand: chain 'Q' and resid 336 through 338 removed outlier: 3.531A pdb=" N TRP Q 389 " --> pdb=" O SER Q 374 " (cutoff:3.500A) Processing sheet with id=60, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.833A pdb=" N ASP S 10 " --> pdb=" O CYS S 30 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU S 41 " --> pdb=" O THR S 33 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR S 138 " --> pdb=" O GLN S 46 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N THR S 48 " --> pdb=" O LYS S 136 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LYS S 136 " --> pdb=" O THR S 48 " (cutoff:3.500A) Processing sheet with id=61, first strand: chain 'S' and resid 20 through 26 removed outlier: 3.947A pdb=" N ARG S 284 " --> pdb=" O GLU S 182 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY S 180 " --> pdb=" O LYS S 286 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU S 181 " --> pdb=" O THR S 169 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR S 169 " --> pdb=" O LEU S 181 " (cutoff:3.500A) Processing sheet with id=62, first strand: chain 'S' and resid 54 through 55 removed outlier: 3.668A pdb=" N LEU S 197 " --> pdb=" O TRP S 204 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TRP S 204 " --> pdb=" O LEU S 197 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ALA S 203 " --> pdb=" O ILE S 268 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THR S 266 " --> pdb=" O MET S 205 " (cutoff:3.500A) Processing sheet with id=63, first strand: chain 'S' and resid 59 through 72 removed outlier: 3.598A pdb=" N ILE S 61 " --> pdb=" O GLU S 123 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N GLU S 123 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLY S 63 " --> pdb=" O CYS S 121 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N CYS S 121 " --> pdb=" O GLY S 63 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ILE S 65 " --> pdb=" O PHE S 119 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE S 119 " --> pdb=" O ILE S 65 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ASN S 67 " --> pdb=" O ALA S 117 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ALA S 117 " --> pdb=" O ASN S 67 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N THR S 69 " --> pdb=" O THR S 115 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR S 115 " --> pdb=" O THR S 69 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASP S 71 " --> pdb=" O LEU S 113 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU S 113 " --> pdb=" O ASP S 71 " (cutoff:3.500A) Processing sheet with id=64, first strand: chain 'S' and resid 59 through 72 removed outlier: 3.598A pdb=" N ILE S 61 " --> pdb=" O GLU S 123 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N GLU S 123 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLY S 63 " --> pdb=" O CYS S 121 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N CYS S 121 " --> pdb=" O GLY S 63 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ILE S 65 " --> pdb=" O PHE S 119 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE S 119 " --> pdb=" O ILE S 65 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ASN S 67 " --> pdb=" O ALA S 117 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ALA S 117 " --> pdb=" O ASN S 67 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N THR S 69 " --> pdb=" O THR S 115 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR S 115 " --> pdb=" O THR S 69 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASP S 71 " --> pdb=" O LEU S 113 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU S 113 " --> pdb=" O ASP S 71 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR S 95 " --> pdb=" O LEU S 113 " (cutoff:3.500A) Processing sheet with id=65, first strand: chain 'S' and resid 172 through 173 removed outlier: 3.979A pdb=" N GLY S 177 " --> pdb=" O LEU S 173 " (cutoff:3.500A) Processing sheet with id=66, first strand: chain 'S' and resid 239 through 241 removed outlier: 3.853A pdb=" N ALA S 241 " --> pdb=" O LYS S 245 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LYS S 245 " --> pdb=" O ALA S 241 " (cutoff:3.500A) Processing sheet with id=67, first strand: chain 'S' and resid 304 through 306 removed outlier: 3.650A pdb=" N VAL S 305 " --> pdb=" O GLU S 323 " (cutoff:3.500A) Processing sheet with id=68, first strand: chain 'S' and resid 336 through 338 Processing sheet with id=69, first strand: chain 'U' and resid 3 through 7 removed outlier: 3.530A pdb=" N THR U 78 " --> pdb=" O ASP U 73 " (cutoff:3.500A) Processing sheet with id=70, first strand: chain 'U' and resid 11 through 12 removed outlier: 3.557A pdb=" N ALA U 97 " --> pdb=" O HIS U 35 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N TRP U 36 " --> pdb=" O VAL U 48 " (cutoff:3.500A) Processing sheet with id=71, first strand: chain 'V' and resid 5 through 6 Processing sheet with id=72, first strand: chain 'V' and resid 11 through 13 removed outlier: 5.833A pdb=" N LEU V 11 " --> pdb=" O GLU V 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=72 Processing sheet with id=73, first strand: chain 'V' and resid 30 through 31 removed outlier: 3.693A pdb=" N LYS V 36 " --> pdb=" O TRP V 31 " (cutoff:3.500A) Processing sheet with id=74, first strand: chain 'V' and resid 51 through 55 removed outlier: 6.745A pdb=" N TRP V 41 " --> pdb=" O LEU V 53 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR V 55 " --> pdb=" O LEU V 39 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU V 39 " --> pdb=" O TYR V 55 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN V 44 " --> pdb=" O LEU V 91 " (cutoff:3.500A) 1120 hydrogen bonds defined for protein. 3036 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: 10.84 Time building geometry restraints manager: 8.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9622 1.35 - 1.48: 7550 1.48 - 1.60: 13324 1.60 - 1.73: 0 1.73 - 1.85: 318 Bond restraints: 30814 Sorted by residual: bond pdb=" C1 BMA Y 5 " pdb=" O5 BMA Y 5 " ideal model delta sigma weight residual 1.410 1.451 -0.041 2.00e-02 2.50e+03 4.21e+00 bond pdb=" C1 BMA J 5 " pdb=" O5 BMA J 5 " ideal model delta sigma weight residual 1.410 1.451 -0.041 2.00e-02 2.50e+03 4.21e+00 bond pdb=" C1 BMA J 5 " pdb=" C2 BMA J 5 " ideal model delta sigma weight residual 1.519 1.559 -0.040 2.00e-02 2.50e+03 3.96e+00 bond pdb=" C1 BMA Y 5 " pdb=" C2 BMA Y 5 " ideal model delta sigma weight residual 1.519 1.559 -0.040 2.00e-02 2.50e+03 3.96e+00 bond pdb=" C5 MAN G 4 " pdb=" O5 MAN G 4 " ideal model delta sigma weight residual 1.418 1.455 -0.037 2.00e-02 2.50e+03 3.33e+00 ... (remaining 30809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 40442 1.94 - 3.87: 1138 3.87 - 5.81: 148 5.81 - 7.74: 40 7.74 - 9.68: 8 Bond angle restraints: 41776 Sorted by residual: angle pdb=" CA PRO C 330 " pdb=" C PRO C 330 " pdb=" N CYS C 331 " ideal model delta sigma weight residual 114.58 118.44 -3.86 1.16e+00 7.43e-01 1.10e+01 angle pdb=" CA PRO Q 330 " pdb=" C PRO Q 330 " pdb=" N CYS Q 331 " ideal model delta sigma weight residual 114.58 118.44 -3.86 1.16e+00 7.43e-01 1.10e+01 angle pdb=" C LEU Q 292 " pdb=" N LYS Q 293 " pdb=" CA LYS Q 293 " ideal model delta sigma weight residual 121.54 127.49 -5.95 1.91e+00 2.74e-01 9.70e+00 angle pdb=" C LEU C 292 " pdb=" N LYS C 293 " pdb=" CA LYS C 293 " ideal model delta sigma weight residual 121.54 127.49 -5.95 1.91e+00 2.74e-01 9.70e+00 angle pdb=" N GLY L 107 " pdb=" CA GLY L 107 " pdb=" C GLY L 107 " ideal model delta sigma weight residual 110.97 115.66 -4.69 1.56e+00 4.11e-01 9.04e+00 ... (remaining 41771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.79: 17696 23.79 - 47.57: 798 47.57 - 71.36: 136 71.36 - 95.15: 92 95.15 - 118.94: 56 Dihedral angle restraints: 18778 sinusoidal: 7840 harmonic: 10938 Sorted by residual: dihedral pdb=" CB CYS O 3 " pdb=" SG CYS O 3 " pdb=" SG CYS O 30 " pdb=" CB CYS O 30 " ideal model delta sinusoidal sigma weight residual -86.00 -165.42 79.42 1 1.00e+01 1.00e-02 7.84e+01 dihedral pdb=" CB CYS A 3 " pdb=" SG CYS A 3 " pdb=" SG CYS A 30 " pdb=" CB CYS A 30 " ideal model delta sinusoidal sigma weight residual -86.00 -165.42 79.42 1 1.00e+01 1.00e-02 7.84e+01 dihedral pdb=" CB CYS A 60 " pdb=" SG CYS A 60 " pdb=" SG CYS A 121 " pdb=" CB CYS A 121 " ideal model delta sinusoidal sigma weight residual -86.00 -27.97 -58.03 1 1.00e+01 1.00e-02 4.52e+01 ... (remaining 18775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 4056 0.056 - 0.111: 742 0.111 - 0.167: 112 0.167 - 0.223: 6 0.223 - 0.278: 12 Chirality restraints: 4928 Sorted by residual: chirality pdb=" C5 BMA J 5 " pdb=" C4 BMA J 5 " pdb=" C6 BMA J 5 " pdb=" O5 BMA J 5 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C5 BMA Y 5 " pdb=" C4 BMA Y 5 " pdb=" C6 BMA Y 5 " pdb=" O5 BMA Y 5 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C5 BMA W 5 " pdb=" C4 BMA W 5 " pdb=" C6 BMA W 5 " pdb=" O5 BMA W 5 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 4925 not shown) Planarity restraints: 5204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 57 " -0.181 9.50e-02 1.11e+02 8.13e-02 4.15e+00 pdb=" NE ARG A 57 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 57 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 57 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 57 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG O 57 " -0.181 9.50e-02 1.11e+02 8.13e-02 4.15e+00 pdb=" NE ARG O 57 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG O 57 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG O 57 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG O 57 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR E 163 " 0.032 5.00e-02 4.00e+02 4.81e-02 3.71e+00 pdb=" N PRO E 164 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO E 164 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 164 " 0.027 5.00e-02 4.00e+02 ... (remaining 5201 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 659 2.68 - 3.24: 29533 3.24 - 3.79: 44634 3.79 - 4.35: 57553 4.35 - 4.90: 97718 Nonbonded interactions: 230097 Sorted by model distance: nonbonded pdb=" OG1 THR C 48 " pdb=" O ILE C 276 " model vdw 2.130 3.040 nonbonded pdb=" OG1 THR Q 48 " pdb=" O ILE Q 276 " model vdw 2.130 3.040 nonbonded pdb=" OG SER O 167 " pdb=" O CYS O 183 " model vdw 2.131 3.040 nonbonded pdb=" OG SER A 167 " pdb=" O CYS A 183 " model vdw 2.131 3.040 nonbonded pdb=" OD1 ASP H 62 " pdb=" O3 MAN J 4 " model vdw 2.146 3.040 ... (remaining 230092 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: 0.01 Found NCS groups: ncs_group { reference = chain '0' selection = chain 'K' selection = chain 'M' selection = chain 'Z' } ncs_group { reference = chain '1' selection = chain 'I' selection = chain 'N' selection = chain 'X' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'O' selection = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'P' selection = chain 'R' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'W' selection = chain 'Y' } ncs_group { reference = chain 'H' selection = chain 'U' } ncs_group { reference = chain 'L' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.240 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: 0.030 Extract box with map and model: 1.270 Check model and map are aligned: 0.230 Set scattering table: 0.300 Process input model: 65.050 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 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 : 0.004 0.044 30884 Z= 0.202 Angle : 0.766 9.679 41956 Z= 0.425 Chirality : 0.046 0.278 4928 Planarity : 0.004 0.081 5192 Dihedral : 16.432 118.936 11704 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.68 (0.13), residues: 3846 helix: 1.02 (0.18), residues: 850 sheet: -1.82 (0.16), residues: 998 loop : -1.69 (0.13), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 20 HIS 0.005 0.001 HIS E 259 PHE 0.020 0.001 PHE P 42 TYR 0.011 0.001 TYR F 52 ARG 0.006 0.000 ARG A 57 Details of bonding type rmsd link_NAG-ASN : bond 0.00499 ( 12) link_NAG-ASN : angle 1.95438 ( 36) link_BETA1-4 : bond 0.00362 ( 20) link_BETA1-4 : angle 1.94959 ( 60) link_ALPHA1-3 : bond 0.00326 ( 4) link_ALPHA1-3 : angle 1.78299 ( 12) hydrogen bonds : bond 0.20581 ( 1094) hydrogen bonds : angle 8.16193 ( 3036) link_BETA1-6 : bond 0.00573 ( 4) link_BETA1-6 : angle 1.24001 ( 12) SS BOND : bond 0.00720 ( 30) SS BOND : angle 1.86968 ( 60) covalent geometry : bond 0.00410 (30814) covalent geometry : angle 0.75760 (41776) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1306 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1306 time to evaluate : 3.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO B 72 " (corrupted residue). Skipping it. Corrupt residue: chain: B residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO P 72 " (corrupted residue). Skipping it. Corrupt residue: chain: P residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.7788 (t) cc_final: 0.7511 (p) REVERT: A 38 LYS cc_start: 0.9235 (mmtt) cc_final: 0.8959 (mmtm) REVERT: A 61 ILE cc_start: 0.8089 (pt) cc_final: 0.7682 (pt) REVERT: A 82 LEU cc_start: 0.8554 (mt) cc_final: 0.8080 (mm) REVERT: A 98 ASP cc_start: 0.8157 (p0) cc_final: 0.7808 (p0) REVERT: A 201 ASN cc_start: 0.6616 (m-40) cc_final: 0.6263 (t0) REVERT: A 234 LEU cc_start: 0.8560 (mt) cc_final: 0.8322 (mp) REVERT: A 287 MET cc_start: 0.8176 (mtp) cc_final: 0.7941 (mtp) REVERT: A 400 PHE cc_start: 0.7321 (m-10) cc_final: 0.6942 (m-10) REVERT: A 453 MET cc_start: 0.7699 (tpt) cc_final: 0.7333 (tpp) REVERT: B 26 TRP cc_start: 0.6803 (m100) cc_final: 0.6586 (m-90) REVERT: B 45 LEU cc_start: 0.8971 (tp) cc_final: 0.8386 (tt) REVERT: B 74 MET cc_start: 0.5698 (mmp) cc_final: 0.4684 (mmp) REVERT: C 15 LEU cc_start: 0.7984 (pp) cc_final: 0.7648 (pt) REVERT: C 26 GLU cc_start: 0.7794 (tt0) cc_final: 0.7515 (tt0) REVERT: C 131 GLN cc_start: 0.7757 (mt0) cc_final: 0.7379 (mt0) REVERT: C 400 PHE cc_start: 0.8133 (m-10) cc_final: 0.7499 (t80) REVERT: C 443 THR cc_start: 0.8300 (m) cc_final: 0.7968 (p) REVERT: D 14 THR cc_start: 0.8262 (p) cc_final: 0.7805 (m) REVERT: D 65 ILE cc_start: 0.9369 (mm) cc_final: 0.9150 (mm) REVERT: E 42 ASP cc_start: 0.8353 (m-30) cc_final: 0.8085 (m-30) REVERT: E 184 SER cc_start: 0.8968 (t) cc_final: 0.8726 (m) REVERT: E 199 MET cc_start: 0.8301 (ttp) cc_final: 0.8077 (ttm) REVERT: E 251 LEU cc_start: 0.8428 (tt) cc_final: 0.8041 (tt) REVERT: E 293 LYS cc_start: 0.8495 (ttpp) cc_final: 0.8230 (tttm) REVERT: E 409 ARG cc_start: 0.8720 (ttm110) cc_final: 0.8517 (ttm-80) REVERT: E 436 GLN cc_start: 0.7979 (mt0) cc_final: 0.7589 (mt0) REVERT: E 442 TYR cc_start: 0.8829 (t80) cc_final: 0.8305 (t80) REVERT: E 447 SER cc_start: 0.8992 (t) cc_final: 0.8731 (t) REVERT: E 484 THR cc_start: 0.8923 (m) cc_final: 0.8553 (p) REVERT: F 12 LEU cc_start: 0.8017 (pp) cc_final: 0.7760 (pp) REVERT: F 16 THR cc_start: 0.8846 (t) cc_final: 0.8586 (m) REVERT: F 32 VAL cc_start: 0.9054 (t) cc_final: 0.8789 (t) REVERT: H 57 ASP cc_start: 0.7357 (t0) cc_final: 0.7005 (t0) REVERT: H 94 TYR cc_start: 0.8314 (m-10) cc_final: 0.7633 (m-80) REVERT: H 110 ASP cc_start: 0.7907 (m-30) cc_final: 0.7675 (m-30) REVERT: L 2 ILE cc_start: 0.8898 (mt) cc_final: 0.8530 (mt) REVERT: L 55 TYR cc_start: 0.8512 (p90) cc_final: 0.8149 (p90) REVERT: O 6 VAL cc_start: 0.7813 (t) cc_final: 0.7543 (p) REVERT: O 38 LYS cc_start: 0.9235 (mmtt) cc_final: 0.8963 (mmtm) REVERT: O 61 ILE cc_start: 0.8075 (pt) cc_final: 0.7676 (pt) REVERT: O 82 LEU cc_start: 0.8520 (mt) cc_final: 0.8052 (mm) REVERT: O 98 ASP cc_start: 0.8157 (p0) cc_final: 0.7806 (p0) REVERT: O 201 ASN cc_start: 0.6575 (m-40) cc_final: 0.6231 (t0) REVERT: O 287 MET cc_start: 0.8173 (mtp) cc_final: 0.7962 (mtp) REVERT: O 400 PHE cc_start: 0.7312 (m-10) cc_final: 0.6912 (m-10) REVERT: O 453 MET cc_start: 0.7706 (tpt) cc_final: 0.7309 (tpp) REVERT: P 26 TRP cc_start: 0.6784 (m100) cc_final: 0.6577 (m-90) REVERT: P 45 LEU cc_start: 0.8975 (tp) cc_final: 0.8403 (tt) REVERT: P 74 MET cc_start: 0.5723 (mmp) cc_final: 0.4290 (mmp) REVERT: Q 15 LEU cc_start: 0.7990 (pp) cc_final: 0.7661 (pt) REVERT: Q 26 GLU cc_start: 0.7782 (tt0) cc_final: 0.7506 (tt0) REVERT: Q 131 GLN cc_start: 0.7758 (mt0) cc_final: 0.7354 (mt0) REVERT: Q 182 GLU cc_start: 0.6552 (tt0) cc_final: 0.6338 (tp30) REVERT: Q 400 PHE cc_start: 0.8139 (m-10) cc_final: 0.7500 (t80) REVERT: Q 443 THR cc_start: 0.8308 (m) cc_final: 0.7970 (p) REVERT: R 14 THR cc_start: 0.8272 (p) cc_final: 0.7817 (m) REVERT: R 35 TRP cc_start: 0.9005 (t60) cc_final: 0.8797 (t60) REVERT: R 65 ILE cc_start: 0.9372 (mm) cc_final: 0.9159 (mm) REVERT: S 36 LYS cc_start: 0.8432 (tptt) cc_final: 0.8155 (tppt) REVERT: S 42 ASP cc_start: 0.8344 (m-30) cc_final: 0.8077 (m-30) REVERT: S 184 SER cc_start: 0.8967 (t) cc_final: 0.8730 (m) REVERT: S 251 LEU cc_start: 0.8427 (tt) cc_final: 0.8034 (tt) REVERT: S 293 LYS cc_start: 0.8572 (ttpp) cc_final: 0.8353 (tttt) REVERT: S 436 GLN cc_start: 0.7975 (mt0) cc_final: 0.7593 (mt0) REVERT: S 442 TYR cc_start: 0.8838 (t80) cc_final: 0.8311 (t80) REVERT: S 447 SER cc_start: 0.8994 (t) cc_final: 0.8733 (t) REVERT: S 484 THR cc_start: 0.8927 (m) cc_final: 0.8565 (p) REVERT: T 12 LEU cc_start: 0.8004 (pp) cc_final: 0.7745 (pp) REVERT: T 16 THR cc_start: 0.8819 (t) cc_final: 0.8565 (m) REVERT: T 32 VAL cc_start: 0.9057 (t) cc_final: 0.8798 (t) REVERT: U 57 ASP cc_start: 0.7355 (t0) cc_final: 0.7047 (t0) REVERT: U 94 TYR cc_start: 0.8319 (m-10) cc_final: 0.7642 (m-80) REVERT: U 110 ASP cc_start: 0.7897 (m-30) cc_final: 0.7667 (m-30) REVERT: V 2 ILE cc_start: 0.8899 (mt) cc_final: 0.8532 (mt) REVERT: V 55 TYR cc_start: 0.8515 (p90) cc_final: 0.8151 (p90) outliers start: 0 outliers final: 0 residues processed: 1306 average time/residue: 0.4083 time to fit residues: 837.8393 Evaluate side-chains 874 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 874 time to evaluate : 3.