Starting phenix.real_space_refine on Mon Aug 25 18:30:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jn5_36433/08_2025/8jn5_36433.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jn5_36433/08_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_36433/08_2025/8jn5_36433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jn5_36433/08_2025/8jn5_36433.map" model { file = "/net/cci-nas-00/data/ceres_data/8jn5_36433/08_2025/8jn5_36433.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jn5_36433/08_2025/8jn5_36433.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 7.34, per 1000 atoms: 0.24 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: 2.82 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.00 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: 5.63 Time building geometry restraints manager: 3.57 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: 0.02 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: 0.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.380 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.280 ------------------------------------------------------------------------------- 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 : 11.28 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.006 0.000 ARG A 57 TYR 0.011 0.001 TYR F 52 PHE 0.020 0.001 PHE P 42 TRP 0.019 0.002 TRP E 20 HIS 0.005 0.001 HIS E 259 Details of bonding type rmsd covalent geometry : bond 0.00410 (30814) covalent geometry : angle 0.75760 (41776) SS BOND : bond 0.00720 ( 30) SS BOND : angle 1.86968 ( 60) hydrogen bonds : bond 0.20581 ( 1094) hydrogen bonds : angle 8.16193 ( 3036) link_ALPHA1-3 : bond 0.00326 ( 4) link_ALPHA1-3 : angle 1.78299 ( 12) link_BETA1-4 : bond 0.00362 ( 20) link_BETA1-4 : angle 1.94959 ( 60) link_BETA1-6 : bond 0.00573 ( 4) link_BETA1-6 : angle 1.24001 ( 12) link_NAG-ASN : bond 0.00499 ( 12) link_NAG-ASN : angle 1.95438 ( 36) *********************** 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 : 1.044 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: 0.2009 time to fit residues: 414.8051 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 : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 9.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 ASN C 144 HIS C 246 GLN C 388 ASN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 GLN 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 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 165 GLN 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.123544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.106995 restraints weight = 52311.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.109937 restraints weight = 25635.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.111792 restraints weight = 15583.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.113076 restraints weight = 11037.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.113887 restraints weight = 8622.457| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30884 Z= 0.153 Angle : 0.720 9.907 41956 Z= 0.361 Chirality : 0.045 0.224 4928 Planarity : 0.005 0.048 5192 Dihedral : 13.360 111.473 4876 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.41 % Allowed : 13.38 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.66 (0.13), residues: 3846 helix: 1.00 (0.18), residues: 882 sheet: -1.69 (0.15), residues: 1088 loop : -1.74 (0.13), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 348 TYR 0.021 0.002 TYR U 111 PHE 0.024 0.002 PHE P 42 TRP 0.015 0.002 TRP S 20 HIS 0.006 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00346 (30814) covalent geometry : angle 0.70415 (41776) SS BOND : bond 0.00592 ( 30) SS BOND : angle 2.12943 ( 60) hydrogen bonds : bond 0.04599 ( 1094) hydrogen bonds : angle 6.11776 ( 3036) link_ALPHA1-3 : bond 0.00984 ( 4) link_ALPHA1-3 : angle 3.43225 ( 12) link_BETA1-4 : bond 0.00340 ( 20) link_BETA1-4 : angle 2.53724 ( 60) link_BETA1-6 : bond 0.01570 ( 4) link_BETA1-6 : angle 3.30577 ( 12) link_NAG-ASN : bond 0.00287 ( 12) link_NAG-ASN : angle 1.67412 ( 36) *********************** 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 1047 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 937 time to evaluate : 1.209 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 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: A 6 VAL cc_start: 0.8005 (t) cc_final: 0.7704 (p) REVERT: A 38 LYS cc_start: 0.9298 (mmtt) cc_final: 0.9092 (mmtm) REVERT: A 82 LEU cc_start: 0.8733 (mt) cc_final: 0.8485 (mm) REVERT: A 98 ASP cc_start: 0.8156 (p0) cc_final: 0.7656 (p0) REVERT: A 181 LEU cc_start: 0.8529 (tp) cc_final: 0.7932 (tp) REVERT: A 201 ASN cc_start: 0.7304 (m-40) cc_final: 0.6383 (t0) REVERT: A 234 LEU cc_start: 0.8513 (mt) cc_final: 0.8275 (mp) REVERT: A 287 MET cc_start: 0.8548 (mtp) cc_final: 0.8056 (mtp) REVERT: A 299 MET cc_start: 0.7195 (mmm) cc_final: 0.6294 (mmt) REVERT: B 26 TRP cc_start: 0.6696 (m100) cc_final: 0.6237 (m-90) REVERT: B 28 GLN cc_start: 0.8061 (tp-100) cc_final: 0.6958 (tp40) REVERT: B 61 VAL cc_start: 0.9290 (t) cc_final: 0.9049 (p) REVERT: C 182 GLU cc_start: 0.7034 (tp30) cc_final: 0.6801 (tp30) REVERT: C 199 MET cc_start: 0.8256 (ptm) cc_final: 0.7992 (ptm) REVERT: C 258 MET cc_start: 0.8857 (tpp) cc_final: 0.8571 (tpp) REVERT: C 380 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7699 (tt) REVERT: C 400 PHE cc_start: 0.7566 (m-10) cc_final: 0.7261 (t80) REVERT: C 401 GLU cc_start: 0.8502 (tp30) cc_final: 0.8022 (tp30) REVERT: C 422 SER cc_start: 0.8548 (p) cc_final: 0.8321 (m) REVERT: C 443 THR cc_start: 0.8467 (m) cc_final: 0.8012 (p) REVERT: D 12 LEU cc_start: 0.8476 (pp) cc_final: 0.8257 (pp) REVERT: D 14 THR cc_start: 0.8278 (p) cc_final: 0.7817 (m) REVERT: D 18 THR cc_start: 0.8732 (p) cc_final: 0.7982 (t) REVERT: D 42 PHE cc_start: 0.8726 (t80) cc_final: 0.8234 (t80) REVERT: D 64 PHE cc_start: 0.9218 (t80) cc_final: 0.8971 (t80) REVERT: D 74 MET cc_start: 0.8509 (tpp) cc_final: 0.8116 (mmm) REVERT: E 8 ASN cc_start: 0.7742 (t0) cc_final: 0.7320 (t0) REVERT: E 20 TRP cc_start: 0.7536 (p90) cc_final: 0.6086 (p90) REVERT: E 108 PHE cc_start: 0.8586 (m-80) cc_final: 0.8183 (m-80) REVERT: E 199 MET cc_start: 0.8314 (ttp) cc_final: 0.8060 (ttm) REVERT: E 251 LEU cc_start: 0.8489 (tt) cc_final: 0.7925 (tt) REVERT: E 295 MET cc_start: 0.7718 (tpt) cc_final: 0.6146 (tmm) REVERT: E 335 PHE cc_start: 0.8271 (OUTLIER) cc_final: 0.6734 (m-80) REVERT: E 484 THR cc_start: 0.8853 (m) cc_final: 0.8466 (p) REVERT: F 13 ASP cc_start: 0.7196 (p0) cc_final: 0.6881 (m-30) REVERT: F 16 THR cc_start: 0.9006 (t) cc_final: 0.8754 (m) REVERT: F 32 VAL cc_start: 0.8953 (t) cc_final: 0.8746 (t) REVERT: H 37 LEU cc_start: 0.8883 (mt) cc_final: 0.8632 (mt) REVERT: H 47 TRP cc_start: 0.8007 (t60) cc_final: 0.7759 (t60) REVERT: H 54 ASP cc_start: 0.6054 (p0) cc_final: 0.5321 (p0) REVERT: H 57 ASP cc_start: 0.7587 (t0) cc_final: 0.7205 (m-30) REVERT: H 117 LEU cc_start: 0.7762 (tt) cc_final: 0.7361 (tp) REVERT: L 2 ILE cc_start: 0.8742 (mt) cc_final: 0.8525 (mt) REVERT: L 45 LYS cc_start: 0.8793 (mttt) cc_final: 0.8540 (mttm) REVERT: L 48 GLN cc_start: 0.6845 (mp10) cc_final: 0.6087 (mp10) REVERT: L 55 TYR cc_start: 0.8643 (p90) cc_final: 0.8356 (p90) REVERT: L 93 TYR cc_start: 0.8883 (m-10) cc_final: 0.8158 (m-10) REVERT: L 104 PHE cc_start: 0.8517 (m-80) cc_final: 0.8236 (m-80) REVERT: O 6 VAL cc_start: 0.7965 (t) cc_final: 0.7673 (p) REVERT: O 82 LEU cc_start: 0.8712 (mt) cc_final: 0.8436 (mm) REVERT: O 98 ASP cc_start: 0.8152 (p0) cc_final: 0.7648 (p0) REVERT: O 161 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7742 (mt-10) REVERT: O 181 LEU cc_start: 0.8554 (tp) cc_final: 0.7959 (tp) REVERT: O 190 ASP cc_start: 0.8092 (t0) cc_final: 0.7861 (t0) REVERT: O 201 ASN cc_start: 0.7122 (m-40) cc_final: 0.6409 (t0) REVERT: O 287 MET cc_start: 0.8551 (mtp) cc_final: 0.8091 (mtp) REVERT: O 299 MET cc_start: 0.7188 (mmm) cc_final: 0.6114 (mtt) REVERT: P 26 TRP cc_start: 0.6679 (m100) cc_final: 0.6466 (m-90) REVERT: P 28 GLN cc_start: 0.8064 (tp-100) cc_final: 0.6905 (tp40) REVERT: P 61 VAL cc_start: 0.9293 (t) cc_final: 0.9054 (p) REVERT: P 74 MET cc_start: 0.4894 (mmp) cc_final: 0.3923 (mmt) REVERT: Q 182 GLU cc_start: 0.6652 (tt0) cc_final: 0.6268 (tp30) REVERT: Q 199 MET cc_start: 0.8259 (ptm) cc_final: 0.7983 (ptm) REVERT: Q 213 ASP cc_start: 0.7353 (m-30) cc_final: 0.7106 (m-30) REVERT: Q 258 MET cc_start: 0.8863 (tpp) cc_final: 0.8573 (tpp) REVERT: Q 380 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7694 (tt) REVERT: Q 400 PHE cc_start: 0.7569 (m-10) cc_final: 0.7267 (t80) REVERT: Q 401 GLU cc_start: 0.8516 (tp30) cc_final: 0.8023 (tp30) REVERT: Q 422 SER cc_start: 0.8545 (p) cc_final: 0.8323 (m) REVERT: Q 443 THR cc_start: 0.8481 (m) cc_final: 0.8023 (p) REVERT: R 12 LEU cc_start: 0.8680 (pp) cc_final: 0.8459 (pp) REVERT: R 14 THR cc_start: 0.8288 (p) cc_final: 0.7827 (m) REVERT: R 18 THR cc_start: 0.8737 (p) cc_final: 0.8004 (t) REVERT: R 35 TRP cc_start: 0.9036 (t60) cc_final: 0.8744 (t60) REVERT: R 42 PHE cc_start: 0.8729 (t80) cc_final: 0.8163 (t80) REVERT: R 64 PHE cc_start: 0.9230 (t80) cc_final: 0.8971 (t80) REVERT: R 74 MET cc_start: 0.8493 (tpp) cc_final: 0.7921 (mmm) REVERT: S 8 ASN cc_start: 0.7815 (t0) cc_final: 0.7575 (t0) REVERT: S 20 TRP cc_start: 0.7550 (p90) cc_final: 0.6097 (p90) REVERT: S 108 PHE cc_start: 0.8577 (m-80) cc_final: 0.8172 (m-80) REVERT: S 251 LEU cc_start: 0.8484 (tt) cc_final: 0.7927 (tt) REVERT: S 295 MET cc_start: 0.7813 (tpt) cc_final: 0.6243 (tmm) REVERT: S 335 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.6712 (m-80) REVERT: S 410 MET cc_start: 0.8648 (mtm) cc_final: 0.8256 (mtp) REVERT: S 484 THR cc_start: 0.8859 (m) cc_final: 0.8469 (p) REVERT: T 13 ASP cc_start: 0.7187 (p0) cc_final: 0.6871 (m-30) REVERT: T 16 THR cc_start: 0.8970 (t) cc_final: 0.8735 (m) REVERT: T 26 TRP cc_start: 0.8094 (m100) cc_final: 0.7877 (m100) REVERT: T 32 VAL cc_start: 0.8965 (t) cc_final: 0.8755 (t) REVERT: U 37 LEU cc_start: 0.8885 (mt) cc_final: 0.8629 (mt) REVERT: U 47 TRP cc_start: 0.8005 (t60) cc_final: 0.7757 (t60) REVERT: U 54 ASP cc_start: 0.6086 (p0) cc_final: 0.5280 (p0) REVERT: U 57 ASP cc_start: 0.7629 (t0) cc_final: 0.7232 (m-30) REVERT: U 117 LEU cc_start: 0.7761 (tt) cc_final: 0.7354 (tp) REVERT: V 2 ILE cc_start: 0.8744 (mt) cc_final: 0.8518 (mt) REVERT: V 45 LYS cc_start: 0.8809 (mttt) cc_final: 0.8549 (mttm) REVERT: V 48 GLN cc_start: 0.6858 (mp10) cc_final: 0.6093 (mp10) REVERT: V 55 TYR cc_start: 0.8641 (p90) cc_final: 0.8350 (p90) REVERT: V 93 TYR cc_start: 0.8887 (m-10) cc_final: 0.8161 (m-10) REVERT: V 104 PHE cc_start: 0.8518 (m-80) cc_final: 0.8233 (m-80) outliers start: 110 outliers final: 58 residues processed: 996 average time/residue: 0.1832 time to fit residues: 300.0032 Evaluate side-chains 892 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 830 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 452 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 C residue 263 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 181 LEU Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain E residue 266 THR 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 455 ILE Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 78 THR 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 452 VAL Chi-restraints excluded: chain O residue 461 LEU Chi-restraints excluded: chain O residue 466 LEU Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain Q residue 263 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 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 U residue 7 SER Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain U residue 63 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 340 optimal weight: 10.0000 chunk 238 optimal weight: 20.0000 chunk 278 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 357 optimal weight: 30.0000 chunk 310 optimal weight: 20.0000 chunk 339 optimal weight: 0.9990 chunk 247 optimal weight: 30.0000 chunk 288 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN L 27 GLN L 51 GLN L 85 GLN ** O 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 100 GLN V 27 GLN V 51 GLN V 85 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.119637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.102591 restraints weight = 52857.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.105492 restraints weight = 26275.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.107370 restraints weight = 16218.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.108604 restraints weight = 11561.