Starting phenix.real_space_refine on Mon Aug 25 18:00:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jn2_36430/08_2025/8jn2_36430.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jn2_36430/08_2025/8jn2_36430.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jn2_36430/08_2025/8jn2_36430.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jn2_36430/08_2025/8jn2_36430.map" model { file = "/net/cci-nas-00/data/ceres_data/8jn2_36430/08_2025/8jn2_36430.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jn2_36430/08_2025/8jn2_36430.cif" } resolution = 4.1 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 204 5.16 5 C 19018 2.51 5 N 5056 2.21 5 O 5710 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 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: 29988 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3759 Classifications: {'peptide': 493} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 476} 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: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 957 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 797 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "G" 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: "I" 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: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 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: "M" 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: "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: 3759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3759 Classifications: {'peptide': 493} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 476} 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: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 957 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "V" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 797 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "W" 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: "X" 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: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 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: "0" 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: "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: 6.64, per 1000 atoms: 0.22 Number of scatterers: 29988 At special positions: 0 Unit cell: (162.45, 241.11, 116.28, 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 204 16.00 O 5710 8.00 N 5056 7.00 C 19018 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 30 " distance=2.02 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 300 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS C 30 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 183 " - pdb=" SG CYS C 283 " distance=2.03 Simple disulfide: pdb=" SG CYS C 300 " - pdb=" SG CYS C 331 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS O 3 " - pdb=" SG CYS O 30 " distance=2.02 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 300 " - pdb=" SG CYS O 331 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 3 " - pdb=" SG CYS Q 30 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS Q 183 " - pdb=" SG CYS Q 283 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 300 " - pdb=" SG CYS Q 331 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 96 " distance=2.03 Simple disulfide: pdb=" SG CYS V 22 " - pdb=" SG CYS V 89 " distance=2.03 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 BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " 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 J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " 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 Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " 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: 2.11 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6948 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 76 sheets defined 26.4% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 100 through 104 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 147 through 151 removed outlier: 3.662A pdb=" N GLN A 150 " --> pdb=" O ASP A 147 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL A 151 " --> pdb=" O GLN A 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 147 through 151' Processing helix chain 'A' and resid 185 through 188 Processing helix chain 'A' and resid 207 through 213 Processing helix chain 'A' and resid 231 through 234 removed outlier: 3.815A pdb=" N LEU A 234 " --> pdb=" O ARG A 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 231 through 234' Processing helix chain 'A' and resid 254 through 262 Processing helix chain 'A' and resid 394 through 414 removed outlier: 3.627A pdb=" N ILE A 412 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 419 removed outlier: 3.540A pdb=" N ASP A 419 " --> pdb=" O THR A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 444 removed outlier: 3.930A pdb=" N ALA A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 466 Processing helix chain 'A' and resid 470 through 489 Processing helix chain 'B' and resid 20 through 39 removed outlier: 4.403A pdb=" N GLN B 28 " --> pdb=" O GLY B 24 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N VAL B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 removed outlier: 3.683A pdb=" N ILE B 44 " --> pdb=" O PRO B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 75 removed outlier: 3.561A pdb=" N THR B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Proline residue: B 72 - end of helix Processing helix chain 'C' and resid 16 through 18 No H-bonds generated for 'chain 'C' and resid 16 through 18' Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.677A pdb=" N GLY C 104 " --> pdb=" O TRP C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 212 removed outlier: 3.640A pdb=" N PHE C 212 " --> pdb=" O ARG C 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 208 through 212' 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: 4.009A pdb=" N TRP C 418 " --> pdb=" O ASP C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 446 Processing helix chain 'C' and resid 450 through 467 Processing helix chain 'C' and resid 470 through 491 Processing helix chain 'D' and resid 20 through 25 Processing helix chain 'D' and resid 26 through 39 Processing helix chain 'D' and resid 40 through 54 removed outlier: 4.239A pdb=" N ILE D 44 " --> pdb=" O PRO D 40 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU D 45 " --> pdb=" O GLY D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 75 Proline residue: D 72 - end of helix Processing helix chain 'E' and resid 82 through 87 removed outlier: 3.736A pdb=" N GLN E 86 " --> pdb=" O PRO E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 104 removed outlier: 3.602A pdb=" N GLY E 104 " --> pdb=" O TRP E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 135 Processing helix chain 'E' and resid 185 through 188 Processing helix chain 'E' and resid 207 through 213 Processing helix chain 'E' and resid 231 through 235 removed outlier: 3.597A pdb=" N LEU E 235 " --> pdb=" O LYS E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 262 Processing helix chain 'E' and resid 394 through 414 Processing helix chain 'E' and resid 415 through 417 No H-bonds generated for 'chain 'E' and resid 415 through 417' Processing helix chain 'E' and resid 425 through 446 Processing helix chain 'E' and resid 450 through 467 Processing helix chain 'E' and resid 471 through 490 removed outlier: 4.311A pdb=" N PHE E 475 " --> pdb=" O THR E 471 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 39 Processing helix chain 'F' and resid 40 through 53 removed outlier: 3.872A pdb=" N ILE F 44 " --> pdb=" O PRO F 40 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU F 45 " --> pdb=" O GLY F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 71 removed outlier: 3.894A pdb=" N THR F 71 " --> pdb=" O LEU F 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 Processing helix chain 'O' and resid 100 through 104 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 147 through 151 removed outlier: 3.662A pdb=" N GLN O 150 " --> pdb=" O ASP O 147 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL O 151 " --> pdb=" O GLN O 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 147 through 151' Processing helix chain 'O' and resid 185 through 188 Processing helix chain 'O' and resid 207 through 213 Processing helix chain 'O' and resid 231 through 234 removed outlier: 3.815A pdb=" N LEU O 234 " --> pdb=" O ARG O 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 231 through 234' Processing helix chain 'O' and resid 254 through 262 Processing helix chain 'O' and resid 394 through 414 removed outlier: 3.627A pdb=" N ILE O 412 " --> pdb=" O ARG O 408 " (cutoff:3.500A) Processing helix chain 'O' and resid 415 through 419 removed outlier: 3.540A pdb=" N ASP O 419 " --> pdb=" O THR O 416 " (cutoff:3.500A) Processing helix chain 'O' and resid 427 through 444 removed outlier: 3.930A pdb=" N ALA O 441 " --> pdb=" O ILE O 437 " (cutoff:3.500A) Processing helix chain 'O' and resid 450 through 466 Processing helix chain 'O' and resid 470 through 489 Processing helix chain 'P' and resid 20 through 39 removed outlier: 4.403A pdb=" N GLN P 28 " --> pdb=" O GLY P 24 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N VAL P 29 " --> pdb=" O ALA P 25 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 53 removed outlier: 3.683A pdb=" N ILE P 44 " --> pdb=" O PRO P 40 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 75 removed outlier: 3.561A pdb=" N THR P 71 " --> pdb=" O LEU P 67 " (cutoff:3.500A) Proline residue: P 72 - end of helix Processing helix chain 'Q' and resid 16 through 18 No H-bonds generated for 'chain 'Q' and resid 16 through 18' Processing helix chain 'Q' and resid 100 through 104 removed outlier: 3.677A pdb=" N GLY Q 104 " --> pdb=" O TRP Q 101 " (cutoff:3.500A) Processing helix chain 'Q' and resid 208 through 212 removed outlier: 3.640A pdb=" N PHE Q 212 " --> pdb=" O ARG Q 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 208 through 212' 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: 4.009A pdb=" N TRP Q 418 " --> pdb=" O ASP Q 415 " (cutoff:3.500A) Processing helix chain 'Q' and resid 425 through 446 Processing helix chain 'Q' and resid 450 through 467 Processing helix chain 'Q' and resid 470 through 491 Processing helix chain 'R' and resid 20 through 25 Processing helix chain 'R' and resid 26 through 39 Processing helix chain 'R' and resid 40 through 54 removed outlier: 4.239A pdb=" N ILE R 44 " --> pdb=" O PRO R 40 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU R 45 " --> pdb=" O GLY R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 75 Proline residue: R 72 - end of helix Processing helix chain 'S' and resid 82 through 87 removed outlier: 3.736A pdb=" N GLN S 86 " --> pdb=" O PRO S 83 " (cutoff:3.500A) Processing helix chain 'S' and resid 100 through 104 removed outlier: 3.602A pdb=" N GLY S 104 " --> pdb=" O TRP S 101 " (cutoff:3.500A) Processing helix chain 'S' and resid 131 through 135 Processing helix chain 'S' and resid 185 through 188 Processing helix chain 'S' and resid 207 through 213 Processing helix chain 'S' and resid 231 through 235 removed outlier: 3.597A pdb=" N LEU S 235 " --> pdb=" O LYS S 232 " (cutoff:3.500A) Processing helix chain 'S' and resid 254 through 262 Processing helix chain 'S' and resid 394 through 414 Processing helix chain 'S' and resid 415 through 417 No H-bonds generated for 'chain 'S' and resid 415 through 417' Processing helix chain 'S' and resid 425 through 446 Processing helix chain 'S' and resid 450 through 467 Processing helix chain 'S' and resid 471 through 490 removed outlier: 4.311A pdb=" N PHE S 475 " --> pdb=" O THR S 471 " (cutoff:3.500A) Processing helix chain 'T' and resid 26 through 39 Processing helix chain 