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 322 optimal weight: 9.9990 chunk 289 optimal weight: 20.0000 chunk 160 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 195 optimal weight: 4.9990 chunk 154 optimal weight: 0.4980 chunk 299 optimal weight: 10.0000 chunk 115 optimal weight: 7.9990 chunk 182 optimal weight: 20.0000 chunk 222 optimal weight: 5.9990 chunk 346 optimal weight: 10.0000 overall best weight: 5.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 ASN ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN C 388 ASN ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 HIS E 314 GLN E 428 ASN ** F 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 GLN L 99 HIS ** O 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 302 ASN ** Q 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 246 GLN Q 388 ASN ** R 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 242 HIS S 314 GLN S 428 ASN ** T 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 100 GLN ** V 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 44 GLN V 85 GLN V 99 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.121389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.104808 restraints weight = 52608.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.107694 restraints weight = 25817.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.109583 restraints weight = 15793.952| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 30884 Z= 0.197 Angle : 0.745 9.723 41956 Z= 0.376 Chirality : 0.046 0.247 4928 Planarity : 0.005 0.051 5192 Dihedral : 13.597 112.433 4876 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.94 % Allowed : 13.50 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.72 (0.13), residues: 3846 helix: 0.93 (0.18), residues: 882 sheet: -1.79 (0.15), residues: 1072 loop : -1.72 (0.13), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 20 HIS 0.007 0.001 HIS O 144 PHE 0.024 0.002 PHE P 42 TYR 0.019 0.002 TYR U 111 ARG 0.006 0.001 ARG A 348 Details of bonding type rmsd link_NAG-ASN : bond 0.00400 ( 12) link_NAG-ASN : angle 1.91405 ( 36) link_BETA1-4 : bond 0.00391 ( 20) link_BETA1-4 : angle 2.65050 ( 60) link_ALPHA1-3 : bond 0.00869 ( 4) link_ALPHA1-3 : angle 3.19311 ( 12) hydrogen bonds : bond 0.04887 ( 1094) hydrogen bonds : angle 6.18190 ( 3036) link_BETA1-6 : bond 0.01703 ( 4) link_BETA1-6 : angle 3.37112 ( 12) SS BOND : bond 0.00639 ( 30) SS BOND : angle 2.16458 ( 60) covalent geometry : bond 0.00458 (30814) covalent geometry : angle 0.72929 (41776) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1017 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 890 time to evaluate : 3.198 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO B 72 " (corrupted residue). Skipping it. Corrupt residue: chain: B residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO P 72 " (corrupted residue). Skipping it. Corrupt residue: chain: P residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.7970 (t) cc_final: 0.7667 (p) REVERT: A 38 LYS cc_start: 0.9313 (mmtt) cc_final: 0.9096 (mmtm) REVERT: A 82 LEU cc_start: 0.8790 (mt) cc_final: 0.8539 (mm) REVERT: A 98 ASP cc_start: 0.8173 (p0) cc_final: 0.7699 (p0) REVERT: A 181 LEU cc_start: 0.8642 (tp) cc_final: 0.8088 (tp) REVERT: A 287 MET cc_start: 0.8580 (mtp) cc_final: 0.8084 (mtp) REVERT: A 299 MET cc_start: 0.7281 (mmm) cc_final: 0.5710 (mtm) REVERT: A 433 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8298 (ptt) REVERT: B 26 TRP cc_start: 0.6754 (m100) cc_final: 0.6253 (m-90) REVERT: B 28 GLN cc_start: 0.8096 (tp-100) cc_final: 0.6757 (tp-100) REVERT: B 45 LEU cc_start: 0.8890 (tp) cc_final: 0.8257 (tt) REVERT: B 61 VAL cc_start: 0.9285 (t) cc_final: 0.9018 (p) REVERT: B 68 MET cc_start: 0.6936 (ttp) cc_final: 0.6696 (tpt) REVERT: B 74 MET cc_start: 0.4966 (mmp) cc_final: 0.4555 (mmp) REVERT: C 182 GLU cc_start: 0.7076 (tp30) cc_final: 0.6710 (tp30) REVERT: C 199 MET cc_start: 0.8274 (ptm) cc_final: 0.8032 (ptm) REVERT: C 380 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7757 (tt) REVERT: C 400 PHE cc_start: 0.7822 (m-10) cc_final: 0.7337 (t80) REVERT: C 443 THR cc_start: 0.8515 (m) cc_final: 0.8076 (p) REVERT: C 480 ILE cc_start: 0.7936 (mm) cc_final: 0.7733 (mm) REVERT: D 12 LEU cc_start: 0.8519 (pp) cc_final: 0.8285 (pp) REVERT: D 14 THR cc_start: 0.8384 (p) cc_final: 0.7918 (m) REVERT: D 74 MET cc_start: 0.8575 (tpp) cc_final: 0.7848 (mmm) REVERT: E 8 ASN cc_start: 0.7752 (t0) cc_final: 0.7440 (t0) REVERT: E 108 PHE cc_start: 0.8649 (m-80) cc_final: 0.8194 (m-80) REVERT: E 199 MET cc_start: 0.8420 (ttp) cc_final: 0.8161 (ttm) REVERT: E 251 LEU cc_start: 0.8572 (tt) cc_final: 0.8007 (tt) REVERT: E 295 MET cc_start: 0.7695 (tpt) cc_final: 0.6179 (tmm) REVERT: E 335 PHE cc_start: 0.8205 (OUTLIER) cc_final: 0.6959 (m-80) REVERT: E 484 THR cc_start: 0.8888 (m) cc_final: 0.8514 (p) REVERT: F 13 ASP cc_start: 0.7172 (p0) cc_final: 0.6850 (m-30) REVERT: F 16 THR cc_start: 0.9034 (t) cc_final: 0.8785 (m) REVERT: F 32 VAL cc_start: 0.8878 (t) cc_final: 0.8655 (t) REVERT: H 37 LEU cc_start: 0.8916 (mt) cc_final: 0.8590 (mt) REVERT: H 47 TRP cc_start: 0.8140 (t60) cc_final: 0.7710 (t60) REVERT: H 54 ASP cc_start: 0.6075 (p0) cc_final: 0.5522 (p0) REVERT: H 57 ASP cc_start: 0.7628 (t0) cc_final: 0.7267 (m-30) REVERT: H 73 ASP cc_start: 0.7864 (p0) cc_final: 0.7659 (p0) REVERT: H 117 LEU cc_start: 0.7788 (tt) cc_final: 0.7382 (tp) REVERT: L 2 ILE cc_start: 0.8679 (mt) cc_final: 0.8455 (mt) REVERT: L 45 LYS cc_start: 0.8803 (mttt) cc_final: 0.8603 (mttp) REVERT: L 48 GLN cc_start: 0.6745 (mp10) cc_final: 0.6133 (mp10) REVERT: L 55 TYR cc_start: 0.8689 (p90) cc_final: 0.8417 (p90) REVERT: L 85 GLN cc_start: 0.7566 (mm-40) cc_final: 0.7363 (mm-40) REVERT: L 104 PHE cc_start: 0.8558 (m-80) cc_final: 0.8291 (m-80) REVERT: L 109 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7836 (mtp85) REVERT: O 6 VAL cc_start: 0.7978 (t) cc_final: 0.7678 (p) REVERT: O 38 LYS cc_start: 0.9309 (mmtt) cc_final: 0.9098 (mmtm) REVERT: O 82 LEU cc_start: 0.8770 (mt) cc_final: 0.8488 (mm) REVERT: O 98 ASP cc_start: 0.8178 (p0) cc_final: 0.7706 (p0) REVERT: O 161 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7627 (mt-10) REVERT: O 181 LEU cc_start: 0.8666 (tp) cc_final: 0.8099 (tp) REVERT: O 201 ASN cc_start: 0.7127 (m-40) cc_final: 0.6427 (t0) REVERT: O 287 MET cc_start: 0.8594 (mtp) cc_final: 0.8097 (mtp) REVERT: O 299 MET cc_start: 0.7269 (mmm) cc_final: 0.5669 (mtm) REVERT: O 433 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8278 (ptt) REVERT: P 26 TRP cc_start: 0.6735 (m100) cc_final: 0.6258 (m-90) REVERT: P 28 GLN cc_start: 0.8101 (tp-100) cc_final: 0.6757 (tp-100) REVERT: P 61 VAL cc_start: 0.9287 (t) cc_final: 0.9036 (p) REVERT: P 68 MET cc_start: 0.6944 (ttp) cc_final: 0.6688 (tpt) REVERT: P 74 MET cc_start: 0.4998 (mmp) cc_final: 0.4564 (mmp) REVERT: Q 182 GLU cc_start: 0.6759 (tt0) cc_final: 0.6307 (tp30) REVERT: Q 199 MET cc_start: 0.8285 (ptm) cc_final: 0.8031 (ptm) REVERT: Q 220 SER cc_start: 0.8053 (p) cc_final: 0.7840 (p) REVERT: Q 380 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7754 (tt) REVERT: Q 400 PHE cc_start: 0.7830 (m-10) cc_final: 0.7347 (t80) REVERT: Q 443 THR cc_start: 0.8529 (m) cc_final: 0.8061 (p) REVERT: R 15 ARG cc_start: 0.7725 (tpt170) cc_final: 0.7454 (ttm170) REVERT: R 35 TRP cc_start: 0.9042 (t60) cc_final: 0.8776 (t60) REVERT: R 74 MET cc_start: 0.8585 (tpp) cc_final: 0.7819 (mmm) REVERT: S 8 ASN cc_start: 0.7818 (t0) cc_final: 0.7527 (t0) REVERT: S 108 PHE cc_start: 0.8638 (m-80) cc_final: 0.8239 (m-80) REVERT: S 251 LEU cc_start: 0.8566 (tt) cc_final: 0.8008 (tt) REVERT: S 295 MET cc_start: 0.7749 (tpt) cc_final: 0.6188 (tmm) REVERT: S 335 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.6957 (m-80) REVERT: S 484 THR cc_start: 0.8895 (m) cc_final: 0.8520 (p) REVERT: T 13 ASP cc_start: 0.7159 (p0) cc_final: 0.6830 (m-30) REVERT: T 16 THR cc_start: 0.8994 (t) cc_final: 0.8779 (m) REVERT: T 32 VAL cc_start: 0.8890 (t) cc_final: 0.8660 (t) REVERT: U 37 LEU cc_start: 0.8918 (mt) cc_final: 0.8592 (mt) REVERT: U 47 TRP cc_start: 0.8138 (t60) cc_final: 0.7710 (t60) REVERT: U 54 ASP cc_start: 0.6086 (p0) cc_final: 0.5524 (p0) REVERT: U 57 ASP cc_start: 0.7664 (t0) cc_final: 0.7301 (m-30) REVERT: U 73 ASP cc_start: 0.7884 (p0) cc_final: 0.7665 (p0) REVERT: U 117 LEU cc_start: 0.7784 (tt) cc_final: 0.7377 (tp) REVERT: V 2 ILE cc_start: 0.8683 (mt) cc_final: 0.8459 (mt) REVERT: V 45 LYS cc_start: 0.8818 (mttt) cc_final: 0.8607 (mttp) REVERT: V 48 GLN cc_start: 0.6759 (mp10) cc_final: 0.6134 (mp10) REVERT: V 55 TYR cc_start: 0.8690 (p90) cc_final: 0.8408 (p90) REVERT: V 104 PHE cc_start: 0.8555 (m-80) cc_final: 0.8280 (m-80) REVERT: V 109 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7849 (mtp85) outliers start: 127 outliers final: 82 residues processed: 963 average time/residue: 0.3724 time to fit residues: 587.9521 Evaluate side-chains 892 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 802 time to evaluate : 3.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 335 PHE Chi-restraints excluded: chain E residue 451 TRP Chi-restraints excluded: chain E residue 455 ILE Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain L residue 109 ARG Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 198 THR Chi-restraints excluded: chain O residue 237 THR Chi-restraints excluded: chain O residue 253 SER Chi-restraints excluded: chain O residue 275 SER Chi-restraints excluded: chain O residue 365 ILE Chi-restraints excluded: chain O residue 413 LEU Chi-restraints excluded: chain O residue 423 VAL Chi-restraints excluded: chain O residue 433 MET Chi-restraints excluded: chain O residue 452 VAL Chi-restraints excluded: chain O residue 455 ILE Chi-restraints excluded: chain O residue 459 VAL Chi-restraints excluded: chain O residue 461 LEU Chi-restraints excluded: chain O residue 466 LEU Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 73 SER Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain Q residue 113 LEU Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 313 THR Chi-restraints excluded: chain Q residue 357 THR Chi-restraints excluded: chain Q residue 380 ILE Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 41 LEU Chi-restraints excluded: chain S residue 64 LYS Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 179 LEU Chi-restraints excluded: chain S residue 181 LEU Chi-restraints excluded: chain S residue 187 THR Chi-restraints excluded: chain S residue 242 HIS Chi-restraints excluded: chain S residue 258 MET Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 318 ILE Chi-restraints excluded: chain S residue 335 PHE Chi-restraints excluded: chain S residue 451 TRP Chi-restraints excluded: chain S residue 455 ILE Chi-restraints excluded: chain S residue 485 LEU Chi-restraints excluded: chain T residue 8 VAL Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain U residue 53 SER Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain V residue 109 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 68 optimal weight: 8.9990 chunk 197 optimal weight: 8.9990 chunk 282 optimal weight: 0.8980 chunk 323 optimal weight: 20.0000 chunk 303 optimal weight: 0.0980 chunk 78 optimal weight: 0.1980 chunk 195 optimal weight: 1.9990 chunk 196 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 144 HIS ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 HIS E 165 GLN E 428 ASN ** F 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN L 27 GLN ** O 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 144 HIS ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 144 HIS S 165 GLN S 428 ASN ** T 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 39 HIS U 100 GLN ** V 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 85 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.124756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.107985 restraints weight = 51966.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.110991 restraints weight = 25390.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.112934 restraints weight = 15382.356| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 30884 Z= 0.131 Angle : 0.684 10.548 41956 Z= 0.339 Chirality : 0.044 0.210 4928 Planarity : 0.004 0.045 5192 Dihedral : 11.371 105.166 4876 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.79 % Allowed : 16.57 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.57 (0.13), residues: 3846 helix: 1.14 (0.18), residues: 884 sheet: -1.61 (0.15), residues: 1062 loop : -1.74 (0.13), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 20 HIS 0.007 0.001 HIS E 242 PHE 0.023 0.001 PHE D 64 TYR 0.021 0.001 TYR H 111 ARG 0.006 0.001 ARG A 348 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 12) link_NAG-ASN : angle 1.72739 ( 36) link_BETA1-4 : bond 0.00331 ( 20) link_BETA1-4 : angle 2.49316 ( 60) link_ALPHA1-3 : bond 0.00903 ( 4) link_ALPHA1-3 : angle 2.93703 ( 12) hydrogen bonds : bond 0.04156 ( 1094) hydrogen bonds : angle 5.68457 ( 3036) link_BETA1-6 : bond 0.01474 ( 4) link_BETA1-6 : angle 2.84118 ( 12) SS BOND : bond 0.00508 ( 30) SS BOND : angle 2.09160 ( 60) covalent geometry : bond 0.00283 (30814) covalent geometry : angle 0.66888 (41776) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1021 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 899 time to evaluate : 3.