Starting phenix.real_space_refine on Wed Jun 25 22:46:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jn5_36433/06_2025/8jn5_36433.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jn5_36433/06_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_36433/06_2025/8jn5_36433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jn5_36433/06_2025/8jn5_36433.map" model { file = "/net/cci-nas-00/data/ceres_data/8jn5_36433/06_2025/8jn5_36433.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jn5_36433/06_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 18.00, per 1000 atoms: 0.60 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: 7.85 Conformation dependent library (CDL) restraints added in 3.4 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: 4.44 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: 10.90 Time building geometry restraints manager: 9.21 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: 0.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.070 Check model and map are aligned: 0.190 Set scattering table: 0.280 Process input model: 67.060 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.210 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.020 ------------------------------------------------------------------------------- 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 : 3.274 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: 0.4171 time to fit residues: 855.8441 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 : 3.462 ------------------------------------------------------------------------------- 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 = 39)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.104781 restraints weight = 52608.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.107697 restraints weight = 25878.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.109596 restraints weight = 15778.431| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- 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 3.19312 ( 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 : 3.176 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: 0.7969 (t) cc_final: 0.7666 (p) REVERT: A 38 LYS cc_start: 0.9312 (mmtt) cc_final: 0.9095 (mmtm) REVERT: A 82 LEU cc_start: 0.8790 (mt) cc_final: 0.8539 (mm) REVERT: A 98 ASP cc_start: 0.8171 (p0) cc_final: 0.7698 (p0) REVERT: A 181 LEU cc_start: 0.8643 (tp) cc_final: 0.8090 (tp) REVERT: A 287 MET cc_start: 0.8582 (mtp) cc_final: 0.8084 (mtp) REVERT: A 299 MET cc_start: 0.7282 (mmm) cc_final: 0.5709 (mtm) REVERT: A 433 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8298 (ptt) REVERT: B 26 TRP cc_start: 0.6753 (m100) cc_final: 0.6253 (m-90) REVERT: B 28 GLN cc_start: 0.8096 (tp-100) cc_final: 0.6758 (tp-100) REVERT: B 45 LEU cc_start: 0.8888 (tp) cc_final: 0.8255 (tt) REVERT: B 61 VAL cc_start: 0.9285 (t) cc_final: 0.9018 (p) REVERT: B 68 MET cc_start: 0.6935 (ttp) cc_final: 0.6693 (tpt) REVERT: B 74 MET cc_start: 0.4969 (mmp) cc_final: 0.4558 (mmp) REVERT: C 182 GLU cc_start: 0.7077 (tp30) cc_final: 0.6709 (tp30) REVERT: C 199 MET cc_start: 0.8273 (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: 0.8383 (p) cc_final: 0.7918 (m) REVERT: D 74 MET cc_start: 0.8574 (tpp) cc_final: 0.7848 (mmm) REVERT: E 8 ASN cc_start: 0.7752 (t0) cc_final: 0.7439 (t0) REVERT: E 108 PHE cc_start: 0.8649 (m-80) cc_final: 0.8194 (m-80) REVERT: E 199 MET cc_start: 0.8419 (ttp) cc_final: 0.8162 (ttm) REVERT: E 251 LEU cc_start: 0.8574 (tt) cc_final: 0.8009 (tt) REVERT: E 295 MET cc_start: 0.7694 (tpt) cc_final: 0.6179 (tmm) REVERT: E 335 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.6961 (m-80) REVERT: E 484 THR cc_start: 0.8889 (m) cc_final: 0.8514 (p) REVERT: F 13 ASP cc_start: 0.7174 (p0) cc_final: 0.6851 (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: 0.8656 (t) REVERT: H 37 LEU cc_start: 0.8916 (mt) cc_final: 0.8590 (mt) REVERT: H 47 TRP cc_start: 0.8141 (t60) cc_final: 0.7710 (t60) REVERT: H 54 ASP cc_start: 0.6075 (p0) cc_final: 0.5521 (p0) REVERT: H 57 ASP cc_start: 0.7629 (t0) cc_final: 0.7267 (m-30) REVERT: H 73 ASP cc_start: 0.7864 (p0) cc_final: 0.7658 (p0) REVERT: H 117 LEU cc_start: 0.7788 (tt) cc_final: 0.7382 (tp) REVERT: L 2 ILE cc_start: 0.8678 (mt) cc_final: 0.8455 (mt) REVERT: L 45 LYS cc_start: 0.8802 (mttt) cc_final: 0.8602 (mttp) REVERT: L 48 GLN cc_start: 0.6744 (mp10) cc_final: 0.6132 (mp10) REVERT: L 55 TYR cc_start: 0.8689 (p90) cc_final: 0.8416 (p90) REVERT: L 85 GLN cc_start: 0.7566 (mm-40) cc_final: 0.7364 (mm-40) REVERT: L 104 PHE cc_start: 0.8559 (m-80) cc_final: 0.8291 (m-80) REVERT: L 109 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7835 (mtp85) REVERT: O 6 VAL cc_start: 0.7977 (t) cc_final: 0.7678 (p) REVERT: O 38 LYS cc_start: 0.9309 (mmtt) cc_final: 0.9099 (mmtm) REVERT: O 82 LEU cc_start: 0.8771 (mt) cc_final: 0.8490 (mm) REVERT: O 98 ASP cc_start: 0.8177 (p0) cc_final: 0.7704 (p0) REVERT: O 161 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7628 (mt-10) REVERT: O 181 LEU cc_start: 0.8666 (tp) cc_final: 0.8098 (tp) REVERT: O 201 ASN cc_start: 0.7131 (m-40) cc_final: 0.6429 (t0) REVERT: O 287 MET cc_start: 0.8597 (mtp) cc_final: 0.8097 (mtp) REVERT: O 299 MET cc_start: 0.7270 (mmm) cc_final: 0.5670 (mtm) REVERT: O 433 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8278 (ptt) REVERT: P 26 TRP cc_start: 0.6736 (m100) cc_final: 0.6258 (m-90) REVERT: P 28 GLN cc_start: 0.8102 (tp-100) cc_final: 0.6758 (tp-100) REVERT: P 61 VAL cc_start: 0.9287 (t) cc_final: 0.9035 (p) REVERT: P 68 MET cc_start: 0.6946 (ttp) cc_final: 0.6686 (tpt) REVERT: P 74 MET cc_start: 0.4997 (mmp) cc_final: 0.4564 (mmp) REVERT: Q 182 GLU cc_start: 0.6760 (tt0) cc_final: 0.6308 (tp30) REVERT: Q 199 MET cc_start: 0.8284 (ptm) cc_final: 0.8031 (ptm) REVERT: Q 220 SER cc_start: 0.8054 (p) cc_final: 0.7839 (p) REVERT: Q 380 ILE cc_start: 0.8027 (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: 0.8528 (m) cc_final: 0.8060 (p) REVERT: R 15 ARG cc_start: 0.7726 (tpt170) cc_final: 0.7454 (ttm170) REVERT: R 35 TRP cc_start: 0.9041 (t60) cc_final: 0.8775 (t60) REVERT: R 74 MET cc_start: 0.8586 (tpp) cc_final: 0.7819 (mmm) REVERT: S 8 ASN cc_start: 0.7819 (t0) cc_final: 0.7528 (t0) REVERT: S 108 PHE cc_start: 0.8639 (m-80) cc_final: 0.8240 (m-80) REVERT: S 251 LEU cc_start: 0.8566 (tt) cc_final: 0.8009 (tt) REVERT: S 295 MET cc_start: 0.7750 (tpt) cc_final: 0.6189 (tmm) REVERT: S 335 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.6958 (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: 0.8995 (t) cc_final: 0.8780 (m) REVERT: T 32 VAL cc_start: 0.8892 (t) cc_final: 0.8661 (t) REVERT: U 37 LEU cc_start: 0.8918 (mt) cc_final: 0.8592 (mt) REVERT: U 47 TRP cc_start: 0.8139 (t60) cc_final: 0.7710 (t60) REVERT: U 54 ASP cc_start: 0.6085 (p0) cc_final: 0.5522 (p0) REVERT: U 57 ASP cc_start: 0.7664 (t0) cc_final: 0.7301 (m-30) REVERT: U 73 ASP cc_start: 0.7883 (p0) cc_final: 0.7664 (p0) REVERT: U 117 LEU cc_start: 0.7784 (tt) cc_final: 0.7376 (tp) REVERT: V 2 ILE cc_start: 0.8682 (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: 0.8409 (p90) REVERT: V 104 PHE cc_start: 0.8554 (m-80) cc_final: 0.8280 (m-80) REVERT: V 109 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7848 (mtp85) outliers start: 127 outliers final: 82 residues processed: 963 average time/residue: 0.3865 time to fit residues: 609.4876 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 : 3.315 ------------------------------------------------------------------------------- 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: 5.9990 chunk 197 optimal weight: 7.9990 chunk 282 optimal weight: 0.6980 chunk 323 optimal weight: 10.0000 chunk 303 optimal weight: 0.0970 chunk 78 optimal weight: 0.4980 chunk 195 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 overall best weight: 1.2580 ------------------------------------------------------------------------------- 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 134 ASN 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.124359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.107531 restraints weight = 52004.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.110554 restraints weight = 25500.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.112511 restraints weight = 15424.972| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30884 Z= 0.131 Angle : 0.684 10.551 41956 Z= 0.339 Chirality : 0.044 0.209 4928 Planarity : 0.004 0.047 5192 Dihedral : 11.347 105.211 4876 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.85 % Allowed : 16.73 % Favored : 79.42 % 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: -1.62 (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 0.009 0.001 HIS S 242 PHE 0.023 0.001 PHE D 64 TYR 0.021 0.001 TYR U 111 ARG 0.006 0.001 ARG A 348 Details of bonding type rmsd link_NAG-ASN : bond 0.00329 ( 12) link_NAG-ASN : angle 1.76939 ( 36) link_BETA1-4 : bond 0.00358 ( 20) link_BETA1-4 : angle 2.50760 ( 60) link_ALPHA1-3 : bond 0.00960 ( 4) link_ALPHA1-3 : angle 2.95789 ( 12) hydrogen bonds : bond 0.04163 ( 1094) hydrogen bonds : angle 5.67791 ( 3036) link_BETA1-6 : bond 0.01425 ( 4) link_BETA1-6 : angle 2.86224 ( 12) SS BOND : bond 0.00505 ( 30) SS BOND : angle 2.09048 ( 60) covalent geometry : bond 0.00285 (30814) covalent geometry : angle 0.66847 (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 1018 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 894 time to evaluate : 3.006 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: 0.8016 (t) cc_final: 0.7648 (p) REVERT: A 98 ASP cc_start: 0.8132 (p0) cc_final: 0.7621 (p0) REVERT: A 181 LEU cc_start: 0.8158 (tp) cc_final: 0.7577 (tp) REVERT: A 205 MET cc_start: 0.7689 (tpp) cc_final: 0.7468 (tpt) REVERT: A 287 MET cc_start: 0.8575 (mtp) cc_final: 0.8076 (mtp) REVERT: A 299 MET cc_start: 0.7063 (mmm) cc_final: 0.6289 (mmt) REVERT: B 26 TRP cc_start: 0.6716 (m100) cc_final: 0.6222 (m-90) REVERT: B 61 VAL cc_start: 0.9240 (t) cc_final: 0.9024 (p) REVERT: B 74 MET cc_start: 0.4942 (mmp) cc_final: 0.4618 (mmp) REVERT: C 122 LEU cc_start: 0.8946 (mt) cc_final: 0.8611 (mt) REVERT: C 182 GLU cc_start: 0.7250 (tp30) cc_final: 0.6948 (tp30) REVERT: C 199 MET cc_start: 0.8307 (ptm) cc_final: 0.8054 (ptm) REVERT: C 258 MET cc_start: 0.9072 (tpp) cc_final: 0.8667 (tpp) REVERT: C 358 LYS cc_start: 0.7361 (OUTLIER) cc_final: 0.6823 (tppt) REVERT: C 360 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6934 (mm-30) REVERT: C 371 PHE cc_start: 0.6065 (p90) cc_final: 0.5544 (p90) REVERT: C 380 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7671 (tt) REVERT: C 400 PHE cc_start: 0.7670 (m-10) cc_final: 0.7233 (t80) REVERT: C 401 GLU cc_start: 0.8358 (tp30) cc_final: 0.7854 (tp30) REVERT: C 432 LYS cc_start: 0.8328 (tttp) cc_final: 0.8085 (ttpp) REVERT: C 436 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8179 (tt0) REVERT: C 462 THR cc_start: 0.9069 (m) cc_final: 0.8862 (p) REVERT: D 12 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8393 (pp) REVERT: D 14 THR cc_start: 0.8232 (p) cc_final: 0.7774 (m) REVERT: D 18 THR cc_start: 0.8634 (p) cc_final: 0.7776 (t) REVERT: D 42 PHE cc_start: 0.8772 (t80) cc_final: 0.8252 (t80) REVERT: D 64 PHE cc_start: 0.9300 (t80) cc_final: 0.9075 (t80) REVERT: D 74 MET cc_start: 0.8618 (tpp) cc_final: 0.8191 (mmm) REVERT: E 8 ASN cc_start: 0.7795 (t0) cc_final: 0.7395 (t0) REVERT: E 20 TRP cc_start: 0.7537 (p90) cc_final: 0.6011 (p90) REVERT: E 108 PHE cc_start: 0.8558 (m-80) cc_final: 0.8149 (m-80) REVERT: E 126 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7054 (tp30) REVERT: E 250 VAL cc_start: 0.8736 (t) cc_final: 0.8470 (m) REVERT: E 270 ASN cc_start: 0.6752 (t0) cc_final: 0.6490 (t0) REVERT: E 295 MET cc_start: 0.7784 (tpt) cc_final: 