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.109421 restraints weight = 9133.113| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3055 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= 0.235 Angle : 0.761 9.781 41956 Z= 0.379 Chirality : 0.047 0.253 4928 Planarity : 0.005 0.049 5192 Dihedral : 11.749 108.289 4876 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 5.21 % Allowed : 16.45 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.13), residues: 3846 helix: 1.12 (0.18), residues: 864 sheet: -1.68 (0.15), residues: 1092 loop : -1.71 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 57 TYR 0.019 0.002 TYR U 111 PHE 0.018 0.002 PHE B 42 TRP 0.017 0.002 TRP Q 218 HIS 0.009 0.002 HIS O 144 Details of bonding type rmsd covalent geometry : bond 0.00547 (30814) covalent geometry : angle 0.74294 (41776) SS BOND : bond 0.00618 ( 30) SS BOND : angle 2.51252 ( 60) hydrogen bonds : bond 0.04566 ( 1094) hydrogen bonds : angle 5.79559 ( 3036) link_ALPHA1-3 : bond 0.00881 ( 4) link_ALPHA1-3 : angle 2.87486 ( 12) link_BETA1-4 : bond 0.00435 ( 20) link_BETA1-4 : angle 2.68499 ( 60) link_BETA1-6 : bond 0.01440 ( 4) link_BETA1-6 : angle 3.14131 ( 12) link_NAG-ASN : bond 0.00506 ( 12) link_NAG-ASN : angle 2.24360 ( 36) *********************** 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 978 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 810 time to evaluate : 1.227 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 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: A 6 VAL cc_start: 0.8131 (t) cc_final: 0.7742 (p) REVERT: A 26 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7789 (mm-30) REVERT: A 38 LYS cc_start: 0.9337 (mmtt) cc_final: 0.9101 (mmtm) REVERT: A 98 ASP cc_start: 0.8115 (p0) cc_final: 0.7669 (p0) REVERT: A 181 LEU cc_start: 0.8553 (tp) cc_final: 0.8021 (tp) REVERT: A 234 LEU cc_start: 0.8336 (mt) cc_final: 0.8106 (mp) REVERT: A 287 MET cc_start: 0.8624 (mtp) cc_final: 0.8086 (mtp) REVERT: A 299 MET cc_start: 0.7039 (mmm) cc_final: 0.5828 (mmm) REVERT: B 12 LEU cc_start: 0.6693 (OUTLIER) cc_final: 0.6107 (pp) REVERT: B 26 TRP cc_start: 0.6817 (m100) cc_final: 0.6563 (m-90) REVERT: B 28 GLN cc_start: 0.7592 (tp-100) cc_final: 0.6766 (tp-100) REVERT: B 61 VAL cc_start: 0.9209 (t) cc_final: 0.8903 (p) REVERT: C 44 GLU cc_start: 0.7783 (pt0) cc_final: 0.7580 (pt0) REVERT: C 182 GLU cc_start: 0.7306 (tp30) cc_final: 0.6999 (tp30) REVERT: C 199 MET cc_start: 0.8239 (ptm) cc_final: 0.7990 (ptm) REVERT: C 258 MET cc_start: 0.8941 (tpp) cc_final: 0.8685 (tpp) REVERT: C 358 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.6987 (tppt) REVERT: C 360 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6978 (mm-30) REVERT: C 380 ILE cc_start: 0.8015 (OUTLIER) cc_final: 0.7750 (tt) REVERT: C 389 TRP cc_start: 0.7517 (t-100) cc_final: 0.7002 (t-100) REVERT: C 400 PHE cc_start: 0.7545 (m-10) cc_final: 0.7255 (t80) REVERT: C 432 LYS cc_start: 0.8351 (tttp) cc_final: 0.8132 (ttpp) REVERT: C 436 GLN cc_start: 0.8795 (tm-30) cc_final: 0.8210 (tt0) REVERT: D 12 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8262 (pp) REVERT: D 18 THR cc_start: 0.8812 (p) cc_final: 0.8005 (t) REVERT: D 42 PHE cc_start: 0.8807 (t80) cc_final: 0.8168 (t80) REVERT: D 74 MET cc_start: 0.8693 (tpp) cc_final: 0.8276 (mmm) REVERT: E 8 ASN cc_start: 0.7886 (t0) cc_final: 0.7518 (t0) REVERT: E 108 PHE cc_start: 0.8657 (m-80) cc_final: 0.8231 (m-80) REVERT: E 181 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8561 (pp) REVERT: E 251 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8457 (tt) REVERT: E 270 ASN cc_start: 0.6839 (t0) cc_final: 0.6559 (t0) REVERT: E 320 ILE cc_start: 0.9346 (mm) cc_final: 0.9120 (mt) REVERT: E 484 THR cc_start: 0.8860 (m) cc_final: 0.8530 (p) REVERT: F 13 ASP cc_start: 0.7840 (p0) cc_final: 0.7152 (m-30) REVERT: H 47 TRP cc_start: 0.8217 (t60) cc_final: 0.7632 (t60) REVERT: H 57 ASP cc_start: 0.7530 (t0) cc_final: 0.7225 (m-30) REVERT: H 114 GLN cc_start: 0.7695 (tp40) cc_final: 0.7351 (tp-100) REVERT: L 2 ILE cc_start: 0.8710 (mt) cc_final: 0.8465 (mt) REVERT: L 48 GLN cc_start: 0.6948 (mp10) cc_final: 0.6114 (mp10) REVERT: L 51 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7995 (pt0) REVERT: L 104 PHE cc_start: 0.8622 (m-80) cc_final: 0.8414 (m-80) REVERT: O 6 VAL cc_start: 0.8138 (t) cc_final: 0.7778 (p) REVERT: O 26 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7779 (mm-30) REVERT: O 42 ASP cc_start: 0.8581 (m-30) cc_final: 0.8152 (m-30) REVERT: O 85 GLU cc_start: 0.8085 (tt0) cc_final: 0.7884 (tt0) REVERT: O 98 ASP cc_start: 0.8106 (p0) cc_final: 0.7661 (p0) REVERT: O 181 LEU cc_start: 0.8559 (tp) cc_final: 0.8019 (tp) REVERT: O 190 ASP cc_start: 0.8093 (t0) cc_final: 0.7803 (t70) REVERT: O 247 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7115 (pm20) REVERT: O 287 MET cc_start: 0.8653 (mtp) cc_final: 0.8135 (mtp) REVERT: O 299 MET cc_start: 0.7028 (mmm) cc_final: 0.5828 (mmm) REVERT: O 460 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7546 (mp) REVERT: P 12 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6519 (pp) REVERT: P 26 TRP cc_start: 0.6808 (m100) cc_final: 0.6580 (m-90) REVERT: P 28 GLN cc_start: 0.7939 (tp-100) cc_final: 0.7669 (tp-100) REVERT: P 61 VAL cc_start: 0.9283 (t) cc_final: 0.9057 (p) REVERT: P 74 MET cc_start: 0.5058 (mmp) cc_final: 0.4560 (mmp) REVERT: Q 182 GLU cc_start: 0.6923 (tt0) cc_final: 0.6697 (tp30) REVERT: Q 199 MET cc_start: 0.8244 (ptm) cc_final: 0.7976 (ptm) REVERT: Q 213 ASP cc_start: 0.7488 (m-30) cc_final: 0.7144 (m-30) REVERT: Q 258 MET cc_start: 0.8953 (tpp) cc_final: 0.8695 (tpp) REVERT: Q 358 LYS cc_start: 0.7409 (OUTLIER) cc_final: 0.7053 (tppt) REVERT: Q 360 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6955 (mm-30) REVERT: Q 380 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7749 (tt) REVERT: Q 389 TRP cc_start: 0.7526 (t-100) cc_final: 0.7015 (t-100) REVERT: Q 400 PHE cc_start: 0.7549 (m-10) cc_final: 0.7271 (t80) REVERT: Q 432 LYS cc_start: 0.8369 (tttp) cc_final: 0.8138 (ttpp) REVERT: Q 436 GLN cc_start: 0.8808 (tm-30) cc_final: 0.8212 (tt0) REVERT: R 12 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8277 (pp) REVERT: R 18 THR cc_start: 0.8812 (p) cc_final: 0.8008 (t) REVERT: R 35 TRP cc_start: 0.9015 (t60) cc_final: 0.8741 (t60) REVERT: R 42 PHE cc_start: 0.8794 (t80) cc_final: 0.8128 (t80) REVERT: R 74 MET cc_start: 0.8715 (tpp) cc_final: 0.8296 (mmm) REVERT: S 8 ASN cc_start: 0.7971 (t0) cc_final: 0.7633 (t0) REVERT: S 108 PHE cc_start: 0.8656 (m-80) cc_final: 0.8278 (m-80) REVERT: S 176 TYR cc_start: 0.8890 (m-80) cc_final: 0.8471 (m-80) REVERT: S 323 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7421 (pm20) REVERT: S 484 THR cc_start: 0.8870 (m) cc_final: 0.8536 (p) REVERT: T 13 ASP cc_start: 0.7841 (p0) cc_final: 0.7159 (m-30) REVERT: U 47 TRP cc_start: 0.8217 (t60) cc_final: 0.7629 (t60) REVERT: U 57 ASP cc_start: 0.7559 (t0) cc_final: 0.7263 (m-30) REVERT: U 114 GLN cc_start: 0.7701 (tp40) cc_final: 0.7378 (tp-100) REVERT: V 2 ILE cc_start: 0.8706 (mt) cc_final: 0.8463 (mt) REVERT: V 48 GLN cc_start: 0.6959 (mp10) cc_final: 0.6119 (mp10) REVERT: V 51 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.8007 (pt0) REVERT: V 104 PHE cc_start: 0.8612 (m-80) cc_final: 0.8406 (m-80) outliers start: 168 outliers final: 122 residues processed: 909 average time/residue: 0.1632 time to fit residues: 244.5960 Evaluate side-chains 891 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 754 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 285 LEU 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 459 VAL Chi-restraints excluded: chain A residue 461 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 34 THR Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 313 THR 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 62 VAL 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 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 255 GLU 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 451 TRP 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 25 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 107 TRP Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 51 GLN Chi-restraints excluded: chain O residue 16 SER Chi-restraints excluded: chain O residue 33 THR 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 253 SER Chi-restraints excluded: chain O residue 275 SER Chi-restraints excluded: chain O residue 285 LEU 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 451 TRP 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 460 LEU Chi-restraints excluded: chain O residue 461 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 34 THR Chi-restraints excluded: chain P residue 67 LEU Chi-restraints excluded: chain P residue 73 SER Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain Q residue 113 LEU Chi-restraints excluded: chain Q residue 158 VAL 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 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 12 LEU Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain S residue 41 LEU Chi-restraints excluded: chain S residue 43 ILE Chi-restraints excluded: chain S residue 79 GLU Chi-restraints excluded: chain S residue 139 VAL 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 255 GLU 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 323 GLU Chi-restraints excluded: chain S residue 451 TRP Chi-restraints excluded: chain S residue 485 LEU Chi-restraints excluded: chain T residue 8 VAL 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 53 SER Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 83 MET Chi-restraints excluded: chain U residue 107 TRP Chi-restraints excluded: chain V residue 51 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 182 optimal weight: 10.0000 chunk 298 optimal weight: 10.0000 chunk 177 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 123 optimal weight: 7.9990 chunk 190 optimal weight: 20.0000 chunk 267 optimal weight: 6.9990 chunk 296 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 230 optimal weight: 8.9990 chunk 370 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 HIS C 246 GLN ** C 353 ASN ** 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 259 HIS E 302 ASN E 428 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN L 27 GLN L 85 GLN ** O 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 HIS ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 144 HIS U 100 GLN V 27 GLN V 85 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.120043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.102891 restraints weight = 52034.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.105824 restraints weight = 25795.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.107777 restraints weight = 15846.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.109006 restraints weight = 11167.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.109822 restraints weight = 8827.750| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 30884 Z= 0.199 Angle : 0.725 9.764 41956 Z= 0.359 Chirality : 0.046 0.240 4928 Planarity : 0.004 0.054 5192 Dihedral : 10.775 103.065 4876 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 6.39 % Allowed : 18.47 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.13), residues: 3846 helix: 1.19 (0.18), residues: 870 sheet: -1.62 (0.15), residues: 1106 loop : -1.80 (0.13), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 348 TYR 0.023 0.002 TYR H 111 PHE 0.020 0.002 PHE T 48 TRP 0.017 0.002 TRP S 20 HIS 0.010 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00461 (30814) covalent geometry : angle 0.70599 (41776) SS BOND : bond 0.00561 ( 30) SS BOND : angle 2.50745 ( 60) hydrogen bonds : bond 0.04268 ( 1094) hydrogen bonds : angle 5.52837 ( 3036) link_ALPHA1-3 : bond 0.00914 ( 4) link_ALPHA1-3 : angle 3.09278 ( 12) link_BETA1-4 : bond 0.00415 ( 20) link_BETA1-4 : angle 2.57656 ( 60) link_BETA1-6 : bond 0.01540 ( 4) link_BETA1-6 : angle 3.06306 ( 12) link_NAG-ASN : bond 0.00449 ( 12) link_NAG-ASN : angle 2.38220 ( 36) *********************** 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 1012 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 806 time to evaluate : 1.080 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 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: 0.8146 (t) cc_final: 0.7731 (p) REVERT: A 26 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7875 (mm-30) REVERT: A 38 LYS cc_start: 0.9347 (mmtt) cc_final: 0.9119 (mmtm) REVERT: A 57 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7015 (ttm110) REVERT: A 98 ASP cc_start: 0.8078 (p0) cc_final: 0.7611 (p0) REVERT: A 181 LEU cc_start: 0.8627 (tp) cc_final: 0.8086 (tp) REVERT: A 201 ASN cc_start: 0.7058 (m-40) cc_final: 0.5835 (t0) REVERT: A 234 LEU cc_start: 0.8291 (mt) cc_final: 0.7957 (mp) REVERT: A 247 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7799 (pm20) REVERT: A 287 MET cc_start: 0.8641 (mtp) cc_final: 0.8069 (mtp) REVERT: A 299 MET cc_start: 0.6887 (mmm) cc_final: 0.5881 (mmm) REVERT: B 12 LEU cc_start: 0.6527 (OUTLIER) cc_final: 0.5940 (pp) REVERT: B 26 TRP cc_start: 0.6859 (m100) cc_final: 0.6614 (m-90) REVERT: B 28 GLN cc_start: 0.7753 (tp-100) cc_final: 0.6484 (tp-100) REVERT: B 61 VAL cc_start: 0.9170 (t) cc_final: 0.8830 (p) REVERT: C 44 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7563 (pt0) REVERT: C 125 ILE cc_start: 0.8840 (tt) cc_final: 0.8471 (tt) REVERT: C 182 GLU cc_start: 0.7301 (tp30) cc_final: 0.6869 (tp30) REVERT: C 199 MET cc_start: 0.8360 (ptm) cc_final: 0.7998 (ptm) REVERT: C 230 ASN cc_start: 0.8129 (m-40) cc_final: 0.7383 (m-40) REVERT: C 258 MET cc_start: 0.9057 (tpp) cc_final: 0.8368 (tpp) REVERT: C 293 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8644 (pptt) REVERT: C 348 ARG cc_start: 0.7867 (ptm-80) cc_final: 0.7286 (ptt-90) REVERT: C 358 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.6811 (tppt) REVERT: C 360 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6953 (mm-30) REVERT: C 380 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7716 (tt) REVERT: C 400 PHE cc_start: 0.7535 (m-10) cc_final: 0.7251 (t80) REVERT: C 432 LYS cc_start: 0.8320 (tttp) cc_final: 0.8076 (ttpp) REVERT: C 436 GLN cc_start: 0.8794 (tm-30) cc_final: 0.8213 (tt0) REVERT: D 12 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8235 (pp) REVERT: D 18 THR cc_start: 0.8828 (p) cc_final: 0.8024 (t) REVERT: D 42 PHE cc_start: 0.8793 (t80) cc_final: 0.8170 (t80) REVERT: D 64 PHE cc_start: 0.9340 (t80) cc_final: 0.9085 (t80) REVERT: D 74 MET cc_start: 0.8775 (tpp) cc_final: 0.8008 (mmm) REVERT: E 8 ASN cc_start: 0.8024 (t0) cc_final: 0.7588 (t0) REVERT: E 20 TRP cc_start: 0.7670 (p90) cc_final: 0.6295 (p90) REVERT: E 108 PHE cc_start: 0.8677 (m-80) cc_final: 0.8289 (m-80) REVERT: E 176 TYR cc_start: 0.8780 (m-80) cc_final: 0.8388 (m-80) REVERT: E 181 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8609 (pp) REVERT: E 259 HIS