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO B 72 " (corrupted residue). Skipping it. Corrupt residue: chain: B residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO P 72 " (corrupted residue). Skipping it. Corrupt residue: chain: P residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8007 (t) cc_final: 0.7640 (p) REVERT: A 98 ASP cc_start: 0.8133 (p0) cc_final: 0.7619 (p0) REVERT: A 181 LEU cc_start: 0.8163 (tp) cc_final: 0.7524 (tp) REVERT: A 205 MET cc_start: 0.7676 (tpp) cc_final: 0.7464 (tpt) REVERT: A 287 MET cc_start: 0.8574 (mtp) cc_final: 0.8081 (mtp) REVERT: A 299 MET cc_start: 0.7054 (mmm) cc_final: 0.6282 (mmt) REVERT: A 433 MET cc_start: 0.8578 (ptp) cc_final: 0.8345 (ptt) REVERT: B 26 TRP cc_start: 0.6707 (m100) cc_final: 0.6205 (m-90) REVERT: B 28 GLN cc_start: 0.7958 (tp-100) cc_final: 0.6815 (tp40) REVERT: B 61 VAL cc_start: 0.9240 (t) cc_final: 0.9029 (p) REVERT: B 74 MET cc_start: 0.4942 (mmp) cc_final: 0.4704 (mmp) REVERT: C 122 LEU cc_start: 0.8935 (mt) cc_final: 0.8604 (mt) REVERT: C 182 GLU cc_start: 0.7258 (tp30) cc_final: 0.6968 (tp30) REVERT: C 199 MET cc_start: 0.8301 (ptm) cc_final: 0.8052 (ptm) REVERT: C 258 MET cc_start: 0.9078 (tpp) cc_final: 0.8683 (tpp) REVERT: C 358 LYS cc_start: 0.7353 (OUTLIER) cc_final: 0.6819 (tppt) REVERT: C 360 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6929 (mm-30) REVERT: C 371 PHE cc_start: 0.6029 (p90) cc_final: 0.5514 (p90) REVERT: C 380 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7665 (tt) REVERT: C 400 PHE cc_start: 0.7663 (m-10) cc_final: 0.7235 (t80) REVERT: C 401 GLU cc_start: 0.8348 (tp30) cc_final: 0.7850 (tp30) REVERT: C 432 LYS cc_start: 0.8328 (tttp) cc_final: 0.8086 (ttpp) REVERT: C 436 GLN cc_start: 0.8757 (tm-30) cc_final: 0.8172 (tt0) REVERT: C 462 THR cc_start: 0.9067 (m) cc_final: 0.8863 (p) REVERT: D 12 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8392 (pp) REVERT: D 14 THR cc_start: 0.8221 (p) cc_final: 0.7774 (m) REVERT: D 18 THR cc_start: 0.8615 (p) cc_final: 0.7752 (t) REVERT: D 42 PHE cc_start: 0.8758 (t80) cc_final: 0.8186 (t80) REVERT: D 74 MET cc_start: 0.8612 (tpp) cc_final: 0.8196 (mmm) REVERT: E 8 ASN cc_start: 0.7791 (t0) cc_final: 0.7390 (t0) REVERT: E 20 TRP cc_start: 0.7523 (p90) cc_final: 0.6001 (p90) REVERT: E 108 PHE cc_start: 0.8550 (m-80) cc_final: 0.8136 (m-80) REVERT: E 126 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7058 (tp30) REVERT: E 250 VAL cc_start: 0.8730 (t) cc_final: 0.8454 (m) REVERT: E 295 MET cc_start: 0.7762 (tpt) cc_final: 0.5872 (tmm) REVERT: E 335 PHE cc_start: 0.8119 (OUTLIER) cc_final: 0.6968 (m-80) REVERT: E 442 TYR cc_start: 0.8801 (t80) cc_final: 0.8223 (t80) REVERT: E 484 THR cc_start: 0.8747 (m) cc_final: 0.8271 (p) REVERT: F 13 ASP cc_start: 0.7795 (p0) cc_final: 0.7160 (m-30) REVERT: F 16 THR cc_start: 0.8937 (t) cc_final: 0.8717 (m) REVERT: F 26 TRP cc_start: 0.8094 (m100) cc_final: 0.7817 (m100) REVERT: F 32 VAL cc_start: 0.8868 (t) cc_final: 0.8610 (t) REVERT: H 47 TRP cc_start: 0.7987 (t60) cc_final: 0.7777 (t60) REVERT: H 54 ASP cc_start: 0.6031 (p0) cc_final: 0.5229 (p0) REVERT: H 57 ASP cc_start: 0.7302 (t0) cc_final: 0.7053 (m-30) REVERT: H 114 GLN cc_start: 0.7938 (tp40) cc_final: 0.7467 (tp-100) REVERT: L 2 ILE cc_start: 0.8672 (mt) cc_final: 0.8439 (mt) REVERT: L 48 GLN cc_start: 0.6780 (mp10) cc_final: 0.5949 (mp10) REVERT: L 80 LYS cc_start: 0.7747 (mtmt) cc_final: 0.7531 (mtmt) REVERT: L 85 GLN cc_start: 0.7600 (mm-40) cc_final: 0.7322 (mm-40) REVERT: L 88 ASP cc_start: 0.6145 (m-30) cc_final: 0.5744 (m-30) REVERT: L 104 PHE cc_start: 0.8522 (m-80) cc_final: 0.8268 (m-80) REVERT: L 109 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7871 (mtp85) REVERT: O 6 VAL cc_start: 0.7996 (t) cc_final: 0.7651 (p) REVERT: O 42 ASP cc_start: 0.8434 (m-30) cc_final: 0.8044 (m-30) REVERT: O 98 ASP cc_start: 0.8141 (p0) cc_final: 0.7613 (p0) REVERT: O 181 LEU cc_start: 0.8150 (tp) cc_final: 0.7570 (tp) REVERT: O 190 ASP cc_start: 0.8086 (t0) cc_final: 0.7822 (t0) REVERT: O 201 ASN cc_start: 0.7153 (m-40) cc_final: 0.6217 (t0) REVERT: O 287 MET cc_start: 0.8589 (mtp) cc_final: 0.8083 (mtp) REVERT: O 299 MET cc_start: 0.7079 (mmm) cc_final: 0.6279 (mmt) REVERT: O 433 MET cc_start: 0.8546 (ptp) cc_final: 0.8306 (ptt) REVERT: P 26 TRP cc_start: 0.6693 (m100) cc_final: 0.6459 (m-90) REVERT: P 74 MET cc_start: 0.4968 (mmp) cc_final: 0.4171 (mmp) REVERT: Q 122 LEU cc_start: 0.8941 (mt) cc_final: 0.8608 (mt) REVERT: Q 182 GLU cc_start: 0.6950 (tt0) cc_final: 0.6576 (tp30) REVERT: Q 199 MET cc_start: 0.8308 (ptm) cc_final: 0.8043 (ptm) REVERT: Q 258 MET cc_start: 0.9092 (tpp) cc_final: 0.8684 (tpp) REVERT: Q 360 GLU cc_start: 0.7158 (mm-30) cc_final: 0.6932 (mm-30) REVERT: Q 371 PHE cc_start: 0.6013 (p90) cc_final: 0.5497 (p90) REVERT: Q 380 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7662 (tt) REVERT: Q 400 PHE cc_start: 0.7664 (m-10) cc_final: 0.7239 (t80) REVERT: Q 401 GLU cc_start: 0.8353 (tp30) cc_final: 0.7853 (tp30) REVERT: Q 436 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8151 (tt0) REVERT: Q 443 THR cc_start: 0.8482 (m) cc_final: 0.8008 (p) REVERT: Q 462 THR cc_start: 0.9076 (m) cc_final: 0.8866 (p) REVERT: R 15 ARG cc_start: 0.7759 (tpt170) cc_final: 0.7518 (ttm170) REVERT: R 18 THR cc_start: 0.8598 (p) cc_final: 0.7737 (t) REVERT: R 35 TRP cc_start: 0.9004 (t60) cc_final: 0.8727 (t60) REVERT: R 42 PHE cc_start: 0.8777 (t80) cc_final: 0.8249 (t80) REVERT: R 74 MET cc_start: 0.8639 (tpp) cc_final: 0.8242 (mmm) REVERT: S 8 ASN cc_start: 0.7875 (t0) cc_final: 0.7523 (t0) REVERT: S 20 TRP cc_start: 0.7544 (p90) cc_final: 0.6012 (p90) REVERT: S 108 PHE cc_start: 0.8538 (m-80) cc_final: 0.8181 (m-80) REVERT: S 295 MET cc_start: 0.7890 (tpt) cc_final: 0.5910 (tmm) REVERT: S 319 LEU cc_start: 0.8808 (mt) cc_final: 0.8594 (mt) REVERT: S 323 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7497 (pm20) REVERT: S 335 PHE cc_start: 0.8095 (OUTLIER) cc_final: 0.6944 (m-80) REVERT: S 410 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8132 (mtp) REVERT: S 484 THR cc_start: 0.8744 (m) cc_final: 0.8395 (p) REVERT: T 13 ASP cc_start: 0.7783 (p0) cc_final: 0.7161 (m-30) REVERT: T 26 TRP cc_start: 0.8124 (m100) cc_final: 0.7867 (m100) REVERT: T 32 VAL cc_start: 0.8872 (t) cc_final: 0.8616 (t) REVERT: U 47 TRP cc_start: 0.7993 (t60) cc_final: 0.7788 (t60) REVERT: U 54 ASP cc_start: 0.6034 (p0) cc_final: 0.5264 (p0) REVERT: U 57 ASP cc_start: 0.7350 (t0) cc_final: 0.7094 (m-30) REVERT: U 114 GLN cc_start: 0.7940 (tp40) cc_final: 0.7463 (tp-100) REVERT: V 2 ILE cc_start: 0.8659 (mt) cc_final: 0.8425 (mt) REVERT: V 48 GLN cc_start: 0.6787 (mp10) cc_final: 0.5939 (mp10) REVERT: V 80 LYS cc_start: 0.7744 (mtmt) cc_final: 0.7542 (mtmt) REVERT: V 85 GLN cc_start: 0.7649 (mm110) cc_final: 0.7326 (mm-40) REVERT: V 88 ASP cc_start: 0.6134 (m-30) cc_final: 0.5768 (m-30) REVERT: V 104 PHE cc_start: 0.8513 (m-80) cc_final: 0.8262 (m-80) REVERT: V 109 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7880 (mtp85) outliers start: 122 outliers final: 66 residues processed: 957 average time/residue: 0.3728 time to fit residues: 582.4866 Evaluate side-chains 883 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 807 time to evaluate : 3.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 335 PHE Chi-restraints excluded: chain E residue 451 TRP Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 107 TRP Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 109 ARG Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 130 VAL Chi-restraints excluded: chain O residue 237 THR Chi-restraints excluded: chain O residue 365 ILE Chi-restraints excluded: chain O residue 394 SER Chi-restraints excluded: chain O residue 413 LEU Chi-restraints excluded: chain O residue 423 VAL Chi-restraints excluded: chain O residue 452 VAL Chi-restraints excluded: chain O residue 460 LEU Chi-restraints excluded: chain O residue 461 LEU Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 357 THR Chi-restraints excluded: chain Q residue 380 ILE Chi-restraints excluded: chain Q residue 491 VAL Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain S residue 41 LEU Chi-restraints excluded: chain S residue 64 LYS Chi-restraints excluded: chain S residue 79 GLU Chi-restraints excluded: chain S residue 92 CYS Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 181 LEU Chi-restraints excluded: chain S residue 242 HIS Chi-restraints excluded: chain S residue 258 MET Chi-restraints excluded: chain S residue 318 ILE Chi-restraints excluded: chain S residue 323 GLU Chi-restraints excluded: chain S residue 335 PHE Chi-restraints excluded: chain S residue 410 MET Chi-restraints excluded: chain S residue 451 TRP Chi-restraints excluded: chain S residue 485 LEU Chi-restraints excluded: chain T residue 14 THR Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain U residue 25 SER Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 107 TRP Chi-restraints excluded: chain U residue 119 THR Chi-restraints excluded: chain V residue 109 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 261 optimal weight: 30.0000 chunk 18 optimal weight: 20.0000 chunk 310 optimal weight: 20.0000 chunk 52 optimal weight: 9.9990 chunk 72 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 316 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 156 optimal weight: 10.0000 chunk 312 optimal weight: 6.9990 chunk 283 optimal weight: 8.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 HIS ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 HIS ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 ASN L 27 GLN ** O 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 HIS Q 246 GLN ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 27 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.119444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.102448 restraints weight = 52583.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.105338 restraints weight = 26049.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.107243 restraints weight = 16006.804| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 30884 Z= 0.260 Angle : 0.786 15.232 41956 Z= 0.390 Chirality : 0.047 0.280 4928 Planarity : 0.005 0.062 5192 Dihedral : 10.719 103.101 4876 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 5.87 % Allowed : 18.68 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.63 (0.13), residues: 3846 helix: 1.07 (0.18), residues: 870 sheet: -1.61 (0.15), residues: 1092 loop : -1.76 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Q 218 HIS 0.010 0.002 HIS A 144 PHE 0.017 0.002 PHE P 48 TYR 0.022 0.002 TYR U 111 ARG 0.009 0.001 ARG E 409 Details of bonding type rmsd link_NAG-ASN : bond 0.00473 ( 12) link_NAG-ASN : angle 2.38382 ( 36) link_BETA1-4 : bond 0.00482 ( 20) link_BETA1-4 : angle 2.60060 ( 60) link_ALPHA1-3 : bond 0.00991 ( 4) link_ALPHA1-3 : angle 2.99918 ( 12) hydrogen bonds : bond 0.04493 ( 1094) hydrogen bonds : angle 5.65606 ( 3036) link_BETA1-6 : bond 0.01413 ( 4) link_BETA1-6 : angle 3.06749 ( 12) SS BOND : bond 0.00687 ( 30) SS BOND : angle 2.94041 ( 60) covalent geometry : bond 0.00607 (30814) covalent geometry : angle 0.76707 (41776) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 979 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 790 time to evaluate : 3.175 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO B 72 " (corrupted residue). Skipping it. Corrupt residue: chain: B residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO P 72 " (corrupted residue). Skipping it. Corrupt residue: chain: P residue: PRO 72 >>> skipping revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8207 (t) cc_final: 0.7828 (p) REVERT: A 57 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7138 (ttm110) REVERT: A 98 ASP cc_start: 0.8138 (p0) cc_final: 0.7681 (p0) REVERT: A 181 LEU cc_start: 0.8643 (tp) cc_final: 0.8178 (tp) REVERT: A 201 ASN cc_start: 0.7056 (m-40) cc_final: 0.5850 (t0) REVERT: A 247 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7819 (pm20) REVERT: A 287 MET cc_start: 0.8660 (mtp) cc_final: 0.8132 (mtp) REVERT: A 299 MET cc_start: 0.6996 (mmm) cc_final: 0.5927 (mmm) REVERT: B 26 TRP cc_start: 0.6882 (m100) cc_final: 0.6666 (m-90) REVERT: B 28 GLN cc_start: 0.7835 (tp-100) cc_final: 0.6502 (tp-100) REVERT: B 61 VAL cc_start: 0.9213 (t) cc_final: 0.8893 (p) REVERT: C 182 GLU cc_start: 0.7277 (tp30) cc_final: 0.6899 (tp30) REVERT: C 199 MET cc_start: 0.8348 (ptm) cc_final: 0.8077 (ptm) REVERT: C 258 MET cc_start: 0.9130 (tpp) cc_final: 0.8781 (tpp) REVERT: C 358 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.6989 (tppt) REVERT: C 360 GLU cc_start: 0.7244 (mm-30) cc_final: 0.7019 (mm-30) REVERT: C 380 ILE cc_start: 0.8050 (OUTLIER) cc_final: 0.7762 (tt) REVERT: C 400 PHE cc_start: 0.7541 (m-10) cc_final: 0.7245 (t80) REVERT: C 432 LYS cc_start: 0.8303 (tttp) cc_final: 0.8001 (ttpp) REVERT: C 462 THR cc_start: 0.9105 (m) cc_final: 0.8899 (p) REVERT: D 12 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8257 (pp) REVERT: D 42 PHE cc_start: 0.8809 (t80) cc_final: 0.8139 (t80) REVERT: D 74 MET cc_start: 0.8750 (tpp) cc_final: 0.8302 (mmm) REVERT: E 8 ASN cc_start: 0.7985 (t0) cc_final: 0.7531 (t0) REVERT: E 20 TRP cc_start: 0.7626 (p90) cc_final: 0.6121 (p90) REVERT: E 108 PHE cc_start: 0.8711 (m-80) cc_final: 0.8327 (m-80) REVERT: E 126 GLU cc_start: 0.7309 (mm-30) cc_final: 0.6811 (tp30) REVERT: E 176 TYR cc_start: 0.8898 (m-80) cc_final: 0.8515 (m-80) REVERT: E 181 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8614 (pp) REVERT: E 250 VAL cc_start: 0.8736 (OUTLIER) cc_final: 0.8495 (m) REVERT: E 251 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8325 (tt) REVERT: E 259 HIS cc_start: 0.8808 (OUTLIER) cc_final: 0.7417 (t70) REVERT: E 270 ASN cc_start: 0.6864 (t0) cc_final: 0.6588 (t0) REVERT: E 484 THR cc_start: 0.8909 (m) cc_final: 0.8526 (p) REVERT: H 3 GLU cc_start: 0.6468 (mm-30) cc_final: 0.6184 (mm-30) REVERT: H 47 TRP cc_start: 0.8225 (t60) cc_final: 0.7584 (t60) REVERT: H 57 ASP cc_start: 0.7439 (t0) cc_final: 0.7213 (m-30) REVERT: H 65 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7392 (mtmt) REVERT: H 114 GLN cc_start: 0.7736 (tp40) cc_final: 0.7231 (tp-100) REVERT: L 2 ILE cc_start: 0.8713 (mt) cc_final: 0.8465 (mt) REVERT: L 48 GLN cc_start: 0.7070 (mp10) cc_final: 0.6158 (mp10) REVERT: L 85 GLN cc_start: 0.7594 (mm-40) cc_final: 0.7250 (mm-40) REVERT: L 104 PHE cc_start: 0.8632 (m-80) cc_final: 0.8431 (m-80) REVERT: L 109 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7847 (mtp85) REVERT: O 6 VAL cc_start: 0.8215 (t) cc_final: 0.7839 (p) REVERT: O 57 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7035 (ttm110) REVERT: O 98 ASP cc_start: 0.8128 (p0) cc_final: 0.7682 (p0) REVERT: O 181 LEU cc_start: 0.8640 (tp) cc_final: 0.8174 (tp) REVERT: O 247 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7735 (pm20) REVERT: O 287 MET cc_start: 0.8656 (mtp) cc_final: 0.8127 (mtp) REVERT: O 299 MET cc_start: 0.6994 (mmm) cc_final: 0.5938 (mmm) REVERT: P 26 TRP cc_start: 0.6863 (m100) cc_final: 0.6651 (m-90) REVERT: P 45 LEU cc_start: 0.8477 (tp) cc_final: 0.8268 (tp) REVERT: P 60 LYS cc_start: 0.5843 (mttp) cc_final: 0.4785 (mtmt) REVERT: Q 199 MET cc_start: 0.8341 (ptm) cc_final: 0.8056 (ptm) REVERT: Q 258 MET cc_start: 0.9132 (tpp) cc_final: 0.8780 (tpp) REVERT: Q 358 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.7059 (tppt) REVERT: Q 360 GLU cc_start: 0.7054 (mm-30) cc_final: 0.6829 (mm-30) REVERT: Q 380 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7755 (tt) REVERT: Q 400 PHE cc_start: 0.7547 (m-10) cc_final: 0.7258 (t80) REVERT: Q 432 LYS cc_start: 0.8317 (tttp) cc_final: 0.7996 (ttpp) REVERT: Q 462 THR cc_start: 0.9105 (m) cc_final: 0.8897 (p) REVERT: R 35 TRP cc_start: 0.9051 (t60) cc_final: 0.8761 (t60) REVERT: R 42 PHE cc_start: 0.8813 (t80) cc_final: 0.8141 (t80) REVERT: R 74 MET cc_start: 0.8748 (tpp) cc_final: 0.8287 (mmm) REVERT: S 8 ASN cc_start: 0.8112 (t0) cc_final: 0.7636 (t0) REVERT: S 20 TRP cc_start: 0.7677 (p90) cc_final: 0.6208 (p90) REVERT: S 108 PHE cc_start: 0.8706 (m-80) cc_final: 0.8310 (m-80) REVERT: S 176 TYR cc_start: 0.8812 (m-80) cc_final: 0.8452 (m-80) REVERT: S 181 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8692 (pp) REVERT: S 259 HIS cc_start: 0.8869 (OUTLIER) cc_final: 0.7358 (t70) REVERT: S 323 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7495 (pm20) REVERT: S 400 PHE cc_start: 0.7863 (m-10) cc_final: 0.7661 (m-10) REVERT: S 410 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8091 (mtp) REVERT: S 438 PHE cc_start: 0.7657 (t80) cc_final: 0.7433 (m-10) REVERT: S 447 SER cc_start: 0.9088 (t) cc_final: 0.8793 (t) REVERT: S 484 THR cc_start: 0.8902 (m) cc_final: 0.8532 (p) REVERT: U 3 GLU cc_start: 0.6472 (mm-30) cc_final: 0.6201 (mm-30) REVERT: U 47 TRP cc_start: 0.8226 (t60) cc_final: 0.7577 (t60) REVERT: U 57 ASP cc_start: 0.7474 (t0) cc_final: 0.7234 (m-30) REVERT: U 65 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7387 (mtmt) REVERT: U 114 GLN cc_start: 0.7732 (tp40) cc_final: 0.7229 (tp-100) REVERT: V 2 ILE cc_start: 0.8703 (mt) cc_final: 0.8470 (mt) REVERT: V 48 GLN cc_start: 0.7078 (mp10) cc_final: 0.6158 (mp10) REVERT: V 109 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7842 (mtp85) outliers start: 189 outliers final: 121 residues processed: 909 average time/residue: 0.3720 time to fit residues: 552.7098 Evaluate side-chains 895 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 753 time to evaluate : 3.