0.5874 (tmm) REVERT: E 319 LEU cc_start: 0.8848 (mt) cc_final: 0.8647 (mt) REVERT: E 335 PHE cc_start: 0.8126 (OUTLIER) cc_final: 0.6977 (m-80) REVERT: E 442 TYR cc_start: 0.8807 (t80) cc_final: 0.8227 (t80) REVERT: E 484 THR cc_start: 0.8751 (m) cc_final: 0.8268 (p) REVERT: F 13 ASP cc_start: 0.7804 (p0) cc_final: 0.7160 (m-30) REVERT: F 26 TRP cc_start: 0.8096 (m100) cc_final: 0.7822 (m100) REVERT: F 32 VAL cc_start: 0.8875 (t) cc_final: 0.8619 (t) REVERT: H 47 TRP cc_start: 0.7979 (t60) cc_final: 0.7664 (t60) REVERT: H 54 ASP cc_start: 0.6030 (p0) cc_final: 0.5232 (p0) REVERT: H 57 ASP cc_start: 0.7302 (t0) cc_final: 0.7053 (m-30) REVERT: H 114 GLN cc_start: 0.7948 (tp40) cc_final: 0.7482 (tp-100) REVERT: L 2 ILE cc_start: 0.8679 (mt) cc_final: 0.8443 (mt) REVERT: L 48 GLN cc_start: 0.6793 (mp10) cc_final: 0.5963 (mp10) REVERT: L 80 LYS cc_start: 0.7475 (mtmt) cc_final: 0.7161 (mtmt) REVERT: L 85 GLN cc_start: 0.7608 (mm-40) cc_final: 0.7322 (mm-40) REVERT: L 88 ASP cc_start: 0.6158 (m-30) cc_final: 0.5766 (m-30) REVERT: L 104 PHE cc_start: 0.8532 (m-80) cc_final: 0.8287 (m-80) REVERT: L 109 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7836 (mtp85) REVERT: O 6 VAL cc_start: 0.8008 (t) cc_final: 0.7658 (p) REVERT: O 42 ASP cc_start: 0.8443 (m-30) cc_final: 0.8016 (m-30) REVERT: O 98 ASP cc_start: 0.8139 (p0) cc_final: 0.7615 (p0) REVERT: O 181 LEU cc_start: 0.8184 (tp) cc_final: 0.7580 (tp) REVERT: O 190 ASP cc_start: 0.8057 (t0) cc_final: 0.7817 (t0) REVERT: O 201 ASN cc_start: 0.7153 (m-40) cc_final: 0.6218 (t0) REVERT: O 287 MET cc_start: 0.8598 (mtp) cc_final: 0.8087 (mtp) REVERT: O 299 MET cc_start: 0.7085 (mmm) cc_final: 0.6290 (mmt) REVERT: O 433 MET cc_start: 0.8581 (ptp) cc_final: 0.8351 (ptt) REVERT: P 26 TRP cc_start: 0.6705 (m100) cc_final: 0.6475 (m-90) REVERT: P 74 MET cc_start: 0.4964 (mmp) cc_final: 0.4627 (mmp) REVERT: Q 122 LEU cc_start: 0.8952 (mt) cc_final: 0.8615 (mt) REVERT: Q 182 GLU cc_start: 0.6962 (tt0) cc_final: 0.6586 (tp30) REVERT: Q 199 MET cc_start: 0.8311 (ptm) cc_final: 0.8056 (ptm) REVERT: Q 258 MET cc_start: 0.9087 (tpp) cc_final: 0.8672 (tpp) REVERT: Q 360 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6942 (mm-30) REVERT: Q 371 PHE cc_start: 0.6043 (p90) cc_final: 0.5523 (p90) REVERT: Q 380 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7666 (tt) REVERT: Q 400 PHE cc_start: 0.7670 (m-10) cc_final: 0.7238 (t80) REVERT: Q 401 GLU cc_start: 0.8357 (tp30) cc_final: 0.7852 (tp30) REVERT: Q 436 GLN cc_start: 0.8769 (tm-30) cc_final: 0.8172 (tt0) REVERT: Q 462 THR cc_start: 0.9079 (m) cc_final: 0.8870 (p) REVERT: R 18 THR cc_start: 0.8619 (p) cc_final: 0.7744 (t) REVERT: R 35 TRP cc_start: 0.9007 (t60) cc_final: 0.8734 (t60) REVERT: R 42 PHE cc_start: 0.8779 (t80) cc_final: 0.8241 (t80) REVERT: R 64 PHE cc_start: 0.9304 (t80) cc_final: 0.9080 (t80) REVERT: R 74 MET cc_start: 0.8650 (tpp) cc_final: 0.8230 (mmm) REVERT: S 8 ASN cc_start: 0.7881 (t0) cc_final: 0.7532 (t0) REVERT: S 20 TRP cc_start: 0.7556 (p90) cc_final: 0.6022 (p90) REVERT: S 108 PHE cc_start: 0.8545 (m-80) cc_final: 0.8189 (m-80) REVERT: S 250 VAL cc_start: 0.8738 (t) cc_final: 0.8484 (m) REVERT: S 295 MET cc_start: 0.7917 (tpt) cc_final: 0.5910 (tmm) REVERT: S 319 LEU cc_start: 0.8813 (mt) cc_final: 0.8592 (mt) REVERT: S 323 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7490 (pm20) REVERT: S 335 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.6947 (m-80) REVERT: S 410 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8113 (mtp) REVERT: S 484 THR cc_start: 0.8747 (m) cc_final: 0.8395 (p) REVERT: T 13 ASP cc_start: 0.7790 (p0) cc_final: 0.7155 (m-30) REVERT: T 26 TRP cc_start: 0.8125 (m100) cc_final: 0.7840 (m100) REVERT: T 32 VAL cc_start: 0.8876 (t) cc_final: 0.8624 (t) REVERT: U 47 TRP cc_start: 0.7984 (t60) cc_final: 0.7673 (t60) REVERT: U 54 ASP cc_start: 0.6036 (p0) cc_final: 0.5239 (p0) REVERT: U 57 ASP cc_start: 0.7354 (t0) cc_final: 0.7091 (m-30) REVERT: U 114 GLN cc_start: 0.7946 (tp40) cc_final: 0.7473 (tp-100) REVERT: V 2 ILE cc_start: 0.8664 (mt) cc_final: 0.8430 (mt) REVERT: V 48 GLN cc_start: 0.6800 (mp10) cc_final: 0.5957 (mp10) REVERT: V 80 LYS cc_start: 0.7481 (mtmt) cc_final: 0.7173 (mtmt) REVERT: V 85 GLN cc_start: 0.7657 (mm110) cc_final: 0.7336 (mm-40) REVERT: V 88 ASP cc_start: 0.6153 (m-30) cc_final: 0.5782 (m-30) REVERT: V 104 PHE cc_start: 0.8524 (m-80) cc_final: 0.8278 (m-80) REVERT: V 109 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7841 (mtp85) outliers start: 124 outliers final: 70 residues processed: 953 average time/residue: 0.3867 time to fit residues: 601.9742 Evaluate side-chains 883 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 803 time to evaluate : 3.220 ------------------------------------------------------------------------------- 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 387 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 10 ASP 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 258 MET 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 96 CYS 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 10 ASP 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 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 96 CYS 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: 30.0000 chunk 52 optimal weight: 9.9990 chunk 72 optimal weight: 20.0000 chunk 103 optimal weight: 20.0000 chunk 316 optimal weight: 10.0000 chunk 34 optimal weight: 30.0000 chunk 156 optimal weight: 9.9990 chunk 312 optimal weight: 5.9990 chunk 283 optimal weight: 4.9990 overall best weight: 8.1992 ------------------------------------------------------------------------------- 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 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 259 HIS E 428 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** S 134 ASN V 27 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.118948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.101759 restraints weight = 52759.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.104697 restraints weight = 26353.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.106606 restraints weight = 16207.309| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 30884 Z= 0.259 Angle : 0.787 14.101 41956 Z= 0.391 Chirality : 0.048 0.275 4928 Planarity : 0.005 0.069 5192 Dihedral : 10.705 103.237 4876 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 5.90 % Allowed : 18.84 % Favored : 75.26 % 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: -1.64 (0.13), residues: 3846 helix: 1.06 (0.18), residues: 870 sheet: -1.62 (0.15), residues: 1092 loop : -1.77 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 218 HIS 0.011 0.002 HIS A 144 PHE 0.018 0.002 PHE P 42 TYR 0.022 0.002 TYR H 111 ARG 0.009 0.001 ARG E 409 Details of bonding type rmsd link_NAG-ASN : bond 0.00517 ( 12) link_NAG-ASN : angle 2.43508 ( 36) link_BETA1-4 : bond 0.00518 ( 20) link_BETA1-4 : angle 2.63161 ( 60) link_ALPHA1-3 : bond 0.00924 ( 4) link_ALPHA1-3 : angle 2.98256 ( 12) hydrogen bonds : bond 0.04530 ( 1094) hydrogen bonds : angle 5.65353 ( 3036) link_BETA1-6 : bond 0.01436 ( 4) link_BETA1-6 : angle 3.11611 ( 12) SS BOND : bond 0.00631 ( 30) SS BOND : angle 2.81867 ( 60) covalent geometry : bond 0.00609 (30814) covalent geometry : angle 0.76794 (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 982 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 792 time to evaluate : 3.173 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 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: 0.8212 (t) cc_final: 0.7825 (p) REVERT: A 98 ASP cc_start: 0.8143 (p0) cc_final: 0.7680 (p0) REVERT: A 181 LEU cc_start: 0.8728 (tp) cc_final: 0.8252 (tp) REVERT: A 201 ASN cc_start: 0.7055 (m-40) cc_final: 0.5850 (t0) REVERT: A 247 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7817 (pm20) REVERT: A 287 MET cc_start: 0.8676 (mtp) cc_final: 0.8129 (mtp) REVERT: A 299 MET cc_start: 0.7013 (mmm) cc_final: 0.5932 (mmm) REVERT: B 26 TRP cc_start: 0.6902 (m100) cc_final: 0.6678 (m-90) REVERT: B 28 GLN cc_start: 0.7854 (tp-100) cc_final: 0.6609 (tp-100) REVERT: B 61 VAL cc_start: 0.9210 (t) cc_final: 0.8888 (p) REVERT: C 182 GLU cc_start: 0.7296 (tp30) cc_final: 0.6908 (tp30) REVERT: C 199 MET cc_start: 0.8356 (ptm) cc_final: 0.8081 (ptm) REVERT: C 258 MET cc_start: 0.9130 (tpp) cc_final: 0.8784 (tpp) REVERT: C 358 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.6993 (tppt) REVERT: C 360 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6983 (mm-30) REVERT: C 380 ILE cc_start: 0.8063 (OUTLIER) cc_final: 0.7767 (tt) REVERT: C 400 PHE cc_start: 0.7541 (m-10) cc_final: 0.7233 (t80) REVERT: C 432 LYS cc_start: 0.8306 (tttp) cc_final: 0.8003 (ttpp) REVERT: C 462 THR cc_start: 0.9105 (m) cc_final: 0.8898 (p) REVERT: D 12 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8209 (pp) REVERT: D 42 PHE cc_start: 0.8811 (t80) cc_final: 0.8151 (t80) REVERT: D 64 PHE cc_start: 0.9361 (t80) cc_final: 0.9083 (t80) REVERT: D 74 MET cc_start: 0.8760 (tpp) cc_final: 0.8329 (mmm) REVERT: E 8 ASN cc_start: 0.8022 (t0) cc_final: 0.7542 (t0) REVERT: E 20 TRP cc_start: 0.7687 (p90) cc_final: 0.6211 (p90) REVERT: E 108 PHE cc_start: 0.8722 (m-80) cc_final: 0.8278 (m-80) REVERT: E 126 GLU cc_start: 0.7312 (mm-30) cc_final: 0.6802 (tp30) REVERT: E 176 TYR cc_start: 0.8823 (m-80) cc_final: 0.8465 (m-80) REVERT: E 181 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8628 (pp) REVERT: E 250 VAL cc_start: 0.8736 (OUTLIER) cc_final: 0.8500 (m) REVERT: E 251 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8318 (tt) REVERT: E 259 HIS cc_start: 0.8561 (OUTLIER) cc_final: 0.6691 (t-90) REVERT: E 270 ASN cc_start: 0.6956 (t0) cc_final: 0.6754 (t0) REVERT: E 484 THR cc_start: 0.8912 (m) cc_final: 0.8534 (p) REVERT: H 3 GLU cc_start: 0.6480 (mm-30) cc_final: 0.6199 (mm-30) REVERT: H 47 TRP cc_start: 0.8274 (t60) cc_final: 0.7663 (t60) REVERT: H 57 ASP cc_start: 0.7446 (t0) cc_final: 0.7210 (m-30) REVERT: H 65 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7369 (mtmt) REVERT: H 114 GLN cc_start: 0.7745 (tp40) cc_final: 0.7253 (tp-100) REVERT: L 2 ILE cc_start: 0.8714 (mt) cc_final: 0.8466 (mt) REVERT: L 48 GLN cc_start: 0.7080 (mp10) cc_final: 0.6166 (mp10) REVERT: L 85 GLN cc_start: 0.7513 (mm-40) cc_final: 0.7174 (mm-40) REVERT: L 104 PHE cc_start: 0.8645 (m-80) cc_final: 0.8440 (m-80) REVERT: L 109 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7848 (mtp85) REVERT: O 6 VAL cc_start: 0.8223 (t) cc_final: 0.7847 (p) REVERT: O 85 GLU cc_start: 0.8066 (tt0) cc_final: 0.7844 (tt0) REVERT: O 98 ASP cc_start: 0.8125 (p0) cc_final: 0.7686 (p0) REVERT: O 181 LEU cc_start: 0.8629 (tp) cc_final: 0.8165 (tp) REVERT: O 247 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7739 (pm20) REVERT: O 287 MET cc_start: 0.8665 (mtp) cc_final: 0.8135 (mtp) REVERT: O 299 MET cc_start: 0.6992 (mmm) cc_final: 0.5939 (mmm) REVERT: P 26 TRP cc_start: 0.6884 (m100) cc_final: 0.6671 (m-90) REVERT: P 45 LEU cc_start: 0.8483 (tp) cc_final: 0.8277 (tp) REVERT: P 61 VAL cc_start: 0.9266 (t) cc_final: 0.9046 (p) REVERT: Q 125 ILE cc_start: 0.8858 (tt) cc_final: 0.8527 (tt) REVERT: Q 182 GLU cc_start: 0.6953 (tt0) cc_final: 0.6734 (tp30) REVERT: Q 199 MET cc_start: 0.8361 (ptm) cc_final: 0.8027 (ptm) REVERT: Q 258 MET cc_start: 0.9136 (tpp) cc_final: 0.8798 (tpp) REVERT: Q 358 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.7064 (tppt) REVERT: Q 360 GLU cc_start: 0.7074 (mm-30) cc_final: 0.6846 (mm-30) REVERT: Q 380 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7768 (tt) REVERT: Q 400 PHE cc_start: 0.7544 (m-10) cc_final: 0.7244 (t80) REVERT: Q 432 LYS cc_start: 0.8314 (tttp) cc_final: 0.7993 (ttpp) REVERT: Q 462 THR cc_start: 0.9109 (m) cc_final: 0.8893 (p) REVERT: R 35 TRP cc_start: 0.9051 (t60) cc_final: 0.8765 (t60) REVERT: R 42 PHE cc_start: 0.8810 (t80) cc_final: 0.8149 (t80) REVERT: R 64 PHE cc_start: 0.9364 (t80) cc_final: 0.9118 (t80) REVERT: R 74 MET cc_start: 0.8754 (tpp) cc_final: 0.8303 (mmm) REVERT: S 8 ASN cc_start: 0.8124 (t0) cc_final: 0.7606 (t0) REVERT: S 20 TRP cc_start: 0.7691 (p90) cc_final: 0.6212 (p90) REVERT: S 59 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7984 (mt) REVERT: S 108 PHE cc_start: 0.8715 (m-80) cc_final: 0.8315 (m-80) REVERT: S 151 VAL cc_start: 0.8117 (m) cc_final: 0.7916 (t) REVERT: S 176 TYR cc_start: 0.8817 (m-80) cc_final: 0.8464 (m-80) REVERT: S 181 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8705 (pp) REVERT: S 250 VAL cc_start: 0.8749 (OUTLIER) cc_final: 0.8492 (m) REVERT: S 251 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8338 (tt) REVERT: S 259 HIS cc_start: 0.8890 (OUTLIER) cc_final: 0.7309 (t70) REVERT: S 305 VAL cc_start: 0.9183 (OUTLIER) cc_final: 0.8709 (p) REVERT: S 323 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7482 (pm20) REVERT: S 400 PHE cc_start: 0.7870 (m-10) cc_final: 0.7667 (m-10) REVERT: S 410 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8098 (mtp) REVERT: S 447 SER cc_start: 0.9083 (t) cc_final: 0.8791 (t) REVERT: S 484 THR cc_start: 0.8900 (m) cc_final: 0.8537 (p) REVERT: U 3 GLU cc_start: 0.6487 (mm-30) cc_final: 0.6213 (mm-30) REVERT: U 47 TRP cc_start: 0.8272 (t60) cc_final: 0.7657 (t60) REVERT: U 57 ASP cc_start: 0.7482 (t0) cc_final: 0.7226 (m-30) REVERT: U 65 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7356 (mtmt) REVERT: U 114 GLN cc_start: 0.7740 (tp40) cc_final: 0.7240 (tp-100) REVERT: V 2 ILE cc_start: 0.8708 (mt) cc_final: 0.8471 (mt) REVERT: V 48 GLN cc_start: 0.7089 (mp10) cc_final: 0.6168 (mp10) REVERT: V 104 PHE cc_start: 0.8642 (m-80) cc_final: 0.8436 (m-80) REVERT: V 109 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7842 (mtp85) outliers start: 190 outliers final: 124 residues processed: 913 average time/residue: 0.3794 time to fit residues: 577.0273 Evaluate side-chains 903 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 756 time to evaluate : 3.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 41 LEU 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 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 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 16 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 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 41 LEU 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 237 THR Chi-restraints excluded: chain O residue 247 GLU Chi-restraints excluded: chain O residue 275 SER Chi-restraints excluded: chain O residue 320 ILE 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 R residue 73 SER Chi-restraints excluded: chain S residue 41 LEU Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain S residue 59 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 250 VAL Chi-restraints excluded: chain S residue 251 LEU 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 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: 0.0040 chunk 226 optimal weight: 8.9990 chunk 343 optimal weight: 20.0000 chunk 199 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 158 optimal weight: 10.0000 chunk 362 optimal weight: 9.9990 chunk 337 optimal weight: 30.0000 chunk 2 optimal weight: 0.6980 chunk 326 optimal weight: 5.9990 overall best weight: 4.3398 ------------------------------------------------------------------------------- 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 ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 HIS C 246 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 302 ASN E 428 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 86 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.120685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.103549 restraints weight = 52013.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.106480 restraints weight = 25802.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.108409 restraints weight = 15870.822| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 30884 Z= 0.169 Angle : 0.707 13.090 41956 Z= 0.349 Chirality : 0.045 0.260 4928 Planarity : 0.004 0.054 5192 Dihedral : 10.120 104.489 4876 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 5.56 % Allowed : 20.86 % Favored : 73.59 % 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: 1.25 (0.18), residues: 876 sheet: -1.45 (0.15), residues: 1092 loop : -1.78 (0.13), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 229 HIS 0.023 0.001 HIS E 259 PHE 0.020 0.002 PHE T 48 TYR 0.021 0.001 TYR H 111 ARG 0.008 0.001 ARG Q 2 Details of bonding type rmsd link_NAG-ASN : bond 0.00431 ( 12) link_NAG-ASN : angle 2.31871 ( 36) link_BETA1-4 : bond 0.00357 ( 20) link_BETA1-4 : angle 2.40049 ( 60) link_ALPHA1-3 : bond 0.00813 ( 4) link_ALPHA1-3 : angle 2.84808 ( 12) hydrogen bonds : bond 0.04116 ( 1094) hydrogen bonds : angle 5.41831 ( 3036) link_BETA1-6 : bond 0.01200 ( 4) link_BETA1-6 : angle 2.88407 ( 12) SS BOND : bond 0.00557 ( 30) SS BOND : angle 2.67709 ( 60) covalent geometry : bond 0.00390 (30814) covalent geometry : angle 0.68902 (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 981 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 802 time to evaluate : 3.505 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 6 VAL cc_start: 0.8130 (t) cc_final: 0.7707 (p) REVERT: A 57 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.6973 (ttm110) REVERT: A 98 ASP cc_start: 0.8102 (p0) cc_final: 0.7590 (p0) REVERT: A 181 LEU cc_start: 0.8699 (tp) cc_final: 0.8185 (tp) REVERT: A 201 ASN cc_start: 0.7032 (m-40) cc_final: 0.5796 (t0) REVERT: A 287 MET cc_start: 0.8658 (mtp) cc_final: 0.8123 (mtp) REVERT: A 299 MET cc_start: 0.6914 (mmm) cc_final: 0.5932 (mmm) REVERT: B 26 TRP cc_start: 0.6876 (m100) cc_final: 0.6627 (m-90) REVERT: B 28 GLN cc_start: 0.7749 (tp-100) cc_final: 0.7449 (tp-100) REVERT: B 61 VAL cc_start: 0.9237 (t) cc_final: 0.8925 (p) REVERT: B 68 MET cc_start: 0.8043 (tpt) cc_final: 0.7344 (ttm) REVERT: C 125 ILE cc_start: 0.8806 (tt) cc_final: 0.8458 (tt) REVERT: C 182 GLU cc_start: 0.7307 (tp30) cc_final: 0.6867 (tp30) REVERT: C 199 MET cc_start: 0.8353 (ptm) cc_final: 0.7957 (ptm) REVERT: C 293 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8752 (pptt) REVERT: C 348 ARG cc_start: 0.8205 (ptm-80) cc_final: 0.7779 (ptm-80) REVERT: C 358 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.6899 (tppt) REVERT: C 380 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7698 (tt) REVERT: C 400 PHE cc_start: 0.7388 (m-10) cc_final: 0.7116 (t80) REVERT: C 432 LYS cc_start: 0.8261 (tttp) cc_final: 0.8050 (ttpp) REVERT: C 436 GLN cc_start: 0.8807 (tm-30) cc_final: 0.8198 (tt0) REVERT: C 462 THR cc_start: 0.9091 (m) cc_final: 0.8851 (p) REVERT: D 12 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8088 (pp) REVERT: D 18 THR cc_start: 0.8897 (p) cc_final: 0.8106 (t) REVERT: D 35 TRP cc_start: 0.9034 (t60) cc_final: 0.8819 (t60) REVERT: D 42 PHE cc_start: 0.8794 (t80) cc_final: 0.7903 (t80) REVERT: D 64 PHE cc_start: 0.9369 (t80) cc_final: 0.9064 (t80) REVERT: D 74 MET cc_start: 0.8796 (tpp) cc_final: 0.8126 (mmm) REVERT: E 8 ASN cc_start: 0.8168 (t0) cc_final: 0.7741 (t0) REVERT: E 20 TRP cc_start: 0.7638 (p90) cc_final: 0.6302 (p90) REVERT: E 108 PHE cc_start: 0.8683 (m-80) cc_final: 0.8254 (m-80) REVERT: E 123 GLU cc_start: 0.7537 (tt0) cc_final: 0.7074 (tt0) REVERT: E 176 TYR cc_start: 0.8781 (m-80) cc_final: 0.8406 (m-80) REVERT: E 181 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8622 (pp) REVERT: E 250 VAL cc_start: 0.8656 (OUTLIER) cc_final: 0.8431 (m) REVERT: E 251 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8300 (tt) REVERT: E 270 ASN cc_start: 0.6998 (t0) cc_final: 0.6760 (t0) REVERT: E 400 PHE cc_start: 0.7872 (m-10) cc_final: 0.7653 (m-10) REVERT: E 442 TYR cc_start: 0.8905 (t80) cc_final: 0.8295 (t80) REVERT: E 484 THR cc_start: 0.8876 (m) cc_final: 0.8420 (p) REVERT: H 3 GLU cc_start: 0.6407 (mm-30) cc_final: 0.6105 (mm-30) REVERT: H 47 TRP cc_start: 0.8244 (t60) cc_final: 0.7569 (t60) REVERT: H 56 ASN cc_start: 0.7578 (m-40) cc_final: 0.7339 (m110) REVERT: H 57 ASP cc_start: 0.7335 (t0) cc_final: 0.7034 (m-30) REVERT: H 65 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7161 (mtmt) REVERT: H 90 ASP cc_start: 0.7448 (t0) cc_final: 0.7234 (t0) REVERT: H 111 TYR cc_start: 0.8507 (m-80) cc_final: 0.8257 (m-10) REVERT: L 2 ILE cc_start: 0.8610 (mt) cc_final: 0.8396 (mt) REVERT: L 48 GLN cc_start: 0.7068 (mp10) cc_final: 0.6205 (mp10) REVERT: L 85 GLN cc_start: 0.7549 (mm-40) cc_final: 0.7310 (mm-40) REVERT: L 104 PHE cc_start: 0.8734 (m-80) cc_final: 0.8454 (m-80) REVERT: L 109 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7807 (mtp85) REVERT: O 6 VAL cc_start: 0.8129 (t) cc_final: 0.7716 (p) REVERT: O 57 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7013 (ttm110) REVERT: O 98 ASP cc_start: 0.8087 (p0) cc_final: 0.7623 (p0) REVERT: O 181 LEU cc_start: 0.8692 (tp) cc_final: 0.8176 (tp) REVERT: O 199 MET cc_start: 0.7500 (ttm) cc_final: 0.7297 (ttp) REVERT: O 287 MET cc_start: 0.8723 (mtp) cc_final: 0.8202 (mtp) REVERT: O 299 MET cc_start: 0.6941 (mmm) cc_final: 0.5942 (mmm) REVERT: O 433 MET cc_start: 0.8610 (ptp) cc_final: 0.8400 (ptt) REVERT: P 26 TRP cc_start: 0.6859 (m100) cc_final: 0.6557 (m-90) REVERT: P 61 VAL cc_start: 0.9271 (t) cc_final: 0.9070 (p) REVERT: P 68 MET cc_start: 0.8054 (tpt) cc_final: 0.7364 (ttm) REVERT: P 74 MET cc_start: 0.5904 (mmp) cc_final: 0.5360 (mmt) REVERT: Q 79 GLU cc_start: 0.7368 (mp0) cc_final: 0.7111 (mp0) REVERT: Q 125 ILE cc_start: 0.8810 (tt) cc_final: 0.8455 (tt) REVERT: Q 182 GLU cc_start: 0.6901 (tt0) cc_final: 0.6682 (tp30) REVERT: Q 199 MET cc_start: 0.8348 (ptm) cc_final: 0.7946 (ptm) REVERT: Q 293 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8743 (pptt) REVERT: Q 348 ARG cc_start: 0.8226 (ptm-80) cc_final: 0.8020 (ptm-80) REVERT: Q 358 LYS cc_start: 0.7533 (OUTLIER) cc_final: 0.7084 (tppt) REVERT: Q 380 ILE cc_start: 0.7981 (OUTLIER) cc_final: 0.7695 (tt) REVERT: Q 400 PHE cc_start: 0.7394 (m-10) cc_final: 0.7129 (t80) REVERT: Q 432 LYS cc_start: 0.8273 (tttp) cc_final: 0.7969 (ttpp) REVERT: Q 436 GLN cc_start: 0.8337 (tm-30) cc_final: 0.7866 (tm-30) REVERT: Q 462 THR cc_start: 0.9089 (m) cc_final: 0.8852 (p) REVERT: R 18 THR cc_start: 0.8890 (p) cc_final: 0.8121 (t) REVERT: R 35 TRP cc_start: 0.9045 (t60) cc_final: 0.8725 (t60) REVERT: R 42 PHE cc_start: 0.8791 (t80) cc_final: 0.7894 (t80) REVERT: R 64 PHE cc_start: 0.9365 (t80) cc_final: 0.9059 (t80) REVERT: R 74 MET cc_start: 0.8783 (tpp) cc_final: 0.8408 (mmm) REVERT: S 8 ASN cc_start: 0.8214 (t0) cc_final: 0.7799 (t0) REVERT: S 20 TRP cc_start: 0.7642 (p90) cc_final: 0.6304 (p90) REVERT: S 108 PHE cc_start: 0.8675 (m-80) cc_final: 0.8300 (m-80) REVERT: S 151 VAL cc_start: 0.8100 (OUTLIER) cc_final: 0.7860 (t) REVERT: S 176 TYR cc_start: 0.8875 (m-80) cc_final: 0.8470 (m-80) REVERT: S 181 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8706 (pp) REVERT: S 250 VAL cc_start: 0.8659 (OUTLIER) cc_final: 0.8428 (m) REVERT: S 251 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8323 (tt) REVERT: S 259 HIS cc_start: 0.8876 (OUTLIER) cc_final: 0.7049 (t70) REVERT: S 323 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7516 (pm20) REVERT: S 400 PHE cc_start: 0.7867 (m-10) cc_final: 0.7640 (m-10) REVERT: S 410 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8092 (mtp) REVERT: S 442 TYR cc_start: 0.8900 (t80) cc_final: 0.8277 (t80) REVERT: S 484 THR cc_start: 0.8877 (m) cc_final: 0.8412 (p) REVERT: U 3 GLU cc_start: 0.6414 (mm-30) cc_final: 0.6117 (mm-30) REVERT: U 47 TRP cc_start: 0.8242 (t60) cc_final: 0.7572 (t60) REVERT: U 57 ASP cc_start: 0.7374 (t0) cc_final: 0.7055 (m-30) REVERT: U 65 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7154 (mtmt) REVERT: U 90 ASP cc_start: 0.7439 (t0) cc_final: 0.7223 (t0) REVERT: U 111 TYR cc_start: 0.8529 (m-80) cc_final: 0.8284 (m-10) REVERT: U 114 GLN cc_start: 0.7853 (tp40) cc_final: 0.7652 (tp-100) REVERT: V 2 ILE cc_start: 0.8611 (mt) cc_final: 0.8391 (mt) REVERT: V 48 GLN cc_start: 0.7085 (mp10) cc_final: 0.6213 (mp10) REVERT: V 104 PHE cc_start: 0.8734 (m-80) cc_final: 0.8460 (m-80) REVERT: V 109 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7800 (mtp85) outliers start: 179 outliers final: 116 residues processed: 917 average time/residue: 0.3850 time to fit residues: 578.3932 Evaluate side-chains 904 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 765 time to evaluate : 3.735 ------------------------------------------------------------------------------- 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 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 237 THR 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 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 48 THR 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 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 318 ILE Chi-restraints excluded: chain E residue 356 VAL 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 65 LYS 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 109 ARG Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 33 THR 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 237 THR 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 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 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 125 ILE Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 181 LEU Chi-restraints excluded: chain S residue 187 THR Chi-restraints excluded: chain S residue 250 VAL Chi-restraints excluded: chain S residue 251 LEU 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 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 65 LYS 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 109 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 202 optimal weight: 8.9990 chunk 311 optimal weight: 20.0000 chunk 158 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 125 optimal weight: 10.0000 chunk 201 optimal weight: 1.9990 chunk 258 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 228 optimal weight: 9.9990 chunk 188 optimal weight: 7.9990 chunk 242 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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** C 246 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 134 ASN E 428 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 GLN ** 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.122404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.105270 restraints weight = 51810.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.108287 restraints weight = 25693.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.110230 restraints weight = 15698.425| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 30884 Z= 0.131 Angle : 0.676 11.952 41956 Z= 0.332 Chirality : 0.043 0.256 4928 Planarity : 0.004 0.056 5192 Dihedral : 9.494 106.050 4876 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 5.37 % Allowed : 21.54 % Favored : 73.09 % 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: 1.37 (0.18), residues: 876 sheet: -1.34 (0.15), residues: 1092 loop : -1.75 (0.13), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 20 HIS 0.005 0.001 HIS E 259 PHE 0.015 0.001 PHE C 335 TYR 0.019 0.001 TYR H 111 ARG 0.007 0.000 ARG A 348 Details of bonding type rmsd link_NAG-ASN : bond 0.00354 ( 12) link_NAG-ASN : angle 2.11153 ( 36) link_BETA1-4 : bond 0.00324 ( 20) link_BETA1-4 : angle 2.25148 ( 60) link_ALPHA1-3 : bond 0.00933 ( 4) link_ALPHA1-3 : angle 2.80268 ( 12) hydrogen bonds : bond 0.03900 ( 1094) hydrogen bonds : angle 5.28938 ( 3036) link_BETA1-6 : bond 0.01031 ( 4) link_BETA1-6 : angle 2.84966 ( 12) SS BOND : bond 0.00528 ( 30) SS BOND : angle 2.57968 ( 60) covalent geometry : bond 0.00300 (30814) covalent geometry : angle 0.65868 (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 988 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 815 time to evaluate : 3.145 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 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: 0.8066 (t) cc_final: 0.7660 (p) REVERT: A 57 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7026 (ttm110) REVERT: A 86 GLN cc_start: 0.7204 (tp40) cc_final: 0.6994 (tm-30) REVERT: A 98 ASP cc_start: 0.8094 (p0) cc_final: 0.7593 (p0) REVERT: A 181 LEU cc_start: 0.8248 (tp) cc_final: 0.7857 (tp) REVERT: A 190 ASP cc_start: 0.8269 (t0) cc_final: 0.7954 (t0) REVERT: A 201 ASN cc_start: 0.7040 (m-40) cc_final: 0.5742 (t0) REVERT: A 205 MET cc_start: 0.7553 (tpp) cc_final: 0.7325 (tpt) REVERT: A 287 MET cc_start: 0.8671 (mtp) cc_final: 0.8195 (mtp) REVERT: A 299 MET cc_start: 0.6933 (mmm) cc_final: 0.5940 (mmm) REVERT: A 302 ASN cc_start: 0.7474 (m110) cc_final: 0.7270 (m-40) REVERT: B 12 LEU cc_start: 0.6167 (OUTLIER) cc_final: 0.5660 (pp) REVERT: B 26 TRP cc_start: 0.6863 (m100) cc_final: 0.6565 (m-90) REVERT: B 61 VAL cc_start: 0.9241 (t) cc_final: 0.8967 (p) REVERT: C 34 MET cc_start: 0.7966 (ptp) cc_final: 0.7761 (ptp) REVERT: C 125 ILE cc_start: 0.8740 (tt) cc_final: 0.8222 (tt) REVERT: C 182 GLU cc_start: 0.7143 (tp30) cc_final: 0.6818 (tp30) REVERT: C 199 MET cc_start: 0.8336 (ptm) cc_final: 0.7907 (ptm) REVERT: C 258 MET cc_start: 0.8923 (tpp) cc_final: 0.8301 (tpp) REVERT: C 293 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8632 (pptt) REVERT: C 348 ARG cc_start: 0.8269 (ptm-80) cc_final: 0.7819 (ptm-80) REVERT: C 358 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.6897 (tppt) REVERT: C 360 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6935 (mm-30) REVERT: C 380 ILE cc_start: 0.7958 (OUTLIER) cc_final: 0.7665 (tt) REVERT: C 432 LYS cc_start: 0.8260 (tttp) cc_final: 0.7996 (ttpp) REVERT: C 436 GLN cc_start: 0.8777 (tm-30) cc_final: 0.8082 (tt0) REVERT: C 462 THR cc_start: 0.9053 (m) cc_final: 0.8782 (p) REVERT: D 12 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8040 (pp) REVERT: D 15 ARG cc_start: 0.7798 (ttm170) cc_final: 0.7310 (ttm-80) REVERT: D 18 THR cc_start: 0.8830 (p) cc_final: 0.8079 (t) REVERT: D 35 TRP cc_start: 0.9029 (t60) cc_final: 0.8827 (t60) REVERT: D 42 PHE cc_start: 0.8781 (t80) cc_final: 0.8082 (t80) REVERT: D 64 PHE cc_start: 0.9375 (t80) cc_final: 0.9107 (t80) REVERT: D 74 MET cc_start: 0.8715 (tpp) cc_final: 0.8018 (mmm) REVERT: E 8 ASN cc_start: 0.8145 (t0) cc_final: 0.7768 (t0) REVERT: E 20 TRP cc_start: 0.7608 (p90) cc_final: 0.6262 (p90) REVERT: E 108 PHE cc_start: 0.8661 (m-80) cc_final: 0.8251 (m-80) REVERT: E 176 TYR cc_start: 0.8757 (m-80) cc_final: 0.8432 (m-80) REVERT: E 181 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8632 (pp) REVERT: E 251 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8184 (tt) REVERT: E 270 ASN cc_start: 0.6960 (t0) cc_final: 0.6726 (t0) REVERT: E 286 LYS cc_start: 0.8601 (ptpt) cc_final: 0.8185 (ptpp) REVERT: E 295 MET cc_start: 0.7876 (tpt) cc_final: 0.6369 (tmm) REVERT: E 442 TYR cc_start: 0.8923 (t80) cc_final: 0.8283 (t80) REVERT: E 473 MET cc_start: 0.3993 (pmm) cc_final: 0.3764 (pmm) REVERT: E 484 THR cc_start: 0.8808 (m) cc_final: 0.8288 (p) REVERT: H 3 GLU cc_start: 0.6542 (mm-30) cc_final: 0.6174 (mm-30) REVERT: H 47 TRP cc_start: 0.8150 (t60) cc_final: 0.7772 (t60) REVERT: H 56 ASN cc_start: 0.7634 (m-40) cc_final: 0.7379 (m110) REVERT: H 57 ASP cc_start: 0.7298 (t0) cc_final: 0.7022 (m-30) REVERT: H 65 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7123 (mtmt) REVERT: H 90 ASP cc_start: 0.7529 (t0) cc_final: 0.7210 (t0) REVERT: H 111 TYR cc_start: 0.8326 (m-80) cc_final: 0.8054 (m-10) REVERT: L 48 GLN cc_start: 0.7679 (mp10) cc_final: 0.6560 (mp10) REVERT: L 85 GLN cc_start: 0.7500 (mm-40) cc_final: 0.7283 (mm-40) REVERT: L 104 PHE cc_start: 0.8640 (m-80) cc_final: 0.8431 (m-80) REVERT: L 109 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7895 (mtp85) REVERT: O 6 VAL cc_start: 0.8073 (t) cc_final: 0.7678 (p) REVERT: O 57 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7004 (ttm110) REVERT: O 98 ASP cc_start: 0.8079 (p0) cc_final: 0.7618 (p0) REVERT: O 181 LEU cc_start: 0.8229 (tp) cc_final: 0.7839 (tp) REVERT: O 190 ASP cc_start: 0.8155 (t0) cc_final: 0.7885 (t0) REVERT: O 193 GLU cc_start: 0.6701 (pt0) cc_final: 0.6455 (pt0) REVERT: O 199 MET cc_start: 0.7490 (ttm) cc_final: 0.7142 (ttp) REVERT: O 287 MET cc_start: 0.8673 (mtp) cc_final: 0.8201 (mtp) REVERT: O 299 MET cc_start: 0.6960 (mmm) cc_final: 0.5967 (mmm) REVERT: O 433 MET cc_start: 0.8587 (ptp) cc_final: 0.8385 (ptt) REVERT: P 12 LEU cc_start: 0.6405 (OUTLIER) cc_final: 0.5927 (pp) REVERT: P 26 TRP cc_start: 0.6856 (m100) cc_final: 0.6513 (m-90) REVERT: Q 34 MET cc_start: 0.7959 (ptp) cc_final: 0.7758 (ptp) REVERT: Q 79 GLU cc_start: 0.7340 (mp0) cc_final: 0.7118 (mp0) REVERT: Q 125 ILE cc_start: 0.8751 (tt) cc_final: 0.8232 (tt) REVERT: Q 182 GLU cc_start: 0.6860 (tt0) cc_final: 0.6646 (tp30) REVERT: Q 199 MET cc_start: 0.8342 (ptm) cc_final: 0.7907 (ptm) REVERT: Q 258 MET cc_start: 0.8929 (tpp) cc_final: 0.8316 (tpp) REVERT: Q 293 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8636 (pptt) REVERT: Q 348 ARG cc_start: 0.8296 (ptm-80) cc_final: 0.7843 (ptm-80) REVERT: Q 358 LYS cc_start: 0.7489 (OUTLIER) cc_final: 0.6973 (tppt) REVERT: Q 360 GLU cc_start: 0.7116 (mm-30) cc_final: 0.6862 (mm-30) REVERT: Q 380 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.7660 (tt) REVERT: Q 432 LYS cc_start: 0.8262 (tttp) cc_final: 0.7924 (ttpp) REVERT: Q 436 GLN cc_start: 0.8373 (tm-30) cc_final: 0.7922 (tm-30) REVERT: Q 462 THR cc_start: 0.9051 (m) cc_final: 0.8775 (p) REVERT: R 18 THR cc_start: 0.8838 (p) cc_final: 0.8083 (t) REVERT: R 35 TRP cc_start: 0.8981 (t60) cc_final: 0.8691 (t60) REVERT: R 42 PHE cc_start: 0.8771 (t80) cc_final: 0.8075 (t80) REVERT: R 64 PHE cc_start: 0.9370 (t80) cc_final: 0.9105 (t80) REVERT: R 74 MET cc_start: 0.8709 (tpp) cc_final: 0.7975 (mmm) REVERT: S 8 ASN cc_start: 0.8219 (t0) cc_final: 0.7806 (t0) REVERT: S 20 TRP cc_start: 0.7606 (p90) cc_final: 0.6318 (p90) REVERT: S 108 PHE cc_start: 0.8659 (m-80) cc_final: 0.8297 (m-80) REVERT: S 176 TYR cc_start: 0.8855 (m-80) cc_final: 0.8474 (m-80) REVERT: S 251 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8192 (tt) REVERT: S 286 LYS cc_start: 0.8594 (ptpt) cc_final: 0.8176 (ptpp) REVERT: S 305 VAL cc_start: 0.9175 (OUTLIER) cc_final: 0.8698 (p) REVERT: S 323 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7467 (pm20) REVERT: S 410 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8007 (mtp) REVERT: S 442 TYR cc_start: 0.8923 (t80) cc_final: 0.8270 (t80) REVERT: S 473 MET cc_start: 0.3965 (pmm) cc_final: 0.3742 (pmm) REVERT: S 484 THR cc_start: 0.8805 (m) cc_final: 0.8286 (p) REVERT: U 3 GLU cc_start: 0.6530 (mm-30) cc_final: 0.6167 (mm-30) REVERT: U 47 TRP cc_start: 0.8150 (t60) cc_final: 0.7757 (t60) REVERT: U 57 ASP cc_start: 0.7322 (t0) cc_final: 0.7047 (m-30) REVERT: U 65 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7119 (mtmt) REVERT: U 90 ASP cc_start: 0.7523 (t0) cc_final: 0.7212 (t0) REVERT: U 95 TYR cc_start: 0.8611 (m-80) cc_final: 0.8184 (m-80) REVERT: U 111 TYR cc_start: 0.8328 (m-80) cc_final: 0.8051 (m-10) REVERT: V 2 ILE cc_start: 0.8577 (mt) cc_final: 0.8371 (mt) REVERT: V 48 GLN cc_start: 0.7672 (mp10) cc_final: 0.6565 (mp10) REVERT: V 104 PHE cc_start: 0.8646 (m-80) cc_final: 0.8435 (m-80) REVERT: V 109 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7881 (mtp85) outliers start: 173 outliers final: 115 residues processed: 916 average time/residue: 0.3877 time to fit residues: 579.6548 Evaluate side-chains 911 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 775 time to evaluate : 3.