cc_start: 0.8573 (OUTLIER) cc_final: 0.6771 (t-90) REVERT: E 270 ASN cc_start: 0.6974 (t0) cc_final: 0.6769 (t0) REVERT: E 320 ILE cc_start: 0.9347 (mm) cc_final: 0.9147 (mt) REVERT: E 484 THR cc_start: 0.8885 (m) cc_final: 0.8524 (p) REVERT: H 3 GLU cc_start: 0.6482 (mm-30) cc_final: 0.6188 (mm-30) REVERT: H 47 TRP cc_start: 0.8257 (t60) cc_final: 0.7631 (t60) REVERT: H 57 ASP cc_start: 0.7465 (t0) cc_final: 0.7098 (m-30) REVERT: H 90 ASP cc_start: 0.7397 (t0) cc_final: 0.7140 (t0) REVERT: H 111 TYR cc_start: 0.8474 (m-80) cc_final: 0.8189 (m-10) REVERT: H 114 GLN cc_start: 0.7717 (tp40) cc_final: 0.7262 (tp-100) REVERT: L 2 ILE cc_start: 0.8612 (mt) cc_final: 0.8403 (mt) REVERT: L 45 LYS cc_start: 0.8979 (mttp) cc_final: 0.8645 (mttp) REVERT: L 48 GLN cc_start: 0.6908 (mp10) cc_final: 0.6224 (mp10) REVERT: L 104 PHE cc_start: 0.8503 (m-80) cc_final: 0.8191 (m-80) REVERT: O 6 VAL cc_start: 0.8167 (t) cc_final: 0.7763 (p) REVERT: O 26 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7869 (mm-30) REVERT: O 57 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7036 (ttm110) REVERT: O 85 GLU cc_start: 0.8155 (tt0) cc_final: 0.7951 (tt0) REVERT: O 98 ASP cc_start: 0.8079 (p0) cc_final: 0.7609 (p0) REVERT: O 181 LEU cc_start: 0.8626 (tp) cc_final: 0.8111 (tp) REVERT: O 190 ASP cc_start: 0.8111 (t0) cc_final: 0.7834 (t0) REVERT: O 287 MET cc_start: 0.8644 (mtp) cc_final: 0.8142 (mtp) REVERT: O 299 MET cc_start: 0.6900 (mmm) cc_final: 0.5899 (mmm) REVERT: P 12 LEU cc_start: 0.6523 (OUTLIER) cc_final: 0.5971 (pp) REVERT: P 26 TRP cc_start: 0.6851 (m100) cc_final: 0.6553 (m-90) REVERT: P 28 GLN cc_start: 0.7895 (tp-100) cc_final: 0.7651 (tp-100) REVERT: P 61 VAL cc_start: 0.9283 (t) cc_final: 0.9075 (p) REVERT: Q 2 ARG cc_start: 0.8360 (ttt-90) cc_final: 0.7826 (ttt-90) REVERT: Q 125 ILE cc_start: 0.8788 (tt) cc_final: 0.8454 (tt) REVERT: Q 182 GLU cc_start: 0.6911 (tt0) cc_final: 0.6632 (tp30) REVERT: Q 199 MET cc_start: 0.8346 (ptm) cc_final: 0.8004 (ptm) REVERT: Q 213 ASP cc_start: 0.7532 (m-30) cc_final: 0.7122 (m-30) REVERT: Q 258 MET cc_start: 0.9066 (tpp) cc_final: 0.8373 (tpp) REVERT: Q 293 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8647 (pptt) REVERT: Q 348 ARG cc_start: 0.7866 (ptm-80) cc_final: 0.7279 (ptt-90) REVERT: Q 358 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7007 (tppt) REVERT: Q 360 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6945 (mm-30) REVERT: Q 380 ILE cc_start: 0.7986 (OUTLIER) cc_final: 0.7714 (tt) REVERT: Q 400 PHE cc_start: 0.7539 (m-10) cc_final: 0.7254 (t80) REVERT: Q 432 LYS cc_start: 0.8331 (tttp) cc_final: 0.8077 (ttpp) REVERT: Q 436 GLN cc_start: 0.8802 (tm-30) cc_final: 0.8210 (tt0) REVERT: R 10 MET cc_start: 0.8472 (mmm) cc_final: 0.8264 (mmm) REVERT: R 12 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8223 (pp) REVERT: R 18 THR cc_start: 0.8834 (p) cc_final: 0.8032 (t) REVERT: R 35 TRP cc_start: 0.9046 (t60) cc_final: 0.8766 (t60) REVERT: R 42 PHE cc_start: 0.8775 (t80) cc_final: 0.8131 (t80) REVERT: R 64 PHE cc_start: 0.9346 (t80) cc_final: 0.9135 (t80) REVERT: R 74 MET cc_start: 0.8794 (tpp) cc_final: 0.8407 (mmm) REVERT: S 8 ASN cc_start: 0.8121 (t0) cc_final: 0.7667 (t0) REVERT: S 20 TRP cc_start: 0.7671 (p90) cc_final: 0.6325 (p90) REVERT: S 108 PHE cc_start: 0.8674 (m-80) cc_final: 0.8273 (m-80) REVERT: S 176 TYR cc_start: 0.8772 (m-80) cc_final: 0.8385 (m-80) REVERT: S 250 VAL cc_start: 0.8817 (t) cc_final: 0.8597 (m) REVERT: S 251 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8435 (tt) REVERT: S 259 HIS cc_start: 0.8879 (OUTLIER) cc_final: 0.7300 (t70) REVERT: S 305 VAL cc_start: 0.9180 (OUTLIER) cc_final: 0.8513 (p) REVERT: S 323 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7135 (pm20) REVERT: S 400 PHE cc_start: 0.7854 (m-10) cc_final: 0.7649 (m-10) REVERT: S 484 THR cc_start: 0.8892 (m) cc_final: 0.8539 (p) REVERT: U 3 GLU cc_start: 0.6514 (mm-30) cc_final: 0.6211 (mm-30) REVERT: U 47 TRP cc_start: 0.8262 (t60) cc_final: 0.7624 (t60) REVERT: U 57 ASP cc_start: 0.7513 (t0) cc_final: 0.7144 (m-30) REVERT: U 114 GLN cc_start: 0.7718 (tp40) cc_final: 0.7273 (tp-100) REVERT: V 2 ILE cc_start: 0.8608 (mt) cc_final: 0.8392 (mt) REVERT: V 27 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.7343 (pt0) REVERT: V 45 LYS cc_start: 0.8986 (mttp) cc_final: 0.8638 (mttp) REVERT: V 48 GLN cc_start: 0.6910 (mp10) cc_final: 0.6225 (mp10) REVERT: V 104 PHE cc_start: 0.8497 (m-80) cc_final: 0.8185 (m-80) outliers start: 206 outliers final: 141 residues processed: 947 average time/residue: 0.1647 time to fit residues: 257.5706 Evaluate side-chains 917 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 755 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 233 GLU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 266 THR 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 451 TRP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 461 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 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 43 ILE Chi-restraints excluded: chain C residue 44 GLU 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 129 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 158 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 380 ILE Chi-restraints excluded: chain C residue 457 ILE Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 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 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 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 25 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 63 SER 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 O residue 33 THR Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 57 ARG Chi-restraints excluded: chain O residue 92 CYS Chi-restraints excluded: chain O residue 121 CYS Chi-restraints excluded: chain O residue 130 VAL Chi-restraints excluded: chain O residue 195 ILE Chi-restraints excluded: chain O residue 198 THR Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 237 THR Chi-restraints excluded: chain O residue 253 SER Chi-restraints excluded: chain O residue 275 SER Chi-restraints excluded: chain O residue 319 LEU Chi-restraints excluded: chain O residue 365 ILE Chi-restraints excluded: chain O residue 387 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 429 SER 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 461 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 34 THR Chi-restraints excluded: chain P residue 67 LEU Chi-restraints excluded: chain P residue 73 SER Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 48 THR Chi-restraints excluded: chain Q residue 91 VAL Chi-restraints excluded: chain Q residue 113 LEU Chi-restraints excluded: chain Q residue 158 VAL Chi-restraints excluded: chain Q residue 236 VAL Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 293 LYS Chi-restraints excluded: chain Q residue 313 THR Chi-restraints excluded: chain Q residue 356 VAL Chi-restraints excluded: chain Q residue 357 THR Chi-restraints excluded: chain Q residue 358 LYS Chi-restraints excluded: chain Q residue 380 ILE Chi-restraints excluded: chain Q residue 457 ILE Chi-restraints excluded: chain Q residue 466 LEU Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 62 VAL Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain S residue 41 LEU Chi-restraints excluded: chain S residue 79 GLU Chi-restraints excluded: chain S residue 92 CYS Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 181 LEU Chi-restraints excluded: chain S residue 187 THR Chi-restraints excluded: chain S residue 242 HIS Chi-restraints excluded: chain S residue 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 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 25 SER Chi-restraints excluded: chain U residue 53 SER Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 107 TRP Chi-restraints excluded: chain V residue 27 GLN Chi-restraints excluded: chain V residue 71 SER Chi-restraints excluded: chain V residue 84 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 25 optimal weight: 6.9990 chunk 225 optimal weight: 40.0000 chunk 123 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 154 optimal weight: 30.0000 chunk 97 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 138 optimal weight: 0.9990 chunk 182 optimal weight: 0.8980 chunk 238 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 ASN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 HIS E 428 ASN L 51 GLN L 85 GLN ** O 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 302 ASN ** O 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 383 ASN ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 428 ASN U 100 GLN V 51 GLN V 85 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.121988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.104843 restraints weight = 51803.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.107869 restraints weight = 25545.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.109802 restraints weight = 15560.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.111042 restraints weight = 11027.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.111874 restraints weight = 8686.614| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30884 Z= 0.134 Angle : 0.677 10.397 41956 Z= 0.333 Chirality : 0.044 0.249 4928 Planarity : 0.004 0.056 5192 Dihedral : 10.106 104.796 4876 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 5.18 % Allowed : 20.79 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.13), residues: 3846 helix: 1.35 (0.18), residues: 876 sheet: -1.46 (0.15), residues: 1092 loop : -1.75 (0.13), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 348 TYR 0.024 0.001 TYR L 55 PHE 0.020 0.001 PHE T 48 TRP 0.015 0.002 TRP E 20 HIS 0.027 0.001 HIS E 259 Details of bonding type rmsd covalent geometry : bond 0.00302 (30814) covalent geometry : angle 0.65991 (41776) SS BOND : bond 0.00467 ( 30) SS BOND : angle 2.34099 ( 60) hydrogen bonds : bond 0.03973 ( 1094) hydrogen bonds : angle 5.33660 ( 3036) link_ALPHA1-3 : bond 0.01012 ( 4) link_ALPHA1-3 : angle 2.90125 ( 12) link_BETA1-4 : bond 0.00351 ( 20) link_BETA1-4 : angle 2.31877 ( 60) link_BETA1-6 : bond 0.01306 ( 4) link_BETA1-6 : angle 2.77133 ( 12) link_NAG-ASN : bond 0.00371 ( 12) link_NAG-ASN : angle 2.15631 ( 36) *********************** 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 987 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 820 time to evaluate : 1.067 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 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: 0.8060 (t) cc_final: 0.7663 (p) REVERT: A 26 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7883 (mm-30) REVERT: A 38 LYS cc_start: 0.9335 (mmtt) cc_final: 0.9102 (mmtm) REVERT: A 98 ASP cc_start: 0.8056 (p0) cc_final: 0.7587 (p0) REVERT: A 181 LEU cc_start: 0.8647 (tp) cc_final: 0.8117 (tp) REVERT: A 234 LEU cc_start: 0.8263 (mt) cc_final: 0.7926 (mp) REVERT: A 247 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7703 (pm20) REVERT: A 287 MET cc_start: 0.8630 (mtp) cc_final: 0.8081 (mtp) REVERT: A 299 MET cc_start: 0.6831 (mmm) cc_final: 0.5859 (mmm) REVERT: B 12 LEU cc_start: 0.6535 (OUTLIER) cc_final: 0.6102 (pp) REVERT: B 26 TRP cc_start: 0.6855 (m100) cc_final: 0.6584 (m-90) REVERT: B 28 GLN cc_start: 0.7855 (tp-100) cc_final: 0.7587 (tp-100) REVERT: B 61 VAL cc_start: 0.9168 (t) cc_final: 0.8839 (p) REVERT: B 68 MET cc_start: 0.8053 (tpt) cc_final: 0.7752 (tpt) REVERT: C 125 ILE cc_start: 0.8719 (tt) cc_final: 0.8321 (tt) REVERT: C 182 GLU cc_start: 0.7445 (tp30) cc_final: 0.6936 (tp30) REVERT: C 199 MET cc_start: 0.8350 (ptm) cc_final: 0.7937 (ptm) REVERT: C 258 MET cc_start: 0.8928 (tpp) cc_final: 0.8232 (tpp) REVERT: C 293 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8599 (pptt) REVERT: C 348 ARG cc_start: 0.7852 (ptm-80) cc_final: 0.7520 (ptm-80) REVERT: C 380 ILE cc_start: 0.7932 (OUTLIER) cc_final: 0.7656 (tt) REVERT: C 400 PHE cc_start: 0.7382 (m-10) cc_final: 0.7146 (t80) REVERT: C 432 LYS cc_start: 0.8277 (tttp) cc_final: 0.8040 (ttpp) REVERT: C 436 GLN cc_start: 0.8768 (tm-30) cc_final: 0.8193 (tt0) REVERT: D 10 MET cc_start: 0.8404 (mmm) cc_final: 0.8159 (mmm) REVERT: D 12 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8192 (pp) REVERT: D 18 THR cc_start: 0.8777 (p) cc_final: 0.7975 (t) REVERT: D 42 PHE cc_start: 0.8776 (t80) cc_final: 0.8078 (t80) REVERT: D 64 PHE cc_start: 0.9372 (t80) cc_final: 0.9076 (t80) REVERT: D 74 MET cc_start: 0.8843 (tpp) cc_final: 0.8255 (mmm) REVERT: E 8 ASN cc_start: 0.8183 (t0) cc_final: 0.7735 (t0) REVERT: E 20 TRP cc_start: 0.7609 (p90) cc_final: 0.6262 (p90) REVERT: E 108 PHE cc_start: 0.8636 (m-80) cc_final: 0.8275 (m-80) REVERT: E 126 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7121 (tp30) REVERT: E 176 TYR cc_start: 0.8802 (m-80) cc_final: 0.8435 (m-80) REVERT: E 181 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8595 (pp) REVERT: E 251 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8398 (tt) REVERT: E 270 ASN cc_start: 0.6958 (t0) cc_final: 0.6715 (t0) REVERT: E 286 LYS cc_start: 0.8634 (ptpt) cc_final: 0.8249 (ptpp) REVERT: E 295 MET cc_start: 0.7790 (tpt) cc_final: 0.6073 (tmm) REVERT: E 442 TYR cc_start: 0.8874 (t80) cc_final: 0.8267 (t80) REVERT: E 484 THR cc_start: 0.8762 (m) cc_final: 0.8279 (p) REVERT: F 52 TYR cc_start: 0.6322 (m-80) cc_final: 0.5909 (m-80) REVERT: H 3 GLU cc_start: 0.6421 (mm-30) cc_final: 0.6143 (mm-30) REVERT: H 47 TRP cc_start: 0.8188 (t60) cc_final: 0.7785 (t60) REVERT: H 57 ASP cc_start: 0.7341 (t0) cc_final: 0.7053 (m-30) REVERT: H 65 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7270 (mtmt) REVERT: H 95 TYR cc_start: 0.8677 (m-80) cc_final: 0.8372 (m-80) REVERT: L 2 ILE cc_start: 0.8576 (mt) cc_final: 