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 451 TRP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 457 ILE Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 255 GLU Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 259 HIS Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 451 TRP Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 107 TRP Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 109 ARG Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 57 ARG Chi-restraints excluded: chain O residue 121 CYS Chi-restraints excluded: chain O residue 130 VAL Chi-restraints excluded: chain O residue 195 ILE Chi-restraints excluded: chain O residue 198 THR Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 237 THR Chi-restraints excluded: chain O residue 247 GLU Chi-restraints excluded: chain O residue 275 SER Chi-restraints excluded: chain O residue 338 GLU Chi-restraints excluded: chain O residue 365 ILE Chi-restraints excluded: chain O residue 413 LEU Chi-restraints excluded: chain O residue 423 VAL Chi-restraints excluded: chain O residue 451 TRP Chi-restraints excluded: chain O residue 452 VAL Chi-restraints excluded: chain O residue 455 ILE Chi-restraints excluded: chain O residue 466 LEU Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 67 LEU Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain Q residue 91 VAL Chi-restraints excluded: chain Q residue 92 CYS Chi-restraints excluded: chain Q residue 113 LEU Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 313 THR Chi-restraints excluded: chain Q residue 356 VAL Chi-restraints excluded: chain Q residue 357 THR Chi-restraints excluded: chain Q residue 358 LYS Chi-restraints excluded: chain Q residue 377 VAL Chi-restraints excluded: chain Q residue 380 ILE Chi-restraints excluded: chain Q residue 457 ILE Chi-restraints excluded: chain Q residue 466 LEU Chi-restraints excluded: chain Q residue 491 VAL Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain S residue 41 LEU Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain S residue 79 GLU Chi-restraints excluded: chain S residue 92 CYS Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 181 LEU Chi-restraints excluded: chain S residue 187 THR Chi-restraints excluded: chain S residue 242 HIS Chi-restraints excluded: chain S residue 255 GLU Chi-restraints excluded: chain S residue 258 MET Chi-restraints excluded: chain S residue 259 HIS Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 318 ILE Chi-restraints excluded: chain S residue 323 GLU Chi-restraints excluded: chain S residue 356 VAL Chi-restraints excluded: chain S residue 410 MET Chi-restraints excluded: chain S residue 451 TRP Chi-restraints excluded: chain S residue 485 LEU Chi-restraints excluded: chain T residue 16 THR Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 61 VAL Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain U residue 25 SER Chi-restraints excluded: chain U residue 53 SER Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 65 LYS Chi-restraints excluded: chain U residue 107 TRP Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 84 VAL Chi-restraints excluded: chain V residue 109 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 27 optimal weight: 20.0000 chunk 49 optimal weight: 0.9980 chunk 226 optimal weight: 9.9990 chunk 343 optimal weight: 30.0000 chunk 199 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 158 optimal weight: 7.9990 chunk 362 optimal weight: 20.0000 chunk 337 optimal weight: 30.0000 chunk 2 optimal weight: 0.0050 chunk 326 optimal weight: 6.9990 overall best weight: 4.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN E 428 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 302 ASN ** T 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 85 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.120808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.103636 restraints weight = 52062.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.106595 restraints weight = 25916.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.108512 restraints weight = 15874.480| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 30884 Z= 0.165 Angle : 0.705 13.268 41956 Z= 0.348 Chirality : 0.045 0.279 4928 Planarity : 0.004 0.054 5192 Dihedral : 10.154 104.884 4876 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 5.06 % Allowed : 21.17 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.49 (0.13), residues: 3846 helix: 1.23 (0.18), residues: 876 sheet: -1.46 (0.15), residues: 1092 loop : -1.76 (0.13), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP S 20 HIS 0.007 0.001 HIS A 144 PHE 0.020 0.002 PHE F 48 TYR 0.011 0.001 TYR Q 90 ARG 0.008 0.001 ARG Q 2 Details of bonding type rmsd link_NAG-ASN : bond 0.00413 ( 12) link_NAG-ASN : angle 2.28099 ( 36) link_BETA1-4 : bond 0.00417 ( 20) link_BETA1-4 : angle 2.42349 ( 60) link_ALPHA1-3 : bond 0.01019 ( 4) link_ALPHA1-3 : angle 2.97947 ( 12) hydrogen bonds : bond 0.04120 ( 1094) hydrogen bonds : angle 5.43235 ( 3036) link_BETA1-6 : bond 0.01243 ( 4) link_BETA1-6 : angle 2.89630 ( 12) SS BOND : bond 0.00540 ( 30) SS BOND : angle 2.62762 ( 60) covalent geometry : bond 0.00381 (30814) covalent geometry : angle 0.68678 (41776) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 955 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 792 time to evaluate : 3.665 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO B 72 " (corrupted residue). Skipping it. Corrupt residue: chain: B residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO P 72 " (corrupted residue). Skipping it. Corrupt residue: chain: P residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8118 (t) cc_final: 0.7694 (p) REVERT: A 86 GLN cc_start: 0.7361 (tp40) cc_final: 0.7101 (tp40) REVERT: A 98 ASP cc_start: 0.8107 (p0) cc_final: 0.7645 (p0) REVERT: A 181 LEU cc_start: 0.8590 (tp) cc_final: 0.8075 (tp) REVERT: A 201 ASN cc_start: 0.7038 (m-40) cc_final: 0.5798 (t0) REVERT: A 247 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7828 (pm20) REVERT: A 287 MET cc_start: 0.8652 (mtp) cc_final: 0.8122 (mtp) REVERT: A 299 MET cc_start: 0.6919 (mmm) cc_final: 0.5931 (mmm) REVERT: A 433 MET cc_start: 0.8608 (ptp) cc_final: 0.8404 (ptt) REVERT: B 26 TRP cc_start: 0.6862 (m100) cc_final: 0.6610 (m-90) REVERT: B 28 GLN cc_start: 0.7810 (tp-100) cc_final: 0.7350 (tp-100) REVERT: B 35 TRP cc_start: 0.8245 (t60) cc_final: 0.7978 (t60) REVERT: B 59 GLN cc_start: 0.7265 (pp30) cc_final: 0.6991 (pp30) REVERT: B 61 VAL cc_start: 0.9232 (t) cc_final: 0.8927 (p) REVERT: C 125 ILE cc_start: 0.8824 (tt) cc_final: 0.8485 (tt) REVERT: C 182 GLU cc_start: 0.7298 (tp30) cc_final: 0.6862 (tp30) REVERT: C 199 MET cc_start: 0.8346 (ptm) cc_final: 0.7962 (ptm) REVERT: C 293 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8785 (pptt) REVERT: C 348 ARG cc_start: 0.8206 (ptm-80) cc_final: 0.7771 (ptm-80) REVERT: C 358 LYS cc_start: 0.7457 (OUTLIER) cc_final: 0.6911 (tppt) REVERT: C 360 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7170 (mm-30) REVERT: C 380 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7700 (tt) REVERT: C 400 PHE cc_start: 0.7383 (m-10) cc_final: 0.7112 (t80) REVERT: C 432 LYS cc_start: 0.8262 (tttp) cc_final: 0.8040 (ttpp) REVERT: C 436 GLN cc_start: 0.8798 (tm-30) cc_final: 0.8188 (tt0) REVERT: C 462 THR cc_start: 0.9093 (m) cc_final: 0.8850 (p) REVERT: D 12 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8135 (pp) REVERT: D 18 THR cc_start: 0.8886 (p) cc_final: 0.8100 (t) REVERT: D 35 TRP cc_start: 0.9034 (t60) cc_final: 0.8830 (t60) REVERT: D 42 PHE cc_start: 0.8791 (t80) cc_final: 0.7963 (t80) REVERT: D 74 MET cc_start: 0.8777 (tpp) cc_final: 0.8112 (mmm) REVERT: E 8 ASN cc_start: 0.8142 (t0) cc_final: 0.7728 (t0) REVERT: E 20 TRP cc_start: 0.7634 (p90) cc_final: 0.6311 (p90) REVERT: E 108 PHE cc_start: 0.8679 (m-80) cc_final: 0.8243 (m-80) REVERT: E 176 TYR cc_start: 0.8859 (m-80) cc_final: 0.8464 (m-80) REVERT: E 181 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8623 (pp) REVERT: E 250 VAL cc_start: 0.8660 (OUTLIER) cc_final: 0.8432 (m) REVERT: E 251 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8308 (tt) REVERT: E 259 HIS cc_start: 0.8941 (OUTLIER) cc_final: 0.7411 (t70) REVERT: E 270 ASN cc_start: 0.6497 (t0) cc_final: 0.6178 (t0) REVERT: E 400 PHE cc_start: 0.7869 (m-10) cc_final: 0.7653 (m-10) REVERT: E 410 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8030 (mtp) REVERT: E 442 TYR cc_start: 0.8890 (t80) cc_final: 0.8272 (t80) REVERT: E 484 THR cc_start: 0.8873 (m) cc_final: 0.8402 (p) REVERT: H 3 GLU cc_start: 0.6430 (mm-30) cc_final: 0.6123 (mm-30) REVERT: H 47 TRP cc_start: 0.8220 (t60) cc_final: 0.7611 (t60) REVERT: H 57 ASP cc_start: 0.7340 (t0) cc_final: 0.7056 (m-30) REVERT: H 90 ASP cc_start: 0.7394 (t0) cc_final: 0.7191 (t0) REVERT: L 2 ILE cc_start: 0.8617 (mt) cc_final: 0.8402 (mt) REVERT: L 48 GLN cc_start: 0.7055 (mp10) cc_final: 0.6174 (mp10) REVERT: L 85 GLN cc_start: 0.7465 (mm-40) cc_final: 0.7248 (mm-40) REVERT: L 104 PHE cc_start: 0.8729 (m-80) cc_final: 0.8434 (m-80) REVERT: L 109 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7806 (mtp85) REVERT: O 6 VAL cc_start: 0.8130 (t) cc_final: 0.7756 (p) REVERT: O 98 ASP cc_start: 0.8091 (p0) cc_final: 0.7613 (p0) REVERT: O 181 LEU cc_start: 0.8578 (tp) cc_final: 0.8061 (tp) REVERT: O 190 ASP cc_start: 0.8212 (t0) cc_final: 0.8009 (t0) REVERT: O 247 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7737 (pm20) REVERT: O 287 MET cc_start: 0.8719 (mtp) cc_final: 0.8221 (mtp) REVERT: O 299 MET cc_start: 0.6946 (mmm) cc_final: 0.5924 (mmm) REVERT: O 433 MET cc_start: 0.8613 (ptp) cc_final: 0.8398 (ptt) REVERT: P 26 TRP cc_start: 0.6840 (m100) cc_final: 0.6532 (m-90) REVERT: P 28 GLN cc_start: 0.7805 (tp-100) cc_final: 0.7529 (tp-100) REVERT: P 74 MET cc_start: 0.5907 (mmp) cc_final: 0.5368 (mmt) REVERT: Q 125 ILE cc_start: 0.8816 (tt) cc_final: 0.8481 (tt) REVERT: Q 199 MET cc_start: 0.8328 (ptm) cc_final: 0.7931 (ptm) REVERT: Q 293 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8775 (pptt) REVERT: Q 348 ARG cc_start: 0.8222 (ptm-80) cc_final: 0.7779 (ptm-80) REVERT: Q 358 LYS cc_start: 0.7525 (OUTLIER) cc_final: 0.7082 (tppt) REVERT: Q 380 ILE cc_start: 0.7980 (OUTLIER) cc_final: 0.7693 (tt) REVERT: Q 400 PHE cc_start: 0.7389 (m-10) cc_final: 0.7124 (t80) REVERT: Q 432 LYS cc_start: 0.8257 (tttp) cc_final: 0.7964 (ttpp) REVERT: Q 436 GLN cc_start: 0.8327 (tm-30) cc_final: 0.7862 (tm-30) REVERT: Q 462 THR cc_start: 0.9094 (m) cc_final: 0.8851 (p) REVERT: R 18 THR cc_start: 0.8854 (p) cc_final: 0.8117 (t) REVERT: R 35 TRP cc_start: 0.9050 (t60) cc_final: 0.8736 (t60) REVERT: R 42 PHE cc_start: 0.8789 (t80) cc_final: 0.7950 (t80) REVERT: R 74 MET cc_start: 0.8785 (tpp) cc_final: 0.8106 (mmm) REVERT: S 8 ASN cc_start: 0.8202 (t0) cc_final: 0.7808 (t0) REVERT: S 20 TRP cc_start: 0.7624 (p90) cc_final: 0.6294 (p90) REVERT: S 108 PHE cc_start: 0.8676 (m-80) cc_final: 0.8294 (m-80) REVERT: S 176 TYR cc_start: 0.8874 (m-80) cc_final: 0.8464 (m-80) REVERT: S 181 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8704 (pp) REVERT: S 259 HIS cc_start: 0.8814 (OUTLIER) cc_final: 0.7058 (t70) REVERT: S 305 VAL cc_start: 0.9197 (OUTLIER) cc_final: 0.8697 (p) REVERT: S 323 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7499 (pm20) REVERT: S 400 PHE cc_start: 0.7862 (m-10) cc_final: 0.7642 (m-10) REVERT: S 410 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8090 (mtp) REVERT: S 438 PHE cc_start: 0.7650 (t80) cc_final: 0.7418 (m-10) REVERT: S 442 TYR cc_start: 0.8883 (t80) cc_final: 0.8270 (t80) REVERT: S 484 THR cc_start: 0.8872 (m) cc_final: 0.8401 (p) REVERT: U 3 GLU cc_start: 0.6444 (mm-30) cc_final: 0.6147 (mm-30) REVERT: U 47 TRP cc_start: 0.8224 (t60) cc_final: 0.7608 (t60) REVERT: U 57 ASP cc_start: 0.7387 (t0) cc_final: 0.7067 (m-30) REVERT: U 90 ASP cc_start: 0.7387 (t0) cc_final: 0.7180 (t0) REVERT: V 2 ILE cc_start: 0.8611 (mt) cc_final: 0.8398 (mt) REVERT: V 48 GLN cc_start: 0.7065 (mp10) cc_final: 0.6180 (mp10) REVERT: V 109 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7800 (mtp85) outliers start: 163 outliers final: 109 residues processed: 897 average time/residue: 0.3744 time to fit residues: 550.0291 Evaluate side-chains 889 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 759 time to evaluate : 3.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 451 TRP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 293 LYS Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 457 ILE Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 259 HIS Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 410 MET Chi-restraints excluded: chain E residue 451 TRP Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain L residue 109 ARG Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 121 CYS Chi-restraints excluded: chain O residue 130 VAL Chi-restraints excluded: chain O residue 195 ILE Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 237 THR Chi-restraints excluded: chain O residue 247 GLU Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 283 CYS Chi-restraints excluded: chain O residue 338 GLU Chi-restraints excluded: chain O residue 365 ILE Chi-restraints excluded: chain O residue 413 LEU Chi-restraints excluded: chain O residue 423 VAL Chi-restraints excluded: chain O residue 429 SER Chi-restraints excluded: chain O residue 451 TRP Chi-restraints excluded: chain O residue 452 VAL Chi-restraints excluded: chain O residue 461 LEU Chi-restraints excluded: chain O residue 466 LEU Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 113 LEU Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 236 VAL Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 293 LYS Chi-restraints excluded: chain Q residue 357 THR Chi-restraints excluded: chain Q residue 358 LYS Chi-restraints excluded: chain Q residue 380 ILE Chi-restraints excluded: chain Q residue 457 ILE Chi-restraints excluded: chain Q residue 491 VAL Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain S residue 41 LEU Chi-restraints excluded: chain S residue 79 GLU Chi-restraints excluded: chain S residue 92 CYS Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 181 LEU Chi-restraints excluded: chain S residue 187 THR Chi-restraints excluded: chain S residue 242 HIS Chi-restraints excluded: chain S residue 255 GLU Chi-restraints excluded: chain S residue 258 MET Chi-restraints excluded: chain S residue 259 HIS Chi-restraints excluded: chain S residue 305 VAL Chi-restraints excluded: chain S residue 318 ILE Chi-restraints excluded: chain S residue 323 GLU Chi-restraints excluded: chain S residue 356 VAL Chi-restraints excluded: chain S residue 410 MET Chi-restraints excluded: chain S residue 451 TRP Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain S residue 485 LEU Chi-restraints excluded: chain T residue 16 THR Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain U residue 53 SER Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 83 MET Chi-restraints excluded: chain V residue 109 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 202 optimal weight: 6.9990 chunk 311 optimal weight: 20.0000 chunk 158 optimal weight: 20.0000 chunk 63 optimal weight: 0.0570 chunk 125 optimal weight: 9.9990 chunk 201 optimal weight: 5.9990 chunk 258 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 228 optimal weight: 20.0000 chunk 188 optimal weight: 7.9990 chunk 242 optimal weight: 9.9990 overall best weight: 5.