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 452 VAL 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 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 263 THR Chi-restraints excluded: chain C residue 293 LYS Chi-restraints excluded: chain C residue 356 VAL 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 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 43 ILE Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 92 CYS 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 251 LEU Chi-restraints excluded: chain E residue 258 MET 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 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 53 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 83 MET 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 92 CYS Chi-restraints excluded: chain O residue 121 CYS Chi-restraints excluded: chain O residue 130 VAL Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 237 THR 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 452 VAL 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 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 236 VAL Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 293 LYS 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 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 79 GLU Chi-restraints excluded: chain S residue 92 CYS Chi-restraints excluded: chain S residue 125 ILE Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 187 THR Chi-restraints excluded: chain S residue 205 MET Chi-restraints excluded: chain S residue 242 HIS Chi-restraints excluded: chain S residue 251 LEU Chi-restraints excluded: chain S residue 255 GLU Chi-restraints excluded: chain S residue 258 MET 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 53 SER Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 65 LYS Chi-restraints excluded: chain U residue 83 MET Chi-restraints excluded: chain V residue 84 VAL Chi-restraints excluded: chain V residue 109 ARG 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: 9.9990 chunk 134 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 363 optimal weight: 7.9990 chunk 144 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 chunk 358 optimal weight: 6.9990 chunk 268 optimal weight: 9.9990 chunk 147 optimal weight: 10.0000 chunk 153 optimal weight: 10.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- 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** C 246 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 428 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 GLN O 52 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.120811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.103653 restraints weight = 51960.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.106588 restraints weight = 25710.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.108499 restraints weight = 15776.990| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 30884 Z= 0.175 Angle : 0.711 15.624 41956 Z= 0.349 Chirality : 0.045 0.301 4928 Planarity : 0.004 0.058 5192 Dihedral : 9.210 105.483 4876 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 5.68 % Allowed : 21.76 % Favored : 72.56 % 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: -1.34 (0.13), residues: 3846 helix: 1.34 (0.18), residues: 870 sheet: -1.26 (0.15), residues: 1084 loop : -1.74 (0.13), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 20 HIS 0.006 0.001 HIS A 144 PHE 0.023 0.002 PHE T 48 TYR 0.024 0.001 TYR L 55 ARG 0.008 0.001 ARG A 348 Details of bonding type rmsd link_NAG-ASN : bond 0.00420 ( 12) link_NAG-ASN : angle 2.31695 ( 36) link_BETA1-4 : bond 0.00326 ( 20) link_BETA1-4 : angle 2.27799 ( 60) link_ALPHA1-3 : bond 0.00848 ( 4) link_ALPHA1-3 : angle 2.81510 ( 12) hydrogen bonds : bond 0.04029 ( 1094) hydrogen bonds : angle 5.28068 ( 3036) link_BETA1-6 : bond 0.00801 ( 4) link_BETA1-6 : angle 2.93449 ( 12) SS BOND : bond 0.00639 ( 30) SS BOND : angle 3.01220 ( 60) covalent geometry : bond 0.00410 (30814) covalent geometry : angle 0.69132 (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: 183 poor density : 781 time to evaluate : 7.004 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 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: 0.8111 (t) cc_final: 0.7665 (p) REVERT: A 20 TRP cc_start: 0.8887 (p-90) cc_final: 0.8557 (p-90) REVERT: A 57 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7098 (ttm110) REVERT: A 98 ASP cc_start: 0.8086 (p0) cc_final: 0.7649 (p0) REVERT: A 181 LEU cc_start: 0.8627 (tp) cc_final: 0.8206 (tp) REVERT: A 238 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.7557 (m-10) REVERT: A 287 MET cc_start: 0.8698 (mtp) cc_final: 0.8198 (mtp) REVERT: A 299 MET cc_start: 0.6946 (mmm) cc_final: 0.6041 (mmm) REVERT: A 394 SER cc_start: 0.7808 (m) cc_final: 0.7538 (p) REVERT: B 12 LEU cc_start: 0.6244 (OUTLIER) cc_final: 0.5666 (pp) REVERT: B 26 TRP cc_start: 0.6862 (m100) cc_final: 0.6606 (m-90) REVERT: B 61 VAL cc_start: 0.9243 (t) cc_final: 0.8971 (p) REVERT: B 69 LEU cc_start: 0.8320 (tp) cc_final: 0.7925 (mp) REVERT: C 34 MET cc_start: 0.8015 (ptp) cc_final: 0.7782 (ptp) REVERT: C 182 GLU cc_start: 0.7313 (tp30) cc_final: 0.6882 (tp30) REVERT: C 293 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8360 (pptt) REVERT: C 348 ARG cc_start: 0.8346 (ptm-80) cc_final: 0.7897 (ptm-80) REVERT: C 358 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7142 (tppt) REVERT: C 380 ILE cc_start: 0.7990 (mt) cc_final: 0.7681 (tt) REVERT: C 436 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8413 (tt0) REVERT: C 462 THR cc_start: 0.9075 (m) cc_final: 0.8790 (p) REVERT: D 12 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.7887 (pp) REVERT: D 35 TRP cc_start: 0.9045 (t60) cc_final: 0.8831 (t60) REVERT: D 42 PHE cc_start: 0.8787 (t80) cc_final: 0.7957 (t80) REVERT: D 64 PHE cc_start: 0.9376 (t80) cc_final: 0.9074 (t80) REVERT: D 69 LEU cc_start: 0.8512 (mt) cc_final: 0.8206 (mt) REVERT: D 74 MET cc_start: 0.8834 (tpp) cc_final: 0.8354 (mmm) REVERT: E 8 ASN cc_start: 0.8157 (t0) cc_final: 0.7817 (t0) REVERT: E 20 TRP cc_start: 0.7714 (p90) cc_final: 0.6361 (p90) REVERT: E 108 PHE cc_start: 0.8710 (m-80) cc_final: 0.8321 (m-80) REVERT: E 176 TYR cc_start: 0.8842 (m-80) cc_final: 0.8460 (m-80) REVERT: E 181 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8713 (pp) REVERT: E 259 HIS cc_start: 0.9106 (OUTLIER) cc_final: 0.7165 (t70) REVERT: E 270 ASN cc_start: 0.7015 (t0) cc_final: 0.6805 (t0) REVERT: E 286 LYS cc_start: 0.8636 (ptpt) cc_final: 0.8111 (ptpp) REVERT: E 400 PHE cc_start: 0.7845 (m-10) cc_final: 0.7612 (m-10) REVERT: E 447 SER cc_start: 0.9011 (t) cc_final: 0.8706 (t) REVERT: E 484 THR cc_start: 0.8883 (m) cc_final: 0.8510 (p) REVERT: H 3 GLU cc_start: 0.6519 (mm-30) cc_final: 0.6214 (mm-30) REVERT: H 47 TRP cc_start: 0.8228 (t60) cc_final: 0.7777 (t60) REVERT: H 56 ASN cc_start: 0.7660 (m-40) cc_final: 0.7406 (m110) REVERT: H 57 ASP cc_start: 0.7237 (t0) cc_final: 0.6995 (m-30) REVERT: H 65 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7137 (mtmt) REVERT: H 90 ASP cc_start: 0.7135 (t0) cc_final: 0.6695 (t0) REVERT: H 95 TYR cc_start: 0.8640 (m-80) cc_final: 0.8379 (m-80) REVERT: L 45 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.7998 (mttp) REVERT: L 48 GLN cc_start: 0.7639 (mp10) cc_final: 0.6760 (mp10) REVERT: L 104 PHE cc_start: 0.8500 (m-80) cc_final: 0.8294 (m-80) REVERT: O 6 VAL cc_start: 0.8104 (t) cc_final: 0.7710 (p) REVERT: O 20 TRP cc_start: 0.8906 (p-90) cc_final: 0.8591 (p-90) REVERT: O 42 ASP cc_start: 0.8470 (m-30) cc_final: 0.7900 (m-30) REVERT: O 57 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7146 (ttm110) REVERT: O 98 ASP cc_start: 0.8075 (p0) cc_final: 0.7641 (p0) REVERT: O 181 LEU cc_start: 0.8627 (tp) cc_final: 0.8192 (tp) REVERT: O 199 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.7211 (ttp) REVERT: O 238 PHE cc_start: 0.8683 (OUTLIER) cc_final: 0.7774 (m-10) REVERT: O 287 MET cc_start: 0.8620 (mtp) cc_final: 0.8139 (mtp) REVERT: O 299 MET cc_start: 0.7024 (mmm) cc_final: 0.6125 (mmm) REVERT: O 394 SER cc_start: 0.7800 (m) cc_final: 0.7505 (p) REVERT: O 433 MET cc_start: 0.8592 (ptp) cc_final: 0.8389 (ptt) REVERT: P 12 LEU cc_start: 0.6177 (OUTLIER) cc_final: 0.5617 (pp) REVERT: P 26 TRP cc_start: 0.6843 (m100) cc_final: 0.6546 (m-90) REVERT: P 69 LEU cc_start: 0.8465 (tp) cc_final: 0.7961 (mp) REVERT: Q 34 MET cc_start: 0.8121 (ptp) cc_final: 0.7857 (ptp) REVERT: Q 79 GLU cc_start: 0.7504 (mp0) cc_final: 0.7237 (mp0) REVERT: Q 182 GLU cc_start: 0.6827 (tt0) cc_final: 0.6558 (tp30) REVERT: Q 293 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8349 (pptt) REVERT: Q 348 ARG cc_start: 0.8355 (ptm-80) cc_final: 0.7903 (ptm-80) REVERT: Q 358 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.7213 (tppt) REVERT: Q 380 ILE cc_start: 0.7984 (mt) cc_final: 0.7678 (tt) REVERT: Q 432 LYS cc_start: 0.8287 (tttp) cc_final: 0.8014 (ttpp) REVERT: Q 436 GLN cc_start: 0.8248 (tm-30) cc_final: 0.7797 (tm-30) REVERT: Q 462 THR cc_start: 0.9072 (m) cc_final: 0.8773 (p) REVERT: R 18 THR cc_start: 0.8912 (p) cc_final: 0.8173 (t) REVERT: R 35 TRP cc_start: 0.9038 (t60) cc_final: 0.8767 (t60) REVERT: R 42 PHE cc_start: 0.8772 (t80) cc_final: 0.7927 (t80) REVERT: R 64 PHE cc_start: 0.9371 (t80) cc_final: 0.9085 (t80) REVERT: R 69 LEU cc_start: 0.8443 (mt) cc_final: 0.8135 (mt) REVERT: R 74 MET cc_start: 0.8825 (tpp) cc_final: 0.8344 (mmm) REVERT: S 8 ASN cc_start: 0.8200 (t0) cc_final: 0.7870 (t0) REVERT: S 20 TRP cc_start: 0.7706 (p90) cc_final: 0.6376 (p90) REVERT: S 108 PHE cc_start: 0.8722 (m-80) cc_final: 0.8319 (m-80) REVERT: S 123 GLU cc_start: 0.7082 (tt0) cc_final: 0.6681 (tt0) REVERT: S 176 TYR cc_start: 0.8857 (m-80) cc_final: 0.8516 (m-80) REVERT: S 251 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.7965 (tt) REVERT: S 259 HIS cc_start: 0.8941 (OUTLIER) cc_final: 0.7245 (t70) REVERT: S 286 LYS cc_start: 0.8597 (ptpt) cc_final: 0.8137 (ptpp) REVERT: S 305 VAL cc_start: 0.9154 (OUTLIER) cc_final: 0.8671 (p) REVERT: S 323 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7513 (pm20) REVERT: S 400 PHE cc_start: 0.7839 (m-10) cc_final: 0.7609 (m-10) REVERT: S 410 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8048 (mtp) REVERT: S 484 THR cc_start: 0.8875 (m) cc_final: 0.8506 (p) REVERT: U 3 GLU cc_start: 0.6511 (mm-30) cc_final: 0.6210 (mm-30) REVERT: U 47 TRP cc_start: 0.8233 (t60) cc_final: 0.7761 (t60) REVERT: U 57 ASP cc_start: 0.7269 (t0) cc_final: 0.7032 (m-30) REVERT: U 65 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7137 (mtmt) REVERT: U 90 ASP cc_start: 0.7137 (t0) cc_final: 0.6666 (t0) REVERT: U 95 TYR cc_start: 0.8631 (m-80) cc_final: 0.8369 (m-80) REVERT: V 48 GLN cc_start: 0.7637 (mp10) cc_final: 0.6760 (mp10) REVERT: V 104 PHE cc_start: 0.8494 (m-80) cc_final: 0.8285 (m-80) outliers start: 183 outliers final: 123 residues processed: 895 average time/residue: 0.4416 time to fit residues: 650.9749 Evaluate side-chains 894 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 749 time to evaluate : 4.305 ------------------------------------------------------------------------------- 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 81 VAL 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 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 413 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 429 SER 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 45 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 313 THR Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 358 LYS 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 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 199 MET 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 356 VAL 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 65 LYS 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 45 LYS 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 199 MET Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 237 THR 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 320 ILE 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 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 236 VAL Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 293 LYS 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 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 79 GLU Chi-restraints excluded: chain S residue 91 VAL Chi-restraints excluded: chain S residue 92 CYS Chi-restraints excluded: chain S residue 125 ILE Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 187 THR Chi-restraints excluded: chain S residue 242 HIS Chi-restraints excluded: chain S residue 251 LEU 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 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 53 SER Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 65 LYS 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: 9.9990 chunk 86 optimal weight: 8.9990 chunk 353 optimal weight: 20.0000 chunk 374 optimal weight: 20.0000 chunk 49 optimal weight: 7.9990 chunk 373 optimal weight: 9.9990 chunk 308 optimal weight: 20.0000 chunk 321 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 154 optimal weight: 20.