0.8371 (mt) REVERT: L 48 GLN cc_start: 0.7072 (mp10) cc_final: 0.6207 (mp10) REVERT: L 104 PHE cc_start: 0.8653 (m-80) cc_final: 0.8420 (m-80) REVERT: O 6 VAL cc_start: 0.8071 (t) cc_final: 0.7688 (p) REVERT: O 26 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7808 (mm-30) REVERT: O 42 ASP cc_start: 0.8446 (m-30) cc_final: 0.8021 (m-30) REVERT: O 98 ASP cc_start: 0.8050 (p0) cc_final: 0.7606 (p0) REVERT: O 181 LEU cc_start: 0.8296 (tp) cc_final: 0.7916 (tp) REVERT: O 190 ASP cc_start: 0.8129 (t0) cc_final: 0.7827 (t0) REVERT: O 247 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7668 (pm20) REVERT: O 287 MET cc_start: 0.8611 (mtp) cc_final: 0.8121 (mtp) REVERT: O 299 MET cc_start: 0.6824 (mmm) cc_final: 0.5823 (mmm) REVERT: P 12 LEU cc_start: 0.6507 (OUTLIER) cc_final: 0.6152 (pp) REVERT: P 26 TRP cc_start: 0.6830 (m100) cc_final: 0.6525 (m-90) REVERT: P 28 GLN cc_start: 0.7870 (tp-100) cc_final: 0.7649 (tp-100) REVERT: P 65 ILE cc_start: 0.8468 (tt) cc_final: 0.8223 (tp) REVERT: P 68 MET cc_start: 0.8064 (tpt) cc_final: 0.7780 (tpt) REVERT: Q 125 ILE cc_start: 0.8711 (tt) cc_final: 0.8263 (tt) REVERT: Q 182 GLU cc_start: 0.6822 (tt0) cc_final: 0.6582 (tp30) REVERT: Q 194 MET cc_start: 0.7803 (mtp) cc_final: 0.7506 (ttp) REVERT: Q 199 MET cc_start: 0.8355 (ptm) cc_final: 0.7923 (ptm) REVERT: Q 258 MET cc_start: 0.8934 (tpp) cc_final: 0.8231 (tpp) REVERT: Q 348 ARG cc_start: 0.7855 (ptm-80) cc_final: 0.7519 (ptm-80) REVERT: Q 380 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7656 (tt) REVERT: Q 400 PHE cc_start: 0.7384 (m-10) cc_final: 0.7156 (t80) REVERT: Q 401 GLU cc_start: 0.8064 (tp30) cc_final: 0.7584 (tp30) REVERT: Q 432 LYS cc_start: 0.8295 (tttp) cc_final: 0.8019 (ttpp) REVERT: Q 436 GLN cc_start: 0.8770 (tm-30) cc_final: 0.8195 (tt0) REVERT: R 10 MET cc_start: 0.8364 (mmm) cc_final: 0.8145 (mmm) REVERT: R 12 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8203 (pp) REVERT: R 18 THR cc_start: 0.8779 (p) cc_final: 0.7962 (t) REVERT: R 35 TRP cc_start: 0.8987 (t60) cc_final: 0.8427 (t60) REVERT: R 42 PHE cc_start: 0.8778 (t80) cc_final: 0.8035 (t80) REVERT: R 64 PHE cc_start: 0.9377 (t80) cc_final: 0.9071 (t80) REVERT: R 74 MET cc_start: 0.8824 (tpp) cc_final: 0.8161 (mmm) REVERT: S 8 ASN cc_start: 0.8210 (t0) cc_final: 0.7806 (t0) REVERT: S 20 TRP cc_start: 0.7612 (p90) cc_final: 0.6322 (p90) REVERT: S 108 PHE cc_start: 0.8635 (m-80) cc_final: 0.8259 (m-80) REVERT: S 176 TYR cc_start: 0.8845 (m-80) cc_final: 0.8439 (m-80) REVERT: S 250 VAL cc_start: 0.8784 (t) cc_final: 0.8528 (m) REVERT: S 251 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8317 (tt) REVERT: S 259 HIS cc_start: 0.8899 (OUTLIER) cc_final: 0.7316 (t70) REVERT: S 305 VAL cc_start: 0.9174 (OUTLIER) cc_final: 0.8682 (p) REVERT: S 323 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7486 (pm20) REVERT: S 442 TYR cc_start: 0.8884 (t80) cc_final: 0.8282 (t80) REVERT: S 484 THR cc_start: 0.8775 (m) cc_final: 0.8292 (p) REVERT: U 3 GLU cc_start: 0.6421 (mm-30) cc_final: 0.6143 (mm-30) REVERT: U 47 TRP cc_start: 0.8189 (t60) cc_final: 0.7787 (t60) REVERT: U 57 ASP cc_start: 0.7438 (t0) cc_final: 0.7120 (m-30) REVERT: U 65 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7257 (mtmt) REVERT: U 90 ASP cc_start: 0.7660 (t0) cc_final: 0.7338 (t0) REVERT: U 95 TYR cc_start: 0.8678 (m-80) cc_final: 0.8356 (m-80) REVERT: U 111 TYR cc_start: 0.8456 (m-80) cc_final: 0.8219 (m-10) REVERT: V 48 GLN cc_start: 0.7067 (mp10) cc_final: 0.6210 (mp10) REVERT: V 80 LYS cc_start: 0.7395 (mtmt) cc_final: 0.6933 (mtmm) REVERT: V 104 PHE cc_start: 0.8635 (m-80) cc_final: 0.8415 (m-80) outliers start: 167 outliers final: 109 residues processed: 923 average time/residue: 0.1698 time to fit residues: 258.9833 Evaluate side-chains 881 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 755 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 283 CYS 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 451 TRP 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 A residue 466 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 158 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 380 ILE Chi-restraints excluded: chain C residue 457 ILE 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 64 LYS 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 151 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 485 LEU 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 53 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 51 GLN 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 237 THR Chi-restraints excluded: chain O residue 247 GLU Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 283 CYS Chi-restraints excluded: chain O residue 365 ILE Chi-restraints excluded: chain O residue 387 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 451 TRP 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 O residue 466 LEU Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 67 LEU Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 43 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 263 THR Chi-restraints excluded: chain Q residue 356 VAL Chi-restraints excluded: chain Q residue 357 THR Chi-restraints excluded: chain Q residue 380 ILE Chi-restraints excluded: chain Q residue 457 ILE Chi-restraints excluded: chain R residue 12 LEU 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 92 CYS 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 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 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 451 TRP 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 53 SER Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 65 LYS Chi-restraints excluded: chain U residue 91 THR Chi-restraints excluded: chain V residue 51 GLN Chi-restraints excluded: chain V residue 84 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 277 optimal weight: 4.9990 chunk 308 optimal weight: 10.0000 chunk 133 optimal weight: 1.9990 chunk 306 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 359 optimal weight: 30.0000 chunk 220 optimal weight: 10.0000 chunk 222 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN ** C 353 ASN ** 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** O 86 GLN ** O 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 246 GLN ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 428 ASN U 100 GLN V 85 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.120270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.103108 restraints weight = 52125.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.106071 restraints weight = 25851.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.107995 restraints weight = 15848.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.109247 restraints weight = 11251.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.110044 restraints weight = 8887.215| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3823 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= 0.190 Angle : 0.726 14.366 41956 Z= 0.357 Chirality : 0.045 0.276 4928 Planarity : 0.004 0.053 5192 Dihedral : 9.740 105.319 4876 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 6.21 % Allowed : 20.92 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.13), residues: 3846 helix: 1.27 (0.18), residues: 876 sheet: -1.40 (0.15), residues: 1080 loop : -1.74 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 348 TYR 0.018 0.001 TYR U 111 PHE 0.021 0.002 PHE F 48 TRP 0.017 0.002 TRP L 41 HIS 0.006 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00447 (30814) covalent geometry : angle 0.70669 (41776) SS BOND : bond 0.00623 ( 30) SS BOND : angle 2.87392 ( 60) hydrogen bonds : bond 0.04134 ( 1094) hydrogen bonds : angle 5.34751 ( 3036) link_ALPHA1-3 : bond 0.00876 ( 4) link_ALPHA1-3 : angle 2.97218 ( 12) link_BETA1-4 : bond 0.00373 ( 20) link_BETA1-4 : angle 2.35684 ( 60) link_BETA1-6 : bond 0.01070 ( 4) link_BETA1-6 : angle 2.91812 ( 12) link_NAG-ASN : bond 0.00421 ( 12) link_NAG-ASN : angle 2.38253 ( 36) *********************** 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 975 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 775 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO B 72 " (corrupted residue). Skipping it. Corrupt residue: chain: B residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO P 72 " (corrupted residue). Skipping it. Corrupt residue: chain: P residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: A 6 VAL cc_start: 0.8137 (t) cc_final: 0.7686 (p) REVERT: A 26 GLU cc_start: 0.8330 (mm-30) cc_final: 0.7904 (mm-30) REVERT: A 38 LYS cc_start: 0.9333 (mmtt) cc_final: 0.9081 (mmtm) REVERT: A 57 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7024 (ttm110) REVERT: A 86 GLN cc_start: 0.7622 (mm110) cc_final: 0.7389 (mm-40) REVERT: A 98 ASP cc_start: 0.8087 (p0) cc_final: 0.7594 (p0) REVERT: A 181 LEU cc_start: 0.8530 (tp) cc_final: 0.8092 (tp) REVERT: A 190 ASP cc_start: 0.8257 (t0) cc_final: 0.8034 (t0) REVERT: A 247 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7783 (pm20) REVERT: A 287 MET cc_start: 0.8657 (mtp) cc_final: 0.8065 (mtp) REVERT: A 299 MET cc_start: 0.6786 (mmm) cc_final: 0.5936 (mmm) REVERT: B 12 LEU cc_start: 0.6265 (OUTLIER) cc_final: 0.5720 (pp) REVERT: B 26 TRP cc_start: 0.6907 (m100) cc_final: 0.6634 (m-90) REVERT: B 28 GLN cc_start: 0.7892 (tp-100) cc_final: 0.7588 (tp-100) REVERT: B 61 VAL cc_start: 0.9161 (t) cc_final: 0.8806 (p) REVERT: B 68 MET cc_start: 0.8124 (tpt) cc_final: 0.7618 (tpt) REVERT: C 44 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7539 (pm20) REVERT: C 125 ILE cc_start: 0.8872 (tt) cc_final: 0.8500 (tt) REVERT: C 182 GLU cc_start: 0.7168 (tp30) cc_final: 0.6856 (tp30) REVERT: C 199 MET cc_start: 0.8368 (ptm) cc_final: 0.7975 (ptm) REVERT: C 258 MET cc_start: 0.8947 (tpp) cc_final: 0.8267 (tpp) REVERT: C 293 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8471 (pptt) REVERT: C 348 ARG cc_start: 0.7892 (ptm-80) cc_final: 0.7593 (ptm-80) REVERT: C 358 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.7080 (tppt) REVERT: C 368 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8156 (pm20) REVERT: C 380 ILE cc_start: 0.7966 (OUTLIER) cc_final: 0.7682 (tt) REVERT: C 432 LYS cc_start: 0.8272 (tttp) cc_final: 0.7944 (ttpp) REVERT: D 12 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8143 (pp) REVERT: D 42 PHE cc_start: 0.8780 (t80) cc_final: 0.8129 (t80) REVERT: D 64 PHE cc_start: 0.9356 (t80) cc_final: 0.9050 (t80) REVERT: D 74 MET cc_start: 0.8865 (tpp) cc_final: 0.8345 (mmm) REVERT: E 8 ASN cc_start: 0.8140 (t0) cc_final: 0.7787 (t0) REVERT: E 20 TRP cc_start: 0.7719 (p90) cc_final: 0.6388 (p90) REVERT: E 108 PHE cc_start: 0.8710 (m-80) cc_final: 0.8304 (m-80) REVERT: E 176 TYR cc_start: 0.8780 (m-80) cc_final: 0.8400 (m-80) REVERT: E 181 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8683 (pp) REVERT: E 251 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8268 (tt) REVERT: E 259 HIS cc_start: 0.8945 (OUTLIER) cc_final: 0.7265 (t70) REVERT: E 270 ASN cc_start: 0.7003 (t0) cc_final: 0.6775 (t0) REVERT: E 447 SER cc_start: 0.8968 (t) cc_final: 0.8660 (t) REVERT: E 484 THR cc_start: 0.8793 (m) cc_final: 0.8435 (p) REVERT: H 3 GLU cc_start: 0.6310 (mm-30) cc_final: 0.6042 (mm-30) REVERT: H 47 TRP cc_start: 0.8207 (t60) cc_final: 0.7601 (t60) REVERT: H 57 ASP cc_start: 0.7364 (t0) cc_final: 0.7103 (m-30) REVERT: H 95 TYR cc_start: 0.8665 (m-80) cc_final: 0.8449 (m-80) REVERT: L 45 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8662 (mttp) REVERT: L 48 GLN cc_start: 0.6999 (mp10) cc_final: 0.6245 (mp10) REVERT: L 51 GLN cc_start: 0.8880 (pm20) cc_final: 0.8417 (pt0) REVERT: L 104 PHE cc_start: 0.8683 (m-80) cc_final: 0.8466 (m-80) REVERT: O 6 VAL cc_start: 0.8134 (t) cc_final: 0.7698 (p) REVERT: O 26 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7880 (mm-30) REVERT: O 57 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.6977 (ttm110) REVERT: O 86 GLN cc_start: 0.7696 (tp-100) cc_final: 0.7482 (tp40) REVERT: O 98 ASP cc_start: 0.8071 (p0) cc_final: 0.7619 (p0) REVERT: O 181 LEU cc_start: 0.8553 (tp) cc_final: 0.8162 (tp) REVERT: O 190 ASP cc_start: 0.8124 (t0) cc_final: 0.7881 (t0) REVERT: O 247 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7751 (pm20) REVERT: O 287 MET cc_start: 0.8652 (mtp) cc_final: 0.8136 (mtp) REVERT: O 299 MET cc_start: 0.6946 (mmm) cc_final: 0.6019 (mmm) REVERT: O 400 PHE cc_start: 0.7280 (m-10) cc_final: 0.6929 (m-10) REVERT: P 12 LEU cc_start: 0.6257 (OUTLIER) cc_final: 0.5752 (pp) REVERT: P 26 TRP cc_start: 0.6847 (m100) cc_final: 0.6540 (m-90) REVERT: P 28 GLN cc_start: 0.7877 (tp-100) cc_final: 0.7669 (tp-100) REVERT: P 68 MET cc_start: 0.8135 (tpt) cc_final: 0.7653 (tpt) REVERT: Q 44 GLU cc_start: 0.7849 (pt0) cc_final: 0.7592 (pt0) REVERT: Q 125 ILE cc_start: 0.8862 (tt) cc_final: 0.8452 (tt) REVERT: Q 182 GLU cc_start: 0.6919 (tt0) cc_final: 0.6667 (tp30) REVERT: Q 194 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7344 (mtp) REVERT: Q 199 MET cc_start: 0.8369 (ptm) cc_final: 0.7943 (ptm) REVERT: Q 258 MET cc_start: 0.8963 (tpp) cc_final: 0.8288 (tpp) REVERT: Q 293 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8632 (pptt) REVERT: Q 348 ARG cc_start: 0.7893 (ptm-80) cc_final: 0.7595 (ptm-80) REVERT: Q 358 LYS cc_start: 0.7570 (OUTLIER) cc_final: 0.7257 (tppt) REVERT: Q 368 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8142 (pm20) REVERT: Q 380 ILE cc_start: 0.7969 (OUTLIER) cc_final: 0.7676 (tt) REVERT: Q 432 LYS cc_start: 0.8311 (tttp) cc_final: 0.8000 (ttpp) REVERT: R 12 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8162 (pp) REVERT: R 18 THR cc_start: 0.8926 (p) cc_final: 0.8149 (t) REVERT: R 35 TRP cc_start: 0.9041 (t60) cc_final: 0.8541 (t60) REVERT: R 