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 ASN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 GLN ** O 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 51 GLN V 85 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.119800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.102607 restraints weight = 52338.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.105530 restraints weight = 25961.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.107441 restraints weight = 15956.971| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 30884 Z= 0.189 Angle : 0.722 12.283 41956 Z= 0.356 Chirality : 0.045 0.265 4928 Planarity : 0.004 0.060 5192 Dihedral : 9.654 105.811 4876 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 6.58 % Allowed : 20.67 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.47 (0.13), residues: 3846 helix: 1.16 (0.18), residues: 876 sheet: -1.41 (0.15), residues: 1084 loop : -1.73 (0.13), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP S 20 HIS 0.007 0.001 HIS O 144 PHE 0.016 0.002 PHE E 475 TYR 0.011 0.001 TYR H 60 ARG 0.008 0.001 ARG A 348 Details of bonding type rmsd link_NAG-ASN : bond 0.00452 ( 12) link_NAG-ASN : angle 2.47983 ( 36) link_BETA1-4 : bond 0.00379 ( 20) link_BETA1-4 : angle 2.37301 ( 60) link_ALPHA1-3 : bond 0.00915 ( 4) link_ALPHA1-3 : angle 2.95409 ( 12) hydrogen bonds : bond 0.04174 ( 1094) hydrogen bonds : angle 5.37307 ( 3036) link_BETA1-6 : bond 0.00955 ( 4) link_BETA1-6 : angle 2.97746 ( 12) SS BOND : bond 0.00542 ( 30) SS BOND : angle 2.74353 ( 60) covalent geometry : bond 0.00442 (30814) covalent geometry : angle 0.70303 (41776) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1001 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 789 time to evaluate : 3.192 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO B 72 " (corrupted residue). Skipping it. Corrupt residue: chain: B residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO P 72 " (corrupted residue). Skipping it. Corrupt residue: chain: P residue: PRO 72 >>> skipping revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8131 (t) cc_final: 0.7701 (p) REVERT: A 57 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.6954 (ttm110) REVERT: A 98 ASP cc_start: 0.8105 (p0) cc_final: 0.7634 (p0) REVERT: A 181 LEU cc_start: 0.8538 (tp) cc_final: 0.8109 (tp) REVERT: A 190 ASP cc_start: 0.8341 (t0) cc_final: 0.8090 (t0) REVERT: A 201 ASN cc_start: 0.6922 (m-40) cc_final: 0.5759 (t0) REVERT: A 287 MET cc_start: 0.8654 (mtp) cc_final: 0.8137 (mtp) REVERT: A 299 MET cc_start: 0.6956 (mmm) cc_final: 0.6035 (mmm) REVERT: B 12 LEU cc_start: 0.6269 (OUTLIER) cc_final: 0.5701 (pp) REVERT: B 26 TRP cc_start: 0.6892 (m100) cc_final: 0.6634 (m-90) REVERT: B 28 GLN cc_start: 0.7799 (tp-100) cc_final: 0.7443 (tp-100) REVERT: B 61 VAL cc_start: 0.9235 (t) cc_final: 0.8932 (p) REVERT: C 34 MET cc_start: 0.8024 (ptp) cc_final: 0.7821 (ptp) REVERT: C 182 GLU cc_start: 0.7209 (tp30) cc_final: 0.6922 (tp30) REVERT: C 293 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8522 (pptt) REVERT: C 348 ARG cc_start: 0.8313 (ptm-80) cc_final: 0.7853 (ptm-80) REVERT: C 358 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7070 (tppt) REVERT: C 380 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7723 (tt) REVERT: C 432 LYS cc_start: 0.8260 (tttp) cc_final: 0.8002 (ttpp) REVERT: C 436 GLN cc_start: 0.8801 (tm-30) cc_final: 0.8083 (tt0) REVERT: C 462 THR cc_start: 0.9069 (m) cc_final: 0.8801 (p) REVERT: D 12 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8061 (pp) REVERT: D 15 ARG cc_start: 0.7838 (ttm170) cc_final: 0.7369 (ttm-80) REVERT: D 18 THR cc_start: 0.8911 (p) cc_final: 0.8161 (t) REVERT: D 42 PHE cc_start: 0.8794 (t80) cc_final: 0.8143 (t80) REVERT: D 74 MET cc_start: 0.8742 (tpp) cc_final: 0.8042 (mmm) REVERT: E 8 ASN cc_start: 0.8129 (t0) cc_final: 0.7665 (t0) REVERT: E 20 TRP cc_start: 0.7725 (p90) cc_final: 0.6390 (p90) REVERT: E 108 PHE cc_start: 0.8726 (m-80) cc_final: 0.8337 (m-80) REVERT: E 122 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6584 (tp) REVERT: E 176 TYR cc_start: 0.8809 (m-80) cc_final: 0.8488 (m-80) REVERT: E 181 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8690 (pp) REVERT: E 259 HIS cc_start: 0.8945 (OUTLIER) cc_final: 0.7285 (t70) REVERT: E 270 ASN cc_start: 0.6602 (t0) cc_final: 0.6245 (t0) REVERT: E 400 PHE cc_start: 0.7868 (m-10) cc_final: 0.7665 (m-10) REVERT: E 410 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.8088 (mtp) REVERT: E 484 THR cc_start: 0.8894 (m) cc_final: 0.8522 (p) REVERT: H 3 GLU cc_start: 0.6424 (mm-30) cc_final: 0.6175 (mm-30) REVERT: H 47 TRP cc_start: 0.8244 (t60) cc_final: 0.7576 (t60) REVERT: H 56 ASN cc_start: 0.7709 (m-40) cc_final: 0.7425 (m110) REVERT: H 57 ASP cc_start: 0.7386 (t0) cc_final: 0.7033 (m-30) REVERT: H 90 ASP cc_start: 0.7542 (t0) cc_final: 0.7334 (t0) REVERT: H 95 TYR cc_start: 0.8683 (m-80) cc_final: 0.8314 (m-80) REVERT: L 2 ILE cc_start: 0.8640 (mt) cc_final: 0.8427 (mt) REVERT: L 48 GLN cc_start: 0.7539 (mp10) cc_final: 0.6689 (mp10) REVERT: L 104 PHE cc_start: 0.8522 (m-80) cc_final: 0.8254 (m-80) REVERT: O 6 VAL cc_start: 0.8138 (t) cc_final: 0.7716 (p) REVERT: O 57 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.6984 (ttm110) REVERT: O 98 ASP cc_start: 0.8091 (p0) cc_final: 0.7649 (p0) REVERT: O 181 LEU cc_start: 0.8614 (tp) cc_final: 0.8122 (tp) REVERT: O 287 MET cc_start: 0.8636 (mtp) cc_final: 0.8133 (mtp) REVERT: O 299 MET cc_start: 0.6997 (mmm) cc_final: 0.6088 (mmm) REVERT: O 433 MET cc_start: 0.8600 (ptp) cc_final: 0.8385 (ptt) REVERT: P 12 LEU cc_start: 0.6209 (OUTLIER) cc_final: 0.5622 (pp) REVERT: P 26 TRP cc_start: 0.6882 (m100) cc_final: 0.6551 (m-90) REVERT: P 74 MET cc_start: 0.5800 (mmp) cc_final: 0.5204 (mmt) REVERT: Q 34 MET cc_start: 0.8010 (ptp) cc_final: 0.7810 (ptp) REVERT: Q 199 MET cc_start: 0.8344 (ptm) cc_final: 0.8140 (ptm) REVERT: Q 293 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.8619 (pptt) REVERT: Q 348 ARG cc_start: 0.8320 (ptm-80) cc_final: 0.7862 (ptm-80) REVERT: Q 358 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7265 (tppt) REVERT: Q 380 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7720 (tt) REVERT: Q 432 LYS cc_start: 0.8256 (tttp) cc_final: 0.7934 (ttpp) REVERT: Q 436 GLN cc_start: 0.8318 (tm-30) cc_final: 0.7624 (tm-30) REVERT: Q 462 THR cc_start: 0.9070 (m) cc_final: 0.8806 (p) REVERT: R 18 THR cc_start: 0.8919 (p) cc_final: 0.8173 (t) REVERT: R 35 TRP cc_start: 0.9043 (t60) cc_final: 0.8782 (t60) REVERT: R 42 PHE cc_start: 0.8789 (t80) cc_final: 0.8137 (t80) REVERT: R 74 MET cc_start: 0.8737 (tpp) cc_final: 0.8035 (mmm) REVERT: S 8 ASN cc_start: 0.8235 (t0) cc_final: 0.7836 (t0) REVERT: S 20 TRP cc_start: 0.7668 (p90) cc_final: 0.6306 (p90) REVERT: S 59 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8207 (mt) REVERT: S 108 PHE cc_start: 0.8725 (m-80) cc_final: 0.8330 (m-80) REVERT: S 122 LEU cc_start: 0.6815 (OUTLIER) cc_final: 0.6572 (tp) REVERT: S 176 TYR cc_start: 0.8774 (m-80) cc_final: 0.8418 (m-80) REVERT: S 181 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8774 (pp) REVERT: S 259 HIS cc_start: 0.8928 (OUTLIER) cc_final: 0.7277 (t70) REVERT: S 305 VAL cc_start: 0.9192 (OUTLIER) cc_final: 0.8611 (p) REVERT: S 323 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7407 (pm20) REVERT: S 400 PHE cc_start: 0.7859 (m-10) cc_final: 0.7654 (m-10) REVERT: S 410 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8069 (mtp) REVERT: S 438 PHE cc_start: 0.7682 (t80) cc_final: 0.7434 (m-10) REVERT: S 447 SER cc_start: 0.9015 (t) cc_final: 0.8720 (t) REVERT: S 484 THR cc_start: 0.8893 (m) cc_final: 0.8524 (p) REVERT: U 3 GLU cc_start: 0.6439 (mm-30) cc_final: 0.6205 (mm-30) REVERT: U 47 TRP cc_start: 0.8248 (t60) cc_final: 0.7582 (t60) REVERT: U 57 ASP cc_start: 0.7346 (t0) cc_final: 0.7043 (m-30) REVERT: U 90 ASP cc_start: 0.7533 (t0) cc_final: 0.7324 (t0) REVERT: U 95 TYR cc_start: 0.8672 (m-80) cc_final: 0.8305 (m-80) REVERT: V 2 ILE cc_start: 0.8632 (mt) cc_final: 0.8414 (mt) REVERT: V 48 GLN cc_start: 0.7557 (mp10) cc_final: 0.6697 (mp10) outliers start: 212 outliers final: 141 residues processed: 919 average time/residue: 0.3776 time to fit residues: 566.9192 Evaluate side-chains 917 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 754 time to evaluate : 3.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 451 TRP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 293 LYS Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 457 ILE Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 259 HIS Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 410 MET Chi-restraints excluded: chain E residue 451 TRP Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 57 ARG Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain O residue 121 CYS Chi-restraints excluded: chain O residue 130 VAL Chi-restraints excluded: chain O residue 195 ILE Chi-restraints excluded: chain O residue 198 THR Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 275 SER Chi-restraints excluded: chain O residue 283 CYS Chi-restraints excluded: chain O residue 338 GLU Chi-restraints excluded: chain O residue 365 ILE Chi-restraints excluded: chain O residue 413 LEU Chi-restraints excluded: chain O residue 423 VAL Chi-restraints excluded: chain O residue 429 SER Chi-restraints excluded: chain O residue 451 TRP Chi-restraints excluded: chain O residue 452 VAL Chi-restraints excluded: chain O residue 466 LEU Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain P residue 67 LEU Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 30 CYS Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 113 LEU Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 135 LEU Chi-restraints excluded: chain Q residue 236 VAL Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 293 LYS Chi-restraints excluded: chain Q residue 313 THR Chi-restraints excluded: chain Q residue 356 VAL Chi-restraints excluded: chain Q residue 357 THR Chi-restraints excluded: chain Q residue 358 LYS Chi-restraints excluded: chain Q residue 377 VAL Chi-restraints excluded: chain Q residue 380 ILE Chi-restraints excluded: chain Q residue 457 ILE Chi-restraints excluded: chain Q residue 466 LEU Chi-restraints excluded: chain Q residue 491 VAL Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain S residue 41 LEU Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 79 GLU Chi-restraints excluded: chain S residue 91 VAL Chi-restraints excluded: chain S residue 92 CYS Chi-restraints excluded: chain S residue 122 LEU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 181 LEU Chi-restraints excluded: chain S residue 187 THR Chi-restraints excluded: chain S residue 242 HIS Chi-restraints excluded: chain S residue 255 GLU Chi-restraints excluded: chain S residue 258 MET Chi-restraints excluded: chain S residue 259 HIS Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 305 VAL Chi-restraints excluded: chain S residue 318 ILE Chi-restraints excluded: chain S residue 323 GLU Chi-restraints excluded: chain S residue 356 VAL Chi-restraints excluded: chain S residue 410 MET Chi-restraints excluded: chain S residue 451 TRP Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain S residue 485 LEU Chi-restraints excluded: chain T residue 16 THR Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain U residue 22 CYS Chi-restraints excluded: chain U residue 25 SER Chi-restraints excluded: chain U residue 53 SER Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 83 MET Chi-restraints excluded: chain U residue 91 THR Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 84 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 125 optimal weight: 20.0000 chunk 232 optimal weight: 10.0000 chunk 134 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 chunk 363 optimal weight: 9.9990 chunk 144 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 358 optimal weight: 6.9990 chunk 268 optimal weight: 3.9990 chunk 147 optimal weight: 10.0000 chunk 153 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 ASN E 428 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 GLN L 85 GLN ** O 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 52 GLN ** O 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 134 ASN ** T 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 51 GLN V 85 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.119728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.102470 restraints weight = 52056.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.105418 restraints weight = 26027.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.107336 restraints weight = 16020.981| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 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 : 0.005 0.060 30884 Z= 0.199 Angle : 0.730 12.904 41956 Z= 0.360 Chirality : 0.045 0.286 4928 Planarity : 0.004 0.059 5192 Dihedral : 9.382 105.497 4876 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 6.15 % Allowed : 21.82 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.44 (0.13), residues: 3846 helix: 1.22 (0.18), residues: 870 sheet: -1.40 (0.15), residues: 1096 loop : -1.71 (0.13), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 20 HIS 0.006 0.001 HIS O 144 PHE 0.024 0.002 PHE E 475 TYR 0.024 0.001 TYR L 55 ARG 0.006 0.001 ARG A 348 Details of bonding type rmsd link_NAG-ASN : bond 0.00433 ( 12) link_NAG-ASN : angle 2.50517 ( 36) link_BETA1-4 : bond 0.00383 ( 20) link_BETA1-4 : angle 2.36205 ( 60) link_ALPHA1-3 : bond 0.00670 ( 4) link_ALPHA1-3 : angle 2.76803 ( 12) hydrogen bonds : bond 0.04177 ( 1094) hydrogen bonds : angle 5.36931 ( 3036) link_BETA1-6 : bond 0.00905 ( 4) link_BETA1-6 : angle 3.02935 ( 12) SS BOND : bond 0.00607 ( 30) SS BOND : angle 2.89662 ( 60) covalent geometry : bond 0.00464 (30814) covalent geometry : angle 0.71043 (41776) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 964 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 766 time to evaluate : 3.295 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO B 72 " (corrupted residue). Skipping it. Corrupt residue: chain: B residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO P 72 " (corrupted residue). Skipping it. Corrupt residue: chain: P residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7119 (ttm110) REVERT: A 98 ASP cc_start: 0.8095 (p0) cc_final: 0.7643 (p0) REVERT: A 181 LEU cc_start: 0.8603 (tp) cc_final: 0.8123 (tp) REVERT: A 238 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8041 (m-10) REVERT: A 287 MET cc_start: 0.8570 (mtp) cc_final: 0.8082 (mtp) REVERT: A 299 MET cc_start: 0.6945 (mmm) cc_final: 0.6062 (mmm) REVERT: A 371 PHE cc_start: 0.9347 (OUTLIER) cc_final: 0.8770 (t80) REVERT: B 12 LEU cc_start: 0.6448 (OUTLIER) cc_final: 0.5822 (pp) REVERT: B 26 TRP cc_start: 0.6907 (m100) cc_final: 0.6626 (m-90) REVERT: B 28 GLN cc_start: 0.7790 (tp-100) cc_final: 0.7424 (tp-100) REVERT: B 61 VAL cc_start: 0.9218 (t) cc_final: 0.8916 (p) REVERT: C 34 MET cc_start: 0.8048 (ptp) cc_final: 0.7801 (ptp) REVERT: C 182 GLU cc_start: 0.7154 (tp30) cc_final: 0.6608 (tp30) REVERT: C 199 MET cc_start: 0.8127 (ptm) cc_final: 0.7827 (ptm) REVERT: C 258 MET cc_start: 0.8928 (tpp) cc_final: 0.8355 (tpp) REVERT: C 293 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8470 (pptt) REVERT: C 348 ARG cc_start: 0.8364 (ptm-80) cc_final: 0.7904 (ptm-80) REVERT: C 358 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7090 (tppt) REVERT: C 380 ILE cc_start: 0.8002 (mt) cc_final: 0.7697 (tt) REVERT: C 436 GLN cc_start: 0.8791 (tm-30) cc_final: 0.8404 (tt0) REVERT: C 462 THR cc_start: 0.9077 (m) cc_final: 0.8822 (p) REVERT: D 12 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8111 (pp) REVERT: D 18 THR cc_start: 0.8919 (p) cc_final: 0.8182 (t) REVERT: D 42 PHE cc_start: 0.8787 (t80) cc_final: 0.8146 (t80) REVERT: D 74 MET cc_start: 0.8765 (tpp) cc_final: 0.8256 (mmm) REVERT: E 8 ASN cc_start: 0.8137 (t0) cc_final: 0.7722 (t0) REVERT: E 20 TRP cc_start: 0.7770 (p90) cc_final: 0.6379 (p90) REVERT: E 108 PHE cc_start: 0.8740 (m-80) cc_final: 0.8358 (m-80) REVERT: E 122 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6609 (tp) REVERT: E 176 TYR cc_start: 0.8856 (m-80) cc_final: 0.8485 (m-80) REVERT: E 181 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8744 (pp) REVERT: E 259 HIS cc_start: 0.8944 (OUTLIER) cc_final: 0.7242 (t70) REVERT: E 270 ASN cc_start: 0.6661 (t0) cc_final: 0.6271 (t0) REVERT: E 286 LYS cc_start: 0.8654 (ptpt) cc_final: 0.8131 (ptpp) REVERT: E 400 PHE cc_start: 0.7859 (m-10) cc_final: 0.7652 (m-10) REVERT: E 410 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8089 (mtp) REVERT: E 442 TYR cc_start: 0.8920 (t80) cc_final: 0.8327 (t80) REVERT: E 447 SER cc_start: 0.9019 (t) cc_final: 0.8717 (t) REVERT: E 484 THR cc_start: 0.8861 (m) cc_final: 0.8431 (p) REVERT: H 3 GLU cc_start: 0.6553 (mm-30) cc_final: 0.6274 (mm-30) REVERT: H 47 TRP cc_start: 0.8132 (t60) cc_final: 0.7378 (t60) REVERT: H 56 ASN cc_start: 0.7625 (m-40) cc_final: 0.7369 (m110) REVERT: H 57 ASP cc_start: 0.7306 (t0) cc_final: 0.7021 (m-30) REVERT: H 95 TYR cc_start: 0.8658 (m-80) cc_final: 0.8375 (m-80) REVERT: O 6 VAL cc_start: 0.8124 (t) cc_final: 0.7688 (p) REVERT: O 57 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7101 (ttm110) REVERT: O 98 ASP cc_start: 0.8080 (p0) cc_final: 0.7665 (p0) REVERT: O 181 LEU cc_start: 0.8609 (tp) cc_final: 0.8109 (tp) REVERT: O 190 ASP cc_start: 0.8150 (t0) cc_final: 0.7932 (t0) REVERT: O 201 ASN cc_start: 0.7160 (m-40) cc_final: 0.6082 (t0) REVERT: O 238 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.8021 (m-10) REVERT: O 287 MET cc_start: 0.8548 (mtp) cc_final: 0.8092 (mtp) REVERT: O 299 MET cc_start: 0.6995 (mmm) cc_final: 0.6133 (mmm) REVERT: O 371 PHE cc_start: 0.9330 (OUTLIER) cc_final: 0.8784 (t80) REVERT: O 433 MET cc_start: 0.8591 (ptp) cc_final: 0.8388 (ptt) REVERT: P 12 LEU cc_start: 0.6197 (OUTLIER) cc_final: 0.5602 (pp) REVERT: P 26 TRP cc_start: 0.6888 (m100) cc_final: 0.6578 (m-90) REVERT: P 74 MET cc_start: 0.5893 (mmp) cc_final: 0.5350 (mmt) REVERT: Q 34 MET cc_start: 0.8034 (ptp) cc_final: 0.7792 (ptp) REVERT: Q 79 GLU cc_start: 0.7462 (mp0) cc_final: 0.7254 (mp0) REVERT: Q 194 MET cc_start: 0.8407 (ttm) cc_final: 0.8155 (mmm) REVERT: Q 199 MET cc_start: 0.8383 (ptm) cc_final: 0.8056 (ptm) REVERT: Q 293 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8465 (pptt) REVERT: Q 348 ARG cc_start: 0.8371 (ptm-80) cc_final: 0.7914 (ptm-80) REVERT: Q 358 LYS cc_start: 0.7716 (OUTLIER) cc_final: 0.7265 (tppt) REVERT: Q 380 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7697 (tt) REVERT: Q 415 ASP cc_start: 0.7199 (t0) cc_final: 0.6991 (m-30) REVERT: Q 436 GLN cc_start: 0.8248 (tm-30) cc_final: 0.7763 (tm-30) REVERT: Q 462 THR cc_start: 0.9073 (m) cc_final: 0.8826 (p) REVERT: R 12 LEU cc_start: 0.7847 (pp) cc_final: 0.7618 (pp) REVERT: R 18 THR cc_start: 0.8935 (p) cc_final: 0.8201 (t) REVERT: R 35 TRP cc_start: 0.9041 (t60) cc_final: 0.8744 (t60) REVERT: R 42 PHE cc_start: 0.8789 (t80) cc_final: 0.8149 (t80) REVERT: R 69 LEU cc_start: 0.8461 (mt) cc_final: 0.8129 (mt) REVERT: R 74 MET cc_start: 0.8771 (tpp) cc_final: 0.8242 (mmm) REVERT: S 8 ASN cc_start: 0.8204 (t0) cc_final: 0.7891 (t0) REVERT: S 20 TRP cc_start: 0.7760 (p90) cc_final: 0.6453 (p90) REVERT: S 59 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8236 (mt) REVERT: S 108 PHE cc_start: 0.8752 (m-80) cc_final: 0.8356 (m-80) REVERT: S 122 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6603 (tp) REVERT: S 176 TYR cc_start: 0.8806 (m-80) cc_final: 0.8452 (m-80) REVERT: S 181 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8784 (pp) REVERT: S 259 HIS cc_start: 0.8935 (OUTLIER) cc_final: 0.7171 (t70) REVERT: S 305 VAL cc_start: 0.9173 (OUTLIER) cc_final: 0.8629 (p) REVERT: S 323 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7464 (pm20) REVERT: S 400 PHE cc_start: 0.7851 (m-10) cc_final: 0.7648 (m-10) REVERT: S 410 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8082 (mtp) REVERT: S 438 PHE cc_start: 0.7716 (t80) cc_final: 0.7457 (m-10) REVERT: S 442 TYR cc_start: 0.8928 (t80) cc_final: 0.8342 (t80) REVERT: S 447 SER cc_start: 0.9011 (t) cc_final: 0.8720 (t) REVERT: S 484 THR cc_start: 0.8916 (m) cc_final: 0.8522 (p) REVERT: U 3 GLU cc_start: 0.6567 (mm-30) cc_final: 0.6289 (mm-30) REVERT: U 47 TRP cc_start: 0.8135 (t60) cc_final: 0.7378 (t60) REVERT: U 57 ASP cc_start: 0.7324 (t0) cc_final: 0.7043 (m-30) REVERT: U 95 TYR cc_start: 0.8653 (m-80) cc_final: 0.8369 (m-80) REVERT: V 2 ILE cc_start: 0.8598 (mt) cc_final: 0.8395 (mt) REVERT: V 48 GLN cc_start: 0.7385 (mp10) cc_final: 0.6733 (mp10) outliers start: 198 outliers final: 138 residues processed: 892 average time/residue: 0.3740 time to fit residues: 543.6613 Evaluate side-chains 899 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 736 time to evaluate : 3.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 451 TRP Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 293 LYS Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 457 ILE Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 259 HIS Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 410 MET Chi-restraints excluded: chain E residue 428 ASN Chi-restraints excluded: chain E residue 451 TRP Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 57 ARG Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain O residue 121 CYS Chi-restraints excluded: chain O residue 130 VAL Chi-restraints excluded: chain O residue 195 ILE Chi-restraints excluded: chain O residue 198 THR Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 234 LEU Chi-restraints excluded: chain O residue 238 PHE Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 283 CYS Chi-restraints excluded: chain O residue 338 GLU Chi-restraints excluded: chain O residue 365 ILE Chi-restraints excluded: chain O residue 371 PHE Chi-restraints excluded: chain O residue 413 LEU Chi-restraints excluded: chain O residue 423 VAL Chi-restraints excluded: chain O residue 429 SER Chi-restraints excluded: chain O residue 451 TRP Chi-restraints excluded: chain O residue 466 LEU Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain Q residue 2 ARG Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 30 CYS Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 113 LEU Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 236 VAL Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 293 LYS Chi-restraints excluded: chain Q residue 313 THR Chi-restraints excluded: chain Q residue 356 VAL Chi-restraints excluded: chain Q residue 357 THR Chi-restraints excluded: chain Q residue 358 LYS Chi-restraints excluded: chain Q residue 371 PHE Chi-restraints excluded: chain Q residue 377 VAL Chi-restraints excluded: chain Q residue 380 ILE Chi-restraints excluded: chain Q residue 457 ILE Chi-restraints excluded: chain Q residue 466 LEU Chi-restraints excluded: chain Q residue 491 VAL Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain S residue 41 LEU Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 79 GLU Chi-restraints excluded: chain S residue 91 VAL Chi-restraints excluded: chain S residue 92 CYS Chi-restraints excluded: chain S residue 122 LEU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 181 LEU Chi-restraints excluded: chain S residue 187 THR Chi-restraints excluded: chain S residue 242 HIS Chi-restraints excluded: chain S residue 258 MET Chi-restraints excluded: chain S residue 259 HIS Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 305 VAL Chi-restraints excluded: chain S residue 318 ILE Chi-restraints excluded: chain S residue 323 GLU Chi-restraints excluded: chain S residue 356 VAL Chi-restraints excluded: chain S residue 410 MET Chi-restraints excluded: chain S residue 451 TRP Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain S residue 485 LEU Chi-restraints excluded: chain T residue 16 THR Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain U residue 53 SER Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 83 MET Chi-restraints excluded: chain U residue 91 THR Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 84 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 7 optimal weight: 7.9990 chunk 35 optimal weight: 0.0020 chunk 86 optimal weight: 0.2980 chunk 353 optimal weight: 20.0000 chunk 374 optimal weight: 20.0000 chunk 49 optimal weight: 6.9990 chunk 373 optimal weight: 20.0000 chunk 308 optimal weight: 20.0000 chunk 321 optimal weight: 20.0000 chunk 65 optimal weight: 4.9990 chunk 154 optimal weight: 20.0000 overall best weight: 4.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 ASN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 51 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.120613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.103386 restraints weight = 51989.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.106358 restraints weight = 25888.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.108291 restraints weight = 15855.814| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 30884 Z= 0.164 Angle : 0.723 14.108 41956 Z= 0.356 Chirality : 0.044 0.278 4928 Planarity : 0.004 0.068 5192 Dihedral : 9.105 105.013 4876 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 5.74 % Allowed : 22.69 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.37 (0.13), residues: 3846 helix: 1.31 (0.18), residues: 870 sheet: -1.40 (0.15), residues: 1102 loop : -1.65 (0.13), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Q 218 HIS 0.004 0.001 HIS O 144 PHE 0.026 0.002 PHE E 475 TYR 0.013 0.001 TYR C 90 ARG 0.008 0.001 ARG O 348 Details of bonding type rmsd link_NAG-ASN : bond 0.00408 ( 12) link_NAG-ASN : angle 2.37702 ( 36) link_BETA1-4 : bond 0.00345 ( 20) link_BETA1-4 : angle 2.30479 ( 60) link_ALPHA1-3 : bond 0.00857 ( 4) link_ALPHA1-3 : angle 2.72767 ( 12) hydrogen bonds : bond 0.04061 ( 1094) hydrogen bonds : angle 5.29847 ( 3036) link_BETA1-6 : bond 0.00898 ( 4) link_BETA1-6 : angle 2.97302 ( 12) SS BOND : bond 0.00805 ( 30) SS BOND : angle 2.94053 ( 60) covalent geometry : bond 0.00383 (30814) covalent geometry : angle 0.70434 (41776) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 951 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 766 time to evaluate : 3.587 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO B 72 " (corrupted residue). Skipping it. Corrupt residue: chain: B residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO P 72 " (corrupted residue). Skipping it. Corrupt residue: chain: P residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7116 (ttm110) REVERT: A 86 GLN cc_start: 0.7532 (tp40) cc_final: 0.7231 (mp10) REVERT: A 93 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7761 (pttp) REVERT: A 98 ASP cc_start: 0.8081 (p0) cc_final: 0.7628 (p0) REVERT: A 181 LEU cc_start: 0.8546 (tp) cc_final: 0.8069 (tp) REVERT: A 205 MET cc_start: 0.7735 (tpp) cc_final: 0.7505 (tpt) REVERT: A 238 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.7929 (m-10) REVERT: A 287 MET cc_start: 0.8550 (mtp) cc_final: 0.8075 (mtp) REVERT: A 299 MET cc_start: 0.6919 (mmm) cc_final: 0.6100 (mmm) REVERT: A 371 PHE cc_start: 0.9273 (OUTLIER) cc_final: 0.8573 (t80) REVERT: B 12 LEU cc_start: 0.6229 (OUTLIER) cc_final: 0.5708 (pp) REVERT: B 26 TRP cc_start: 0.6913 (m100) cc_final: 0.6630 (m-90) REVERT: B 28 GLN cc_start: 0.7763 (tp-100) cc_final: 0.7425 (tp-100) REVERT: B 61 VAL cc_start: 0.9210 (t) cc_final: 0.8926 (p) REVERT: C 34 MET cc_start: 0.8053 (ptp) cc_final: 0.7789 (ptp) REVERT: C 182 GLU cc_start: 0.7272 (tp30) cc_final: 0.6836 (tp30) REVERT: C 199 MET cc_start: 0.8164 (ptm) cc_final: 0.7823 (ptm) REVERT: C 258 MET cc_start: 0.8910 (tpp) cc_final: 0.8334 (tpp) REVERT: C 293 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8441 (pptt) REVERT: C 348 ARG cc_start: 0.8371 (ptm-80) cc_final: 0.7915 (ptm-80) REVERT: C 358 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.7069 (tppt) REVERT: C 380 ILE cc_start: 0.7981 (OUTLIER) cc_final: 0.7671 (tt) REVERT: C 436 GLN cc_start: 0.8724 (tm-30) cc_final: 0.8316 (tt0) REVERT: C 462 THR cc_start: 0.9086 (m) cc_final: 0.8786 (p) REVERT: D 12 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.8035 (pp) REVERT: D 18 THR cc_start: 0.8917 (p) cc_final: 0.8172 (t) REVERT: D 42 PHE cc_start: 0.8774 (t80) cc_final: 0.7969 (t80) REVERT: D 69 LEU cc_start: 0.8471 (mt) cc_final: 0.8229 (mt) REVERT: D 74 MET cc_start: 0.8774 (tpp) cc_final: 0.8266 (mmm) REVERT: E 8 ASN cc_start: 0.8024 (t0) cc_final: 0.7666 (t0) REVERT: E 20 TRP cc_start: 0.7766 (p90) cc_final: 0.6452 (p90) REVERT: E 108 PHE cc_start: 0.8732 (m-80) cc_final: 0.8359 (m-80) REVERT: E 122 LEU cc_start: 0.6835 (OUTLIER) cc_final: 0.6561 (tp) REVERT: E 176 TYR cc_start: 0.8841 (m-80) cc_final: 0.8446 (m-80) REVERT: E 181 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8693 (pp) REVERT: E 259 HIS cc_start: 0.8916 (OUTLIER) cc_final: 0.7163 (t70) REVERT: E 270 ASN cc_start: 0.6648 (t0) cc_final: 0.6246 (t0) REVERT: E 286 LYS cc_start: 0.8626 (ptpt) cc_final: 0.8233 (mtmm) REVERT: E 400 PHE cc_start: 0.7848 (m-10) cc_final: 0.7632 (m-10) REVERT: E 410 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8067 (mtp) REVERT: E 428 ASN cc_start: 0.8090 (m-40) cc_final: 0.7749 (t0) REVERT: E 442 TYR cc_start: 0.8937 (t80) cc_final: 0.8335 (t80) REVERT: E 447 SER cc_start: 0.8980 (t) cc_final: 0.8689 (t) REVERT: E 484 THR cc_start: 0.8823 (m) cc_final: 0.8311 (p) REVERT: H 3 GLU cc_start: 0.6612 (mm-30) cc_final: 0.6315 (mm-30) REVERT: H 47 TRP cc_start: 0.8291 (t60) cc_final: 0.7778 (t60) REVERT: H 95 TYR cc_start: 0.8659 (m-80) cc_final: 0.8442 (m-80) REVERT: L 48 GLN cc_start: 0.7212 (mp10) cc_final: 0.6406 (mp10) REVERT: O 57 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7087 (ttm110) REVERT: O 93 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7835 (pttp) REVERT: O 98 ASP cc_start: 0.8063 (p0) cc_final: 0.7644 (p0) REVERT: O 181 LEU cc_start: 0.8520 (tp) cc_final: 0.8038 (tp) REVERT: O 238 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.7912 (m-10) REVERT: O 287 MET cc_start: 0.8590 (mtp) cc_final: 0.8158 (mtp) REVERT: O 299 MET cc_start: 0.6960 (mmm) cc_final: 0.6152 (mmm) REVERT: O 371 PHE cc_start: 0.9243 (OUTLIER) cc_final: 0.8593 (t80) REVERT: O 392 LYS cc_start: 0.8393 (pttp) cc_final: 0.8176 (ptpt) REVERT: P 12 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.6182 (pp) REVERT: P 26 TRP cc_start: 0.6916 (m100) cc_final: 0.6568 (m-90) REVERT: P 69 LEU cc_start: 0.8369 (tp) cc_final: 0.7962 (mp) REVERT: P 74 MET cc_start: 0.5913 (mmp) cc_final: 0.5366 (mmt) REVERT: Q 34 MET cc_start: 0.8044 (ptp) cc_final: 0.7774 (ptp) REVERT: Q 79 GLU cc_start: 0.7437 (mp0) cc_final: 0.7233 (mp0) REVERT: Q 194 MET cc_start: 0.8216 (ttm) cc_final: 0.7968 (mmm) REVERT: Q 199 MET cc_start: 0.8387 (ptm) cc_final: 0.8051 (ptm) REVERT: Q 293 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8295 (pptt) REVERT: Q 348 ARG cc_start: 0.8389 (ptm-80) cc_final: 0.7940 (ptm-80) REVERT: Q 358 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7250 (tppt) REVERT: Q 380 ILE cc_start: 0.7981 (OUTLIER) cc_final: 0.7669 (tt) REVERT: Q 436 GLN cc_start: 0.8351 (tm-30) cc_final: 0.7867 (tm-30) REVERT: Q 462 THR cc_start: 0.9085 (m) cc_final: 0.8782 (p) REVERT: R 12 LEU cc_start: 0.7818 (pp) cc_final: 0.7514 (pp) REVERT: R 18 THR cc_start: 0.8916 (p) cc_final: 0.8197 (t) REVERT: R 35 TRP cc_start: 0.9034 (t60) cc_final: 0.8518 (t60) REVERT: R 42 PHE cc_start: 0.8776 (t80) cc_final: 0.8007 (t80) REVERT: R 64 PHE cc_start: 0.9373 (t80) cc_final: 0.9071 (t80) REVERT: R 69 LEU cc_start: 0.8397 (mt) cc_final: 0.8196 (mt) REVERT: R 74 MET cc_start: 0.8836 (tpp) cc_final: 0.8351 (mmm) REVERT: S 8 ASN cc_start: 0.8208 (t0) cc_final: 0.7944 (t0) REVERT: S 20 TRP cc_start: 0.7781 (p90) cc_final: 0.6466 (p90) REVERT: S 59 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8228 (mt) REVERT: S 108 PHE cc_start: 0.8731 (m-80) cc_final: 0.7992 (m-80) REVERT: S 181 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8781 (pp) REVERT: S 259 HIS cc_start: 0.8903 (OUTLIER) cc_final: 0.7042 (t70) REVERT: S 305 VAL cc_start: 0.9164 (OUTLIER) cc_final: 0.8593 (p) REVERT: S 323 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7431 (pm20) REVERT: S 400 PHE cc_start: 0.7844 (m-10) cc_final: 0.7629 (m-10) REVERT: S 410 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8064 (mtp) REVERT: S 438 PHE cc_start: 0.7705 (t80) cc_final: 0.7440 (m-10) REVERT: S 442 TYR cc_start: 0.8943 (t80) cc_final: 0.8339 (t80) REVERT: S 447 SER cc_start: 0.8965 (t) cc_final: 0.8670 (t) REVERT: S 484 THR cc_start: 0.8816 (m) cc_final: 0.8305 (p) REVERT: U 3 GLU cc_start: 0.6620 (mm-30) cc_final: 0.6332 (mm-30) REVERT: U 47 TRP cc_start: 0.8304 (t60) cc_final: 0.7791 (t60) REVERT: U 57 ASP cc_start: 0.7277 (t0) cc_final: 0.7027 (m-30) REVERT: U 95 TYR cc_start: 0.8655 (m-80) cc_final: 0.8441 (m-80) outliers start: 185 outliers final: 134 residues processed: 884 average time/residue: 0.3750 time to fit residues: 538.9751 Evaluate side-chains 899 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 738 time to evaluate : 3.