'T' and resid 40 through 53 removed outlier: 3.872A pdb=" N ILE T 44 " --> pdb=" O PRO T 40 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU T 45 " --> pdb=" O GLY T 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 56 through 71 removed outlier: 3.894A pdb=" N THR T 71 " --> pdb=" O LEU T 67 " (cutoff:3.500A) Processing helix chain 'V' and resid 80 through 84 Processing sheet with id=1, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.171A pdb=" N ASP A 10 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 140 " --> pdb=" O GLU A 44 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N THR A 138 " --> pdb=" O GLN A 46 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N THR A 48 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N LYS A 136 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 20 through 25 removed outlier: 3.564A pdb=" N VAL A 21 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 281 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 58 through 59 Processing sheet with id=4, first strand: chain 'A' and resid 65 through 72 removed outlier: 4.583A pdb=" N ILE A 68 " --> pdb=" O CYS A 116 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N CYS A 116 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR A 70 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL A 114 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N SER A 72 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N SER A 112 " --> pdb=" O SER A 72 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR A 115 " --> pdb=" O LYS A 93 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS A 93 " --> pdb=" O THR A 115 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'A' and resid 195 through 196 removed outlier: 3.690A pdb=" N ALA A 203 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE A 268 " --> pdb=" O ALA A 203 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'A' and resid 236 through 237 Processing sheet with id=7, first strand: chain 'A' and resid 240 through 241 removed outlier: 3.541A pdb=" N ALA A 241 " --> pdb=" O LYS A 245 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=7 Processing sheet with id=8, first strand: chain 'A' and resid 305 through 308 removed outlier: 3.853A pdb=" N LYS A 307 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N LYS A 321 " --> pdb=" O LYS A 307 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU A 368 " --> pdb=" O ARG A 348 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG A 348 " --> pdb=" O GLU A 368 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'A' and resid 336 through 339 removed outlier: 3.667A pdb=" N TRP A 389 " --> pdb=" O SER A 374 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.484A pdb=" N ASP C 10 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL C 139 " --> pdb=" O ALA C 160 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'C' and resid 20 through 26 removed outlier: 3.552A pdb=" N LEU C 281 " --> pdb=" O LEU C 25 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'C' and resid 48 through 50 removed outlier: 3.672A pdb=" N THR C 48 " --> pdb=" O ILE C 276 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'C' and resid 54 through 55 removed outlier: 4.062A pdb=" N MET C 205 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR C 266 " --> pdb=" O MET C 205 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'C' and resid 59 through 60 Processing sheet with id=15, first strand: chain 'C' and resid 63 through 64 removed outlier: 3.554A pdb=" N GLN C 120 " --> pdb=" O LYS C 64 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'C' and resid 68 through 72 removed outlier: 3.523A pdb=" N ALA C 117 " --> pdb=" O VAL C 91 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'C' and resid 68 through 72 removed outlier: 3.515A pdb=" N GLY C 109 " --> pdb=" O ARG C 99 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'C' and resid 237 through 240 removed outlier: 4.065A pdb=" N THR C 237 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL C 249 " --> pdb=" O THR C 237 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU C 247 " --> pdb=" O LYS C 239 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'C' and resid 304 through 306 removed outlier: 3.524A pdb=" N SER C 311 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'C' and resid 304 through 306 Processing sheet with id=21, first strand: chain 'C' and resid 336 through 338 removed outlier: 3.704A pdb=" N GLY C 372 " --> pdb=" O LYS C 391 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.229A pdb=" N ASP E 10 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR E 138 " --> pdb=" O GLN E 46 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR E 48 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LYS E 136 " --> pdb=" O THR E 48 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'E' and resid 20 through 26 Processing sheet with id=24, first strand: chain 'E' and resid 54 through 55 Processing sheet with id=25, first strand: chain 'E' and resid 59 through 62 removed outlier: 3.697A pdb=" N ILE E 61 " --> pdb=" O GLU E 123 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N GLU E 123 " --> pdb=" O ILE E 61 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'E' and resid 65 through 72 removed outlier: 4.713A pdb=" N ILE E 68 " --> pdb=" O CYS E 116 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N CYS E 116 " --> pdb=" O ILE E 68 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N THR E 70 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL E 114 " --> pdb=" O THR E 70 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N SER E 72 " --> pdb=" O SER E 112 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N SER E 112 " --> pdb=" O SER E 72 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR E 115 " --> pdb=" O LYS E 93 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'E' and resid 237 through 239 Processing sheet with id=28, first strand: chain 'E' and resid 269 through 270 removed outlier: 3.626A pdb=" N GLN E 269 " --> pdb=" O SER E 275 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'E' and resid 304 through 306 removed outlier: 3.758A pdb=" N VAL E 305 " --> pdb=" O GLU E 323 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THR E 317 " --> pdb=" O THR E 313 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER E 311 " --> pdb=" O LEU E 319 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'E' and resid 304 through 306 removed outlier: 3.758A pdb=" N VAL E 305 " --> pdb=" O GLU E 323 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL E 322 " --> pdb=" O VAL E 363 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'E' and resid 336 through 339 removed outlier: 3.776A pdb=" N SER E 336 " --> pdb=" O VAL E 377 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN E 375 " --> pdb=" O GLU E 338 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'H' and resid 3 through 4 removed outlier: 3.892A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'H' and resid 33 through 34 Processing sheet with id=34, first strand: chain 'H' and resid 45 through 47 Processing sheet with id=35, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.719A pdb=" N LEU L 107 " --> pdb=" O ALA L 85 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA L 85 " --> pdb=" O LEU L 107 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN L 38 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.719A pdb=" N LEU L 107 " --> pdb=" O ALA L 85 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA L 85 " --> pdb=" O LEU L 107 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.847A pdb=" N VAL L 18 " --> pdb=" O ILE L 76 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE L 76 " --> pdb=" O VAL L 18 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.847A pdb=" N VAL L 18 " --> pdb=" O ILE L 76 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE L 76 " --> pdb=" O VAL L 18 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'O' and resid 10 through 11 removed outlier: 6.171A pdb=" N ASP O 10 " --> pdb=" O THR O 32 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE O 140 " --> pdb=" O GLU O 44 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N THR O 138 " --> pdb=" O GLN O 46 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N THR O 48 " --> pdb=" O LYS O 136 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N LYS O 136 " --> pdb=" O THR O 48 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'O' and resid 20 through 25 removed outlier: 3.564A pdb=" N VAL O 21 " --> pdb=" O LEU O 285 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU O 281 " --> pdb=" O LEU O 25 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'O' and resid 58 through 59 Processing sheet with id=42, first strand: chain 'O' and resid 65 through 72 removed outlier: 4.583A pdb=" N ILE O 68 " --> pdb=" O CYS O 116 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N CYS O 116 " --> pdb=" O ILE O 68 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR O 70 " --> pdb=" O VAL O 114 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL O 114 " --> pdb=" O THR O 70 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N SER O 72 " --> pdb=" O SER O 112 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N SER O 112 " --> pdb=" O SER O 72 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR O 115 " --> pdb=" O LYS O 93 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS O 93 " --> pdb=" O THR O 115 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'O' and resid 195 through 196 removed outlier: 3.690A pdb=" N ALA O 203 " --> pdb=" O ILE O 268 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE O 268 " --> pdb=" O ALA O 203 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'O' and resid 236 through 237 Processing sheet with id=45, first strand: chain 'O' and resid 240 through 241 removed outlier: 3.541A pdb=" N ALA O 241 " --> pdb=" O LYS O 245 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS O 245 " --> pdb=" O ALA O 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=45 Processing sheet with id=46, first strand: chain 'O' and resid 305 through 308 removed outlier: 3.853A pdb=" N LYS O 307 " --> pdb=" O LYS O 321 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N LYS O 321 " --> pdb=" O LYS O 307 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU O 368 " --> pdb=" O ARG O 348 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG O 348 " --> pdb=" O GLU O 368 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'O' and resid 336 through 339 removed outlier: 3.667A pdb=" N TRP O 389 " --> pdb=" O SER O 374 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'Q' and resid 10 through 11 removed outlier: 6.484A pdb=" N ASP Q 10 " --> pdb=" O THR Q 32 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL Q 139 " --> pdb=" O ALA Q 160 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'Q' and resid 20 through 26 removed outlier: 3.552A pdb=" N LEU Q 281 " --> pdb=" O LEU Q 25 " (cutoff:3.500A) Processing sheet with id=50, first strand: chain 'Q' and resid 48 through 50 removed outlier: 3.672A pdb=" N THR Q 48 " --> pdb=" O ILE Q 276 " (cutoff:3.500A) Processing sheet with id=51, first strand: chain 'Q' and resid 54 through 55 removed outlier: 4.062A pdb=" N MET Q 205 " --> pdb=" O THR Q 266 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR Q 266 " --> pdb=" O MET Q 205 " (cutoff:3.500A) Processing sheet with id=52, first strand: chain 'Q' and resid 59 through 60 Processing sheet with id=53, first strand: chain 'Q' and resid 63 through 64 removed outlier: 3.554A pdb=" N GLN Q 120 " --> pdb=" O LYS Q 64 " (cutoff:3.500A) Processing sheet with id=54, first strand: chain 'Q' and resid 68 through 72 removed outlier: 3.523A pdb=" N ALA Q 117 " --> pdb=" O VAL Q 91 " (cutoff:3.500A) Processing sheet with id=55, first