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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 242 HIS E 259 HIS ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 GLN L 85 GLN ** 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 150 GLN S 242 HIS ** T 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 51 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.118265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.100873 restraints weight = 52484.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.103803 restraints weight = 26314.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.105691 restraints weight = 16258.732| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 30884 Z= 0.263 Angle : 0.799 14.763 41956 Z= 0.396 Chirality : 0.048 0.313 4928 Planarity : 0.005 0.058 5192 Dihedral : 9.190 103.397 4876 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 6.30 % Allowed : 21.85 % Favored : 71.85 % 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: -1.52 (0.13), residues: 3846 helix: 1.10 (0.18), residues: 876 sheet: -1.46 (0.15), residues: 1102 loop : -1.74 (0.13), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP Q 218 HIS 0.009 0.002 HIS O 144 PHE 0.019 0.002 PHE F 48 TYR 0.016 0.002 TYR U 60 ARG 0.008 0.001 ARG A 9 Details of bonding type rmsd link_NAG-ASN : bond 0.00538 ( 12) link_NAG-ASN : angle 2.82757 ( 36) link_BETA1-4 : bond 0.00442 ( 20) link_BETA1-4 : angle 2.39479 ( 60) link_ALPHA1-3 : bond 0.00796 ( 4) link_ALPHA1-3 : angle 2.94921 ( 12) hydrogen bonds : bond 0.04473 ( 1094) hydrogen bonds : angle 5.43514 ( 3036) link_BETA1-6 : bond 0.00715 ( 4) link_BETA1-6 : angle 3.03153 ( 12) SS BOND : bond 0.00656 ( 30) SS BOND : angle 3.32434 ( 60) covalent geometry : bond 0.00619 (30814) covalent geometry : angle 0.77741 (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 969 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 766 time to evaluate : 3.123 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 6 VAL cc_start: 0.8179 (t) cc_final: 0.7739 (p) REVERT: A 48 THR cc_start: 0.8806 (OUTLIER) cc_final: 0.8542 (t) REVERT: A 57 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7045 (ttm110) REVERT: A 98 ASP cc_start: 0.8096 (p0) cc_final: 0.7708 (p0) REVERT: A 181 LEU cc_start: 0.8695 (tp) cc_final: 0.8225 (tp) REVERT: A 238 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.8023 (m-10) REVERT: A 287 MET cc_start: 0.8589 (mtp) cc_final: 0.8097 (mtp) REVERT: A 299 MET cc_start: 0.6963 (mmm) cc_final: 0.6187 (mtt) REVERT: A 371 PHE cc_start: 0.9286 (OUTLIER) cc_final: 0.8525 (t80) REVERT: B 12 LEU cc_start: 0.6864 (OUTLIER) cc_final: 0.6194 (pp) REVERT: B 23 GLU cc_start: 0.5915 (pm20) cc_final: 0.5600 (pm20) REVERT: B 26 TRP cc_start: 0.6934 (m100) cc_final: 0.6672 (m-90) REVERT: B 61 VAL cc_start: 0.9243 (t) cc_final: 0.8949 (p) REVERT: C 34 MET cc_start: 0.8104 (ptp) cc_final: 0.7843 (ptp) REVERT: C 182 GLU cc_start: 0.7343 (tp30) cc_final: 0.6904 (tp30) REVERT: C 194 MET cc_start: 0.8389 (ttm) cc_final: 0.8115 (mmm) REVERT: C 199 MET cc_start: 0.8141 (ptm) cc_final: 0.7869 (ptm) REVERT: C 293 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8268 (pptt) REVERT: C 348 ARG cc_start: 0.8405 (ptm-80) cc_final: 0.7926 (ptm-80) REVERT: C 358 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7328 (tppt) REVERT: C 380 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7737 (tt) REVERT: C 462 THR cc_start: 0.9086 (m) cc_final: 0.8848 (p) REVERT: D 12 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7718 (pp) REVERT: D 42 PHE cc_start: 0.8834 (t80) cc_final: 0.8235 (t80) REVERT: D 64 PHE cc_start: 0.9372 (t80) cc_final: 0.9098 (t80) REVERT: D 69 LEU cc_start: 0.8548 (mt) cc_final: 0.8319 (mt) REVERT: D 74 MET cc_start: 0.8837 (tpp) cc_final: 0.8342 (mmm) REVERT: E 8 ASN cc_start: 0.8214 (t0) cc_final: 0.7916 (t0) REVERT: E 20 TRP cc_start: 0.7915 (p90) cc_final: 0.6450 (p90) REVERT: E 108 PHE cc_start: 0.8792 (m-80) cc_final: 0.8366 (m-80) REVERT: E 176 TYR cc_start: 0.8907 (m-80) cc_final: 0.8532 (m-80) REVERT: E 181 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8746 (pp) REVERT: E 259 HIS cc_start: 0.8879 (OUTLIER) cc_final: 0.6468 (t-90) REVERT: E 270 ASN cc_start: 0.7141 (t0) cc_final: 0.6933 (t0) REVERT: E 286 LYS cc_start: 0.8651 (ptpt) cc_final: 0.8253 (mtmm) REVERT: E 400 PHE cc_start: 0.7868 (m-10) cc_final: 0.7663 (m-10) REVERT: E 442 TYR cc_start: 0.8951 (t80) cc_final: 0.8399 (t80) REVERT: E 447 SER cc_start: 0.9079 (t) cc_final: 0.8774 (t) REVERT: E 473 MET cc_start: 0.4748 (pmm) cc_final: 0.4439 (pmm) REVERT: E 484 THR cc_start: 0.8928 (m) cc_final: 0.8541 (p) REVERT: H 47 TRP cc_start: 0.8233 (t60) cc_final: 0.7333 (t60) REVERT: H 56 ASN cc_start: 0.7661 (m-40) cc_final: 0.7458 (m110) REVERT: H 65 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7860 (mtpp) REVERT: H 90 ASP cc_start: 0.7131 (t0) cc_final: 0.6857 (t0) REVERT: H 95 TYR cc_start: 0.8653 (m-80) cc_final: 0.8449 (m-80) REVERT: L 48 GLN cc_start: 0.7729 (mp10) cc_final: 0.7503 (mp10) REVERT: L 109 ARG cc_start: 0.8362 (mtp85) cc_final: 0.8107 (mtp85) REVERT: O 6 VAL cc_start: 0.8169 (t) cc_final: 0.7736 (p) REVERT: O 57 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7020 (ttm110) REVERT: O 98 ASP cc_start: 0.8095 (p0) cc_final: 0.7731 (p0) REVERT: O 168 THR cc_start: 0.9024 (OUTLIER) cc_final: 0.8640 (p) REVERT: O 181 LEU cc_start: 0.8695 (tp) cc_final: 0.8146 (tp) REVERT: O 199 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7366 (ttm) REVERT: O 201 ASN cc_start: 0.7257 (m-40) cc_final: 0.6029 (t0) REVERT: O 238 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.8011 (m-10) REVERT: O 287 MET cc_start: 0.8577 (mtp) cc_final: 0.8103 (mtp) REVERT: O 299 MET cc_start: 0.7025 (mmm) cc_final: 0.6301 (mtt) REVERT: O 371 PHE cc_start: 0.9257 (OUTLIER) cc_final: 0.8476 (t80) REVERT: O 433 MET cc_start: 0.8610 (ptp) cc_final: 0.8403 (ptt) REVERT: P 12 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6129 (pp) REVERT: P 23 GLU cc_start: 0.5884 (pm20) cc_final: 0.5566 (pm20) REVERT: P 26 TRP cc_start: 0.6917 (m100) cc_final: 0.6616 (m-90) REVERT: Q 34 MET cc_start: 0.8181 (ptp) cc_final: 0.7889 (ptp) REVERT: Q 79 GLU cc_start: 0.7568 (mp0) cc_final: 0.7340 (mp0) REVERT: Q 182 GLU cc_start: 0.6967 (tt0) cc_final: 0.6682 (tp30) REVERT: Q 199 MET cc_start: 0.8161 (ptm) cc_final: 0.7896 (ptm) REVERT: Q 230 ASN cc_start: 0.8567 (m-40) cc_final: 0.7356 (m-40) REVERT: Q 293 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8258 (pptt) REVERT: Q 348 ARG cc_start: 0.8410 (ptm-80) cc_final: 0.7935 (ptm-80) REVERT: Q 358 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7325 (tppt) REVERT: Q 380 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7745 (tt) REVERT: Q 436 GLN cc_start: 0.8274 (tm-30) cc_final: 0.7782 (tt0) REVERT: Q 462 THR cc_start: 0.9074 (m) cc_final: 0.8839 (p) REVERT: R 35 TRP cc_start: 0.9033 (t60) cc_final: 0.8748 (t60) REVERT: R 42 PHE cc_start: 0.8818 (t80) cc_final: 0.8144 (t80) REVERT: R 64 PHE cc_start: 0.9371 (t80) cc_final: 0.9093 (t80) REVERT: R 69 LEU cc_start: 0.8459 (mt) cc_final: 0.8234 (mt) REVERT: R 74 MET cc_start: 0.8815 (tpp) cc_final: 0.8313 (mmm) REVERT: S 8 ASN cc_start: 0.8237 (t0) cc_final: 0.7954 (t0) REVERT: S 20 TRP cc_start: 0.7914 (p90) cc_final: 0.6458 (p90) REVERT: S 26 GLU cc_start: 0.7604 (mp0) cc_final: 0.7315 (pm20) REVERT: S 108 PHE cc_start: 0.8807 (m-80) cc_final: 0.8062 (m-80) REVERT: S 151 VAL cc_start: 0.8197 (OUTLIER) cc_final: 0.7827 (t) REVERT: S 259 HIS cc_start: 0.8946 (OUTLIER) cc_final: 0.7205 (t70) REVERT: S 286 LYS cc_start: 0.8652 (ptpt) cc_final: 0.8191 (mtmt) REVERT: S 305 VAL cc_start: 0.9185 (OUTLIER) cc_final: 0.8586 (p) REVERT: S 323 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7409 (pm20) REVERT: S 400 PHE cc_start: 0.7866 (m-10) cc_final: 0.7659 (m-10) REVERT: S 410 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8106 (mtp) REVERT: S 442 TYR cc_start: 0.8952 (t80) cc_final: 0.8386 (t80) REVERT: S 447 SER cc_start: 0.9124 (t) cc_final: 0.8845 (t) REVERT: S 473 MET cc_start: 0.4733 (pmm) cc_final: 0.4428 (pmm) REVERT: S 484 THR cc_start: 0.8926 (m) cc_final: 0.8547 (p) REVERT: U 47 TRP cc_start: 0.8237 (t60) cc_final: 0.7331 (t60) REVERT: U 65 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7856 (mtpp) REVERT: U 90 ASP cc_start: 0.7131 (t0) cc_final: 0.6772 (t0) REVERT: V 48 GLN cc_start: 0.7740 (mp10) cc_final: 0.7080 (mp10) outliers start: 203 outliers final: 138 residues processed: 895 average time/residue: 0.4404 time to fit residues: 653.4218 Evaluate side-chains 917 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 752 time to evaluate : 3.668 ------------------------------------------------------------------------------- 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 81 VAL 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 320 ILE 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 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 45 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 195 ILE 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 350 ILE 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 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 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 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 65 LYS 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 168 THR Chi-restraints excluded: chain O residue 195 ILE Chi-restraints excluded: chain O residue 198 THR Chi-restraints excluded: chain O residue 199 MET 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 320 ILE 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 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 65 ILE 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 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 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 91 VAL Chi-restraints excluded: chain S residue 125 ILE Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 151 VAL 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 22 CYS 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 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: 5.9990 chunk 208 optimal weight: 1.9990 chunk 367 optimal weight: 0.4980 chunk 167 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 307 optimal weight: 9.9990 chunk 148 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 369 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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** ** 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** H 100 GLN ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 GLN ** 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 8 ASN ** 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 = 0.3433 r_free = 0.3433 target = 0.121848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.104617 restraints weight = 51660.