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 451 TRP Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 293 LYS Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 457 ILE Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 259 HIS Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 410 MET Chi-restraints excluded: chain E residue 451 TRP Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 57 ARG Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain O residue 93 LYS Chi-restraints excluded: chain O residue 121 CYS Chi-restraints excluded: chain O residue 130 VAL Chi-restraints excluded: chain O residue 195 ILE Chi-restraints excluded: chain O residue 198 THR Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 238 PHE Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 275 SER Chi-restraints excluded: chain O residue 283 CYS Chi-restraints excluded: chain O residue 338 GLU Chi-restraints excluded: chain O residue 365 ILE Chi-restraints excluded: chain O residue 371 PHE Chi-restraints excluded: chain O residue 413 LEU Chi-restraints excluded: chain O residue 423 VAL Chi-restraints excluded: chain O residue 429 SER Chi-restraints excluded: chain O residue 451 TRP Chi-restraints excluded: chain O residue 460 LEU Chi-restraints excluded: chain O residue 466 LEU Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 30 CYS Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 113 LEU Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 201 ASN Chi-restraints excluded: chain Q residue 236 VAL Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 293 LYS Chi-restraints excluded: chain Q residue 350 ILE Chi-restraints excluded: chain Q residue 356 VAL Chi-restraints excluded: chain Q residue 357 THR Chi-restraints excluded: chain Q residue 358 LYS Chi-restraints excluded: chain Q residue 371 PHE Chi-restraints excluded: chain Q residue 380 ILE Chi-restraints excluded: chain Q residue 457 ILE Chi-restraints excluded: chain Q residue 491 VAL Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain S residue 26 GLU Chi-restraints excluded: chain S residue 41 LEU Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 79 GLU Chi-restraints excluded: chain S residue 91 VAL Chi-restraints excluded: chain S residue 92 CYS Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 181 LEU Chi-restraints excluded: chain S residue 187 THR Chi-restraints excluded: chain S residue 242 HIS Chi-restraints excluded: chain S residue 258 MET Chi-restraints excluded: chain S residue 259 HIS Chi-restraints excluded: chain S residue 305 VAL Chi-restraints excluded: chain S residue 318 ILE Chi-restraints excluded: chain S residue 323 GLU Chi-restraints excluded: chain S residue 356 VAL Chi-restraints excluded: chain S residue 410 MET Chi-restraints excluded: chain S residue 451 TRP Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain S residue 485 LEU Chi-restraints excluded: chain T residue 16 THR Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain U residue 22 CYS Chi-restraints excluded: chain U residue 25 SER Chi-restraints excluded: chain U residue 53 SER Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 83 MET Chi-restraints excluded: chain U residue 91 THR Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 84 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 207 optimal weight: 10.0000 chunk 353 optimal weight: 20.0000 chunk 208 optimal weight: 0.6980 chunk 367 optimal weight: 8.9990 chunk 167 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 307 optimal weight: 7.9990 chunk 148 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 29 optimal weight: 20.0000 chunk 369 optimal weight: 10.0000 overall best weight: 6.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 HIS E 428 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 GLN ** L 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 8 ASN ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 242 HIS ** T 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.119026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.101671 restraints weight = 52320.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.104579 restraints weight = 26090.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.106515 restraints weight = 16117.344| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 30884 Z= 0.218 Angle : 0.765 15.537 41956 Z= 0.379 Chirality : 0.046 0.319 4928 Planarity : 0.004 0.061 5192 Dihedral : 8.967 103.065 4876 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 5.71 % Allowed : 23.15 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.42 (0.13), residues: 3846 helix: 1.15 (0.18), residues: 882 sheet: -1.36 (0.15), residues: 1090 loop : -1.69 (0.13), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 218 HIS 0.006 0.001 HIS O 144 PHE 0.025 0.002 PHE E 475 TYR 0.014 0.001 TYR S 176 ARG 0.008 0.001 ARG O 348 Details of bonding type rmsd link_NAG-ASN : bond 0.00500 ( 12) link_NAG-ASN : angle 2.64201 ( 36) link_BETA1-4 : bond 0.00388 ( 20) link_BETA1-4 : angle 2.34305 ( 60) link_ALPHA1-3 : bond 0.00806 ( 4) link_ALPHA1-3 : angle 2.79537 ( 12) hydrogen bonds : bond 0.04248 ( 1094) hydrogen bonds : angle 5.35223 ( 3036) link_BETA1-6 : bond 0.00778 ( 4) link_BETA1-6 : angle 2.86785 ( 12) SS BOND : bond 0.00613 ( 30) SS BOND : angle 3.11842 ( 60) covalent geometry : bond 0.00514 (30814) covalent geometry : angle 0.74539 (41776) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 929 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 745 time to evaluate : 3.435 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PRO B 72 " (corrupted residue). Skipping it. Corrupt residue: chain: B residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO P 72 " (corrupted residue). Skipping it. Corrupt residue: chain: P residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7014 (ttm110) REVERT: A 93 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7988 (pttp) REVERT: A 98 ASP cc_start: 0.8082 (p0) cc_final: 0.7682 (p0) REVERT: A 168 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8661 (p) REVERT: A 181 LEU cc_start: 0.8623 (tp) cc_final: 0.8073 (tp) REVERT: A 238 PHE cc_start: 0.8851 (OUTLIER) cc_final: 0.7997 (m-10) REVERT: A 287 MET cc_start: 0.8561 (mtp) cc_final: 0.8094 (mtp) REVERT: A 299 MET cc_start: 0.6952 (mmm) cc_final: 0.6225 (mtt) REVERT: A 371 PHE cc_start: 0.9290 (OUTLIER) cc_final: 0.8516 (t80) REVERT: A 392 LYS cc_start: 0.8394 (pttp) cc_final: 0.8181 (ptpt) REVERT: B 12 LEU cc_start: 0.6844 (OUTLIER) cc_final: 0.6188 (pp) REVERT: B 26 TRP cc_start: 0.6949 (m100) cc_final: 0.6678 (m-90) REVERT: B 28 GLN cc_start: 0.7746 (tp-100) cc_final: 0.7385 (tp-100) REVERT: B 61 VAL cc_start: 0.9213 (t) cc_final: 0.8915 (p) REVERT: B 74 MET cc_start: 0.6218 (tpp) cc_final: 0.5716 (tpp) REVERT: C 34 MET cc_start: 0.8100 (ptp) cc_final: 0.7814 (ptp) REVERT: C 182 GLU cc_start: 0.7367 (tp30) cc_final: 0.6938 (tp30) REVERT: C 199 MET cc_start: 0.8171 (ptm) cc_final: 0.7877 (ptm) REVERT: C 258 MET cc_start: 0.8911 (tpp) cc_final: 0.8357 (tpp) REVERT: C 293 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8211 (pptt) REVERT: C 348 ARG cc_start: 0.8407 (ptm-80) cc_final: 0.7933 (ptm-80) REVERT: C 358 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7228 (tppt) REVERT: C 380 ILE cc_start: 0.8015 (OUTLIER) cc_final: 0.7697 (tt) REVERT: C 462 THR cc_start: 0.9084 (m) cc_final: 0.8811 (p) REVERT: D 12 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7826 (pp) REVERT: D 42 PHE cc_start: 0.8793 (t80) cc_final: 0.8156 (t80) REVERT: D 69 LEU cc_start: 0.8517 (mt) cc_final: 0.8294 (mt) REVERT: D 71 THR cc_start: 0.8834 (m) cc_final: 0.8472 (p) REVERT: D 74 MET cc_start: 0.8787 (tpp) cc_final: 0.8311 (mmm) REVERT: E 8 ASN cc_start: 0.8051 (t0) cc_final: 0.7712 (t0) REVERT: E 20 TRP cc_start: 0.7892 (p90) cc_final: 0.6377 (p90) REVERT: E 108 PHE cc_start: 0.8782 (m-80) cc_final: 0.8356 (m-80) REVERT: E 122 LEU cc_start: 0.6868 (OUTLIER) cc_final: 0.6615 (tp) REVERT: E 175 GLU cc_start: 0.7174 (tp30) cc_final: 0.6871 (tp30) REVERT: E 176 TYR cc_start: 0.8881 (m-80) cc_final: 0.8570 (m-80) REVERT: E 181 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8750 (pp) REVERT: E 259 HIS cc_start: 0.8980 (OUTLIER) cc_final: 0.7081 (t70) REVERT: E 270 ASN cc_start: 0.6722 (t0) cc_final: 0.6500 (t0) REVERT: E 286 LYS cc_start: 0.8632 (ptpt) cc_final: 0.8269 (mtmm) REVERT: E 323 GLU cc_start: 0.7519 (tt0) cc_final: 0.7139 (pt0) REVERT: E 400 PHE cc_start: 0.7854 (m-10) cc_final: 0.7643 (m-10) REVERT: E 410 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8063 (mtp) REVERT: E 442 TYR cc_start: 0.8963 (t80) cc_final: 0.8327 (t80) REVERT: E 447 SER cc_start: 0.9063 (t) cc_final: 0.8768 (t) REVERT: E 484 THR cc_start: 0.8918 (m) cc_final: 0.8505 (p) REVERT: H 47 TRP cc_start: 0.8161 (t60) cc_final: 0.7350 (t60) REVERT: H 95 TYR cc_start: 0.8628 (m-80) cc_final: 0.8427 (m-80) REVERT: L 48 GLN cc_start: 0.7135 (mp10) cc_final: 0.6767 (mp10) REVERT: O 57 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7063 (ttm110) REVERT: O 93 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8028 (pttp) REVERT: O 98 ASP cc_start: 0.8071 (p0) cc_final: 0.7698 (p0) REVERT: O 168 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8614 (p) REVERT: O 181 LEU cc_start: 0.8611 (tp) cc_final: 0.8066 (tp) REVERT: O 201 ASN cc_start: 0.7475 (m-40) cc_final: 0.6402 (t0) REVERT: O 238 PHE cc_start: 0.8815 (OUTLIER) cc_final: 0.7959 (m-10) REVERT: O 287 MET cc_start: 0.8541 (mtp) cc_final: 0.8101 (mtp) REVERT: O 299 MET cc_start: 0.7004 (mmm) cc_final: 0.6290 (mtt) REVERT: O 371 PHE cc_start: 0.9263 (OUTLIER) cc_final: 0.8542 (t80) REVERT: O 392 LYS cc_start: 0.8391 (pttp) cc_final: 0.8161 (ptpt) REVERT: P 12 LEU cc_start: 0.6799 (OUTLIER) cc_final: 0.6137 (pp) REVERT: P 26 TRP cc_start: 0.6961 (m100) cc_final: 0.6646 (m-90) REVERT: P 74 MET cc_start: 0.5883 (mmp) cc_final: 0.5330 (mmt) REVERT: Q 34 MET cc_start: 0.8078 (ptp) cc_final: 0.7796 (ptp) REVERT: Q 199 MET cc_start: 0.8404 (ptm) cc_final: 0.8077 (ptm) REVERT: Q 293 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8216 (pptt) REVERT: Q 348 ARG cc_start: 0.8425 (ptm-80) cc_final: 0.7975 (ptm-80) REVERT: Q 358 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7201 (tppt) REVERT: Q 380 ILE cc_start: 0.8016 (mt) cc_final: 0.7697 (tt) REVERT: Q 436 GLN cc_start: 0.8348 (tm-30) cc_final: 0.7823 (tm-30) REVERT: Q 462 THR cc_start: 0.9089 (m) cc_final: 0.8812 (p) REVERT: R 35 TRP cc_start: 0.9035 (t60) cc_final: 0.8774 (t60) REVERT: R 42 PHE cc_start: 0.8794 (t80) cc_final: 0.8126 (t80) REVERT: R 69 LEU cc_start: 0.8444 (mt) cc_final: 0.8226 (mt) REVERT: R 74 MET cc_start: 0.8782 (tpp) cc_final: 0.8286 (mmm) REVERT: S 8 ASN cc_start: 0.8116 (t0) cc_final: 0.7779 (t0) REVERT: S 20 TRP cc_start: 0.7921 (p90) cc_final: 0.6447 (p90) REVERT: S 59 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8072 (mt) REVERT: S 108 PHE cc_start: 0.8783 (m-80) cc_final: 0.8040 (m-80) REVERT: S 122 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6606 (tp) REVERT: S 181 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8832 (pp) REVERT: S 259 HIS cc_start: 0.8945 (OUTLIER) cc_final: 0.7016 (t70) REVERT: S 305 VAL cc_start: 0.9164 (OUTLIER) cc_final: 0.8566 (p) REVERT: S 323 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7384 (pm20) REVERT: S 400 PHE cc_start: 0.7853 (m-10) cc_final: 0.7644 (m-10) REVERT: S 410 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8070 (mtp) REVERT: S 438 PHE cc_start: 0.7754 (t80) cc_final: 0.7466 (m-10) REVERT: S 442 TYR cc_start: 0.8971 (t80) cc_final: 0.8364 (t80) REVERT: S 447 SER cc_start: 0.9031 (t) cc_final: 0.8756 (t) REVERT: S 484 THR cc_start: 0.8916 (m) cc_final: 0.8509 (p) REVERT: U 3 GLU cc_start: 0.6319 (mm-30) cc_final: 0.6019 (mm-30) REVERT: U 47 TRP cc_start: 0.8195 (t60) cc_final: 0.7318 (t60) REVERT: U 57 ASP cc_start: 0.7188 (t0) cc_final: 0.6774 (t0) REVERT: U 95 TYR cc_start: 0.8631 (m-80) cc_final: 0.8428 (m-80) REVERT: V 27 GLN cc_start: 0.8298 (pt0) cc_final: 0.8087 (pt0) REVERT: V 48 GLN cc_start: 0.7355 (mp10) cc_final: 0.7044 (mp10) outliers start: 184 outliers final: 142 residues processed: 867 average time/residue: 0.3784 time to fit residues: 534.1941 Evaluate side-chains 903 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 732 time to evaluate : 3.