strand: chain 'Q' and resid 68 through 72 removed outlier: 3.515A pdb=" N GLY Q 109 " --> pdb=" O ARG Q 99 " (cutoff:3.500A) Processing sheet with id=56, first strand: chain 'Q' and resid 237 through 240 removed outlier: 4.065A pdb=" N THR Q 237 " --> pdb=" O VAL Q 249 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL Q 249 " --> pdb=" O THR Q 237 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU Q 247 " --> pdb=" O LYS Q 239 " (cutoff:3.500A) Processing sheet with id=57, first strand: chain 'Q' and resid 304 through 306 removed outlier: 3.524A pdb=" N SER Q 311 " --> pdb=" O LEU Q 319 " (cutoff:3.500A) Processing sheet with id=58, first strand: chain 'Q' and resid 304 through 306 Processing sheet with id=59, first strand: chain 'Q' and resid 336 through 338 removed outlier: 3.704A pdb=" N GLY Q 372 " --> pdb=" O LYS Q 391 " (cutoff:3.500A) Processing sheet with id=60, first strand: chain 'S' and resid 10 through 11 removed outlier: 6.229A pdb=" N ASP S 10 " --> pdb=" O THR S 32 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR S 138 " --> pdb=" O GLN S 46 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR S 48 " --> pdb=" O LYS S 136 " (cutoff:3.500A) removed outlier: 6.104A 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 Processing sheet with id=62, first strand: chain 'S' and resid 54 through 55 Processing sheet with id=63, first strand: chain 'S' and resid 59 through 62 removed outlier: 3.697A pdb=" N ILE S 61 " --> pdb=" O GLU S 123 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N GLU S 123 " --> pdb=" O ILE S 61 " (cutoff:3.500A) Processing sheet with id=64, first strand: chain 'S' and resid 65 through 72 removed outlier: 4.713A pdb=" N ILE S 68 " --> pdb=" O CYS S 116 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N CYS S 116 " --> pdb=" O ILE S 68 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N THR S 70 " --> pdb=" O VAL S 114 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL S 114 " --> pdb=" O THR S 70 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N SER S 72 " --> pdb=" O SER S 112 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N SER S 112 " --> pdb=" O SER S 72 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR S 115 " --> pdb=" O LYS S 93 " (cutoff:3.500A) Processing sheet with id=65, first strand: chain 'S' and resid 237 through 239 Processing sheet with id=66, first strand: chain 'S' and resid 269 through 270 removed outlier: 3.626A pdb=" N GLN S 269 " --> pdb=" O SER S 275 " (cutoff:3.500A) Processing sheet with id=67, first strand: chain 'S' and resid 304 through 306 removed outlier: 3.758A pdb=" N VAL S 305 " --> pdb=" O GLU S 323 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THR S 317 " --> pdb=" O THR S 313 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER S 311 " --> pdb=" O LEU S 319 " (cutoff:3.500A) Processing sheet with id=68, first strand: chain 'S' and resid 304 through 306 removed outlier: 3.758A pdb=" N VAL S 305 " --> pdb=" O GLU S 323 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL S 322 " --> pdb=" O VAL S 363 " (cutoff:3.500A) Processing sheet with id=69, first strand: chain 'S' and resid 336 through 339 removed outlier: 3.776A pdb=" N SER S 336 " --> pdb=" O VAL S 377 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN S 375 " --> pdb=" O GLU S 338 " (cutoff:3.500A) Processing sheet with id=70, first strand: chain 'U' and resid 3 through 4 removed outlier: 3.892A pdb=" N GLN U 3 " --> pdb=" O SER U 25 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER U 25 " --> pdb=" O GLN U 3 " (cutoff:3.500A) Processing sheet with id=71, first strand: chain 'U' and resid 33 through 34 Processing sheet with id=72, first strand: chain 'U' and resid 45 through 47 Processing sheet with id=73, first strand: chain 'V' and resid 10 through 11 removed outlier: 3.719A pdb=" N LEU V 107 " --> pdb=" O ALA V 85 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA V 85 " --> pdb=" O LEU V 107 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP V 36 " --> pdb=" O LEU V 48 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN V 38 " --> pdb=" O LYS V 46 " (cutoff:3.500A) Processing sheet with id=74, first strand: chain 'V' and resid 10 through 11 removed outlier: 3.719A pdb=" N LEU V 107 " --> pdb=" O ALA V 85 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA V 85 " --> pdb=" O LEU V 107 " (cutoff:3.500A) Processing sheet with id=75, first strand: chain 'V' and resid 18 through 23 removed outlier: 3.847A pdb=" N VAL V 18 " --> pdb=" O ILE V 76 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE V 76 " --> pdb=" O VAL V 18 " (cutoff:3.500A) Processing sheet with id=76, first strand: chain 'V' and resid 18 through 23 removed outlier: 3.847A pdb=" N VAL V 18 " --> pdb=" O ILE V 76 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE V 76 " --> pdb=" O VAL V 18 " (cutoff:3.500A) 1126 hydrogen bonds defined for protein. 3024 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: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9604 1.34 - 1.47: 7226 1.47 - 1.59: 13444 1.59 - 1.71: 0 1.71 - 1.83: 322 Bond restraints: 30596 Sorted by residual: bond pdb=" CA ALA O 417 " pdb=" C ALA O 417 " ideal model delta sigma weight residual 1.522 1.485 0.037 1.38e-02 5.25e+03 7.36e+00 bond pdb=" CA ALA A 417 " pdb=" C ALA A 417 " ideal model delta sigma weight residual 1.522 1.485 0.037 1.38e-02 5.25e+03 7.36e+00 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.06e+00 bond pdb=" C1 NAG 1 1 " pdb=" O5 NAG 1 1 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.06e+00 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.559 -0.040 2.00e-02 2.50e+03 3.93e+00 ... (remaining 30591 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 40316 1.98 - 3.95: 1004 3.95 - 5.93: 134 5.93 - 7.90: 26 7.90 - 9.88: 4 Bond angle restraints: 41484 Sorted by residual: angle pdb=" N GLY U 56 " pdb=" CA GLY U 56 " pdb=" C GLY U 56 " ideal model delta sigma weight residual 112.37 116.99 -4.62 1.40e+00 5.10e-01 1.09e+01 angle pdb=" N GLY H 56 " pdb=" CA GLY H 56 " pdb=" C GLY H 56 " ideal model delta sigma weight residual 112.37 116.99 -4.62 1.40e+00 5.10e-01 1.09e+01 angle pdb=" CB MET S 473 " pdb=" CG MET S 473 " pdb=" SD MET S 473 " ideal model delta sigma weight residual 112.70 122.58 -9.88 3.00e+00 1.11e-01 1.08e+01 angle pdb=" CB MET E 473 " pdb=" CG MET E 473 " pdb=" SD MET E 473 " ideal model delta sigma weight residual 112.70 122.58 -9.88 3.00e+00 1.11e-01 1.08e+01 angle pdb=" C THR Q 224 " pdb=" N GLU Q 225 " pdb=" CA GLU Q 225 " ideal model delta sigma weight residual 121.54 127.82 -6.28 1.91e+00 2.74e-01 1.08e+01 ... (remaining 41479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.12: 17388 23.12 - 46.24: 924 46.24 - 69.35: 86 69.35 - 92.47: 96 92.47 - 115.59: 40 Dihedral angle restraints: 18534 sinusoidal: 7644 harmonic: 10890 Sorted by residual: 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 93.00 4.41 88.59 1 1.00e+01 1.00e-02 9.36e+01 dihedral pdb=" CB CYS O 60 " pdb=" SG CYS O 60 " pdb=" SG CYS O 121 " pdb=" CB CYS O 121 " ideal model delta sinusoidal sigma weight residual 93.00 4.41 88.59 1 1.00e+01 1.00e-02 9.36e+01 dihedral pdb=" CB CYS C 300 " pdb=" SG CYS C 300 " pdb=" SG CYS C 331 " pdb=" CB CYS C 331 " ideal model delta sinusoidal sigma weight residual 93.00 11.35 81.65 1 1.00e+01 1.00e-02 8.21e+01 ... (remaining 18531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 3844 0.053 - 0.107: 884 0.107 - 0.160: 114 0.160 - 0.213: 10 0.213 - 0.267: 10 Chirality restraints: 4862 Sorted by residual: chirality pdb=" C5 BMA W 3 " pdb=" C4 BMA W 3 " pdb=" C6 BMA W 3 " pdb=" O5 BMA W 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" C5 BMA Z 3 " pdb=" C4 BMA Z 3 " pdb=" C6 BMA Z 3 " pdb=" O5 BMA Z 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 4859 not shown) Planarity restraints: 5194 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 451 " -0.018 2.00e-02 2.50e+03 1.46e-02 5.34e+00 pdb=" CG TRP E 451 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP E 451 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP E 451 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP E 451 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 451 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP E 451 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 451 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 451 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 451 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP S 451 " -0.018 2.00e-02 2.50e+03 1.46e-02 5.34e+00 pdb=" CG TRP S 451 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP S 451 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP S 451 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP S 451 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP S 451 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP S 451 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP S 451 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP S 451 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP S 451 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 163 " 0.031 5.00e-02 4.00e+02 4.77e-02 3.63e+00 pdb=" N PRO C 164 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 164 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 164 " 0.026 5.00e-02 4.00e+02 ... (remaining 5191 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 485 2.65 - 3.21: 29172 3.21 - 3.78: 43991 3.78 - 4.34: 57725 4.34 - 4.90: 96147 Nonbonded interactions: 227520 Sorted by model distance: nonbonded pdb=" OG1 THR S 48 " pdb=" O ILE S 276 " model vdw 2.089 3.040 nonbonded pdb=" OG1 THR E 48 " pdb=" O ILE E 276 " model vdw 2.089 3.040 nonbonded pdb=" O GLN E 46 " pdb=" OG1 THR E 138 " model vdw 2.103 3.040 nonbonded pdb=" O GLN S 46 " pdb=" OG1 THR S 138 " model vdw 2.103 3.040 nonbonded pdb=" OG SER V 27 " pdb=" OG SER V 95 " model vdw 2.169 3.040 ... (remaining 227515 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 '1' selection = chain 'G' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'W' selection = chain 'Z' } ncs_group { reference = (chain 'A' and (resid 1 through 492 or (resid 493 and (name N or name CA or name \ C or name CB )))) selection = chain 'C' selection = chain 'E' selection = (chain 'O' and (resid 1 through 492 or (resid 493 and (name N or name CA or name \ C or name CB )))) 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 'H' selection = chain 'U' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'X' selection = chain 'Y' } 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: 0.010 Normalize map: mean=0, sd=1: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 26.060 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 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 : 0.005 0.045 30656 Z= 0.220 Angle : 0.767 9.875 41636 Z= 0.420 Chirality : 0.046 0.267 4862 Planarity : 0.004 0.048 5182 Dihedral : 15.804 115.590 11502 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: -1.72 (0.13), residues: 3838 helix: 0.83 (0.18), residues: 884 sheet: -1.13 (0.17), residues: 972 loop : -2.12 (0.13), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Q 186 TYR 0.014 0.002 TYR C 324 PHE 0.017 0.002 PHE C 304 TRP 0.040 0.002 TRP E 451 HIS 0.006 0.001 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00453 (30596) covalent geometry : angle 0.76010 (41484) SS BOND : bond 0.00449 ( 28) SS BOND : angle 1.13975 ( 56) hydrogen bonds : bond 0.21275 ( 1098) hydrogen bonds : angle 8.83837 ( 3024) link_BETA1-4 : bond 0.00676 ( 20) link_BETA1-4 : angle 1.97810 ( 60) link_NAG-ASN : bond 0.00489 ( 12) link_NAG-ASN : angle 2.63283 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1146 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1146 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO D 72 " (corrupted residue). Skipping it. Corrupt residue: chain: D 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 R 72 " (corrupted residue). Skipping it. Corrupt residue: chain: R residue: PRO 72 >>> skipping REVERT: A 42 ASP cc_start: 0.8466 (t0) cc_final: 0.8255 (t0) REVERT: A 49 GLU cc_start: 0.8254 (mp0) cc_final: 0.7865 (mp0) REVERT: A 69 THR cc_start: 0.9207 (p) cc_final: 0.8569 (p) REVERT: A 71 ASP cc_start: 0.8172 (p0) cc_final: 0.7936 (t70) REVERT: A 133 GLU cc_start: 0.8097 (pp20) cc_final: 0.7771 (pp20) REVERT: A 182 GLU cc_start: 0.7581 (mm-30) cc_final: 0.6956 (tp30) REVERT: A 195 ILE cc_start: 0.9014 (mt) cc_final: 0.8349 (tt) REVERT: A 453 MET cc_start: 0.8238 (tpp) cc_final: 0.7945 (tpt) REVERT: A 486 TYR cc_start: 0.8381 (t80) cc_final: 0.8097 (t80) REVERT: A 487 LEU cc_start: 0.8792 (tt) cc_final: 0.8514 (tt) REVERT: A 492 GLN cc_start: 0.8450 (mt0) cc_final: 0.7886 (tm-30) REVERT: B 60 LYS cc_start: 0.7970 (mttt) cc_final: 0.7766 (mttt) REVERT: C 1 MET cc_start: 0.8829 (mmp) cc_final: 0.7900 (mmm) REVERT: C 41 LEU cc_start: 0.9537 (pp) cc_final: 0.9317 (pt) REVERT: C 47 LYS cc_start: 0.8502 (mttp) cc_final: 0.8058 (pttt) REVERT: C 49 GLU cc_start: 0.7949 (mp0) cc_final: 0.7507 (mp0) REVERT: C 148 GLN cc_start: 0.8943 (tt0) cc_final: 0.8414 (tm-30) REVERT: C 196 LEU cc_start: 0.8891 (mt) cc_final: 0.8687 (mp) REVERT: C 237 THR cc_start: 0.9177 (p) cc_final: 0.8890 (p) REVERT: C 366 GLU cc_start: 0.7883 (pm20) cc_final: 0.7602 (pm20) REVERT: D 68 MET cc_start: 0.8613 (mmm) cc_final: 0.7421 (tmm) REVERT: D 74 MET cc_start: 0.8533 (mmm) cc_final: 0.8140 (mmm) REVERT: E 12 VAL cc_start: 0.9540 (p) cc_final: 0.9336 (t) REVERT: E 116 CYS cc_start: 0.5758 (m) cc_final: 0.5478 (m) REVERT: E 125 ILE cc_start: 0.9595 (tt) cc_final: 0.9124 (tt) REVERT: E 183 CYS cc_start: 0.8658 (m) cc_final: 0.8397 (m) REVERT: E 306 LEU cc_start: 0.9204 (tp) cc_final: 0.8920 (tp) REVERT: E 335 PHE cc_start: 0.8435 (t80) cc_final: 0.8179 (t80) REVERT: E 399 MET cc_start: 0.7892 (tmm) cc_final: 0.7442 (tmm) REVERT: E 419 ASP cc_start: 0.7714 (m-30) cc_final: 0.7373 (m-30) REVERT: F 51 HIS cc_start: 0.7549 (t-90) cc_final: 0.7007 (t-90) REVERT: F 59 GLN cc_start: 0.8088 (tt0) cc_final: 0.7184 (tt0) REVERT: F 68 MET cc_start: 0.8592 (tpt) cc_final: 0.8365 (ttt) REVERT: H 3 GLN cc_start: 0.7644 (pm20) cc_final: 0.7295 (pm20) REVERT: H 29 PHE cc_start: 0.6233 (t80) cc_final: 0.5714 (t80) REVERT: H 36 TRP cc_start: 0.6991 (m100) cc_final: 0.6169 (m100) REVERT: H 43 GLN cc_start: 0.7420 (mm-40) cc_final: 0.7053 (mm-40) REVERT: H 81 MET cc_start: 0.7553 (ttt) cc_final: 0.5054 (ttt) REVERT: H 111 TYR cc_start: 0.7820 (m-80) cc_final: 0.7537 (m-80) REVERT: L 3 VAL cc_start: 0.6786 (p) cc_final: 0.6149 (m) REVERT: L 32 ASN cc_start: 0.8135 (m-40) cc_final: 0.7730 (m-40) REVERT: L 52 ASN cc_start: 0.7052 (t0) cc_final: 0.6850 (t0) REVERT: O 42 ASP cc_start: 0.8470 (t0) cc_final: 0.8255 (t0) REVERT: O 49 GLU cc_start: 0.8271 (mp0) cc_final: 0.7840 (mp0) REVERT: O 69 THR cc_start: 0.9205 (p) cc_final: 0.8568 (p) REVERT: O 71 ASP cc_start: 0.8177 (p0) cc_final: 0.7936 (t70) REVERT: O 133 GLU cc_start: 0.8100 (pp20) cc_final: 0.7768 (pp20) REVERT: O 182 GLU cc_start: 0.7563 (mm-30) cc_final: 0.6950 (tp30) REVERT: O 195 ILE cc_start: 0.9011 (mt) cc_final: 0.8370 (tt) REVERT: O 453 MET cc_start: 0.8244 (tpp) cc_final: 0.7938 (tpt) REVERT: O 486 TYR cc_start: 0.8383 (t80) cc_final: 0.8090 (t80) REVERT: O 487 LEU cc_start: 0.8782 (tt) cc_final: 0.8498 (tt) REVERT: O 492 GLN cc_start: 0.8448 (mt0) cc_final: 0.7879 (tm-30) REVERT: P 60 LYS cc_start: 0.7954 (mttt) cc_final: 0.7750 (mttt) REVERT: Q 1 MET cc_start: 0.8827 (mmp) cc_final: 0.7909 (mmm) REVERT: Q 41 LEU cc_start: 0.9535 (pp) cc_final: 0.9317 (pt) REVERT: Q 47 LYS cc_start: 0.8499 (mttp) cc_final: 0.8059 (pttt) REVERT: Q 49 GLU cc_start: 0.7951 (mp0) cc_final: 0.7512 (mp0) REVERT: Q 148 GLN cc_start: 0.8941 (tt0) cc_final: 0.8410 (tm-30) REVERT: Q 196 LEU cc_start: 0.8886 (mt) cc_final: 0.8680 (mp) REVERT: Q 237 THR cc_start: 0.9158 (p) cc_final: 0.8854 (p) REVERT: Q 366 GLU cc_start: 0.7877 (pm20) cc_final: 0.7599 (pm20) REVERT: Q 463 TRP cc_start: 0.8144 (t-100) cc_final: 0.7943 (t-100) REVERT: R 68 MET cc_start: 0.8612 (mmm) cc_final: 0.7416 (tmm) REVERT: R 74 MET cc_start: 0.8536 (mmm) cc_final: 0.8141 (mmm) REVERT: S 12 VAL cc_start: 0.9530 (p) cc_final: 0.9328 (t) REVERT: S 116 CYS cc_start: 0.5734 (m) cc_final: 0.5463 (m) REVERT: S 125 ILE cc_start: 0.9597 (tt) cc_final: 0.9129 (tt) REVERT: S 183 CYS cc_start: 0.8656 (m) cc_final: 0.8389 (m) REVERT: S 306 LEU cc_start: 0.9229 (tp) cc_final: 0.8958 (tp) REVERT: S 335 PHE cc_start: 0.8440 (t80) cc_final: 0.8189 (t80) REVERT: S 399 MET cc_start: 0.7896 (tmm) cc_final: 0.7443 (tmm) REVERT: S 419 ASP cc_start: 0.7726 (m-30) cc_final: 0.7383 (m-30) REVERT: T 51 HIS cc_start: 0.7545 (t-90) cc_final: 0.6999 (t-90) REVERT: T 59 GLN cc_start: 0.8070 (tt0) cc_final: 0.7172 (tt0) REVERT: T 68 MET cc_start: 0.8598 (tpt) cc_final: 0.8369 (ttt) REVERT: U 3 GLN cc_start: 0.7640 (pm20) cc_final: 0.7287 (pm20) REVERT: U 29 PHE cc_start: 0.6252 (t80) cc_final: 0.5729 (t80) REVERT: U 36 TRP cc_start: 0.6990 (m100) cc_final: 0.6167 (m100) REVERT: U 43 GLN cc_start: 0.7417 (mm-40) cc_final: 0.7046 (mm-40) REVERT: U 81 MET cc_start: 0.7562 (ttt) cc_final: 0.5069 (ttt) REVERT: U 111 TYR cc_start: 0.7819 (m-80) cc_final: 0.7539 (m-80) REVERT: V 3 VAL cc_start: 0.6777 (p) cc_final: 0.6145 (m) REVERT: V 32 ASN cc_start: 0.8143 (m-40) cc_final: 0.7732 (m-40) outliers start: 0 outliers final: 0 residues processed: 1146 average time/residue: 0.1829 time to fit residues: 339.9961 Evaluate side-chains 848 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 848 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 5.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 HIS C 209 GLN ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 467 ASN E 27 HIS E 201 ASN ** E 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN O 192 ASN ** O 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 269 GLN P 51 HIS ** P 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 209 GLN ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 467 ASN S 27 HIS S 201 ASN ** S 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 38 GLN ** V 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.133674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.115507 restraints weight = 51094.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.118226 restraints weight = 28224.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.120048 restraints weight = 18127.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.121267 restraints weight = 13049.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.122049 restraints weight = 10284.451| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30656 Z= 0.181 Angle : 0.726 11.963 41636 Z= 0.369 Chirality : 0.046 0.205 4862 Planarity : 0.004 0.049 5182 Dihedral : 11.108 89.795 4716 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.25 % Allowed : 6.50 % Favored : 93.25 % 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: -1.59 (0.13), residues: 3838 helix: 0.85 (0.17), residues: 898 sheet: -1.12 (0.17), residues: 958 loop : -1.97 (0.13), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 284 TYR 0.021 0.002 TYR T 52 PHE 0.018 0.002 PHE F 42 TRP 0.029 0.002 TRP S 451 HIS 0.006 0.001 HIS U 65 Details of bonding type rmsd covalent geometry : bond 0.00410 (30596) covalent geometry : angle 0.71519 (41484) SS BOND : bond 0.00566 ( 28) SS BOND : angle 1.78091 ( 56) hydrogen bonds : bond 0.04957 ( 1098) hydrogen bonds : angle 6.63066 ( 3024) link_BETA1-4 : bond 0.00605 ( 20) link_BETA1-4 : angle 2.29502 ( 60) link_NAG-ASN : bond 0.00295 ( 12) link_NAG-ASN : angle 2.60824 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1053 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 1045 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO D 72 " (corrupted residue). Skipping it. Corrupt residue: chain: D residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO R 72 " (corrupted residue). Skipping it. Corrupt residue: chain: R residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8375 (mmm) cc_final: 0.7804 (mmm) REVERT: A 42 ASP cc_start: 0.8159 (t0) cc_final: 0.7901 (t0) REVERT: A 49 GLU cc_start: 0.8310 (mp0) cc_final: 0.7856 (mp0) REVERT: A 69 THR cc_start: 0.9220 (p) cc_final: 0.8526 (p) REVERT: A 71 ASP cc_start: 0.8185 (p0) cc_final: 0.7816 (t70) REVERT: A 76 THR cc_start: 0.7977 (p) cc_final: 0.7749 (p) REVERT: A 182 GLU cc_start: 0.7057 (mm-30) cc_final: 0.6460 (tp30) REVERT: A 195 ILE cc_start: 0.8994 (mt) cc_final: 0.8113 (tt) REVERT: A 453 MET cc_start: 0.8533 (tpp) cc_final: 0.8253 (tpp) REVERT: A 486 TYR cc_start: 0.8353 (t80) cc_final: 0.8077 (t80) REVERT: A 487 LEU cc_start: 0.8686 (tt) cc_final: 0.8388 (tp) REVERT: A 492 GLN cc_start: 0.8398 (mt0) cc_final: 0.7771 (tm-30) REVERT: C 1 MET cc_start: 0.8781 (mmp) cc_final: 0.7881 (mmm) REVERT: C 47 LYS cc_start: 0.8600 (mttp) cc_final: 0.8185 (pttt) REVERT: C 71 ASP cc_start: 0.8875 (t70) cc_final: 0.8627 (t0) REVERT: C 148 GLN cc_start: 0.8784 (tt0) cc_final: 0.8340 (tm-30) REVERT: C 186 ARG cc_start: 0.8848 (mmm160) cc_final: 0.8310 (mmt180) REVERT: C 199 MET cc_start: 0.9123 (ptm) cc_final: 0.8858 (ptm) REVERT: C 204 TRP cc_start: 0.9483 (m-90) cc_final: 0.8588 (m-90) REVERT: C 286 LYS cc_start: 0.8272 (tttt) cc_final: 0.7791 (mtpp) REVERT: C 389 TRP cc_start: 0.7983 (t60) cc_final: 0.7648 (t-100) REVERT: C 453 MET cc_start: 0.9022 (mmp) cc_final: 0.8760 (tpp) REVERT: D 38 ARG cc_start: 0.8255 (ttp-170) cc_final: 0.8049 (ttp-170) REVERT: D 68 MET cc_start: 0.8676 (mmm) cc_final: 0.7504 (tmm) REVERT: E 132 TYR cc_start: 0.8614 (t80) cc_final: 0.8184 (t80) REVERT: E 239 LYS cc_start: 0.7942 (ttmt) cc_final: 0.7634 (ttpt) REVERT: E 247 GLU cc_start: 0.7569 (pm20) cc_final: 0.7306 (pm20) REVERT: E 399 MET cc_start: 0.7895 (tmm) cc_final: 0.7437 (tmm) REVERT: E 419 ASP cc_start: 0.7382 (m-30) cc_final: 0.7154 (m-30) REVERT: E 455 ILE cc_start: 0.9246 (tp) cc_final: 0.8998 (tp) REVERT: F 51 HIS cc_start: 0.7845 (t-90) cc_final: 0.7551 (t-90) REVERT: H 3 GLN cc_start: 0.7638 (pm20) cc_final: 0.7062 (pm20) REVERT: H 21 SER cc_start: 0.8518 (p) cc_final: 0.8288 (p) REVERT: H 27 TYR cc_start: 0.7980 (p90) cc_final: 0.7438 (p90) REVERT: H 29 PHE cc_start: 0.6379 (t80) cc_final: 0.5809 (t80) REVERT: H 43 GLN cc_start: 0.7463 (mm-40) cc_final: 0.7252 (mm-40) REVERT: H 111 TYR cc_start: 0.7715 (m-80) cc_final: 0.7406 (m-80) REVERT: L 3 VAL cc_start: 0.6853 (p) cc_final: 0.6122 (m) REVERT: L 96 LEU cc_start: 0.8530 (mp) cc_final: 0.8267 (mt) REVERT: O 1 MET cc_start: 0.8382 (mmm) cc_final: 0.7824 (mmm) REVERT: O 42 ASP cc_start: 0.8168 (t0) cc_final: 0.7911 (t0) REVERT: O 49 GLU cc_start: 0.8340 (mp0) cc_final: 0.7876 (mp0) REVERT: O 69 THR cc_start: 0.9210 (p) cc_final: 0.8519 (p) REVERT: O 71 ASP cc_start: 0.8192 (p0) cc_final: 0.7802 (t70) REVERT: O 76 THR cc_start: 0.8008 (p) cc_final: 0.7768 (p) REVERT: O 182 GLU cc_start: 0.7056 (mm-30) cc_final: 0.6437 (tp30) REVERT: O 190 ASP cc_start: 0.8526 (t0) cc_final: 0.7846 (t0) REVERT: O 195 ILE cc_start: 0.8981 (mt) cc_final: 0.8281 (mp) REVERT: O 453 MET cc_start: 0.8535 (tpp) cc_final: 0.8242 (tpp) REVERT: O 486 TYR cc_start: 0.8340 (t80) cc_final: 0.8066 (t80) REVERT: O 487 LEU cc_start: 0.8680 (tt) cc_final: 0.8379 (tp) REVERT: O 492 GLN cc_start: 0.8396 (mt0) cc_final: 0.7761 (tm-30) REVERT: Q 1 MET cc_start: 0.8783 (mmp) cc_final: 0.7900 (mmm) REVERT: Q 47 LYS cc_start: 0.8603 (mttp) cc_final: 0.8187 (pttt) REVERT: Q 71 ASP cc_start: 0.8917 (t70) cc_final: 0.8659 (t0) REVERT: Q 148 GLN cc_start: 0.8777 (tt0) cc_final: 0.8336 (tm-30) REVERT: Q 186 ARG cc_start: 0.8843 (mmm160) cc_final: 0.8582 (mmt180) REVERT: Q 199 MET cc_start: 0.9138 (ptm) cc_final: 0.8867 (ptm) REVERT: Q 204 TRP cc_start: 0.9477 (m-90) cc_final: 0.8591 (m-90) REVERT: Q 286 LYS cc_start: 0.8273 (tttt) cc_final: 0.7789 (mtpp) REVERT: Q 389 TRP cc_start: 0.7984 (t60) cc_final: 0.7640 (t-100) REVERT: Q 453 MET cc_start: 0.9013 (mmp) cc_final: 0.8756 (tpp) REVERT: Q 463 TRP cc_start: 0.8220 (t-100) cc_final: 0.8006 (t-100) REVERT: R 38 ARG cc_start: 0.8248 (ttp-170) cc_final: 0.8040 (ttp-170) REVERT: R 68 MET cc_start: 0.8690 (mmm) cc_final: 0.7511 (tmm) REVERT: S 132 TYR cc_start: 0.8608 (t80) cc_final: 0.8182 (t80) REVERT: S 239 LYS cc_start: 0.7935 (ttmt) cc_final: 0.7618 (ttpt) REVERT: S 247 GLU cc_start: 0.7574 (pm20) cc_final: 0.7300 (pm20) REVERT: S 399 MET cc_start: 0.7900 (tmm) cc_final: 0.7434 (tmm) REVERT: S 419 ASP cc_start: 0.7408 (m-30) cc_final: 0.7167 (m-30) REVERT: S 455 ILE cc_start: 0.9239 (tp) cc_final: 0.8993 (tp) REVERT: T 51 HIS cc_start: 0.7854 (t-90) cc_final: 0.7553 (t-90) REVERT: U 3 GLN cc_start: 0.7637 (pm20) cc_final: 0.7072 (pm20) REVERT: U 21 SER cc_start: 0.8510 (p) cc_final: 0.8280 (p) REVERT: U 27 TYR cc_start: 0.7968 (p90) cc_final: 0.7422 (p90) REVERT: U 29 PHE cc_start: 0.6394 (t80) cc_final: 0.5810 (t80) REVERT: U 43 GLN cc_start: 0.7459 (mm-40) cc_final: 0.7249 (mm-40) REVERT: U 98 ARG cc_start: 0.6939 (ttp-170) cc_final: 0.6737 (ttp-110) REVERT: U 111 TYR cc_start: 0.7750 (m-80) cc_final: 0.7454 (m-80) REVERT: V 3 VAL cc_start: 0.6839 (p) cc_final: 0.6129 (m) REVERT: V 91 THR cc_start: 0.8778 (t) cc_final: 0.8492 (m) REVERT: V 96 LEU cc_start: 0.8542 (mp) cc_final: 0.8270 (mt) outliers start: 8 outliers final: 2 residues processed: 1047 average time/residue: 0.1694 time to fit residues: 287.1072 Evaluate side-chains 838 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 836 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 233 optimal weight: 20.0000 chunk 293 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 171 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 209 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 140 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 ASN ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 GLN ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 467 ASN E 27 HIS E 428 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 ASN ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** O 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 192 ASN ** O 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 467 ASN R 17 GLN S 27 HIS ** S 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 428 ASN ** T 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 ASN ** V 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 38 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.133272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.115327 restraints weight = 51883.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.117997 restraints weight = 28878.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.119754 restraints weight = 18691.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.120934 restraints weight = 13587.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.121703 restraints weight = 10793.008| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30656 Z= 0.186 Angle : 0.707 9.727 41636 Z= 0.359 Chirality : 0.046 0.267 4862 Planarity : 0.004 0.081 5182 Dihedral : 9.536 82.826 4716 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.12 % Allowed : 5.53 % Favored : 94.34 % 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: -1.60 (0.13), residues: 3838 helix: 0.79 (0.17), residues: 910 sheet: -1.08 (0.17), residues: 964 loop : -1.99 (0.13), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Q 99 TYR 0.016 0.002 TYR P 52 PHE 0.016 0.002 PHE Q 335 TRP 0.025 0.002 TRP E 451 HIS 0.007 0.001 HIS D 39 Details of bonding type rmsd covalent geometry : bond 0.00424 (30596) covalent geometry : angle 0.69680 (41484) SS BOND : bond 0.00477 ( 28) SS BOND : angle 1.80303 ( 56) hydrogen bonds : bond 0.04509 ( 1098) hydrogen bonds : angle 6.24419 ( 3024) link_BETA1-4 : bond 0.00653 ( 20) link_BETA1-4 : angle 2.12009 ( 60) link_NAG-ASN : bond 0.00316 ( 12) link_NAG-ASN : angle 2.49117 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1019 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1015 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO D 72 " (corrupted residue). Skipping it. Corrupt residue: chain: D residue: PRO 72 >>> skipping revert: symmetry clash TARDY: cannot create tardy model for: "PRO F 72 " (corrupted residue). Skipping it. Corrupt residue: chain: F residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO R 72 " (corrupted residue). Skipping it. Corrupt residue: chain: R residue: PRO 72 >>> skipping revert: symmetry clash TARDY: cannot create tardy model for: "PRO T 72 " (corrupted residue). Skipping it. Corrupt residue: chain: T residue: PRO 72 >>> skipping REVERT: A 1 MET cc_start: 0.8373 (mmm) cc_final: 0.7430 (mmm) REVERT: A 42 ASP cc_start: 0.8116 (t0) cc_final: 0.7772 (t0) REVERT: A 49 GLU cc_start: 0.8375 (mp0) cc_final: 0.8098 (mp0) REVERT: A 195 ILE cc_start: 0.8917 (mt) cc_final: 0.8176 (tt) REVERT: A 283 CYS cc_start: 0.8643 (t) cc_final: 0.8268 (t) REVERT: A 453 MET cc_start: 0.8441 (tpp) cc_final: 0.7990 (tpp) REVERT: A 486 TYR cc_start: 0.8335 (t80) cc_final: 0.8092 (t80) REVERT: A 487 LEU cc_start: 0.8761 (tt) cc_final: 0.8524 (tp) REVERT: A 492 GLN cc_start: 0.8411 (mt0) cc_final: 0.7765 (tm-30) REVERT: B 45 LEU cc_start: 0.9303 (tp) cc_final: 0.9094 (tp) REVERT: B 60 LYS cc_start: 0.8413 (mttm) cc_final: 0.8095 (mmtm) REVERT: C 1 MET cc_start: 0.8850 (mmp) cc_final: 0.7937 (mmm) REVERT: C 34 MET cc_start: 0.8593 (ptp) cc_final: 0.8129 (ptp) REVERT: C 47 LYS cc_start: 0.8673 (mttp) cc_final: 0.8262 (pttt) REVERT: C 71 ASP cc_start: 0.8792 (t70) cc_final: 0.8578 (t0) REVERT: C 148 GLN cc_start: 0.8794 (tt0) cc_final: 0.8341 (tm-30) REVERT: C 193 GLU cc_start: 0.6342 (pm20) cc_final: 0.5297 (pm20) REVERT: C 204 TRP cc_start: 0.9443 (m-90) cc_final: 0.8692 (m-90) REVERT: C 390 TYR cc_start: 0.8511 (t80) cc_final: 0.8251 (t80) REVERT: D 68 MET cc_start: 0.8484 (mmm) cc_final: 0.7548 (tmm) REVERT: E 286 LYS cc_start: 0.9067 (mttt) cc_final: 0.8856 (mttm) REVERT: E 399 MET cc_start: 0.7850 (tmm) cc_final: 0.7398 (tmm) REVERT: E 419 ASP cc_start: 0.7407 (m-30) cc_final: 0.7176 (m-30) REVERT: E 455 ILE cc_start: 0.9388 (tp) cc_final: 0.9040 (tp) REVERT: F 43 THR cc_start: 0.8999 (m) cc_final: 0.8778 (m) REVERT: F 51 HIS cc_start: 0.7854 (t-90) cc_final: 0.7599 (t-90) REVERT: H 3 GLN cc_start: 0.7617 (pm20) cc_final: 0.7098 (pm20) REVERT: H 21 SER cc_start: 0.8460 (p) cc_final: 0.8220 (p) REVERT: H 27 TYR cc_start: 0.8167 (p90) cc_final: 0.7563 (p90) REVERT: H 29 PHE cc_start: 0.6643 (t80) cc_final: 0.6163 (t80) REVERT: H 36 TRP cc_start: 0.7524 (m100) cc_final: 0.6859 (m100) REVERT: H 61 HIS cc_start: 0.8927 (t-90) cc_final: 0.8523 (t-90) REVERT: H 111 TYR cc_start: 0.7898 (m-80) cc_final: 0.7624 (m-80) REVERT: L 3 VAL cc_start: 0.6849 (p) cc_final: 0.6080 (m) REVERT: O 1 MET cc_start: 0.8380 (mmm) cc_final: 0.7416 (mmm) REVERT: O 42 ASP cc_start: 0.8121 (t0) cc_final: 0.7759 (t0) REVERT: O 49 GLU cc_start: 0.8378 (mp0) cc_final: 0.8107 (mp0) REVERT: O 69 THR cc_start: 0.9258 (p) cc_final: 0.8561 (p) REVERT: O 76 THR cc_start: 0.8584 (p) cc_final: 0.8379 (p) REVERT: O 190 ASP cc_start: 0.8457 (t0) cc_final: 0.8001 (t0) REVERT: O 195 ILE cc_start: 0.8913 (mt) cc_final: 0.8358 (mp) REVERT: O 283 CYS cc_start: 0.8373 (t) cc_final: 0.7970 (t) REVERT: O 453 MET cc_start: 0.8441 (tpp) cc_final: 0.8006 (tpp) REVERT: O 486 TYR cc_start: 0.8328 (t80) cc_final: 0.8089 (t80) REVERT: O 487 LEU cc_start: 0.8747 (tt) cc_final: 0.8516 (tp) REVERT: O 492 GLN cc_start: 0.8414 (mt0) cc_final: 0.7775 (tm-30) REVERT: P 10 MET cc_start: 0.7526 (tpp) cc_final: 0.7042 (mmm) REVERT: P 60 LYS cc_start: 0.8378 (mttm) cc_final: 0.8090 (mmtm) REVERT: Q 1 MET cc_start: 0.8851 (mmp) cc_final: 0.7949 (mmm) REVERT: Q 34 MET cc_start: 0.8603 (ptp) cc_final: 0.8125 (ptp) REVERT: Q 47 LYS cc_start: 0.8676 (mttp) cc_final: 0.8262 (pttt) REVERT: Q 71 ASP cc_start: 0.8940 (t70) cc_final: 0.8644 (t0) REVERT: Q 148 GLN cc_start: 0.8782 (tt0) cc_final: 0.8329 (tm-30) REVERT: Q 193 GLU cc_start: 0.6362 (pm20) cc_final: 0.5310 (pm20) REVERT: Q 204 TRP cc_start: 0.9439 (m-90) cc_final: 0.8697 (m-90) REVERT: Q 287 MET cc_start: 0.8371 (mtp) cc_final: 0.7563 (ttp) REVERT: Q 390 TYR cc_start: 0.8505 (t80) cc_final: 0.8244 (t80) REVERT: Q 463 TRP cc_start: 0.8243 (t-100) cc_final: 0.8025 (t-100) REVERT: R 68 MET cc_start: 0.8497 (mmm) cc_final: 0.7552 (tmm) REVERT: S 186 ARG cc_start: 0.8225 (mmt-90) cc_final: 0.8024 (mmm160) REVERT: S 286 LYS cc_start: 0.9066 (mttt) cc_final: 0.8859 (mttm) REVERT: S 399 MET cc_start: 0.7854 (tmm) cc_final: 0.7395 (tmm) REVERT: S 419 ASP cc_start: 0.7435 (m-30) cc_final: 0.7216 (m-30) REVERT: S 455 ILE cc_start: 0.9384 (tp) cc_final: 0.9039 (tp) REVERT: T 43 THR cc_start: 0.8984 (m) cc_final: 0.8768 (m) REVERT: T 51 HIS cc_start: 0.7855 (t-90) cc_final: 0.7592 (t-90) REVERT: U 3 GLN cc_start: 0.7623 (pm20) cc_final: 0.7103 (pm20) REVERT: U 21 SER cc_start: 0.8448 (p) cc_final: 0.8208 (p) REVERT: U 27 TYR cc_start: 0.8015 (p90) cc_final: 0.7483 (p90) REVERT: U 29 PHE cc_start: 0.6651 (t80) cc_final: 0.6171 (t80) REVERT: U 36 TRP cc_start: 0.7514 (m100) cc_final: 0.6842 (m100) REVERT: U 54 ILE cc_start: 0.8464 (tp) cc_final: 0.8263 (tp) REVERT: U 61 HIS cc_start: 0.8921 (t-90) cc_final: 0.8515 (t-90) REVERT: U 111 TYR cc_start: 0.8030 (m-80) cc_final: 0.7725 (m-80) REVERT: V 3 VAL cc_start: 0.6848 (p) cc_final: 0.6078 (m) outliers start: 4 outliers final: 0 residues processed: 1017 average time/residue: 0.1691 time to fit residues: 281.3854 Evaluate side-chains 823 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 823 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 291 optimal weight: 9.9990 chunk 142 optimal weight: 7.9990 chunk 189 optimal weight: 20.0000 chunk 141 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 chunk 274 optimal weight: 9.9990 chunk 353 optimal weight: 6.9990 chunk 184 optimal weight: 2.9990 chunk 96 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 239 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN A 230 ASN B 51 HIS C 209 GLN C 280 HIS ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 467 ASN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 ASN ** E 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 GLN F 59 GLN L 16 GLN L 38 GLN O 192 ASN O 207 HIS O 230 ASN P 51 HIS Q 209 GLN Q 280 HIS ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 467 ASN ** S 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 192 ASN ** S 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 17 GLN T 59 GLN V 16 GLN V 38 GLN V 52 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.125366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.106849 restraints weight = 52796.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.109486 restraints weight = 29725.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.111246 restraints weight = 19443.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.112451 restraints weight = 14223.