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.107617 restraints weight = 25576.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.109542 restraints weight = 15618.701| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 30884 Z= 0.133 Angle : 0.708 13.512 41956 Z= 0.348 Chirality : 0.044 0.256 4928 Planarity : 0.004 0.062 5192 Dihedral : 8.732 102.627 4876 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.62 % Allowed : 23.68 % Favored : 71.69 % 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: -1.35 (0.13), residues: 3846 helix: 1.35 (0.18), residues: 876 sheet: -1.40 (0.15), residues: 1126 loop : -1.66 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP Q 218 HIS 0.019 0.001 HIS E 242 PHE 0.025 0.001 PHE E 475 TYR 0.027 0.001 TYR V 55 ARG 0.009 0.001 ARG A 348 Details of bonding type rmsd link_NAG-ASN : bond 0.00370 ( 12) link_NAG-ASN : angle 2.28334 ( 36) link_BETA1-4 : bond 0.00289 ( 20) link_BETA1-4 : angle 2.21988 ( 60) link_ALPHA1-3 : bond 0.00891 ( 4) link_ALPHA1-3 : angle 2.59783 ( 12) hydrogen bonds : bond 0.03946 ( 1094) hydrogen bonds : angle 5.23824 ( 3036) link_BETA1-6 : bond 0.00917 ( 4) link_BETA1-6 : angle 2.69857 ( 12) SS BOND : bond 0.00590 ( 30) SS BOND : angle 2.71531 ( 60) covalent geometry : bond 0.00302 (30814) covalent geometry : angle 0.69093 (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 940 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 791 time to evaluate : 3.650 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 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 57 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7288 (ttm110) REVERT: A 98 ASP cc_start: 0.8050 (p0) cc_final: 0.7611 (p0) REVERT: A 181 LEU cc_start: 0.8308 (tp) cc_final: 0.7878 (tp) REVERT: A 287 MET cc_start: 0.8643 (mtp) cc_final: 0.8169 (mtp) REVERT: A 299 MET cc_start: 0.6834 (mmm) cc_final: 0.6028 (mmm) REVERT: A 371 PHE cc_start: 0.9255 (OUTLIER) cc_final: 0.8536 (t80) REVERT: A 390 TYR cc_start: 0.8754 (t80) cc_final: 0.8197 (t80) REVERT: A 392 LYS cc_start: 0.8380 (pttp) cc_final: 0.8169 (ptpt) REVERT: B 12 LEU cc_start: 0.6275 (OUTLIER) cc_final: 0.5782 (pp) REVERT: B 26 TRP cc_start: 0.6890 (m100) cc_final: 0.6559 (m-90) REVERT: B 61 VAL cc_start: 0.9242 (t) cc_final: 0.8988 (p) REVERT: B 69 LEU cc_start: 0.8217 (tp) cc_final: 0.7859 (mp) REVERT: C 34 MET cc_start: 0.8053 (ptp) cc_final: 0.7794 (ptp) REVERT: C 182 GLU cc_start: 0.7292 (tp30) cc_final: 0.6862 (tp30) REVERT: C 194 MET cc_start: 0.8155 (ttm) cc_final: 0.7718 (mmm) REVERT: C 199 MET cc_start: 0.8123 (ptm) cc_final: 0.7804 (ptm) REVERT: C 258 MET cc_start: 0.8875 (tpp) cc_final: 0.8319 (tpp) REVERT: C 293 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8214 (pptt) REVERT: C 348 ARG cc_start: 0.8374 (ptm-80) cc_final: 0.7937 (ptm-80) REVERT: C 358 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.6979 (tppt) REVERT: C 380 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7644 (tt) REVERT: C 436 GLN cc_start: 0.8720 (tm-30) cc_final: 0.8242 (tt0) REVERT: C 462 THR cc_start: 0.9079 (m) cc_final: 0.8812 (p) REVERT: D 12 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7599 (pp) REVERT: D 35 TRP cc_start: 0.9044 (t60) cc_final: 0.8594 (t60) REVERT: D 42 PHE cc_start: 0.8781 (t80) cc_final: 0.8128 (t80) REVERT: D 64 PHE cc_start: 0.9357 (t80) cc_final: 0.9060 (t80) REVERT: D 69 LEU cc_start: 0.8480 (mt) cc_final: 0.8262 (mt) REVERT: D 74 MET cc_start: 0.8838 (tpp) cc_final: 0.8336 (mmm) REVERT: E 8 ASN cc_start: 0.8057 (t0) cc_final: 0.7734 (t0) REVERT: E 20 TRP cc_start: 0.7762 (p90) cc_final: 0.6373 (p90) REVERT: E 108 PHE cc_start: 0.8709 (m-80) cc_final: 0.8338 (m-80) REVERT: E 175 GLU cc_start: 0.7134 (tp30) cc_final: 0.6848 (tp30) REVERT: E 176 TYR cc_start: 0.8830 (m-80) cc_final: 0.8507 (m-80) REVERT: E 181 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8704 (pp) REVERT: E 270 ASN cc_start: 0.7038 (t0) cc_final: 0.6831 (t0) REVERT: E 323 GLU cc_start: 0.7510 (tt0) cc_final: 0.7114 (pt0) REVERT: E 400 PHE cc_start: 0.7846 (m-10) cc_final: 0.7612 (m-10) REVERT: E 442 TYR cc_start: 0.8949 (t80) cc_final: 0.8388 (t80) REVERT: E 447 SER cc_start: 0.8934 (t) cc_final: 0.8629 (t) REVERT: E 473 MET cc_start: 0.4446 (pmm) cc_final: 0.4103 (pmm) REVERT: E 484 THR cc_start: 0.8811 (m) cc_final: 0.8303 (p) REVERT: F 17 GLN cc_start: 0.8398 (tt0) cc_final: 0.7920 (tt0) REVERT: H 3 GLU cc_start: 0.6415 (mm-30) cc_final: 0.6203 (mm-30) REVERT: H 47 TRP cc_start: 0.8257 (t60) cc_final: 0.7748 (t60) REVERT: H 65 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7876 (mtpp) REVERT: H 90 ASP cc_start: 0.7191 (t0) cc_final: 0.6558 (t0) REVERT: L 48 GLN cc_start: 0.7881 (mp10) cc_final: 0.7103 (mp10) REVERT: O 42 ASP cc_start: 0.8424 (m-30) cc_final: 0.7987 (m-30) REVERT: O 53 LEU cc_start: 0.7867 (mt) cc_final: 0.7644 (mt) REVERT: O 57 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7046 (ttm110) REVERT: O 98 ASP cc_start: 0.8047 (p0) cc_final: 0.7632 (p0) REVERT: O 181 LEU cc_start: 0.8290 (tp) cc_final: 0.7851 (tp) REVERT: O 199 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7114 (ttp) REVERT: O 201 ASN cc_start: 0.7146 (m-40) cc_final: 0.6017 (t0) REVERT: O 287 MET cc_start: 0.8635 (mtp) cc_final: 0.8175 (mtp) REVERT: O 299 MET cc_start: 0.7082 (mmm) cc_final: 0.6348 (mmm) REVERT: O 371 PHE cc_start: 0.9227 (OUTLIER) cc_final: 0.8541 (t80) REVERT: O 390 TYR cc_start: 0.8789 (t80) cc_final: 0.8309 (t80) REVERT: O 392 LYS cc_start: 0.8356 (pttp) cc_final: 0.8139 (ptpt) REVERT: P 12 LEU cc_start: 0.6186 (OUTLIER) cc_final: 0.5786 (pp) REVERT: P 26 TRP cc_start: 0.6871 (m100) cc_final: 0.6566 (m-90) REVERT: P 45 LEU cc_start: 0.8355 (tp) cc_final: 0.7871 (tt) REVERT: P 69 LEU cc_start: 0.8207 (tp) cc_final: 0.7859 (mp) REVERT: Q 34 MET cc_start: 0.8019 (ptp) cc_final: 0.7767 (ptp) REVERT: Q 79 GLU cc_start: 0.7496 (mp0) cc_final: 0.7277 (mp0) REVERT: Q 182 GLU cc_start: 0.6859 (tt0) cc_final: 0.6564 (tp30) REVERT: Q 199 MET cc_start: 0.8139 (ptm) cc_final: 0.7828 (ptm) REVERT: Q 258 MET cc_start: 0.8894 (tpp) cc_final: 0.8341 (tpp) REVERT: Q 293 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8211 (pptt) REVERT: Q 348 ARG cc_start: 0.8389 (ptm-80) cc_final: 0.7944 (ptm-80) REVERT: Q 358 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7186 (tppt) REVERT: Q 380 ILE cc_start: 0.7952 (mt) cc_final: 0.7647 (tt) REVERT: Q 436 GLN cc_start: 0.8339 (tm-30) cc_final: 0.8038 (tt0) REVERT: Q 462 THR cc_start: 0.9067 (m) cc_final: 0.8806 (p) REVERT: R 35 TRP cc_start: 0.8973 (t60) cc_final: 0.8416 (t60) REVERT: R 42 PHE cc_start: 0.8769 (t80) cc_final: 0.8122 (t80) REVERT: R 64 PHE cc_start: 0.9338 (t80) cc_final: 0.9050 (t80) REVERT: R 74 MET cc_start: 0.8807 (tpp) cc_final: 0.8297 (mmm) REVERT: S 20 TRP cc_start: 0.7833 (p90) cc_final: 0.6420 (p90) REVERT: S 59 LEU cc_start: 0.8418 (mt) cc_final: 0.8178 (mt) REVERT: S 108 PHE cc_start: 0.8725 (m-80) cc_final: 0.7974 (m-80) REVERT: S 259 HIS cc_start: 0.8863 (OUTLIER) cc_final: 0.6948 (t70) REVERT: S 305 VAL cc_start: 0.9148 (OUTLIER) cc_final: 0.8574 (p) REVERT: S 323 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7423 (pm20) REVERT: S 400 PHE cc_start: 0.7841 (m-10) cc_final: 0.7609 (m-10) REVERT: S 410 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8063 (mtp) REVERT: S 442 TYR cc_start: 0.8948 (t80) cc_final: 0.8372 (t80) REVERT: S 447 SER cc_start: 0.8940 (t) cc_final: 0.8630 (t) REVERT: S 473 MET cc_start: 0.4420 (pmm) cc_final: 0.4087 (pmm) REVERT: S 484 THR cc_start: 0.8870 (m) cc_final: 0.8402 (p) REVERT: U 3 GLU cc_start: 0.6428 (mm-30) cc_final: 0.6134 (mm-30) REVERT: U 47 TRP cc_start: 0.8274 (t60) cc_final: 0.7743 (t60) REVERT: U 65 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7872 (mtpp) REVERT: U 90 ASP cc_start: 0.7200 (t0) cc_final: 0.6855 (t0) REVERT: V 45 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.7989 (mttp) REVERT: V 48 GLN cc_start: 0.7906 (mp10) cc_final: 0.7099 (mp10) outliers start: 149 outliers final: 109 residues processed: 880 average time/residue: 0.5334 time to fit residues: 760.8456 Evaluate side-chains 890 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 760 time to evaluate : 3.544 ------------------------------------------------------------------------------- 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 81 VAL 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 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 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 30 CYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 129 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 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 91 VAL Chi-restraints excluded: chain E residue 92 CYS 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 318 ILE Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 485 LEU 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 65 LYS Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 76 ASP 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 198 THR Chi-restraints excluded: chain O residue 199 MET 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 460 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 65 ILE Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 201 ASN 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 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 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 91 VAL Chi-restraints excluded: chain S residue 92 CYS Chi-restraints excluded: chain S residue 125 ILE Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 151 VAL 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 464 ILE Chi-restraints excluded: chain S residue 485 LEU 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 63 SER Chi-restraints excluded: chain U residue 65 LYS Chi-restraints excluded: chain U residue 83 MET Chi-restraints excluded: chain U residue 91 THR Chi-restraints excluded: chain V residue 45 LYS Chi-restraints excluded: chain V residue 76 ASP 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: 20.0000 chunk 80 optimal weight: 8.9990 chunk 127 optimal weight: 7.9990 chunk 332 optimal weight: 0.3980 chunk 131 optimal weight: 20.0000 chunk 293 optimal weight: 3.9990 chunk 288 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 chunk 338 optimal weight: 6.9990 chunk 323 optimal weight: 3.9990 overall best weight: 4.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 GLN ** 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 242 HIS E 428 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN ** L 51 GLN ** 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 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.120622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.103381 restraints weight = 51944.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.106323 restraints weight = 25720.