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 451 TRP Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 293 LYS Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 457 ILE Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 259 HIS Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 410 MET Chi-restraints excluded: chain E residue 451 TRP Chi-restraints excluded: chain E residue 455 ILE Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 57 ARG Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain O residue 93 LYS Chi-restraints excluded: chain O residue 121 CYS Chi-restraints excluded: chain O residue 130 VAL Chi-restraints excluded: chain O residue 168 THR Chi-restraints excluded: chain O residue 195 ILE Chi-restraints excluded: chain O residue 198 THR Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain O residue 238 PHE Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 275 SER Chi-restraints excluded: chain O residue 283 CYS Chi-restraints excluded: chain O residue 338 GLU Chi-restraints excluded: chain O residue 365 ILE Chi-restraints excluded: chain O residue 371 PHE Chi-restraints excluded: chain O residue 413 LEU Chi-restraints excluded: chain O residue 423 VAL Chi-restraints excluded: chain O residue 429 SER Chi-restraints excluded: chain O residue 451 TRP Chi-restraints excluded: chain O residue 466 LEU Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 30 CYS Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 113 LEU Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 135 LEU Chi-restraints excluded: chain Q residue 201 ASN Chi-restraints excluded: chain Q residue 236 VAL Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 293 LYS Chi-restraints excluded: chain Q residue 350 ILE Chi-restraints excluded: chain Q residue 356 VAL Chi-restraints excluded: chain Q residue 357 THR Chi-restraints excluded: chain Q residue 358 LYS Chi-restraints excluded: chain Q residue 371 PHE Chi-restraints excluded: chain Q residue 377 VAL Chi-restraints excluded: chain Q residue 457 ILE Chi-restraints excluded: chain Q residue 466 LEU Chi-restraints excluded: chain Q residue 491 VAL Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain S residue 26 GLU Chi-restraints excluded: chain S residue 41 LEU Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 91 VAL Chi-restraints excluded: chain S residue 122 LEU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 181 LEU Chi-restraints excluded: chain S residue 187 THR Chi-restraints excluded: chain S residue 242 HIS Chi-restraints excluded: chain S residue 258 MET Chi-restraints excluded: chain S residue 259 HIS Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 305 VAL Chi-restraints excluded: chain S residue 318 ILE Chi-restraints excluded: chain S residue 323 GLU Chi-restraints excluded: chain S residue 336 SER Chi-restraints excluded: chain S residue 356 VAL Chi-restraints excluded: chain S residue 410 MET Chi-restraints excluded: chain S residue 451 TRP Chi-restraints excluded: chain S residue 455 ILE Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain S residue 485 LEU Chi-restraints excluded: chain T residue 10 MET Chi-restraints excluded: chain T residue 16 THR Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain U residue 22 CYS Chi-restraints excluded: chain U residue 34 MET Chi-restraints excluded: chain U residue 53 SER Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 83 MET Chi-restraints excluded: chain U residue 91 THR Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 84 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 156 optimal weight: 10.0000 chunk 309 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 chunk 127 optimal weight: 8.9990 chunk 332 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 293 optimal weight: 8.9990 chunk 288 optimal weight: 5.9990 chunk 207 optimal weight: 10.0000 chunk 338 optimal weight: 7.9990 chunk 323 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 144 HIS A 209 GLN ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 GLN ** O 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 51 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.118306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.101055 restraints weight = 52338.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.103965 restraints weight = 26073.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.105856 restraints weight = 16041.775| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 30884 Z= 0.242 Angle : 0.789 15.307 41956 Z= 0.392 Chirality : 0.047 0.301 4928 Planarity : 0.005 0.061 5192 Dihedral : 8.878 103.706 4876 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 5.90 % Allowed : 23.40 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.48 (0.13), residues: 3846 helix: 1.09 (0.18), residues: 882 sheet: -1.39 (0.15), residues: 1090 loop : -1.73 (0.13), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP O 229 HIS 0.006 0.001 HIS A 144 PHE 0.027 0.002 PHE E 475 TYR 0.015 0.002 TYR U 60 ARG 0.009 0.001 ARG O 348 Details of bonding type rmsd link_NAG-ASN : bond 0.00532 ( 12) link_NAG-ASN : angle 2.76656 ( 36) link_BETA1-4 : bond 0.00408 ( 20) link_BETA1-4 : angle 2.40025 ( 60) link_ALPHA1-3 : bond 0.00801 ( 4) link_ALPHA1-3 : angle 2.75770 ( 12) hydrogen bonds : bond 0.04322 ( 1094) hydrogen bonds : angle 5.40251 ( 3036) link_BETA1-6 : bond 0.00766 ( 4) link_BETA1-6 : angle 2.71171 ( 12) SS BOND : bond 0.00639 ( 30) SS BOND : angle 3.13968 ( 60) covalent geometry : bond 0.00568 (30814) covalent geometry : angle 0.76894 (41776) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 934 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 744 time to evaluate : 3.747 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PRO B 72 " (corrupted residue). Skipping it. Corrupt residue: chain: B residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO P 72 " (corrupted residue). Skipping it. Corrupt residue: chain: P residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 THR cc_start: 0.8923 (OUTLIER) cc_final: 0.8677 (t) REVERT: A 57 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7007 (ttm110) REVERT: A 93 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7990 (pttp) REVERT: A 98 ASP cc_start: 0.8083 (p0) cc_final: 0.7718 (p0) REVERT: A 168 THR cc_start: 0.9146 (OUTLIER) cc_final: 0.8628 (p) REVERT: A 181 LEU cc_start: 0.8650 (tp) cc_final: 0.8094 (tp) REVERT: A 238 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.8060 (m-10) REVERT: A 287 MET cc_start: 0.8558 (mtp) cc_final: 0.8096 (mtp) REVERT: A 299 MET cc_start: 0.6968 (mmm) cc_final: 0.6306 (mtt) REVERT: A 371 PHE cc_start: 0.9283 (OUTLIER) cc_final: 0.8428 (t80) REVERT: A 390 TYR cc_start: 0.8837 (t80) cc_final: 0.8390 (t80) REVERT: A 392 LYS cc_start: 0.8399 (pttp) cc_final: 0.8194 (ptpt) REVERT: B 12 LEU cc_start: 0.6857 (OUTLIER) cc_final: 0.6194 (pp) REVERT: B 26 TRP cc_start: 0.7027 (m100) cc_final: 0.6789 (m-90) REVERT: B 28 GLN cc_start: 0.7730 (tp-100) cc_final: 0.7357 (tp-100) REVERT: B 33 GLU cc_start: 0.6997 (mm-30) cc_final: 0.6496 (pt0) REVERT: B 61 VAL cc_start: 0.9215 (t) cc_final: 0.8907 (p) REVERT: C 182 GLU cc_start: 0.7381 (tp30) cc_final: 0.6939 (tp30) REVERT: C 199 MET cc_start: 0.8202 (ptm) cc_final: 0.7916 (ptm) REVERT: C 258 MET cc_start: 0.8917 (tpp) cc_final: 0.8361 (tpp) REVERT: C 293 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8105 (pptt) REVERT: C 348 ARG cc_start: 0.8348 (ptm-80) cc_final: 0.7876 (ptm-80) REVERT: C 358 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7261 (tppt) REVERT: C 380 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7709 (tt) REVERT: C 462 THR cc_start: 0.9092 (m) cc_final: 0.8815 (p) REVERT: D 12 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7948 (pp) REVERT: D 42 PHE cc_start: 0.8804 (t80) cc_final: 0.8141 (t80) REVERT: D 69 LEU cc_start: 0.8532 (mt) cc_final: 0.8251 (mt) REVERT: D 74 MET cc_start: 0.8802 (tpp) cc_final: 0.8334 (mmm) REVERT: E 8 ASN cc_start: 0.8096 (t0) cc_final: 0.7749 (t0) REVERT: E 20 TRP cc_start: 0.7923 (p90) cc_final: 0.6327 (p90) REVERT: E 108 PHE cc_start: 0.8804 (m-80) cc_final: 0.8077 (m-80) REVERT: E 122 LEU cc_start: 0.6908 (OUTLIER) cc_final: 0.6657 (tp) REVERT: E 175 GLU cc_start: 0.7214 (tp30) cc_final: 0.6911 (tp30) REVERT: E 176 TYR cc_start: 0.8895 (m-80) cc_final: 0.8576 (m-80) REVERT: E 181 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8764 (pp) REVERT: E 259 HIS cc_start: 0.8976 (OUTLIER) cc_final: 0.7076 (t70) REVERT: E 270 ASN cc_start: 0.6770 (t0) cc_final: 0.6548 (t0) REVERT: E 286 LYS cc_start: 0.8623 (ptpt) cc_final: 0.8187 (mtmt) REVERT: E 323 GLU cc_start: 0.7549 (tt0) cc_final: 0.7184 (pt0) REVERT: E 400 PHE cc_start: 0.7857 (m-10) cc_final: 0.7653 (m-10) REVERT: E 410 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8074 (mtp) REVERT: E 442 TYR cc_start: 0.8990 (t80) cc_final: 0.8372 (t80) REVERT: E 447 SER cc_start: 0.9074 (t) cc_final: 0.8790 (t) REVERT: E 484 THR cc_start: 0.8927 (m) cc_final: 0.8525 (p) REVERT: H 47 TRP cc_start: 0.8223 (t60) cc_final: 0.7290 (t60) REVERT: H 90 ASP cc_start: 0.7696 (t0) cc_final: 0.7333 (t0) REVERT: L 48 GLN cc_start: 0.7490 (mp10) cc_final: 0.7190 (mp10) REVERT: O 57 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7013 (ttm110) REVERT: O 93 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8045 (pttp) REVERT: O 98 ASP cc_start: 0.8071 (p0) cc_final: 0.7737 (p0) REVERT: O 168 THR cc_start: 0.9146 (OUTLIER) cc_final: 0.8632 (p) REVERT: O 181 LEU cc_start: 0.8632 (tp) cc_final: 0.8084 (tp) REVERT: O 201 ASN cc_start: 0.7834 (m-40) cc_final: 0.6572 (t0) REVERT: O 238 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.8024 (m-10) REVERT: O 287 MET cc_start: 0.8529 (mtp) cc_final: 0.8073 (mtp) REVERT: O 299 MET cc_start: 0.7007 (mmm) cc_final: 0.6340 (mtt) REVERT: O 371 PHE cc_start: 0.9262 (OUTLIER) cc_final: 0.8453 (t80) REVERT: O 392 LYS cc_start: 0.8387 (pttp) cc_final: 0.8162 (ptpt) REVERT: P 12 LEU cc_start: 0.6794 (OUTLIER) cc_final: 0.6122 (pp) REVERT: P 26 TRP cc_start: 0.7042 (m100) cc_final: 0.6710 (m-90) REVERT: P 74 MET cc_start: 0.5570 (mmp) cc_final: 0.4725 (mmt) REVERT: Q 199 MET cc_start: 0.8429 (ptm) cc_final: 0.8123 (ptm) REVERT: Q 293 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8096 (pptt) REVERT: Q 348 ARG cc_start: 0.8420 (ptm-80) cc_final: 0.7971 (ptm-80) REVERT: Q 358 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7342 (tppt) REVERT: Q 380 ILE cc_start: 0.8022 (mt) cc_final: 0.7704 (tt) REVERT: Q 462 THR cc_start: 0.9093 (m) cc_final: 0.8817 (p) REVERT: R 35 TRP cc_start: 0.9037 (t60) cc_final: 0.8742 (t60) REVERT: R 42 PHE cc_start: 0.8798 (t80) cc_final: 0.8126 (t80) REVERT: R 69 LEU cc_start: 0.8466 (mt) cc_final: 0.8193 (mt) REVERT: R 74 MET cc_start: 0.8793 (tpp) cc_final: 0.8312 (mmm) REVERT: S 8 ASN cc_start: 0.8128 (t0) cc_final: 0.7798 (t0) REVERT: S 20 TRP cc_start: 0.7950 (p90) cc_final: 0.6380 (p90) REVERT: S 59 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8093 (mt) REVERT: S 108 PHE cc_start: 0.8807 (m-80) cc_final: 0.8082 (m-80) REVERT: S 122 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6633 (tp) REVERT: S 259 HIS cc_start: 0.8937 (OUTLIER) cc_final: 0.6950 (t70) REVERT: S 305 VAL cc_start: 0.9167 (OUTLIER) cc_final: 0.8554 (p) REVERT: S 323 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7359 (pm20) REVERT: S 400 PHE cc_start: 0.7858 (m-10) cc_final: 0.7654 (m-10) REVERT: S 410 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8081 (mtp) REVERT: S 438 PHE cc_start: 0.7807 (t80) cc_final: 0.7458 (m-10) REVERT: S 442 TYR cc_start: 0.8989 (t80) cc_final: 0.8390 (t80) REVERT: S 447 SER cc_start: 0.9052 (t) cc_final: 0.8776 (t) REVERT: S 484 THR cc_start: 0.8854 (m) cc_final: 0.8458 (p) REVERT: U 47 TRP cc_start: 0.8303 (t60) cc_final: 0.7338 (t60) REVERT: U 57 ASP cc_start: 0.7288 (t0) cc_final: 0.6923 (t0) REVERT: U 90 ASP cc_start: 0.7693 (t0) cc_final: 0.7333 (t0) REVERT: V 27 GLN cc_start: 0.8289 (pt0) cc_final: 0.8023 (pt0) REVERT: V 48 GLN cc_start: 0.7346 (mp10) cc_final: 0.7052 (mp10) outliers start: 190 outliers final: 144 residues processed: 869 average time/residue: 0.4007 time to fit residues: 567.2463 Evaluate side-chains 912 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 739 time to evaluate : 3.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 451 TRP Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 293 LYS Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 457 ILE Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 259 HIS Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 410 MET Chi-restraints excluded: chain E residue 451 TRP Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 57 ARG Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain O residue 93 LYS Chi-restraints excluded: chain O residue 121 CYS Chi-restraints excluded: chain O residue 130 VAL Chi-restraints excluded: chain O residue 168 THR Chi-restraints excluded: chain O residue 195 ILE Chi-restraints excluded: chain O residue 198 THR Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 233 GLU Chi-restraints excluded: chain O residue 238 PHE Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 275 SER Chi-restraints excluded: chain O residue 283 CYS Chi-restraints excluded: chain O residue 338 GLU Chi-restraints excluded: chain O residue 365 ILE Chi-restraints excluded: chain O residue 371 PHE Chi-restraints excluded: chain O residue 413 LEU Chi-restraints excluded: chain O residue 423 VAL Chi-restraints excluded: chain O residue 429 SER Chi-restraints excluded: chain O residue 451 TRP Chi-restraints excluded: chain O residue 466 LEU Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 67 LEU Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 30 CYS Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 113 LEU Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 135 LEU Chi-restraints excluded: chain Q residue 201 ASN Chi-restraints excluded: chain Q residue 236 VAL Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 293 LYS Chi-restraints excluded: chain Q residue 350 ILE Chi-restraints excluded: chain Q residue 356 VAL Chi-restraints excluded: chain Q residue 357 THR Chi-restraints excluded: chain Q residue 358 LYS Chi-restraints excluded: chain Q residue 371 PHE Chi-restraints excluded: chain Q residue 457 ILE Chi-restraints excluded: chain Q residue 466 LEU Chi-restraints excluded: chain Q residue 491 VAL Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain S residue 26 GLU Chi-restraints excluded: chain S residue 41 LEU Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 91 VAL Chi-restraints excluded: chain S residue 92 CYS Chi-restraints excluded: chain S residue 122 LEU Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 181 LEU Chi-restraints excluded: chain S residue 187 THR Chi-restraints excluded: chain S residue 242 HIS Chi-restraints excluded: chain S residue 258 MET Chi-restraints excluded: chain S residue 259 HIS Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 305 VAL Chi-restraints excluded: chain S residue 318 ILE Chi-restraints excluded: chain S residue 323 GLU Chi-restraints excluded: chain S residue 336 SER Chi-restraints excluded: chain S residue 356 VAL Chi-restraints excluded: chain S residue 410 MET Chi-restraints excluded: chain S residue 451 TRP Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain S residue 485 LEU Chi-restraints excluded: chain T residue 16 THR Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain U residue 22 CYS Chi-restraints excluded: chain U residue 34 MET Chi-restraints excluded: chain U residue 53 SER Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 83 MET Chi-restraints excluded: chain U residue 91 THR Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 84 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 132 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 334 optimal weight: 10.0000 chunk 247 optimal weight: 30.0000 chunk 2 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 203 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 86 optimal weight: 8.9990 chunk 169 optimal weight: 6.9990 chunk 305 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 GLN ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 HIS ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN ** O 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 209 GLN ** O 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 46 GLN ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.121417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.104279 restraints weight = 51719.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.107213 restraints weight = 25595.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.109136 restraints weight = 15732.868| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 30884 Z= 0.143 Angle : 0.724 15.787 41956 Z= 0.357 Chirality : 0.044 0.280 4928 Planarity : 0.004 0.062 5192 Dihedral : 8.394 100.301 4876 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.56 % Allowed : 24.83 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.32 (0.13), residues: 3846 helix: 1.31 (0.18), residues: 882 sheet: -1.33 (0.15), residues: 1114 loop : -1.65 (0.13), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 229 HIS 0.004 0.001 HIS A 94 PHE 0.029 0.001 PHE E 475 TYR 0.011 0.001 TYR U 94 ARG 0.008 0.000 ARG A 348 Details of bonding type rmsd link_NAG-ASN : bond 0.00403 ( 12) link_NAG-ASN : angle 2.30938 ( 36) link_BETA1-4 : bond 0.00337 ( 20) link_BETA1-4 : angle 2.24505 ( 60) link_ALPHA1-3 : bond 0.00898 ( 4) link_ALPHA1-3 : angle 2.53699 ( 12) hydrogen bonds : bond 0.03952 ( 1094) hydrogen bonds : angle 5.22991 ( 3036) link_BETA1-6 : bond 0.00882 ( 4) link_BETA1-6 : angle 2.28627 ( 12) SS BOND : bond 0.00555 ( 30) SS BOND : angle 2.79243 ( 60) covalent geometry : bond 0.00329 (30814) covalent geometry : angle 0.70665 (41776) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11607.02 seconds wall clock time: 203 minutes 26.97 seconds (12206.97 seconds total)