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.113225 restraints weight = 11317.423| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 30656 Z= 0.291 Angle : 0.792 11.380 41636 Z= 0.402 Chirality : 0.049 0.205 4862 Planarity : 0.005 0.073 5182 Dihedral : 8.422 72.349 4716 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 0.12 % Allowed : 6.59 % Favored : 93.28 % 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: -1.77 (0.13), residues: 3838 helix: 0.57 (0.17), residues: 910 sheet: -1.14 (0.17), residues: 992 loop : -2.09 (0.13), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 57 TYR 0.019 0.002 TYR E 297 PHE 0.020 0.002 PHE E 11 TRP 0.027 0.002 TRP E 451 HIS 0.018 0.002 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00667 (30596) covalent geometry : angle 0.78402 (41484) SS BOND : bond 0.00674 ( 28) SS BOND : angle 1.81220 ( 56) hydrogen bonds : bond 0.04771 ( 1098) hydrogen bonds : angle 6.21674 ( 3024) link_BETA1-4 : bond 0.00529 ( 20) link_BETA1-4 : angle 1.98897 ( 60) link_NAG-ASN : bond 0.00595 ( 12) link_NAG-ASN : angle 2.45555 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 969 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 965 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO D 72 " (corrupted residue). Skipping it. Corrupt residue: chain: D 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 R 72 " (corrupted residue). Skipping it. Corrupt residue: chain: R residue: PRO 72 >>> skipping revert: symmetry clash REVERT: A 1 MET cc_start: 0.8504 (mmm) cc_final: 0.8280 (mmm) REVERT: A 20 TRP cc_start: 0.8755 (p-90) cc_final: 0.8462 (p-90) REVERT: A 42 ASP cc_start: 0.7992 (t0) cc_final: 0.7697 (t0) REVERT: A 49 GLU cc_start: 0.8439 (mp0) cc_final: 0.8092 (mp0) REVERT: A 69 THR cc_start: 0.9251 (p) cc_final: 0.8731 (p) REVERT: A 176 TYR cc_start: 0.8337 (m-10) cc_final: 0.8005 (m-10) REVERT: A 190 ASP cc_start: 0.8604 (t0) cc_final: 0.8034 (t0) REVERT: A 195 ILE cc_start: 0.8962 (mt) cc_final: 0.8279 (mt) REVERT: A 210 TRP cc_start: 0.9175 (t60) cc_final: 0.8842 (t60) REVERT: A 262 LEU cc_start: 0.9310 (pt) cc_final: 0.8966 (pp) REVERT: A 283 CYS cc_start: 0.8849 (t) cc_final: 0.8616 (t) REVERT: A 453 MET cc_start: 0.8617 (tpp) cc_final: 0.8236 (tpp) REVERT: A 486 TYR cc_start: 0.8434 (t80) cc_final: 0.8172 (t80) REVERT: A 492 GLN cc_start: 0.8486 (mt0) cc_final: 0.7782 (tm-30) REVERT: B 60 LYS cc_start: 0.8543 (mttm) cc_final: 0.8084 (mmtm) REVERT: C 1 MET cc_start: 0.8543 (mmp) cc_final: 0.7502 (mmm) REVERT: C 193 GLU cc_start: 0.6302 (pm20) cc_final: 0.5443 (pm20) REVERT: C 204 TRP cc_start: 0.9403 (m-90) cc_final: 0.8661 (m-90) REVERT: C 233 GLU cc_start: 0.7641 (tp30) cc_final: 0.7436 (tm-30) REVERT: C 324 TYR cc_start: 0.8804 (t80) cc_final: 0.7844 (t80) REVERT: C 433 MET cc_start: 0.8068 (tpp) cc_final: 0.7736 (tpp) REVERT: E 26 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7870 (mt-10) REVERT: E 61 ILE cc_start: 0.9262 (tp) cc_final: 0.9043 (tp) REVERT: E 247 GLU cc_start: 0.7446 (pm20) cc_final: 0.7145 (pm20) REVERT: E 286 LYS cc_start: 0.9252 (mttt) cc_final: 0.9018 (mttm) REVERT: E 399 MET cc_start: 0.7981 (tmm) cc_final: 0.7440 (tmm) REVERT: F 43 THR cc_start: 0.9071 (m) cc_final: 0.8815 (m) REVERT: F 47 LEU cc_start: 0.8312 (mt) cc_final: 0.8099 (mt) REVERT: H 3 GLN cc_start: 0.7577 (pm20) cc_final: 0.7220 (pm20) REVERT: H 12 LYS cc_start: 0.6875 (mmtm) cc_final: 0.6497 (mmtt) REVERT: H 27 TYR cc_start: 0.8051 (p90) cc_final: 0.7454 (p90) REVERT: H 29 PHE cc_start: 0.6634 (t80) cc_final: 0.6102 (t80) REVERT: H 36 TRP cc_start: 0.7587 (m100) cc_final: 0.6872 (m100) REVERT: H 46 GLU cc_start: 0.8970 (pm20) cc_final: 0.8432 (pm20) REVERT: H 111 TYR cc_start: 0.7799 (m-80) cc_final: 0.7597 (m-80) REVERT: L 3 VAL cc_start: 0.6945 (p) cc_final: 0.6155 (m) REVERT: L 28 ASN cc_start: 0.8465 (p0) cc_final: 0.7774 (p0) REVERT: L 87 TYR cc_start: 0.7939 (m-80) cc_final: 0.7351 (m-10) REVERT: O 42 ASP cc_start: 0.7984 (t0) cc_final: 0.7685 (t0) REVERT: O 49 GLU cc_start: 0.8545 (mp0) cc_final: 0.7698 (mp0) REVERT: O 69 THR cc_start: 0.9243 (p) cc_final: 0.8741 (p) REVERT: O 76 THR cc_start: 0.8195 (p) cc_final: 0.7983 (p) REVERT: O 176 TYR cc_start: 0.8341 (m-10) cc_final: 0.8007 (m-10) REVERT: O 190 ASP cc_start: 0.8611 (t0) cc_final: 0.8090 (t0) REVERT: O 195 ILE cc_start: 0.9010 (mt) cc_final: 0.8371 (mp) REVERT: O 210 TRP cc_start: 0.9192 (t60) cc_final: 0.8825 (t60) REVERT: O 262 LEU cc_start: 0.9280 (pt) cc_final: 0.8923 (pp) REVERT: O 453 MET cc_start: 0.8625 (tpp) cc_final: 0.8227 (tpp) REVERT: O 486 TYR cc_start: 0.8422 (t80) cc_final: 0.8164 (t80) REVERT: O 492 GLN cc_start: 0.8511 (mt0) cc_final: 0.8296 (mt0) REVERT: P 60 LYS cc_start: 0.8570 (mttm) cc_final: 0.8229 (mmtm) REVERT: Q 1 MET cc_start: 0.8547 (mmp) cc_final: 0.7508 (mmm) REVERT: Q 71 ASP cc_start: 0.8991 (t70) cc_final: 0.8709 (t0) REVERT: Q 193 GLU cc_start: 0.6348 (pm20) cc_final: 0.5477 (pm20) REVERT: Q 204 TRP cc_start: 0.9401 (m-90) cc_final: 0.8664 (m-90) REVERT: Q 324 TYR cc_start: 0.8787 (t80) cc_final: 0.7836 (t80) REVERT: Q 433 MET cc_start: 0.8066 (tpp) cc_final: 0.7723 (tpp) REVERT: S 26 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7887 (mt-10) REVERT: S 61 ILE cc_start: 0.9267 (tp) cc_final: 0.9038 (tp) REVERT: S 247 GLU cc_start: 0.7464 (pm20) cc_final: 0.7138 (pm20) REVERT: S 286 LYS cc_start: 0.9249 (mttt) cc_final: 0.9018 (mttm) REVERT: S 399 MET cc_start: 0.7973 (tmm) cc_final: 0.7427 (tmm) REVERT: T 28 GLN cc_start: 0.7874 (mm-40) cc_final: 0.7671 (mm-40) REVERT: T 43 THR cc_start: 0.9061 (m) cc_final: 0.8783 (m) REVERT: T 47 LEU cc_start: 0.8311 (mt) cc_final: 0.8098 (mt) REVERT: U 3 GLN cc_start: 0.7595 (pm20) cc_final: 0.7227 (pm20) REVERT: U 12 LYS cc_start: 0.6869 (mmtm) cc_final: 0.6494 (mmtt) REVERT: U 27 TYR cc_start: 0.8047 (p90) cc_final: 0.7404 (p90) REVERT: U 29 PHE cc_start: 0.6652 (t80) cc_final: 0.6121 (t80) REVERT: U 36 TRP cc_start: 0.7577 (m100) cc_final: 0.6862 (m100) REVERT: U 46 GLU cc_start: 0.8964 (pm20) cc_final: 0.8425 (pm20) REVERT: U 111 TYR cc_start: 0.7831 (m-80) cc_final: 0.7585 (m-80) REVERT: V 3 VAL cc_start: 0.6955 (p) cc_final: 0.6173 (m) REVERT: V 28 ASN cc_start: 0.8509 (p0) cc_final: 0.8171 (p0) REVERT: V 87 TYR cc_start: 0.7943 (m-80) cc_final: 0.7343 (m-10) outliers start: 4 outliers final: 2 residues processed: 966 average time/residue: 0.1849 time to fit residues: 290.2098 Evaluate side-chains 806 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 804 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 127 optimal weight: 0.0370 chunk 135 optimal weight: 8.9990 chunk 157 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 265 optimal weight: 6.9990 chunk 163 optimal weight: 5.9990 chunk 184 optimal weight: 8.9990 chunk 333 optimal weight: 6.9990 chunk 347 optimal weight: 5.9990 chunk 275 optimal weight: 5.9990 overall best weight: 4.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN A 207 HIS B 59 GLN C 77 GLN C 353 ASN C 467 ASN D 17 GLN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN L 16 GLN L 38 GLN O 192 ASN P 59 GLN Q 77 GLN Q 353 ASN Q 467 ASN R 17 GLN ** S 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 59 GLN V 16 GLN V 38 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.130914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.112743 restraints weight = 51781.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.115444 restraints weight = 28881.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.117253 restraints weight = 18738.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.118439 restraints weight = 13579.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.119243 restraints weight = 10788.645| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 30656 Z= 0.184 Angle : 0.710 10.780 41636 Z= 0.359 Chirality : 0.047 0.244 4862 Planarity : 0.004 0.058 5182 Dihedral : 7.445 63.080 4716 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.12 % Allowed : 3.00 % Favored : 96.88 % 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: 3838 helix: 0.69 (0.17), residues: 908 sheet: -1.14 (0.17), residues: 982 loop : -2.02 (0.13), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 85 TYR 0.021 0.002 TYR B 52 PHE 0.021 0.002 PHE T 42 TRP 0.024 0.002 TRP S 451 HIS 0.014 0.001 HIS O 207 Details of bonding type rmsd covalent geometry : bond 0.00429 (30596) covalent geometry : angle 0.70187 (41484) SS BOND : bond 0.00464 ( 28) SS BOND : angle 1.77260 ( 56) hydrogen bonds : bond 0.04244 ( 1098) hydrogen bonds : angle 5.96798 ( 3024) link_BETA1-4 : bond 0.00465 ( 20) link_BETA1-4 : angle 1.82449 ( 60) link_NAG-ASN : bond 0.00320 ( 12) link_NAG-ASN : angle 2.24164 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1017 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1013 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO D 72 " (corrupted residue). Skipping it. Corrupt residue: chain: D residue: PRO 72 >>> skipping revert: symmetry clash TARDY: cannot create tardy model for: "PRO F 72 " (corrupted residue). Skipping it. Corrupt residue: chain: F residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO R 72 " (corrupted residue). Skipping it. Corrupt residue: chain: R residue: PRO 72 >>> skipping revert: symmetry clash TARDY: cannot create tardy model for: "PRO T 72 " (corrupted residue). Skipping it. Corrupt residue: chain: T residue: PRO 72 >>> skipping revert: symmetry clash REVERT: A 42 ASP cc_start: 0.7937 (t0) cc_final: 0.7603 (t0) REVERT: A 49 GLU cc_start: 0.8424 (mp0) cc_final: 0.8078 (mp0) REVERT: A 69 THR cc_start: 0.9216 (p) cc_final: 0.8558 (p) REVERT: A 176 TYR cc_start: 0.8366 (m-10) cc_final: 0.8155 (m-10) REVERT: A 190 ASP cc_start: 0.8480 (t0) cc_final: 0.8151 (t0) REVERT: A 209 GLN cc_start: 0.7337 (tm-30) cc_final: 0.6782 (tm-30) REVERT: A 262 LEU cc_start: 0.9300 (pt) cc_final: 0.9065 (pp) REVERT: A 353 ASN cc_start: 0.8478 (t0) cc_final: 0.7735 (t0) REVERT: A 408 ARG cc_start: 0.8029 (ttm170) cc_final: 0.7668 (tpp80) REVERT: A 453 MET cc_start: 0.8544 (tpp) cc_final: 0.8137 (tpp) REVERT: A 486 TYR cc_start: 0.8325 (t80) cc_final: 0.8093 (t80) REVERT: A 492 GLN cc_start: 0.8480 (mt0) cc_final: 0.7804 (tm-30) REVERT: B 60 LYS cc_start: 0.8164 (mttm) cc_final: 0.7928 (mttt) REVERT: C 1 MET cc_start: 0.8489 (mmp) cc_final: 0.7829 (mmm) REVERT: C 204 TRP cc_start: 0.9341 (m-90) cc_final: 0.8699 (m-90) REVERT: C 286 LYS cc_start: 0.8299 (tttm) cc_final: 0.7857 (mtpp) REVERT: C 408 ARG cc_start: 0.8921 (tpp80) cc_final: 0.8666 (tpp80) REVERT: C 433 MET cc_start: 0.8022 (tpp) cc_final: 0.7657 (tpp) REVERT: D 30 GLU cc_start: 0.8186 (tp30) cc_final: 0.7792 (tp30) REVERT: D 68 MET cc_start: 0.8424 (mmm) cc_final: 0.7294 (tmm) REVERT: E 61 ILE cc_start: 0.9248 (tp) cc_final: 0.9032 (tp) REVERT: E 186 ARG cc_start: 0.8055 (mmm160) cc_final: 0.7622 (mmm-85) REVERT: E 399 MET cc_start: 0.7798 (tmm) cc_final: 0.7378 (tmm) REVERT: E 455 ILE cc_start: 0.9331 (tp) cc_final: 0.9053 (tp) REVERT: F 15 ARG cc_start: 0.7982 (mmt180) cc_final: 0.7772 (mmm-85) REVERT: H 3 GLN cc_start: 0.7482 (pm20) cc_final: 0.7147 (pm20) REVERT: H 21 SER cc_start: 0.8446 (p) cc_final: 0.8224 (p) REVERT: H 27 TYR cc_start: 0.8055 (p90) cc_final: 0.7655 (p90) REVERT: H 29 PHE cc_start: 0.6764 (t80) cc_final: 0.6231 (t80) REVERT: H 36 TRP cc_start: 0.7410 (m100) cc_final: 0.7025 (m100) REVERT: H 50 TRP cc_start: 0.8445 (m-10) cc_final: 0.8065 (m-10) REVERT: H 98 ARG cc_start: 0.6884 (ttp-170) cc_final: 0.6207 (ttp-110) REVERT: H 111 TYR cc_start: 0.7840 (m-80) cc_final: 0.7445 (m-80) REVERT: H 118 VAL cc_start: 0.8065 (m) cc_final: 0.7858 (p) REVERT: L 3 VAL cc_start: 0.6886 (p) cc_final: 0.6010 (m) REVERT: L 28 ASN cc_start: 0.8453 (p0) cc_final: 0.7894 (p0) REVERT: L 87 TYR cc_start: 0.7519 (m-80) cc_final: 0.7258 (m-10) REVERT: O 42 ASP cc_start: 0.7947 (t0) cc_final: 0.7619 (t0) REVERT: O 49 GLU cc_start: 0.8643 (mp0) cc_final: 0.8282 (mp0) REVERT: O 69 THR cc_start: 0.9199 (p) cc_final: 0.8584 (p) REVERT: O 176 TYR cc_start: 0.8361 (m-10) cc_final: 0.8152 (m-10) REVERT: O 190 ASP cc_start: 0.8395 (t0) cc_final: 0.7988 (t0) REVERT: O 209 GLN cc_start: 0.7280 (tm-30) cc_final: 0.6376 (tm-30) REVERT: O 210 TRP cc_start: 0.9063 (t60) cc_final: 0.8709 (t60) REVERT: O 262 LEU cc_start: 0.9283 (pt) cc_final: 0.9014 (pp) REVERT: O 283 CYS cc_start: 0.8774 (t) cc_final: 0.8562 (t) REVERT: O 353 ASN cc_start: 0.8493 (t0) cc_final: 0.7743 (t0) REVERT: O 408 ARG cc_start: 0.8011 (ttm170) cc_final: 0.7682 (tpp80) REVERT: O 453 MET cc_start: 0.8506 (tpp) cc_final: 0.8115 (tpp) REVERT: O 486 TYR cc_start: 0.8320 (t80) cc_final: 0.8099 (t80) REVERT: O 492 GLN cc_start: 0.8474 (mt0) cc_final: 0.7767 (tm-30) REVERT: P 60 LYS cc_start: 0.8150 (mttm) cc_final: 0.7917 (mttt) REVERT: Q 1 MET cc_start: 0.8477 (mmp) cc_final: 0.7848 (mmm) REVERT: Q 71 ASP cc_start: 0.8924 (t70) cc_final: 0.8649 (t0) REVERT: Q 204 TRP cc_start: 0.9332 (m-90) cc_final: 0.8700 (m-90) REVERT: Q 286 LYS cc_start: 0.8286 (tttm) cc_final: 0.7857 (mtpp) REVERT: Q 408 ARG cc_start: 0.8920 (tpp80) cc_final: 0.8667 (tpp80) REVERT: Q 433 MET cc_start: 0.7991 (tpp) cc_final: 0.7639 (tpp) REVERT: Q 463 TRP cc_start: 0.8229 (t-100) cc_final: 0.7995 (t-100) REVERT: R 30 GLU cc_start: 0.8193 (tp30) cc_final: 0.7804 (tp30) REVERT: R 68 MET cc_start: 0.8427 (mmm) cc_final: 0.7280 (tmm) REVERT: S 44 GLU cc_start: 0.8781 (tt0) cc_final: 0.8520 (tt0) REVERT: S 61 ILE cc_start: 0.9245 (tp) cc_final: 0.9026 (tp) REVERT: S 399 MET cc_start: 0.7801 (tmm) cc_final: 0.7368 (tmm) REVERT: S 455 ILE cc_start: 0.9337 (tp) cc_final: 0.9055 (tp) REVERT: T 15 ARG cc_start: 0.7986 (mmt180) cc_final: 0.7771 (mmm-85) REVERT: T 28 GLN cc_start: 0.7610 (mm-40) cc_final: 0.7404 (mm-40) REVERT: U 3 GLN cc_start: 0.7513 (pm20) cc_final: 0.7156 (pm20) REVERT: U 21 SER cc_start: 0.8427 (p) cc_final: 0.8209 (p) REVERT: U 27 TYR cc_start: 0.8018 (p90) cc_final: 0.7515 (p90) REVERT: U 29 PHE cc_start: 0.6758 (t80) cc_final: 0.6218 (t80) REVERT: U 36 TRP cc_start: 0.7399 (m100) cc_final: 0.7018 (m100) REVERT: U 50 TRP cc_start: 0.8437 (m-10) cc_final: 0.8062 (m-10) REVERT: U 111 TYR cc_start: 0.7796 (m-80) cc_final: 0.7444 (m-80) REVERT: U 118 VAL cc_start: 0.8056 (m) cc_final: 0.7853 (p) REVERT: V 3 VAL cc_start: 0.6942 (p) cc_final: 0.6118 (m) REVERT: V 28 ASN cc_start: 0.8528 (p0) cc_final: 0.8125 (p0) REVERT: V 87 TYR cc_start: 0.7518 (m-80) cc_final: 0.7277 (m-10) outliers start: 4 outliers final: 0 residues processed: 1014 average time/residue: 0.1911 time to fit residues: 313.8977 Evaluate side-chains 832 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 832 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 117 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 283 optimal weight: 8.9990 chunk 273 optimal weight: 10.0000 chunk 152 optimal weight: 10.0000 chunk 370 optimal weight: 5.9990 chunk 125 optimal weight: 8.9990 chunk 127 optimal weight: 8.9990 chunk 94 optimal weight: 20.0000 chunk 314 optimal weight: 8.9990 chunk 137 optimal weight: 7.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN B 51 HIS C 46 GLN C 149 HIS C 209 GLN ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 17 GLN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS E 428 ASN F 59 GLN L 16 GLN L 38 GLN L 52 ASN O 192 ASN P 51 HIS Q 209 GLN ** Q 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN ** S 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 428 ASN T 59 GLN V 16 GLN V 38 GLN V 52 ASN V 53 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.122886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.105229 restraints weight = 53258.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.107622 restraints weight = 30955.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.109227 restraints weight = 20718.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.110319 restraints weight = 15449.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.110956 restraints weight = 12444.071| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 30656 Z= 0.309 Angle : 0.808 10.416 41636 Z= 0.412 Chirality : 0.049 0.214 4862 Planarity : 0.005 0.067 5182 Dihedral : 7.316 53.085 4716 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 0.22 % Allowed : 3.84 % Favored : 95.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.13), residues: 3838 helix: 0.50 (0.17), residues: 908 sheet: -1.21 (0.17), residues: 980 loop : -2.13 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 2 TYR 0.019 0.002 TYR O 132 PHE 0.020 0.002 PHE S 11 TRP 0.029 0.002 TRP O 218 HIS 0.013 0.002 HIS C 149 Details of bonding type rmsd covalent geometry : bond 0.00714 (30596) covalent geometry : angle 0.80150 (41484) SS BOND : bond 0.00637 ( 28) SS BOND : angle 1.74699 ( 56) hydrogen bonds : bond 0.04711 ( 1098) hydrogen bonds : angle 6.11030 ( 3024) link_BETA1-4 : bond 0.00461 ( 20) link_BETA1-4 : angle 1.74235 ( 60) link_NAG-ASN : bond 0.00694 ( 12) link_NAG-ASN : angle 2.40488 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 980 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 973 time to evaluate : 1.227 Fit side-chains 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 D 72 " (corrupted residue). Skipping it. Corrupt residue: chain: D residue: PRO 72 >>> skipping revert: symmetry clash TARDY: cannot create tardy model for: "PRO F 72 " (corrupted residue). Skipping it. Corrupt residue: chain: F 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 R 72 " (corrupted residue). Skipping it. Corrupt residue: chain: R residue: PRO 72 >>> skipping revert: symmetry clash TARDY: cannot create tardy model for: "PRO T 72 " (corrupted residue). Skipping it. Corrupt residue: chain: T residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8399 (mmm) cc_final: 0.8045 (mmm) REVERT: A 42 ASP cc_start: 0.7661 (t0) cc_final: 0.7322 (t0) REVERT: A 49 GLU cc_start: 0.8700 (mp0) cc_final: 0.8379 (mp0) REVERT: A 69 THR cc_start: 0.9282 (p) cc_final: 0.8728 (p) REVERT: A 176 TYR cc_start: 0.8425 (m-10) cc_final: 0.8194 (m-10) REVERT: A 209 GLN cc_start: 0.7799 (tm-30) cc_final: 0.7119 (tm-30) REVERT: A 210 TRP cc_start: 0.9213 (t60) cc_final: 0.8828 (t60) REVERT: A 262 LEU cc_start: 0.9251 (pt) cc_final: 0.8992 (pp) REVERT: A 283 CYS cc_start: 0.8809 (t) cc_final: 0.8451 (t) REVERT: A 418 TRP cc_start: 0.8220 (t-100) cc_final: 0.7705 (t-100) REVERT: A 453 MET cc_start: 0.8655 (tpp) cc_final: 0.8332 (tpp) REVERT: A 486 TYR cc_start: 0.8411 (t80) cc_final: 0.8128 (t80) REVERT: A 492 GLN cc_start: 0.8551 (mt0) cc_final: 0.8306 (mt0) REVERT: B 60 LYS cc_start: 0.8293 (mttm) cc_final: 0.8021 (mmtm) REVERT: C 1 MET cc_start: 0.8253 (mmp) cc_final: 0.7141 (mmm) REVERT: C 46 GLN cc_start: 0.9197 (OUTLIER) cc_final: 0.8377 (pp30) REVERT: C 71 ASP cc_start: 0.8846 (t70) cc_final: 0.8637 (t0) REVERT: C 193 GLU cc_start: 0.6061 (pm20) cc_final: 0.5219 (pm20) REVERT: C 204 TRP cc_start: 0.9389 (m-90) cc_final: 0.8765 (m-90) REVERT: C 324 TYR cc_start: 0.8521 (t80) cc_final: 0.7966 (t80) REVERT: D 30 GLU cc_start: 0.8201 (tp30) cc_final: 0.7846 (tp30) REVERT: E 186 ARG cc_start: 0.8086 (mmm160) cc_final: 0.7655 (mpt180) REVERT: E 281 LEU cc_start: 0.8895 (tp) cc_final: 0.8677 (tp) REVERT: E 399 MET cc_start: 0.7927 (tmm) cc_final: 0.7431 (tmm) REVERT: E 455 ILE cc_start: 0.9436 (tp) cc_final: 0.9133 (tp) REVERT: F 28 GLN cc_start: 0.7531 (mm-40) cc_final: 0.7225 (mm-40) REVERT: F 43 THR cc_start: 0.9096 (m) cc_final: 0.8876 (m) REVERT: H 3 GLN cc_start: 0.7626 (pm20) cc_final: 0.7173 (pm20) REVERT: H 29 PHE cc_start: 0.6717 (t80) cc_final: 0.6509 (t80) REVERT: H 36 TRP cc_start: 0.7689 (m100) cc_final: 0.7281 (m100) REVERT: H 50 TRP cc_start: 0.8435 (m-10) cc_final: 0.8125 (m-10) REVERT: H 98 ARG cc_start: 0.7013 (ttp-170) cc_final: 0.6721 (ttp-110) REVERT: L 3 VAL cc_start: 0.6885 (p) cc_final: 0.6030 (m) REVERT: L 28 ASN cc_start: 0.8538 (p0) cc_final: 0.8031 (p0) REVERT: L 47 LEU cc_start: 0.7362 (tt) cc_final: 0.7083 (tt) REVERT: O 42 ASP cc_start: 0.7686 (t0) cc_final: 0.7386 (t0) REVERT: O 49 GLU cc_start: 0.8780 (mp0) cc_final: 0.8507 (mp0) REVERT: O 69 THR cc_start: 0.9276 (p) cc_final: 0.8731 (p) REVERT: O 176 TYR cc_start: 0.8427 (m-10) cc_final: 0.8198 (m-10) REVERT: O 209 GLN cc_start: 0.7594 (tm-30) cc_final: 0.7331 (tm-30) REVERT: O 210 TRP cc_start: 0.9175 (t60) cc_final: 0.8828 (t60) REVERT: O 262 LEU cc_start: 0.9230 (pt) cc_final: 0.8982 (pp) REVERT: O 283 CYS cc_start: 0.8735 (t) cc_final: 0.8396 (t) REVERT: O 418 TRP cc_start: 0.8231 (t-100) cc_final: 0.7712 (t-100) REVERT: O 453 MET cc_start: 0.8636 (tpp) cc_final: 0.8308 (tpp) REVERT: O 486 TYR cc_start: 0.8412 (t80) cc_final: 0.8128 (t80) REVERT: O 492 GLN cc_start: 0.8547 (mt0) cc_final: 0.8313 (mt0) REVERT: P 60 LYS cc_start: 0.8260 (mttm) cc_final: 0.8018 (mmtm) REVERT: Q 1 MET cc_start: 0.8442 (mmp) cc_final: 0.7284 (mmm) REVERT: Q 57 ARG cc_start: 0.9291 (tpp80) cc_final: 0.9071 (tpp80) REVERT: Q 71 ASP cc_start: 0.8983 (t70) cc_final: 0.8722 (t0) REVERT: Q 193 GLU cc_start: 0.6099 (pm20) cc_final: 0.5249 (pm20) REVERT: Q 204 TRP cc_start: 0.9381 (m-90) cc_final: 0.8773 (m-90) REVERT: Q 324 TYR cc_start: 0.8553 (t80) cc_final: 0.8009 (t80) REVERT: R 30 GLU cc_start: 0.8198 (tp30) cc_final: 0.7837 (tp30) REVERT: S 281 LEU cc_start: 0.8874 (tp) cc_final: 0.8666 (tp) REVERT: S 399 MET cc_start: 0.7929 (tmm) cc_final: 0.7430 (tmm) REVERT: S 455 ILE cc_start: 0.9434 (tp) cc_final: 0.9137 (tp) REVERT: T 15 ARG cc_start: 0.8118 (mmt180) cc_final: 0.7908 (mmm-85) REVERT: T 28 GLN cc_start: 0.7764 (mm-40) cc_final: 0.7553 (mm-40) REVERT: U 3 GLN cc_start: 0.7635 (pm20) cc_final: 0.7170 (pm20) REVERT: U 36 TRP cc_start: 0.7669 (m100) cc_final: 0.7309 (m100) REVERT: U 50 TRP cc_start: 0.8427 (m-10) cc_final: 0.8105 (m-10) REVERT: V 3 VAL cc_start: 0.6881 (p) cc_final: 0.6009 (m) REVERT: V 28 ASN cc_start: 0.8642 (p0) cc_final: 0.8309 (p0) REVERT: V 47 LEU cc_start: 0.7359 (tt) cc_final: 0.7095 (tt) outliers start: 7 outliers final: 4 residues processed: 978 average time/residue: 0.1678 time to fit residues: 271.1215 Evaluate side-chains 803 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 798 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 55 optimal weight: 5.9990 chunk 122 optimal weight: 0.5980 chunk 366 optimal weight: 9.9990 chunk 269 optimal weight: 1.9990 chunk 182 optimal weight: 20.0000 chunk 118 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 205 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 137 optimal weight: 0.8980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 144 HIS A 192 ASN A 230 ASN B 59 GLN C 77 GLN ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 17 GLN E 27 HIS E 201 ASN F 59 GLN L 16 GLN L 38 GLN L 53 ASN O 89 ASN O 144 HIS O 192 ASN O 230 ASN Q 77 GLN ** Q 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN S 27 HIS S 201 ASN T 59 GLN V 16 GLN V 38 GLN V 53 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.126217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.107837 restraints weight = 52741.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.110537 restraints weight = 29369.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.112319 restraints weight = 19065.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.113518 restraints weight = 13823.