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.108249 restraints weight = 15828.001| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 30884 Z= 0.176 Angle : 0.735 16.514 41956 Z= 0.362 Chirality : 0.045 0.283 4928 Planarity : 0.004 0.062 5192 Dihedral : 8.573 101.762 4876 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 4.59 % Allowed : 23.90 % Favored : 71.51 % 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: -1.35 (0.13), residues: 3846 helix: 1.30 (0.18), residues: 876 sheet: -1.32 (0.15), residues: 1114 loop : -1.69 (0.13), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP P 35 HIS 0.006 0.001 HIS S 242 PHE 0.021 0.002 PHE E 475 TYR 0.010 0.001 TYR H 60 ARG 0.009 0.001 ARG A 348 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 12) link_NAG-ASN : angle 2.43618 ( 36) link_BETA1-4 : bond 0.00353 ( 20) link_BETA1-4 : angle 2.25856 ( 60) link_ALPHA1-3 : bond 0.00845 ( 4) link_ALPHA1-3 : angle 2.64577 ( 12) hydrogen bonds : bond 0.04054 ( 1094) hydrogen bonds : angle 5.24551 ( 3036) link_BETA1-6 : bond 0.00828 ( 4) link_BETA1-6 : angle 2.50533 ( 12) SS BOND : bond 0.00635 ( 30) SS BOND : angle 2.96261 ( 60) covalent geometry : bond 0.00414 (30814) covalent geometry : angle 0.71713 (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 901 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 753 time to evaluate : 3.385 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7041 (ttm110) REVERT: A 98 ASP cc_start: 0.8054 (p0) cc_final: 0.7653 (p0) REVERT: A 168 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8616 (p) REVERT: A 181 LEU cc_start: 0.8466 (tp) cc_final: 0.7995 (tp) REVERT: A 190 ASP cc_start: 0.8093 (t0) cc_final: 0.7852 (t70) REVERT: A 287 MET cc_start: 0.8548 (mtp) cc_final: 0.8085 (mtp) REVERT: A 299 MET cc_start: 0.6947 (mmm) cc_final: 0.6213 (mtt) REVERT: A 371 PHE cc_start: 0.9263 (OUTLIER) cc_final: 0.8446 (t80) REVERT: A 390 TYR cc_start: 0.8760 (t80) cc_final: 0.8285 (t80) REVERT: A 392 LYS cc_start: 0.8395 (pttp) cc_final: 0.8170 (ptpt) REVERT: B 12 LEU cc_start: 0.6866 (OUTLIER) cc_final: 0.6401 (pp) REVERT: B 26 TRP cc_start: 0.6918 (m100) cc_final: 0.6579 (m-90) REVERT: B 61 VAL cc_start: 0.9241 (t) cc_final: 0.8950 (p) REVERT: C 34 MET cc_start: 0.8080 (ptp) cc_final: 0.7808 (ptp) REVERT: C 182 GLU cc_start: 0.7315 (tp30) cc_final: 0.6877 (tp30) REVERT: C 194 MET cc_start: 0.8169 (ttm) cc_final: 0.7829 (mmm) REVERT: C 199 MET cc_start: 0.8130 (ptm) cc_final: 0.7837 (ptm) REVERT: C 258 MET cc_start: 0.8883 (tpp) cc_final: 0.8329 (tpp) REVERT: C 293 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8091 (pptt) REVERT: C 348 ARG cc_start: 0.8409 (ptm-80) cc_final: 0.7972 (ptm-80) REVERT: C 358 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7098 (tppt) REVERT: C 380 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7659 (tt) REVERT: C 462 THR cc_start: 0.9096 (m) cc_final: 0.8791 (p) REVERT: D 12 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7614 (pp) REVERT: D 35 TRP cc_start: 0.9043 (t60) cc_final: 0.8602 (t60) REVERT: D 42 PHE cc_start: 0.8792 (t80) cc_final: 0.7936 (t80) REVERT: D 64 PHE cc_start: 0.9362 (t80) cc_final: 0.9034 (t80) REVERT: D 69 LEU cc_start: 0.8455 (mt) cc_final: 0.8243 (mt) REVERT: D 74 MET cc_start: 0.8750 (tpp) cc_final: 0.8322 (mmm) REVERT: E 8 ASN cc_start: 0.8061 (t0) cc_final: 0.7760 (t0) REVERT: E 20 TRP cc_start: 0.7873 (p90) cc_final: 0.6403 (p90) REVERT: E 108 PHE cc_start: 0.8748 (m-80) cc_final: 0.8374 (m-80) REVERT: E 175 GLU cc_start: 0.7144 (tp30) cc_final: 0.6855 (tp30) REVERT: E 176 TYR cc_start: 0.8854 (m-80) cc_final: 0.8558 (m-80) REVERT: E 179 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.7832 (pt) REVERT: E 270 ASN cc_start: 0.7087 (t0) cc_final: 0.6887 (t0) REVERT: E 400 PHE cc_start: 0.7823 (m-10) cc_final: 0.7591 (m-10) REVERT: E 442 TYR cc_start: 0.8967 (t80) cc_final: 0.8410 (t80) REVERT: E 447 SER cc_start: 0.8998 (t) cc_final: 0.8700 (t) REVERT: E 473 MET cc_start: 0.4563 (pmm) cc_final: 0.4217 (pmm) REVERT: E 484 THR cc_start: 0.8875 (m) cc_final: 0.8407 (p) REVERT: H 47 TRP cc_start: 0.8246 (t60) cc_final: 0.7516 (t60) REVERT: H 65 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7861 (mtpp) REVERT: H 73 ASP cc_start: 0.7561 (p0) cc_final: 0.6415 (p0) REVERT: H 90 ASP cc_start: 0.7477 (t0) cc_final: 0.6904 (t0) REVERT: L 45 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8173 (mmtp) REVERT: L 111 GLU cc_start: 0.6180 (tp30) cc_final: 0.5665 (tp30) REVERT: O 53 LEU cc_start: 0.7904 (mt) cc_final: 0.7667 (mt) REVERT: O 57 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7059 (ttm110) REVERT: O 98 ASP cc_start: 0.8048 (p0) cc_final: 0.7665 (p0) REVERT: O 181 LEU cc_start: 0.8185 (tp) cc_final: 0.7808 (tp) REVERT: O 199 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.7381 (ttp) REVERT: O 201 ASN cc_start: 0.7240 (m-40) cc_final: 0.6044 (t0) REVERT: O 287 MET cc_start: 0.8531 (mtp) cc_final: 0.8094 (mtp) REVERT: O 299 MET cc_start: 0.6979 (mmm) cc_final: 0.6278 (mtt) REVERT: O 371 PHE cc_start: 0.9247 (OUTLIER) cc_final: 0.8470 (t80) REVERT: P 12 LEU cc_start: 0.6402 (OUTLIER) cc_final: 0.5993 (pp) REVERT: P 26 TRP cc_start: 0.6883 (m100) cc_final: 0.6575 (m-90) REVERT: Q 25 LEU cc_start: 0.8360 (mt) cc_final: 0.7961 (mp) REVERT: Q 34 MET cc_start: 0.8148 (ptp) cc_final: 0.7852 (ptp) REVERT: Q 79 GLU cc_start: 0.7518 (mp0) cc_final: 0.7305 (mp0) REVERT: Q 182 GLU cc_start: 0.6815 (tt0) cc_final: 0.6543 (tp30) REVERT: Q 199 MET cc_start: 0.8155 (ptm) cc_final: 0.7848 (ptm) REVERT: Q 258 MET cc_start: 0.8899 (tpp) cc_final: 0.8348 (tpp) REVERT: Q 293 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8091 (pptt) REVERT: Q 348 ARG cc_start: 0.8413 (ptm-80) cc_final: 0.7968 (ptm-80) REVERT: Q 358 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7280 (tppt) REVERT: Q 380 ILE cc_start: 0.7990 (mt) cc_final: 0.7675 (tt) REVERT: Q 436 GLN cc_start: 0.8353 (tm-30) cc_final: 0.7966 (tm-30) REVERT: Q 462 THR cc_start: 0.9089 (m) cc_final: 0.8802 (p) REVERT: R 35 TRP cc_start: 0.9020 (t60) cc_final: 0.8508 (t60) REVERT: R 42 PHE cc_start: 0.8783 (t80) cc_final: 0.7917 (t80) REVERT: R 64 PHE cc_start: 0.9360 (t80) cc_final: 0.9038 (t80) REVERT: R 74 MET cc_start: 0.8718 (tpp) cc_final: 0.8280 (mmm) REVERT: S 20 TRP cc_start: 0.7820 (p90) cc_final: 0.6451 (p90) REVERT: S 108 PHE cc_start: 0.8767 (m-80) cc_final: 0.8029 (m-80) REVERT: S 126 GLU cc_start: 0.6771 (mm-30) cc_final: 0.6433 (tp30) REVERT: S 259 HIS cc_start: 0.8902 (OUTLIER) cc_final: 0.6916 (t70) REVERT: S 305 VAL cc_start: 0.9160 (OUTLIER) cc_final: 0.8589 (p) REVERT: S 323 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7422 (pm20) REVERT: S 400 PHE cc_start: 0.7821 (m-10) cc_final: 0.7592 (m-10) REVERT: S 410 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8052 (mtp) REVERT: S 442 TYR cc_start: 0.8967 (t80) cc_final: 0.8400 (t80) REVERT: S 447 SER cc_start: 0.8991 (t) cc_final: 0.8692 (t) REVERT: S 473 MET cc_start: 0.4536 (pmm) cc_final: 0.4204 (pmm) REVERT: S 484 THR cc_start: 0.8893 (m) cc_final: 0.8418 (p) REVERT: U 47 TRP cc_start: 0.8254 (t60) cc_final: 0.7579 (t60) REVERT: U 65 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7868 (mtpp) REVERT: U 90 ASP cc_start: 0.7480 (t0) cc_final: 0.6896 (t0) REVERT: V 48 GLN cc_start: 0.7659 (mp10) cc_final: 0.7450 (mp10) outliers start: 148 outliers final: 112 residues processed: 845 average time/residue: 0.3998 time to fit residues: 552.2591 Evaluate side-chains 880 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 746 time to evaluate : 3.086 ------------------------------------------------------------------------------- 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 81 VAL 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 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 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 452 VAL Chi-restraints excluded: chain A residue 460 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 30 CYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 129 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 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 16 THR Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain E residue 92 CYS 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 187 THR Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 428 ASN Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 485 LEU 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 65 LYS Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 76 ASP 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 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 199 MET 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 460 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 65 ILE Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 201 ASN 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 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 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 8 ASN Chi-restraints excluded: chain S residue 41 LEU Chi-restraints excluded: chain S residue 91 VAL Chi-restraints excluded: chain S residue 92 CYS Chi-restraints excluded: chain S residue 125 ILE Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 187 THR 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 464 ILE Chi-restraints excluded: chain S residue 485 LEU Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain U residue 22 CYS Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 65 LYS Chi-restraints excluded: chain U residue 83 MET Chi-restraints excluded: chain U residue 91 THR Chi-restraints excluded: chain V residue 45 LYS Chi-restraints excluded: chain V residue 76 ASP 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: 8.9990 chunk 136 optimal weight: 5.9990 chunk 334 optimal weight: 0.9980 chunk 247 optimal weight: 30.0000 chunk 2 optimal weight: 6.9990 chunk 129 optimal weight: 0.8980 chunk 203 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 169 optimal weight: 6.9990 chunk 305 optimal weight: 7.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN L 27 GLN ** O 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 209 GLN ** O 353 ASN ** 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 8 ASN ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 27 GLN V 51 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.123061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.105998 restraints weight = 51374.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.108973 restraints weight = 25265.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.110926 restraints weight = 15457.394| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 30884 Z= 0.132 Angle : 0.713 15.655 41956 Z= 0.351 Chirality : 0.044 0.242 4928 Planarity : 0.004 0.062 5192 Dihedral : 8.284 99.427 4876 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.28 % Allowed : 24.39 % Favored : 71.32 % 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: -1.24 (0.13), residues: 3846 helix: 1.35 (0.18), residues: 876 sheet: -1.19 (0.15), residues: 1114 loop : -1.64 (0.13), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP P 35 HIS 0.004 0.001 HIS P 39 PHE 0.022 0.001 PHE E 475 TYR 0.010 0.001 TYR V 93 ARG 0.011 0.001 ARG S 9 Details of bonding type rmsd link_NAG-ASN : bond 0.00326 ( 12) link_NAG-ASN : angle 2.14051 ( 36) link_BETA1-4 : bond 0.00334 ( 20) link_BETA1-4 : angle 2.14932 ( 60) link_ALPHA1-3 : bond 0.00975 ( 4) link_ALPHA1-3 : angle 2.55149 ( 12) hydrogen bonds : bond 0.03857 ( 1094) hydrogen bonds : angle 5.16801 ( 3036) link_BETA1-6 : bond 0.00967 ( 4) link_BETA1-6 : angle 2.29986 ( 12) SS BOND : bond 0.00569 ( 30) SS BOND : angle 2.70982 ( 60) covalent geometry : bond 0.00291 (30814) covalent geometry : angle 0.69754 (41776) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12916.04 seconds wall clock time: 229 minutes 18.33 seconds (13758.33 seconds total)