42 PHE cc_start: 0.8785 (t80) cc_final: 0.8149 (t80) REVERT: R 64 PHE cc_start: 0.9387 (t80) cc_final: 0.9109 (t80) REVERT: R 74 MET cc_start: 0.8858 (tpp) cc_final: 0.8328 (mmm) REVERT: S 8 ASN cc_start: 0.8220 (t0) cc_final: 0.7822 (t0) REVERT: S 20 TRP cc_start: 0.7743 (p90) cc_final: 0.6393 (p90) REVERT: S 108 PHE cc_start: 0.8699 (m-80) cc_final: 0.8285 (m-80) REVERT: S 122 LEU cc_start: 0.6852 (OUTLIER) cc_final: 0.6619 (tp) REVERT: S 176 TYR cc_start: 0.8744 (m-80) cc_final: 0.8356 (m-80) REVERT: S 181 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8769 (pp) REVERT: S 250 VAL cc_start: 0.8794 (t) cc_final: 0.8543 (m) REVERT: S 259 HIS cc_start: 0.8922 (OUTLIER) cc_final: 0.7363 (t70) REVERT: S 305 VAL cc_start: 0.9184 (OUTLIER) cc_final: 0.8569 (p) REVERT: S 323 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7454 (pm20) REVERT: S 400 PHE cc_start: 0.7849 (m-10) cc_final: 0.7635 (m-10) REVERT: S 484 THR cc_start: 0.8803 (m) cc_final: 0.8446 (p) REVERT: U 3 GLU cc_start: 0.6409 (mm-30) cc_final: 0.6138 (mm-30) REVERT: U 47 TRP cc_start: 0.8253 (t60) cc_final: 0.7764 (t60) REVERT: U 57 ASP cc_start: 0.7451 (t0) cc_final: 0.7094 (m-30) REVERT: U 95 TYR cc_start: 0.8667 (m-80) cc_final: 0.8459 (m-80) REVERT: U 111 TYR cc_start: 0.8428 (m-80) cc_final: 0.8094 (m-10) REVERT: V 45 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8543 (mttp) REVERT: V 48 GLN cc_start: 0.7014 (mp10) cc_final: 0.6237 (mp10) REVERT: V 51 GLN cc_start: 0.8666 (pm20) cc_final: 0.8368 (pt0) REVERT: V 104 PHE cc_start: 0.8681 (m-80) cc_final: 0.8474 (m-80) outliers start: 200 outliers final: 144 residues processed: 910 average time/residue: 0.1705 time to fit residues: 257.1062 Evaluate side-chains 922 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 750 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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 233 GLU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 320 ILE 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 451 TRP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 461 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 34 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 44 GLU 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 158 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 368 GLU Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 457 ILE Chi-restraints excluded: chain C residue 459 VAL 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 64 LYS Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 151 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 251 LEU 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 H residue 7 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 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 33 THR Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 43 ILE 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 247 GLU Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 283 CYS Chi-restraints excluded: chain O residue 285 LEU Chi-restraints excluded: chain O residue 365 ILE Chi-restraints excluded: chain O residue 387 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 455 ILE Chi-restraints excluded: chain O residue 461 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 34 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 43 ILE Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 91 VAL Chi-restraints excluded: chain Q residue 113 LEU Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 194 MET 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 368 GLU Chi-restraints excluded: chain Q residue 371 PHE Chi-restraints excluded: chain Q residue 380 ILE Chi-restraints excluded: chain Q residue 457 ILE Chi-restraints excluded: chain Q residue 459 VAL Chi-restraints excluded: chain Q residue 466 LEU Chi-restraints excluded: chain Q residue 491 VAL Chi-restraints excluded: chain R residue 12 LEU 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 91 VAL Chi-restraints excluded: chain S residue 92 CYS Chi-restraints excluded: chain S residue 122 LEU 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 196 LEU Chi-restraints excluded: chain S residue 242 HIS Chi-restraints excluded: chain S residue 255 GLU Chi-restraints excluded: chain S residue 258 MET Chi-restraints excluded: chain S residue 259 HIS Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 305 VAL Chi-restraints excluded: chain S residue 318 ILE Chi-restraints excluded: chain S residue 323 GLU Chi-restraints excluded: chain S residue 356 VAL Chi-restraints excluded: chain S residue 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 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 83 MET Chi-restraints excluded: chain U residue 91 THR Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 45 LYS Chi-restraints excluded: chain V residue 84 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 62 optimal weight: 8.9990 chunk 308 optimal weight: 20.0000 chunk 251 optimal weight: 3.9990 chunk 266 optimal weight: 3.9990 chunk 282 optimal weight: 6.9990 chunk 208 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 72 optimal weight: 9.9990 chunk 227 optimal weight: 8.9990 chunk 211 optimal weight: 6.9990 chunk 272 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 HIS E 259 HIS E 428 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 GLN ** O 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 302 ASN S 428 ASN ** T 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 100 GLN V 51 GLN V 85 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.119882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.102626 restraints weight = 52138.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.105578 restraints weight = 26123.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.107496 restraints weight = 16075.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.108742 restraints weight = 11436.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.109523 restraints weight = 9048.055| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 30884 Z= 0.202 Angle : 0.740 14.282 41956 Z= 0.365 Chirality : 0.045 0.322 4928 Planarity : 0.004 0.049 5192 Dihedral : 9.422 105.463 4876 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 6.42 % Allowed : 21.20 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.13), residues: 3846 helix: 1.28 (0.18), residues: 870 sheet: -1.35 (0.15), residues: 1080 loop : -1.77 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 348 TYR 0.018 0.001 TYR U 111 PHE 0.022 0.002 PHE S 475 TRP 0.018 0.002 TRP C 218 HIS 0.007 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00473 (30814) covalent geometry : angle 0.71995 (41776) SS BOND : bond 0.00635 ( 30) SS BOND : angle 3.08207 ( 60) hydrogen bonds : bond 0.04174 ( 1094) hydrogen bonds : angle 5.34493 ( 3036) link_ALPHA1-3 : bond 0.00881 ( 4) link_ALPHA1-3 : angle 2.91527 ( 12) link_BETA1-4 : bond 0.00372 ( 20) link_BETA1-4 : angle 2.35156 ( 60) link_BETA1-6 : bond 0.00870 ( 4) link_BETA1-6 : angle 3.01767 ( 12) link_NAG-ASN : bond 0.00455 ( 12) link_NAG-ASN : angle 2.51494 ( 36) *********************** 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 983 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 776 time to evaluate : 1.208 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PRO B 72 " (corrupted residue). Skipping it. Corrupt residue: chain: B residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: A 20 TRP cc_start: 0.8966 (p-90) cc_final: 0.8606 (p-90) REVERT: A 26 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7889 (mm-30) REVERT: A 38 LYS cc_start: 0.9330 (mmtt) cc_final: 0.9067 (mmtm) REVERT: A 57 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7139 (ttm110) REVERT: A 98 ASP cc_start: 0.8079 (p0) cc_final: 0.7626 (p0) REVERT: A 168 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8630 (p) REVERT: A 181 LEU cc_start: 0.8627 (tp) cc_final: 0.8077 (tp) REVERT: A 196 LEU cc_start: 0.7329 (mt) cc_final: 0.6921 (mt) REVERT: A 238 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.8000 (m-10) REVERT: A 287 MET cc_start: 0.8652 (mtp) cc_final: 0.8062 (mtp) REVERT: A 299 MET cc_start: 0.6912 (mmm) cc_final: 0.6105 (mmm) REVERT: A 371 PHE cc_start: 0.9339 (OUTLIER) cc_final: 0.8778 (t80) REVERT: B 12 LEU cc_start: 0.6387 (OUTLIER) cc_final: 0.5763 (pp) REVERT: B 23 GLU cc_start: 0.5853 (pm20) cc_final: 0.5634 (pm20) REVERT: B 26 TRP cc_start: 0.6940 (m100) cc_final: 0.6637 (m-90) REVERT: B 61 VAL cc_start: 0.9161 (t) cc_final: 0.8813 (p) REVERT: B 68 MET cc_start: 0.8204 (tpt) cc_final: 0.7601 (tpt) REVERT: C 79 GLU cc_start: 0.7465 (mp0) cc_final: 0.7254 (mp0) REVERT: C 182 GLU cc_start: 0.7156 (tp30) cc_final: 0.6629 (tp30) REVERT: C 258 MET cc_start: 0.9025 (tpp) cc_final: 0.8456 (tpp) REVERT: C 293 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8539 (pptt) REVERT: C 358 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7037 (tppt) REVERT: C 380 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7673 (tt) REVERT: C 436 GLN cc_start: 0.8272 (tm-30) cc_final: 0.7947 (tt0) REVERT: D 12 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.7885 (pp) REVERT: D 42 PHE cc_start: 0.8778 (t80) cc_final: 0.8148 (t80) REVERT: D 64 PHE cc_start: 0.9377 (t80) cc_final: 0.9054 (t80) REVERT: D 74 MET cc_start: 0.8864 (tpp) cc_final: 0.8421 (mmm) REVERT: E 8 ASN cc_start: 0.8150 (t0) cc_final: 0.7747 (t0) REVERT: E 20 TRP cc_start: 0.7793 (p90) cc_final: 0.6400 (p90) REVERT: E 108 PHE cc_start: 0.8737 (m-80) cc_final: 0.8348 (m-80) REVERT: E 176 TYR cc_start: 0.8799 (m-80) cc_final: 0.8443 (m-80) REVERT: E 179 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.7969 (pt) REVERT: E 259 HIS cc_start: 0.8887 (OUTLIER) cc_final: 0.6518 (t-90) REVERT: E 270 ASN cc_start: 0.7048 (t0) cc_final: 0.6807 (t0) REVERT: E 286 LYS cc_start: 0.8664 (ptpt) cc_final: 0.8108 (ptpp) REVERT: E 323 GLU cc_start: 0.7557 (tt0) cc_final: 0.7330 (pt0) REVERT: E 401 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7767 (mm-30) REVERT: E 442 TYR cc_start: 0.8904 (t80) cc_final: 0.8322 (t80) REVERT: E 447 SER cc_start: 0.9025 (t) cc_final: 0.8728 (t) REVERT: E 484 THR cc_start: 0.8891 (m) cc_final: 0.8506 (p) REVERT: H 3 GLU cc_start: 0.6635 (mm-30) cc_final: 0.6392 (mm-30) REVERT: H 47 TRP cc_start: 0.8264 (t60) cc_final: 0.7587 (t60) REVERT: H 57 ASP cc_start: 0.7321 (t0) cc_final: 0.7014 (m-30) REVERT: H 90 ASP cc_start: 0.7409 (t0) cc_final: 0.7045 (t0) REVERT: L 48 GLN cc_start: 0.7409 (mp10) cc_final: 0.6711 (mp10) REVERT: O 6 VAL cc_start: 0.8132 (t) cc_final: 0.7704 (p) REVERT: O 20 TRP cc_start: 0.8934 (p-90) cc_final: 0.8550 (p-90) REVERT: O 26 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7876 (mm-30) REVERT: O 42 ASP cc_start: 0.8471 (m-30) cc_final: 0.8087 (m-30) REVERT: O 57 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7107 (ttm110) REVERT: O 98 ASP cc_start: 0.8066 (p0) cc_final: 0.7653 (p0) REVERT: O 168 THR cc_start: 0.9013 (OUTLIER) cc_final: 0.8647 (p) REVERT: O 181 LEU cc_start: 0.8586 (tp) cc_final: 0.8135 (tp) REVERT: O 190 ASP cc_start: 0.8142 (t0) cc_final: 0.7928 (t0) REVERT: O 238 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.7984 (m-10) REVERT: O 287 MET cc_start: 0.8645 (mtp) cc_final: 0.8126 (mtp) REVERT: O 299 MET cc_start: 0.6896 (mmm) cc_final: 0.6058 (mmm) REVERT: O 371 PHE cc_start: 0.9329 (OUTLIER) cc_final: 0.8788 (t80) REVERT: P 12 LEU cc_start: 0.6783 (OUTLIER) cc_final: 0.6176 (pp) REVERT: P 23 GLU cc_start: 0.5853 (pm20) cc_final: 0.5630 (pm20) REVERT: P 26 TRP cc_start: 0.6876 (m100) cc_final: 0.6540 (m-90) REVERT: P 28 GLN cc_start: 0.7871 (tp-100) cc_final: 0.7668 (tp-100) REVERT: P 68 MET cc_start: 0.8173 (tpt) cc_final: 0.7572 (tpt) REVERT: Q 79 GLU cc_start: 0.7368 (mp0) cc_final: 0.7091 (mp0) REVERT: Q 182 GLU cc_start: 0.6898 (tt0) cc_final: 0.6631 (tp30) REVERT: Q 213 ASP cc_start: 0.7534 (m-30) cc_final: 0.7170 (m-30) REVERT: Q 258 MET cc_start: 0.9026 (tpp) cc_final: 0.8480 (tpp) REVERT: Q 293 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8405 (pptt) REVERT: Q 358 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7195 (tppt) REVERT: Q 380 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7667 (tt) REVERT: Q 436 GLN cc_start: 0.8274 (tm-30) cc_final: 0.7944 (tt0) REVERT: R 12 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7582 (pp) REVERT: R 35 TRP cc_start: 0.9048 (t60) cc_final: 0.8782 (t60) REVERT: R 42 PHE cc_start: 0.8787 (t80) cc_final: 0.8151 (t80) REVERT: R 64 PHE cc_start: 0.9390 (t80) cc_final: 0.9097 (t80) REVERT: R 69 LEU cc_start: 0.8522 (mt) cc_final: 0.8260 (mt) REVERT: R 74 MET cc_start: 0.8854 (tpp) cc_final: 0.8369 (mmm) REVERT: S 8 ASN cc_start: 0.8206 (t0) cc_final: 0.7889 (t0) REVERT: S 20 TRP cc_start: 0.7814 (p90) cc_final: 0.6472 (p90) REVERT: S 108 PHE cc_start: 0.8722 (m-80) cc_final: 0.8325 (m-80) REVERT: S 122 LEU cc_start: 0.6909 (OUTLIER) cc_final: 0.6644 (tp) REVERT: S 176 TYR cc_start: 0.8766 (m-80) cc_final: 0.8365 (m-80) REVERT: S 250 VAL cc_start: 0.8770 (t) cc_final: 0.8529 (m) REVERT: S 259 HIS cc_start: 0.8975 (OUTLIER) cc_final: 0.7266 (t70) REVERT: S 305 VAL cc_start: 0.9193 (OUTLIER) cc_final: 0.8569 (p) REVERT: S 323 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7461 (pm20) REVERT: S 400 PHE cc_start: 0.7850 (m-10) cc_final: 0.7631 (m-10) REVERT: S 442 TYR cc_start: 0.8916 (t80) cc_final: 0.8329 (t80) REVERT: S 447 SER cc_start: 0.8975 (t) cc_final: 0.8684 (t) REVERT: S 484 THR cc_start: 0.8901 (m) cc_final: 0.8517 (p) REVERT: T 52 TYR cc_start: 0.6469 (m-80) cc_final: 0.5871 (m-80) REVERT: U 3 GLU cc_start: 0.6541 (mm-30) cc_final: 0.6253 (mm-30) REVERT: U 47 TRP cc_start: 0.8277 (t60) cc_final: 0.7553 (t60) REVERT: U 57 ASP cc_start: 0.7396 (t0) cc_final: 0.7168 (m-30) REVERT: U 58 LYS cc_start: 0.8238 (mttt) cc_final: 0.8030 (mttt) REVERT: U 90 ASP cc_start: 0.7385 (t0) cc_final: 0.6777 (t0) REVERT: U 111 TYR cc_start: 0.8477 (m-80) cc_final: 0.8166 (m-10) REVERT: V 48 GLN cc_start: 0.7404 (mp10) cc_final: 0.6713 (mp10) outliers start: 207 outliers final: 149 residues processed: 921 average time/residue: 0.1774 time to fit residues: 270.7300 Evaluate side-chains 922 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 749 time to evaluate : 1.176 ------------------------------------------------------------------------------- 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 168 THR Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 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 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 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 461 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 34 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 158 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 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 459 VAL 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 64 LYS 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 151 VAL Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 244 LYS 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 428 ASN Chi-restraints excluded: chain E residue 451 TRP Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 51 GLN Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 43 ILE 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 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 275 SER Chi-restraints excluded: chain O residue 283 CYS Chi-restraints excluded: chain O residue 320 ILE Chi-restraints excluded: chain O residue 365 ILE Chi-restraints excluded: chain O residue 371 PHE Chi-restraints excluded: chain O residue 387 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 455 ILE Chi-restraints excluded: chain O residue 461 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 34 THR Chi-restraints excluded: chain P residue 67 LEU Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 30 CYS Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 43 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 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 380 ILE Chi-restraints excluded: chain Q residue 457 ILE Chi-restraints excluded: chain Q residue 459 VAL Chi-restraints excluded: chain Q residue 466 LEU Chi-restraints excluded: chain Q residue 491 VAL Chi-restraints excluded: chain R residue 12 LEU 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 91 VAL Chi-restraints excluded: chain S residue 92 CYS Chi-restraints excluded: chain S residue 122 LEU Chi-restraints excluded: chain S residue 125 ILE 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 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 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 83 MET Chi-restraints excluded: chain U residue 91 THR Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 51 GLN 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 63 optimal weight: 6.9990 chunk 310 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 174 optimal weight: 20.0000 chunk 123 optimal weight: 10.0000 chunk 253 optimal weight: 5.9990 chunk 324 optimal weight: 0.3980 chunk 237 optimal weight: 8.9990 chunk 162 optimal weight: 0.9980 chunk 91 optimal weight: 20.0000 chunk 66 optimal weight: 9.9990 overall best weight: 3.8786 ------------------------------------------------------------------------------- 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** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** 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 114 GLN L 51 GLN ** O 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 428 ASN ** T 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 100 GLN U 114 GLN V 51 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.120911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.103620 restraints weight = 52019.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.106596 restraints weight = 25922.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.108553 restraints weight = 15920.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.109802 restraints weight = 11268.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.110582 restraints weight = 8917.347| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 30884 Z= 0.160 Angle : 0.713 14.594 41956 Z= 0.351 Chirality : 0.044 0.284 4928 Planarity : 0.004 0.049 5192 Dihedral : 9.149 104.960 4876 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 5.74 % Allowed : 22.16 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.13), residues: 3846 helix: 1.38 (0.18), residues: 870 sheet: -1.42 (0.15), residues: 1110 loop : -1.71 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 348 TYR 0.026 0.001 TYR V 55 PHE 0.024 0.001 PHE E 475 TRP 0.016 0.002 TRP A 229 HIS 0.013 0.001 HIS E 259 Details of bonding type rmsd covalent geometry : bond 0.00373 (30814) covalent geometry : angle 0.69369 (41776) SS BOND : bond 0.00589 ( 30) SS BOND : angle 2.89787 ( 60) hydrogen bonds : bond 0.04050 ( 1094) hydrogen bonds : angle 5.28086 ( 3036) link_ALPHA1-3 : bond 0.00884 ( 4) link_ALPHA1-3 : angle 2.76758 ( 12) link_BETA1-4 : bond 0.00336 ( 20) link_BETA1-4 : angle 2.28897 ( 60) link_BETA1-6 : bond 0.00849 ( 4) link_BETA1-6 : angle 2.93960 ( 12) link_NAG-ASN : bond 0.00405 ( 12) link_NAG-ASN : angle 2.37844 ( 36) *********************** 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 955 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 770 time to evaluate : 1.215 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: A 26 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7883 (mm-30) REVERT: A 38 LYS cc_start: 0.9312 (mmtt) cc_final: 0.9028 (mmtm) REVERT: A 57 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7132 (ttm110) REVERT: A 98 ASP cc_start: 0.8066 (p0) cc_final: 0.7610 (p0) REVERT: A 168 THR cc_start: 0.8988 (OUTLIER) cc_final: 0.8607 (p) REVERT: A 181 LEU cc_start: 0.8557 (tp) cc_final: 0.8001 (tp) REVERT: A 287 MET cc_start: 0.8641 (mtp) cc_final: 0.8064 (mtp) REVERT: A 299 MET cc_start: 0.6910 (mmm) cc_final: 0.6120 (mmm) REVERT: A 371 PHE cc_start: 0.9326 (OUTLIER) cc_final: 0.8771 (t80) REVERT: B 12 LEU cc_start: 0.6790 (OUTLIER) cc_final: 0.6324 (pp) REVERT: B 26 TRP cc_start: 0.6936 (m100) cc_final: 0.6635 (m-90) REVERT: B 61 VAL cc_start: 0.9175 (t) cc_final: 0.8845 (p) REVERT: B 68 MET cc_start: 0.8235 (tpt) cc_final: 0.7616 (tpt) REVERT: C 182 GLU cc_start: 0.7252 (tp30) cc_final: 0.6814 (tp30) REVERT: C 194 MET cc_start: 0.8118 (ttm) cc_final: 0.7858 (mmm) REVERT: C 199 MET cc_start: 0.8149 (ptm) cc_final: 0.7801 (ptm) REVERT: C 258 MET cc_start: 0.8911 (tpp) cc_final: 0.8258 (tpp) REVERT: C 293 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8166 (pptt) REVERT: C 358 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7015 (tppt) REVERT: C 380 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7646 (tt) REVERT: C 436 GLN cc_start: 0.8287 (tm-30) cc_final: 0.7817 (tm-30) REVERT: D 12 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7773 (pp) REVERT: D 42 PHE cc_start: 0.8771 (t80) cc_final: 0.7987 (t80) REVERT: D 64 PHE cc_start: 0.9381 (t80) cc_final: 0.9083 (t80) REVERT: D 74 MET cc_start: 0.8831 (tpp) cc_final: 0.8390 (mmm) REVERT: E 8 ASN cc_start: 0.8107 (t0) cc_final: 0.7889 (t0) REVERT: E 20 TRP cc_start: 0.7759 (p90) cc_final: 0.6457 (p90) REVERT: E 108 PHE cc_start: 0.8728 (m-80) cc_final: 0.8344 (m-80) REVERT: E 176 TYR cc_start: 0.8784 (m-80) cc_final: 0.8399 (m-80) REVERT: E 179 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.7898 (pt) REVERT: E 259 HIS cc_start: 0.8453 (OUTLIER) cc_final: 0.6811 (t70) REVERT: E 270 ASN cc_start: 0.7023 (t0) cc_final: 0.6788 (t0) REVERT: E 286 LYS cc_start: 0.8644 (ptpt) cc_final: 0.8229 (mtmm) REVERT: E 401 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7769 (mm-30) REVERT: E 428 ASN cc_start: 0.8074 (m-40) cc_final: 0.7737 (t0) REVERT: E 442 TYR cc_start: 0.8925 (t80) cc_final: 0.8322 (t80) REVERT: E 447 SER cc_start: 0.8974 (t) cc_final: 0.8663 (t) REVERT: E 484 THR cc_start: 0.8852 (m) cc_final: 0.8393 (p) REVERT: H 47 TRP cc_start: 0.8265 (t60) cc_final: 0.7736 (t60) REVERT: H 90 ASP cc_start: 0.7865 (t0) cc_final: 0.7178 (t0) REVERT: L 45 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8606 (mttp) REVERT: L 48 GLN cc_start: 0.7356 (mp10) cc_final: 0.6730 (mp10) REVERT: O 26 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7866 (mm-30) REVERT: O 57 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.6940 (ttm110) REVERT: O 98 ASP cc_start: 0.8060 (p0) cc_final: 0.7635 (p0) REVERT: O 168 THR cc_start: 0.8996 (OUTLIER) cc_final: 0.8631 (p) REVERT: O 181 LEU cc_start: 0.8524 (tp) cc_final: 0.8082 (tp) REVERT: O 190 ASP cc_start: 0.8166 (t0) cc_final: 0.7937 (t0) REVERT: O 196 LEU cc_start: 0.7857 (mt) cc_final: 0.7607 (mt) REVERT: O 287 MET cc_start: 0.8622 (mtp) cc_final: 0.8128 (mtp) REVERT: O 299 MET cc_start: 0.6886 (mmm) cc_final: 0.6082 (mmm) REVERT: O 371 PHE cc_start: 0.9246 (OUTLIER) cc_final: 0.8599 (t80) REVERT: P 12 LEU cc_start: 0.6767 (OUTLIER) cc_final: 0.6298 (pp) REVERT: P 26 TRP cc_start: 0.6872 (m100) cc_final: 0.6531 (m-90) REVERT: P 28 GLN cc_start: 0.7163 (tp-100) cc_final: 0.6621 (tp-100) REVERT: P 68 MET cc_start: 0.8205 (tpt) cc_final: 0.7578 (tpt) REVERT: Q 79 GLU cc_start: 0.7443 (mp0) cc_final: 0.7161 (mp0) REVERT: Q 182 GLU cc_start: 0.6820 (tt0) cc_final: 0.6541 (tp30) REVERT: Q 199 MET cc_start: 0.8157 (ptm) cc_final: 0.7880 (ptm) REVERT: Q 258 MET cc_start: 0.8929 (tpp) cc_final: 0.8310 (tpp) REVERT: Q 293 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8269 (pptt) REVERT: Q 358 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.7184 (tppt) REVERT: Q 380 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7648 (tt) REVERT: Q 436 GLN cc_start: 0.8283 (tm-30) cc_final: 0.7803 (tm-30) REVERT: R 10 MET cc_start: 0.8564 (mmm) cc_final: 0.8352 (mmm) REVERT: R 18 THR cc_start: 0.8929 (p) cc_final: 0.8196 (t) REVERT: R 35 TRP cc_start: 0.8982 (t60) cc_final: 0.8424 (t60) REVERT: R 42 PHE cc_start: 0.8772 (t80) cc_final: 0.7934 (t80) REVERT: R 64 PHE cc_start: 0.9394 (t80) cc_final: 0.9090 (t80) REVERT: R 74 MET cc_start: 0.8831 (tpp) cc_final: 0.8348 (mmm) REVERT: S 8 ASN cc_start: 0.8197 (t0) cc_final: 0.7916 (t0) REVERT: S 20 TRP cc_start: 0.7779 (p90) cc_final: 0.6448 (p90) REVERT: S 108 PHE cc_start: 0.8714 (m-80) cc_final: 0.8319 (m-80) REVERT: S 122 LEU cc_start: 0.6874 (OUTLIER) cc_final: 0.6614 (tp) REVERT: S 176 TYR cc_start: 0.8756 (m-80) cc_final: 0.8402 (m-80) REVERT: S 250 VAL cc_start: 0.8764 (t) cc_final: 0.8503 (m) REVERT: S 259 HIS cc_start: 0.8944 (OUTLIER) cc_final: 0.7151 (t70) REVERT: S 305 VAL cc_start: 0.9183 (OUTLIER) cc_final: 0.8907 (p) REVERT: S 323 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7656 (pm20) REVERT: S 400 PHE cc_start: 0.7840 (m-10) cc_final: 0.7618 (m-10) REVERT: S 442 TYR cc_start: 0.8930 (t80) cc_final: 0.8330 (t80) REVERT: S 447 SER cc_start: 0.8981 (t) cc_final: 0.8690 (t) REVERT: S 484 THR cc_start: 0.8802 (m) cc_final: 0.8299 (p) REVERT: U 3 GLU cc_start: 0.6541 (mm-30) cc_final: 0.6247 (mm-30) REVERT: U 47 TRP cc_start: 0.8270 (t60) cc_final: 0.7755 (t60) REVERT: U 57 ASP cc_start: 0.7382 (t0) cc_final: 0.7179 (m-30) REVERT: U 58 LYS cc_start: 0.8206 (mttt) cc_final: 0.7998 (mttt) REVERT: U 65 LYS cc_start: 0.8132 (mmmt) cc_final: 0.7780 (mtpp) REVERT: U 90 ASP cc_start: 0.7359 (t0) cc_final: 0.6901 (t0) REVERT: V 48 GLN cc_start: 0.7358 (mp10) cc_final: 0.6718 (mp10) REVERT: V 80 LYS cc_start: 0.7835 (mtmm) cc_final: 0.7581 (mtmm) outliers start: 185 outliers final: 143 residues processed: 897 average time/residue: 0.1750 time to fit residues: 258.5889 Evaluate side-chains 908 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 743 time to evaluate : 1.110 ------------------------------------------------------------------------------- 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 168 THR Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 283 CYS 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 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 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 34 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 43 ILE 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 158 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 350 ILE Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 371 PHE Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 457 ILE Chi-restraints excluded: chain C residue 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 64 LYS 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 151 VAL Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 242 HIS 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 310 VAL 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 57 LEU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 43 ILE 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 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 285 LEU Chi-restraints excluded: chain O residue 320 ILE Chi-restraints excluded: chain O residue 365 ILE Chi-restraints excluded: chain O residue 371 PHE Chi-restraints excluded: chain O residue 387 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 455 ILE 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 34 THR Chi-restraints excluded: chain P residue 67 LEU Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 30 CYS Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 43 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 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 371 PHE 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 16 THR 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 91 VAL Chi-restraints excluded: chain S residue 92 CYS Chi-restraints excluded: chain S residue 122 LEU Chi-restraints excluded: chain S residue 125 ILE 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 196 LEU 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 428 ASN 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 57 LEU Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain U residue 22 CYS Chi-restraints excluded: chain U residue 25 SER Chi-restraints excluded: chain U residue 53 SER Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 83 MET Chi-restraints excluded: chain U residue 91 THR Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 84 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 155 optimal weight: 9.9990 chunk 233 optimal weight: 20.0000 chunk 207 optimal weight: 10.0000 chunk 235 optimal weight: 20.0000 chunk 148 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 348 optimal weight: 10.0000 chunk 234 optimal weight: 5.9990 chunk 343 optimal weight: 30.0000 chunk 336 optimal weight: 8.9990 chunk 67 optimal weight: 8.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 GLN ** O 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 242 HIS ** T 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 100 GLN V 51 GLN V 85 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.118407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.100907 restraints weight = 52482.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.103841 restraints weight = 26436.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.105767 restraints weight = 16369.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.106997 restraints weight = 11687.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.107782 restraints weight = 9293.552| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 30884 Z= 0.253 Angle : 0.794 17.106 41956 Z= 0.394 Chirality : 0.047 0.316 4928 Planarity : 0.005 0.049 5192 Dihedral : 9.096 103.197 4876 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 5.93 % Allowed : 22.72 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.13), residues: 3846 helix: 1.13 (0.18), residues: 882 sheet: -1.44 (0.15), residues: 1086 loop : -1.77 (0.13), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 348 TYR 0.043 0.002 TYR H 111 PHE 0.026 0.002 PHE T 48 TRP 0.022 0.002 TRP C 218 HIS 0.009 0.002 HIS E 259 Details of bonding type rmsd covalent geometry : bond 0.00596 (30814) covalent geometry : angle 0.77381 (41776) SS BOND : bond 0.00648 ( 30) SS BOND : angle 3.22606 ( 60) hydrogen bonds : bond 0.04366 ( 1094) hydrogen bonds : angle 5.38844 ( 3036) link_ALPHA1-3 : bond 0.00808 ( 4) link_ALPHA1-3 : angle 2.88193 ( 12) link_BETA1-4 : bond 0.00426 ( 20) link_BETA1-4 : angle 2.38249 ( 60) link_BETA1-6 : bond 0.00727 ( 4) link_BETA1-6 : angle 3.02061 ( 12) link_NAG-ASN : bond 0.00557 ( 12) link_NAG-ASN : angle 2.76829 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7692 Ramachandran restraints generated. 3846 Oldfield, 0 Emsley, 3846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 929 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 738 time to evaluate : 0.951 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PRO B 72 " (corrupted residue). Skipping it. Corrupt residue: chain: B residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 26 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7668 (mm-30) REVERT: A 38 LYS cc_start: 0.9309 (mmtt) cc_final: 0.9039 (mmtm) REVERT: A 57 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7011 (ttm110) REVERT: A 98 ASP cc_start: 0.8076 (p0) cc_final: 0.7694 (p0) REVERT: A 168 THR cc_start: 0.9011 (OUTLIER) cc_final: 0.8612 (p) REVERT: A 181 LEU cc_start: 0.8660 (tp) cc_final: 0.8110 (tp) REVERT: A 196 LEU cc_start: 0.7312 (mt) cc_final: 0.7023 (mt) REVERT: A 238 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.7905 (m-10) REVERT: A 287 MET cc_start: 0.8669 (mtp) cc_final: 0.8076 (mtp) REVERT: A 299 MET cc_start: 0.6955 (mmm) cc_final: 0.6282 (mtt) REVERT: A 371 PHE cc_start: 0.9286 (OUTLIER) cc_final: 0.8518 (t80) REVERT: B 12 LEU cc_start: 0.6794 (OUTLIER) cc_final: 0.6141 (pp) REVERT: B 26 TRP cc_start: 0.6968 (m100) cc_final: 0.6685 (m-90) REVERT: C 23 VAL cc_start: 0.9248 (m) cc_final: 0.9040 (m) REVERT: C 44 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8042 (pm20) REVERT: C 182 GLU cc_start: 0.7347 (tp30) cc_final: 0.6917 (tp30) REVERT: C 199 MET cc_start: 0.8186 (ptm) cc_final: 0.7863 (ptm) REVERT: C 258 MET cc_start: 0.9060 (tpp) cc_final: 0.8475 (tpp) REVERT: C 293 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8159 (pptt) REVERT: C 358 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7270 (tppt) REVERT: C 380 ILE cc_start: 0.8004 (mt) cc_final: 0.7708 (tt) REVERT: D 12 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7711 (pp) REVERT: D 42 PHE cc_start: 0.8798 (t80) cc_final: 0.8145 (t80) REVERT: D 74 MET cc_start: 0.8847 (tpp) cc_final: 0.8374 (mmm) REVERT: E 8 ASN cc_start: 0.8081 (t0) cc_final: 0.7721 (t0) REVERT: E 20 TRP cc_start: 0.7911 (p90) cc_final: 0.6388 (p90) REVERT: E 108 PHE cc_start: 0.8800 (m-80) cc_final: 0.8061 (m-80) REVERT: E 151 VAL cc_start: 0.8258 (OUTLIER) cc_final: 0.7891 (t) REVERT: E 175 GLU cc_start: 0.7224 (tp30) cc_final: 0.6929 (tp30) REVERT: E 176 TYR cc_start: 0.8740 (m-80) cc_final: 0.8417 (m-80) REVERT: E 259 HIS cc_start: 0.9111 (OUTLIER) cc_final: 0.7238 (t70) REVERT: E 270 ASN cc_start: 0.6734 (t0) cc_final: 0.6513 (t0) REVERT: E 286 LYS cc_start: 0.8657 (ptpt) cc_final: 0.8184 (mtmt) REVERT: E 442 TYR cc_start: 0.8958 (t80) cc_final: 0.8359 (t80) REVERT: E 447 SER cc_start: 0.9034 (t) cc_final: 0.8738 (t) REVERT: E 484 THR cc_start: 0.8912 (m) cc_final: 0.8523 (p) REVERT: H 47 TRP cc_start: 0.8191 (t60) cc_final: 0.7369 (t60) REVERT: H 65 LYS cc_start: 0.8184 (mmmt) cc_final: 0.7786 (mtpp) REVERT: H 90 ASP cc_start: 0.7899 (t0) cc_final: 0.7381 (t0) REVERT: L 48 GLN cc_start: 0.7448 (mp10) cc_final: 0.6752 (mp10) REVERT: O 26 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7663 (mm-30) REVERT: O 42 ASP cc_start: 0.8485 (m-30) cc_final: 0.8080 (m-30) REVERT: O 57 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7027 (ttm110) REVERT: O 98 ASP cc_start: 0.8069 (p0) cc_final: 0.7718 (p0) REVERT: O 168 THR cc_start: 0.9160 (OUTLIER) cc_final: 0.8667 (p) REVERT: O 181 LEU cc_start: 0.8656 (tp) cc_final: 0.8215 (tp) REVERT: O 190 ASP cc_start: 0.8228 (t0) cc_final: 0.7991 (t0) REVERT: O 201 ASN cc_start: 0.7386 (m-40) cc_final: 0.6163 (t0) REVERT: O 238 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.8057 (m-10) REVERT: O 287 MET cc_start: 0.8659 (mtp) cc_final: 0.8132 (mtp) REVERT: O 299 MET cc_start: 0.6930 (mmm) cc_final: 0.6271 (mtt) REVERT: O 371 PHE cc_start: 0.9283 (OUTLIER) cc_final: 0.8536 (t80) REVERT: P 12 LEU cc_start: 0.6814 (OUTLIER) cc_final: 0.6133 (pp) REVERT: P 26 TRP cc_start: 0.6889 (m100) cc_final: 0.6513 (m-90) REVERT: P 28 GLN cc_start: 0.7176 (tp-100) cc_final: 0.6689 (tp-100) REVERT: Q 23 VAL cc_start: 0.9243 (m) cc_final: 0.9028 (m) REVERT: Q 79 GLU cc_start: 0.7552 (mp0) cc_final: 0.7294 (mp0) REVERT: Q 182 GLU cc_start: 0.6847 (tt0) cc_final: 0.6542 (tp30) REVERT: Q 199 MET cc_start: 0.8201 (ptm) cc_final: 0.7906 (ptm) REVERT: Q 213 ASP cc_start: 0.7582 (m-30) cc_final: 0.7246 (m-30) REVERT: Q 258 MET cc_start: 0.9063 (tpp) cc_final: 0.8495 (tpp) REVERT: Q 293 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8189 (pptt) REVERT: Q 358 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7322 (tppt) REVERT: Q 380 ILE cc_start: 0.8010 (mt) cc_final: 0.7705 (tt) REVERT: R 35 TRP cc_start: 0.9037 (t60) cc_final: 0.8748 (t60) REVERT: R 42 PHE cc_start: 0.8800 (t80) cc_final: 0.8164 (t80) REVERT: R 69 LEU cc_start: 0.8526 (mt) cc_final: 0.8296 (mt) REVERT: R 74 MET cc_start: 0.8790 (tpp) cc_final: 0.8296 (mmm) REVERT: S 8 ASN cc_start: 0.8235 (t0) cc_final: 0.7971 (t0) REVERT: S 20 TRP cc_start: 0.7945 (p90) cc_final: 0.6385 (p90) REVERT: S 108 PHE cc_start: 0.8783 (m-80) cc_final: 0.8035 (m-80) REVERT: S 151 VAL cc_start: 0.8259 (OUTLIER) cc_final: 0.7886 (t) REVERT: S 250 VAL cc_start: 0.8789 (t) cc_final: 0.8587 (m) REVERT: S 259 HIS cc_start: 0.8820 (OUTLIER) cc_final: 0.7023 (t70) REVERT: S 305 VAL cc_start: 0.9166 (OUTLIER) cc_final: 0.8583 (p) REVERT: S 323 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7424 (pm20) REVERT: S 400 PHE cc_start: 0.7853 (m-10) cc_final: 0.7643 (m-10) REVERT: S 442 TYR cc_start: 0.8966 (t80) cc_final: 0.8360 (t80) REVERT: S 447 SER cc_start: 0.9039 (t) cc_final: 0.8757 (t) REVERT: S 484 THR cc_start: 0.8917 (m) cc_final: 0.8532 (p) REVERT: U 47 TRP cc_start: 0.8209 (t60) cc_final: 0.7305 (t60) REVERT: U 57 ASP cc_start: 0.7440 (t0) cc_final: 0.7191 (m-30) REVERT: U 58 LYS cc_start: 0.8197 (mttt) cc_final: 0.7984 (mttt) REVERT: U 65 LYS cc_start: 0.8130 (mmmt) cc_final: 0.7777 (mtpp) REVERT: U 90 ASP cc_start: 0.7901 (t0) cc_final: 0.7192 (t0) REVERT: V 48 GLN cc_start: 0.7453 (mp10) cc_final: 0.6747 (mp10) REVERT: V 56 GLU cc_start: 0.6742 (mp0) cc_final: 0.6479 (mp0) outliers start: 191 outliers final: 146 residues processed: 875 average time/residue: 0.1744 time to fit residues: 252.4367 Evaluate side-chains 893 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 725 time to evaluate : 1.119 ------------------------------------------------------------------------------- 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 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 238 PHE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 283 CYS 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 413 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 451 TRP Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 44 GLU 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 158 VAL Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 293 LYS Chi-restraints excluded: chain C residue 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 371 PHE Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 457 ILE Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain 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 125 ILE Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 259 HIS Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 310 VAL 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 451 TRP Chi-restraints excluded: chain E residue 455 ILE Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 485 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 51 GLN Chi-restraints excluded: chain L residue 84 VAL Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain O residue 57 ARG Chi-restraints excluded: chain O residue 121 CYS Chi-restraints excluded: chain O residue 130 VAL Chi-restraints excluded: chain O residue 168 THR Chi-restraints excluded: chain O residue 195 ILE 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 285 LEU Chi-restraints excluded: chain O residue 320 ILE Chi-restraints excluded: chain O residue 365 ILE Chi-restraints excluded: chain O residue 371 PHE Chi-restraints excluded: chain O residue 387 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 455 ILE Chi-restraints excluded: chain O residue 466 LEU Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 67 LEU Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 30 CYS Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 113 LEU Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 201 ASN Chi-restraints excluded: chain Q residue 236 VAL Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 293 LYS Chi-restraints excluded: chain Q residue 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 457 ILE Chi-restraints excluded: chain Q residue 466 LEU Chi-restraints excluded: chain Q residue 491 VAL Chi-restraints excluded: chain R residue 16 THR Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain S residue 26 GLU Chi-restraints excluded: chain S residue 41 LEU Chi-restraints excluded: chain S residue 91 VAL Chi-restraints excluded: chain S residue 122 LEU Chi-restraints excluded: chain S residue 125 ILE Chi-restraints excluded: chain S residue 142 THR 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 196 LEU 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 333 ILE Chi-restraints excluded: chain S residue 356 VAL Chi-restraints excluded: chain S residue 451 TRP Chi-restraints excluded: chain S residue 455 ILE Chi-restraints excluded: chain S residue 464 ILE Chi-restraints excluded: chain S residue 485 LEU Chi-restraints excluded: chain T residue 16 THR Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 17 SER Chi-restraints excluded: chain U residue 22 CYS Chi-restraints excluded: chain U residue 25 SER Chi-restraints excluded: chain U residue 53 SER Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 83 MET Chi-restraints excluded: chain U residue 91 THR Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 51 GLN 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 38 optimal weight: 6.9990 chunk 272 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 354 optimal weight: 2.9990 chunk 67 optimal weight: 8.9990 chunk 273 optimal weight: 8.9990 chunk 224 optimal weight: 10.0000 chunk 163 optimal weight: 7.9990 chunk 118 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 342 optimal weight: 4.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 GLN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 259 HIS ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 209 GLN ** O 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 353 ASN ** 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** U 100 GLN V 51 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.119374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.102064 restraints weight = 51910.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.105016 restraints weight = 26080.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.106924 restraints weight = 16088.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.108146 restraints weight = 11462.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.108951 restraints weight = 9099.939| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 30884 Z= 0.202 Angle : 0.765 16.818 41956 Z= 0.379 Chirality : 0.046 0.299 4928 Planarity : 0.004 0.053 5192 Dihedral : 8.921 103.333 4876 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 5.21 % Allowed : 23.77 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.13), residues: 3846 helix: 1.23 (0.18), residues: 876 sheet: -1.41 (0.15), residues: 1090 loop : -1.74 (0.13), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 348 TYR 0.033 0.001 TYR H 111 PHE 0.027 0.002 PHE E 475 TRP 0.019 0.002 TRP O 229 HIS 0.008 0.001 HIS E 242 Details of bonding type rmsd covalent geometry : bond 0.00472 (30814) covalent geometry : angle 0.74549 (41776) SS BOND : bond 0.00633 ( 30) SS BOND : angle 3.03096 ( 60) hydrogen bonds : bond 0.04233 ( 1094) hydrogen bonds : angle 5.34007 ( 3036) link_ALPHA1-3 : bond 0.00827 ( 4) link_ALPHA1-3 : angle 2.77232 ( 12) link_BETA1-4 : bond 0.00379 ( 20) link_BETA1-4 : angle 2.33244 ( 60) link_BETA1-6 : bond 0.00808 ( 4) link_BETA1-6 : angle 2.82656 ( 12) link_NAG-ASN : bond 0.00487 ( 12) link_NAG-ASN : angle 2.65634 ( 36) ********************** 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 908 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 740 time to evaluate : 1.204 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PRO B 72 " (corrupted residue). Skipping it. Corrupt residue: chain: B residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 38 LYS cc_start: 0.9440 (mmtt) cc_final: 0.9114 (mmtm) REVERT: A 57 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7052 (ttm110) REVERT: A 98 ASP cc_start: 0.8054 (p0) cc_final: 0.7667 (p0) REVERT: A 168 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8596 (p) REVERT: A 181 LEU cc_start: 0.8604 (tp) cc_final: 0.8060 (tp) REVERT: A 196 LEU cc_start: 0.7222 (mt) cc_final: 0.6943 (mt) REVERT: A 287 MET cc_start: 0.8646 (mtp) cc_final: 0.8060 (mtp) REVERT: A 299 MET cc_start: 0.7049 (mmm) cc_final: 0.6484 (mtt) REVERT: A 371 PHE cc_start: 0.9265 (OUTLIER) cc_final: 0.8479 (t80) REVERT: B 12 LEU cc_start: 0.6734 (OUTLIER) cc_final: 0.6080 (pp) REVERT: B 26 TRP cc_start: 0.6959 (m100) cc_final: 0.6694 (m-90) REVERT: B 61 VAL cc_start: 0.9220 (t) cc_final: 0.8878 (p) REVERT: B 68 MET cc_start: 0.8476 (tpt) cc_final: 0.7627 (tpt) REVERT: C 23 VAL cc_start: 0.9253 (m) cc_final: 0.9038 (m) REVERT: C 44 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8040 (pm20) REVERT: C 182 GLU cc_start: 0.7311 (tp30) cc_final: 0.6908 (tp30) REVERT: C 199 MET cc_start: 0.8206 (ptm) cc_final: 0.7871 (ptm) REVERT: C 258 MET cc_start: 0.9033 (tpp) cc_final: 0.8449 (tpp) REVERT: C 293 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8074 (pptt) REVERT: C 358 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7256 (tppt) REVERT: C 380 ILE cc_start: 0.7978 (mt) cc_final: 0.7677 (tt) REVERT: C 436 GLN cc_start: 0.8738 (tm-30) cc_final: 0.8520 (tm-30) REVERT: D 42 PHE cc_start: 0.8791 (t80) cc_final: 0.8176 (t80) REVERT: D 64 PHE cc_start: 0.9311 (t80) cc_final: 0.9070 (t80) REVERT: D 74 MET cc_start: 0.8827 (tpp) cc_final: 0.8347 (mmm) REVERT: E 8 ASN cc_start: 0.8073 (t0) cc_final: 0.7744 (t0) REVERT: E 20 TRP cc_start: 0.7886 (p90) cc_final: 0.6345 (p90) REVERT: E 108 PHE cc_start: 0.8781 (m-80) cc_final: 0.8046 (m-80) REVERT: E 131 GLN cc_start: 0.7547 (pm20) cc_final: 0.5874 (pt0) REVERT: E 151 VAL cc_start: 0.8229 (OUTLIER) cc_final: 0.7851 (t) REVERT: E 176 TYR cc_start: 0.8715 (m-80) cc_final: 0.8438 (m-80) REVERT: E 179 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8370 (pt) REVERT: E 259 HIS cc_start: 0.8870 (OUTLIER) cc_final: 0.6551 (t-90) REVERT: E 270 ASN cc_start: 0.6726 (t0) cc_final: 0.6501 (t0) REVERT: E 286 LYS cc_start: 0.8626 (ptpt) cc_final: 0.8192 (mtmt) REVERT: E 323 GLU cc_start: 0.7578 (tt0) cc_final: 0.7221 (pt0) REVERT: E 442 TYR cc_start: 0.8970 (t80) cc_final: 0.8378 (t80) REVERT: E 447 SER cc_start: 0.8991 (t) cc_final: 0.8680 (t) REVERT: E 484 THR cc_start: 0.8905 (m) cc_final: 0.8507 (p) REVERT: H 47 TRP cc_start: 0.8186 (t60) cc_final: 0.7360 (t60) REVERT: H 58 LYS cc_start: 0.8148 (mttt) cc_final: 0.7919 (mmtp) REVERT: H 65 LYS cc_start: 0.8198 (mmmt) cc_final: 0.7814 (mtpp) REVERT: H 90 ASP cc_start: 0.8075 (t0) cc_final: 0.7392 (t0) REVERT: L 45 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8730 (mttp) REVERT: L 48 GLN cc_start: 0.7376 (mp10) cc_final: 0.6726 (mp10) REVERT: O 26 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7643 (mm-30) REVERT: O 57 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7015 (ttm110) REVERT: O 98 ASP cc_start: 0.8041 (p0) cc_final: 0.7696 (p0) REVERT: O 168 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8653 (p) REVERT: O 181 LEU cc_start: 0.8584 (tp) cc_final: 0.8151 (tp) REVERT: O 190 ASP cc_start: 0.8194 (t0) cc_final: 0.7979 (t0) REVERT: O 201 ASN cc_start: 0.7342 (m-40) cc_final: 0.6244 (t0) REVERT: O 238 PHE cc_start: 0.8755 (OUTLIER) cc_final: 0.8008 (m-10) REVERT: O 287 MET cc_start: 0.8642 (mtp) cc_final: 0.8143 (mtp) REVERT: O 299 MET cc_start: 0.6931 (mmm) cc_final: 0.6287 (mtt) REVERT: O 371 PHE cc_start: 0.9266 (OUTLIER) cc_final: 0.8491 (t80) REVERT: P 12 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.6610 (pp) REVERT: P 26 TRP cc_start: 0.6860 (m100) cc_final: 0.6541 (m-90) REVERT: P 28 GLN cc_start: 0.7158 (tp-100) cc_final: 0.6648 (tp-100) REVERT: P 68 MET cc_start: 0.8443 (tpt) cc_final: 0.7570 (tpt) REVERT: Q 2 ARG cc_start: 0.8625 (ttt-90) cc_final: 0.8386 (ttm-80) REVERT: Q 23 VAL cc_start: 0.9237 (m) cc_final: 0.9009 (m) REVERT: Q 79 GLU cc_start: 0.7595 (mp0) cc_final: 0.7344 (mp0) REVERT: Q 182 GLU cc_start: 0.6803 (tt0) cc_final: 0.6598 (tp30) REVERT: Q 199 MET cc_start: 0.8215 (ptm) cc_final: 0.7914 (ptm) REVERT: Q 258 MET cc_start: 0.9035 (tpp) cc_final: 0.8470 (tpp) REVERT: Q 293 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8084 (pptt) REVERT: Q 358 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7298 (tppt) REVERT: Q 380 ILE cc_start: 0.7976 (mt) cc_final: 0.7672 (tt) REVERT: Q 436 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8510 (tm-30) REVERT: R 35 TRP cc_start: 0.9037 (t60) cc_final: 0.8560 (t60) REVERT: R 42 PHE cc_start: 0.8792 (t80) cc_final: 0.8196 (t80) REVERT: R 64 PHE cc_start: 0.9322 (t80) cc_final: 0.9072 (t80) REVERT: R 69 LEU cc_start: 0.8510 (mt) cc_final: 0.8291 (mt) REVERT: R 74 MET cc_start: 0.8771 (tpp) cc_final: 0.8269 (mmm) REVERT: S 8 ASN cc_start: 0.8108 (t0) cc_final: 0.7802 (t0) REVERT: S 20 TRP cc_start: 0.7928 (p90) cc_final: 0.6351 (p90) REVERT: S 108 PHE cc_start: 0.8763 (m-80) cc_final: 0.8017 (m-80) REVERT: S 131 GLN cc_start: 0.7624 (pm20) cc_final: 0.5965 (pt0) REVERT: S 250 VAL cc_start: 0.8767 (t) cc_final: 0.8561 (m) REVERT: S 259 HIS cc_start: 0.8911 (OUTLIER) cc_final: 0.7131 (t70) REVERT: S 305 VAL cc_start: 0.9168 (OUTLIER) cc_final: 0.8540 (p) REVERT: S 323 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7392 (pm20) REVERT: S 400 PHE cc_start: 0.7846 (m-10) cc_final: 0.7637 (m-10) REVERT: S 442 TYR cc_start: 0.8973 (t80) cc_final: 0.8381 (t80) REVERT: S 447 SER cc_start: 0.8996 (t) cc_final: 0.8710 (t) REVERT: S 484 THR cc_start: 0.8915 (m) cc_final: 0.8527 (p) REVERT: U 3 GLU cc_start: 0.6628 (mm-30) cc_final: 0.6264 (mm-30) REVERT: U 47 TRP cc_start: 0.8196 (t60) cc_final: 0.7305 (t60) REVERT: U 57 ASP cc_start: 0.7401 (t0) cc_final: 0.7150 (m-30) REVERT: U 58 LYS cc_start: 0.8189 (mttt) cc_final: 0.7916 (mttt) REVERT: U 65 LYS cc_start: 0.8139 (mmmt) cc_final: 0.7768 (mtpp) REVERT: U 90 ASP cc_start: 0.7851 (t0) cc_final: 0.7324 (t0) REVERT: V 48 GLN cc_start: 0.7392 (mp10) cc_final: 0.6739 (mp10) outliers start: 168 outliers final: 137 residues processed: 853 average time/residue: 0.1797 time to fit residues: 252.7736 Evaluate side-chains 883 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 725 time to evaluate : 1.162 ------------------------------------------------------------------------------- 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 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 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 413 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 451 TRP Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 44 GLU 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 158 VAL Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 293 LYS Chi-restraints excluded: chain C residue 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 371 PHE 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 57 LEU Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 259 HIS Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 310 VAL 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 57 LEU Chi-restraints excluded: chain F residue 58 THR 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 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 33 THR Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain O residue 57 ARG Chi-restraints excluded: chain O residue 121 CYS Chi-restraints excluded: chain O residue 130 VAL Chi-restraints excluded: chain O residue 168 THR Chi-restraints excluded: chain O residue 195 ILE Chi-restraints excluded: chain O residue 198 THR 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 285 LEU Chi-restraints excluded: chain O residue 320 ILE Chi-restraints excluded: chain O residue 365 ILE Chi-restraints excluded: chain O residue 371 PHE Chi-restraints excluded: chain O residue 387 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 451 TRP Chi-restraints excluded: chain O residue 455 ILE Chi-restraints excluded: chain O residue 466 LEU Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 14 THR Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 30 CYS Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 113 LEU Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 135 LEU Chi-restraints excluded: chain Q residue 201 ASN Chi-restraints excluded: chain Q residue 236 VAL Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 293 LYS Chi-restraints excluded: chain Q residue 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 371 PHE Chi-restraints excluded: chain Q residue 457 ILE Chi-restraints excluded: chain Q residue 459 VAL 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 1 MET Chi-restraints excluded: chain S residue 26 GLU Chi-restraints excluded: chain S residue 41 LEU Chi-restraints excluded: chain S residue 91 VAL Chi-restraints excluded: chain S residue 122 LEU Chi-restraints excluded: chain S residue 125 ILE Chi-restraints excluded: chain S residue 142 THR 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 196 LEU 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 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 83 MET Chi-restraints excluded: chain U residue 91 THR Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 51 GLN 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 372 optimal weight: 8.9990 chunk 357 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 281 optimal weight: 0.3980 chunk 330 optimal weight: 4.9990 chunk 325 optimal weight: 0.9980 chunk 11 optimal weight: 7.9990 chunk 285 optimal weight: 4.9990 chunk 178 optimal weight: 9.9990 chunk 326 optimal weight: 8.9990 chunk 256 optimal weight: 6.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- 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** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 GLN ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 17 GLN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN L 51 GLN ** O 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 100 GLN V 51 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.120735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.103559 restraints weight = 52102.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.106507 restraints weight = 25805.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.108408 restraints weight = 15861.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.109672 restraints weight = 11302.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.110470 restraints weight = 8895.890| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 30884 Z= 0.151 Angle : 0.735 16.580 41956 Z= 0.362 Chirality : 0.044 0.278 4928 Planarity : 0.004 0.053 5192 Dihedral : 8.664 102.329 4876 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 4.87 % Allowed : 24.05 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.13), residues: 3846 helix: 1.36 (0.18), residues: 876 sheet: -1.41 (0.15), residues: 1114 loop : -1.69 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 348 TYR 0.026 0.001 TYR H 111 PHE 0.028 0.002 PHE E 475 TRP 0.019 0.002 TRP B 35 HIS 0.019 0.001 HIS E 259 Details of bonding type rmsd covalent geometry : bond 0.00350 (30814) covalent geometry : angle 0.71725 (41776) SS BOND : bond 0.00571 ( 30) SS BOND : angle 2.92395 ( 60) hydrogen bonds : bond 0.04048 ( 1094) hydrogen bonds : angle 5.24641 ( 3036) link_ALPHA1-3 : bond 0.00867 ( 4) link_ALPHA1-3 : angle 2.60675 ( 12) link_BETA1-4 : bond 0.00340 ( 20) link_BETA1-4 : angle 2.25708 ( 60) link_BETA1-6 : bond 0.00874 ( 4) link_BETA1-6 : angle 2.58458 ( 12) link_NAG-ASN : bond 0.00429 ( 12) link_NAG-ASN : angle 2.42513 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6007.33 seconds wall clock time: 104 minutes 35.95 seconds (6275.95 seconds total)