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.114308 restraints weight = 10952.664| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30656 Z= 0.141 Angle : 0.703 12.273 41636 Z= 0.351 Chirality : 0.046 0.187 4862 Planarity : 0.004 0.046 5182 Dihedral : 6.598 53.965 4716 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.06 % Allowed : 2.09 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.13), residues: 3838 helix: 0.69 (0.17), residues: 912 sheet: -1.08 (0.17), residues: 976 loop : -2.00 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 2 TYR 0.028 0.002 TYR B 52 PHE 0.019 0.002 PHE F 42 TRP 0.026 0.002 TRP O 451 HIS 0.007 0.001 HIS O 207 Details of bonding type rmsd covalent geometry : bond 0.00321 (30596) covalent geometry : angle 0.69577 (41484) SS BOND : bond 0.00435 ( 28) SS BOND : angle 1.68194 ( 56) hydrogen bonds : bond 0.04057 ( 1098) hydrogen bonds : angle 5.73156 ( 3024) link_BETA1-4 : bond 0.00483 ( 20) link_BETA1-4 : angle 1.58631 ( 60) link_NAG-ASN : bond 0.00278 ( 12) link_NAG-ASN : angle 2.10965 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1041 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1039 time to evaluate : 1.172 Fit side-chains 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 D 72 " (corrupted residue). Skipping it. Corrupt residue: chain: D residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO R 72 " (corrupted residue). Skipping it. Corrupt residue: chain: R residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.7744 (t0) cc_final: 0.7376 (t0) REVERT: A 49 GLU cc_start: 0.8644 (mp0) cc_final: 0.8168 (mp0) REVERT: A 69 THR cc_start: 0.9239 (p) cc_final: 0.8488 (p) REVERT: A 209 GLN cc_start: 0.7112 (tm-30) cc_final: 0.6899 (tm-30) REVERT: A 262 LEU cc_start: 0.9312 (pt) cc_final: 0.8958 (pp) REVERT: A 283 CYS cc_start: 0.8710 (t) cc_final: 0.8402 (t) REVERT: A 323 GLU cc_start: 0.8450 (tp30) cc_final: 0.8209 (tp30) REVERT: A 353 ASN cc_start: 0.8548 (t0) cc_final: 0.7717 (t0) REVERT: A 453 MET cc_start: 0.8493 (tpp) cc_final: 0.8158 (tpp) REVERT: A 486 TYR cc_start: 0.8317 (t80) cc_final: 0.8049 (t80) REVERT: B 60 LYS cc_start: 0.8224 (mttm) cc_final: 0.7915 (mtpt) REVERT: C 1 MET cc_start: 0.8414 (mmp) cc_final: 0.7414 (mmm) REVERT: C 71 ASP cc_start: 0.8720 (t70) cc_final: 0.8482 (t0) REVERT: C 101 TRP cc_start: 0.8620 (m-10) cc_final: 0.8120 (m-10) REVERT: C 204 TRP cc_start: 0.9233 (m-90) cc_final: 0.8656 (m-90) REVERT: C 286 LYS cc_start: 0.8158 (tttm) cc_final: 0.7777 (mtpp) REVERT: C 292 LEU cc_start: 0.9352 (tp) cc_final: 0.9133 (tp) REVERT: C 324 TYR cc_start: 0.8572 (t80) cc_final: 0.8158 (t80) REVERT: C 366 GLU cc_start: 0.7724 (pm20) cc_final: 0.7483 (pm20) REVERT: C 408 ARG cc_start: 0.8941 (tpp80) cc_final: 0.8688 (tpp80) REVERT: D 30 GLU cc_start: 0.8204 (tp30) cc_final: 0.7794 (tp30) REVERT: D 68 MET cc_start: 0.8460 (mmm) cc_final: 0.7196 (tmm) REVERT: E 26 GLU cc_start: 0.8451 (mt-10) cc_final: 0.7924 (mt-10) REVERT: E 41 LEU cc_start: 0.9042 (pt) cc_final: 0.8755 (pt) REVERT: E 61 ILE cc_start: 0.9235 (tp) cc_final: 0.8946 (tp) REVERT: E 132 TYR cc_start: 0.8413 (t80) cc_final: 0.8173 (t80) REVERT: E 399 MET cc_start: 0.7978 (tmm) cc_final: 0.7608 (tmm) REVERT: E 455 ILE cc_start: 0.9323 (tp) cc_final: 0.9042 (tp) REVERT: F 10 MET cc_start: 0.8100 (mmp) cc_final: 0.7607 (mmt) REVERT: F 28 GLN cc_start: 0.7278 (mm-40) cc_final: 0.7049 (mm-40) REVERT: F 43 THR cc_start: 0.8977 (m) cc_final: 0.8758 (m) REVERT: H 3 GLN cc_start: 0.7334 (pm20) cc_final: 0.6965 (pm20) REVERT: H 21 SER cc_start: 0.8393 (p) cc_final: 0.8128 (p) REVERT: H 27 TYR cc_start: 0.8086 (p90) cc_final: 0.7619 (p90) REVERT: H 29 PHE cc_start: 0.6596 (t80) cc_final: 0.6160 (t80) REVERT: H 36 TRP cc_start: 0.7443 (m100) cc_final: 0.7018 (m100) REVERT: H 38 ARG cc_start: 0.8163 (tmm-80) cc_final: 0.7830 (tmm-80) REVERT: H 98 ARG cc_start: 0.6856 (ttp-170) cc_final: 0.6566 (ttp-110) REVERT: L 3 VAL cc_start: 0.6777 (p) cc_final: 0.5945 (m) REVERT: L 28 ASN cc_start: 0.8520 (p0) cc_final: 0.7929 (p0) REVERT: O 42 ASP cc_start: 0.7778 (t0) cc_final: 0.7360 (t0) REVERT: O 49 GLU cc_start: 0.8706 (mp0) cc_final: 0.8394 (mp0) REVERT: O 69 THR cc_start: 0.9217 (p) cc_final: 0.8493 (p) REVERT: O 209 GLN cc_start: 0.7366 (tm-30) cc_final: 0.6448 (tm-30) REVERT: O 283 CYS cc_start: 0.8697 (t) cc_final: 0.8399 (t) REVERT: O 323 GLU cc_start: 0.8473 (tp30) cc_final: 0.8224 (tp30) REVERT: O 353 ASN cc_start: 0.8565 (t0) cc_final: 0.7738 (t0) REVERT: O 453 MET cc_start: 0.8571 (tpp) cc_final: 0.8269 (tpp) REVERT: O 486 TYR cc_start: 0.8320 (t80) cc_final: 0.7999 (t80) REVERT: O 492 GLN cc_start: 0.8506 (mt0) cc_final: 0.7775 (tm-30) REVERT: P 60 LYS cc_start: 0.8141 (mttm) cc_final: 0.7874 (mtpt) REVERT: Q 1 MET cc_start: 0.8288 (mmp) cc_final: 0.7253 (mmm) REVERT: Q 71 ASP cc_start: 0.8878 (t70) cc_final: 0.8583 (t0) REVERT: Q 101 TRP cc_start: 0.8604 (m-10) cc_final: 0.8136 (m-10) REVERT: Q 193 GLU cc_start: 0.6140 (pm20) cc_final: 0.5016 (pm20) REVERT: Q 204 TRP cc_start: 0.9234 (m-90) cc_final: 0.8648 (m-90) REVERT: Q 286 LYS cc_start: 0.8162 (tttm) cc_final: 0.7790 (mtpp) REVERT: Q 292 LEU cc_start: 0.9357 (tp) cc_final: 0.9147 (tp) REVERT: Q 324 TYR cc_start: 0.8586 (t80) cc_final: 0.8244 (t80) REVERT: Q 366 GLU cc_start: 0.7707 (pm20) cc_final: 0.7475 (pm20) REVERT: Q 408 ARG cc_start: 0.8945 (tpp80) cc_final: 0.8692 (tpp80) REVERT: R 30 GLU cc_start: 0.8210 (tp30) cc_final: 0.7785 (tp30) REVERT: S 26 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8053 (mt-10) REVERT: S 41 LEU cc_start: 0.9111 (pt) cc_final: 0.8861 (pt) REVERT: S 61 ILE cc_start: 0.9231 (tp) cc_final: 0.8940 (tp) REVERT: S 281 LEU cc_start: 0.8795 (tp) cc_final: 0.8595 (tp) REVERT: S 399 MET cc_start: 0.7979 (tmm) cc_final: 0.7599 (tmm) REVERT: S 455 ILE cc_start: 0.9325 (tp) cc_final: 0.9041 (tp) REVERT: T 10 MET cc_start: 0.8140 (mmp) cc_final: 0.7618 (mmt) REVERT: U 3 GLN cc_start: 0.7330 (pm20) cc_final: 0.6955 (pm20) REVERT: U 21 SER cc_start: 0.8379 (p) cc_final: 0.8127 (p) REVERT: U 27 TYR cc_start: 0.8486 (p90) cc_final: 0.7727 (p90) REVERT: U 36 TRP cc_start: 0.7437 (m100) cc_final: 0.7010 (m100) REVERT: U 38 ARG cc_start: 0.8166 (tmm-80) cc_final: 0.7844 (tmm-80) REVERT: V 3 VAL cc_start: 0.6778 (p) cc_final: 0.5921 (m) REVERT: V 28 ASN cc_start: 0.8638 (p0) cc_final: 0.8295 (p0) REVERT: V 47 LEU cc_start: 0.7318 (tt) cc_final: 0.6999 (tt) outliers start: 2 outliers final: 0 residues processed: 1041 average time/residue: 0.1616 time to fit residues: 276.8817 Evaluate side-chains 860 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 860 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 69 optimal weight: 8.9990 chunk 313 optimal weight: 10.0000 chunk 379 optimal weight: 10.0000 chunk 376 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 266 optimal weight: 5.9990 chunk 231 optimal weight: 9.9990 chunk 161 optimal weight: 2.9990 chunk 183 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 177 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN B 51 HIS ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 GLN ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 ASN F 59 GLN ** H 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 16 GLN L 38 GLN L 52 ASN L 53 ASN O 192 ASN P 51 HIS Q 209 GLN ** Q 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 428 ASN T 59 GLN ** U 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 16 GLN V 38 GLN V 52 ASN V 53 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.124720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.106129 restraints weight = 53558.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.108830 restraints weight = 29943.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.110627 restraints weight = 19498.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.111840 restraints weight = 14179.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.112654 restraints weight = 11244.188| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 30656 Z= 0.251 Angle : 0.780 10.701 41636 Z= 0.393 Chirality : 0.048 0.224 4862 Planarity : 0.005 0.058 5182 Dihedral : 6.600 52.074 4716 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 0.19 % Allowed : 1.94 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.13), residues: 3838 helix: 0.66 (0.17), residues: 908 sheet: -1.15 (0.17), residues: 996 loop : -2.09 (0.13), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Q 405 TYR 0.015 0.002 TYR L 50 PHE 0.041 0.002 PHE T 42 TRP 0.027 0.002 TRP O 218 HIS 0.006 0.001 HIS P 51 Details of bonding type rmsd covalent geometry : bond 0.00584 (30596) covalent geometry : angle 0.77320 (41484) SS BOND : bond 0.00504 ( 28) SS BOND : angle 1.71057 ( 56) hydrogen bonds : bond 0.04369 ( 1098) hydrogen bonds : angle 5.83153 ( 3024) link_BETA1-4 : bond 0.00477 ( 20) link_BETA1-4 : angle 1.59015 ( 60) link_NAG-ASN : bond 0.00571 ( 12) link_NAG-ASN : angle 2.29992 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 969 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 963 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO D 72 " (corrupted residue). Skipping it. Corrupt residue: chain: D residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO R 72 " (corrupted residue). Skipping it. Corrupt residue: chain: R residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.8015 (t0) cc_final: 0.7606 (t0) REVERT: A 49 GLU cc_start: 0.8696 (mp0) cc_final: 0.8244 (mp0) REVERT: A 69 THR cc_start: 0.9305 (p) cc_final: 0.8676 (p) REVERT: A 71 ASP cc_start: 0.7301 (t70) cc_final: 0.7028 (t0) REVERT: A 209 GLN cc_start: 0.7614 (tm-30) cc_final: 0.7368 (tm-30) REVERT: A 258 MET cc_start: 0.8465 (tpp) cc_final: 0.8209 (tpp) REVERT: A 283 CYS cc_start: 0.8718 (t) cc_final: 0.8364 (t) REVERT: A 453 MET cc_start: 0.8634 (tpp) cc_final: 0.8263 (tpp) REVERT: A 486 TYR cc_start: 0.8444 (t80) cc_final: 0.8175 (t80) REVERT: C 1 MET cc_start: 0.8248 (mmp) cc_final: 0.7507 (mmm) REVERT: C 71 ASP cc_start: 0.8740 (t70) cc_final: 0.8453 (t0) REVERT: C 101 TRP cc_start: 0.8706 (m-10) cc_final: 0.8217 (m-10) REVERT: C 193 GLU cc_start: 0.6275 (pm20) cc_final: 0.5216 (pm20) REVERT: C 204 TRP cc_start: 0.9323 (m-90) cc_final: 0.8737 (m-90) REVERT: C 286 LYS cc_start: 0.8200 (tttm) cc_final: 0.7820 (mtpp) REVERT: C 324 TYR cc_start: 0.8591 (t80) cc_final: 0.8328 (t80) REVERT: C 408 ARG cc_start: 0.8979 (tpp80) cc_final: 0.8711 (tpp80) REVERT: D 30 GLU cc_start: 0.8274 (tp30) cc_final: 0.7841 (tp30) REVERT: E 26 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7610 (mt-10) REVERT: E 61 ILE cc_start: 0.9298 (tp) cc_final: 0.8971 (tp) REVERT: E 132 TYR cc_start: 0.8636 (t80) cc_final: 0.7239 (t80) REVERT: E 281 LEU cc_start: 0.8840 (tp) cc_final: 0.8623 (tp) REVERT: E 399 MET cc_start: 0.8026 (tmm) cc_final: 0.7453 (tmm) REVERT: E 455 ILE cc_start: 0.9369 (tp) cc_final: 0.9078 (tp) REVERT: F 10 MET cc_start: 0.8170 (mmp) cc_final: 0.7900 (mmp) REVERT: F 28 GLN cc_start: 0.7467 (mm-40) cc_final: 0.7132 (mm-40) REVERT: F 43 THR cc_start: 0.9067 (m) cc_final: 0.8819 (m) REVERT: F 47 LEU cc_start: 0.8728 (mt) cc_final: 0.8523 (mt) REVERT: H 3 GLN cc_start: 0.7641 (pm20) cc_final: 0.7246 (pm20) REVERT: H 12 LYS cc_start: 0.6750 (mmtm) cc_final: 0.6510 (mmpt) REVERT: H 21 SER cc_start: 0.8450 (p) cc_final: 0.8235 (p) REVERT: H 27 TYR cc_start: 0.8029 (p90) cc_final: 0.7557 (p90) REVERT: H 29 PHE cc_start: 0.6625 (t80) cc_final: 0.6239 (t80) REVERT: H 36 TRP cc_start: 0.7663 (m100) cc_final: 0.7288 (m100) REVERT: H 38 ARG cc_start: 0.8217 (tmm-80) cc_final: 0.7961 (tmm-80) REVERT: H 50 TRP cc_start: 0.8248 (m-10) cc_final: 0.7901 (m-10) REVERT: H 61 HIS cc_start: 0.8709 (t-90) cc_final: 0.8138 (t-90) REVERT: H 98 ARG cc_start: 0.6938 (ttp-170) cc_final: 0.6638 (ttp-110) REVERT: L 3 VAL cc_start: 0.6836 (p) cc_final: 0.5998 (m) REVERT: L 28 ASN cc_start: 0.8631 (p0) cc_final: 0.8147 (p0) REVERT: L 32 ASN cc_start: 0.8019 (m-40) cc_final: 0.7818 (m-40) REVERT: L 47 LEU cc_start: 0.7203 (tt) cc_final: 0.6927 (tt) REVERT: L 88 TYR cc_start: 0.8325 (m-10) cc_final: 0.8071 (m-10) REVERT: O 42 ASP cc_start: 0.8024 (t0) cc_final: 0.7730 (t0) REVERT: O 49 GLU cc_start: 0.8610 (mp0) cc_final: 0.8335 (mp0) REVERT: O 69 THR cc_start: 0.9295 (p) cc_final: 0.8654 (p) REVERT: O 209 GLN cc_start: 0.7637 (tm-30) cc_final: 0.7283 (tm-30) REVERT: O 283 CYS cc_start: 0.8738 (t) cc_final: 0.8362 (t) REVERT: O 453 MET cc_start: 0.8681 (tpp) cc_final: 0.8409 (tpp) REVERT: O 486 TYR cc_start: 0.8412 (t80) cc_final: 0.8127 (t80) REVERT: O 492 GLN cc_start: 0.8563 (mt0) cc_final: 0.8347 (mt0) REVERT: Q 1 MET cc_start: 0.8287 (mmp) cc_final: 0.7124 (mmm) REVERT: Q 71 ASP cc_start: 0.8968 (t70) cc_final: 0.8625 (t0) REVERT: Q 101 TRP cc_start: 0.8617 (m-10) cc_final: 0.8137 (m-10) REVERT: Q 193 GLU cc_start: 0.6301 (pm20) cc_final: 0.5269 (pm20) REVERT: Q 204 TRP cc_start: 0.9313 (m-90) cc_final: 0.8728 (m-90) REVERT: Q 286 LYS cc_start: 0.8212 (tttm) cc_final: 0.7828 (mtpp) REVERT: Q 324 TYR cc_start: 0.8706 (t80) cc_final: 0.8459 (t80) REVERT: Q 366 GLU cc_start: 0.7780 (pm20) cc_final: 0.7561 (pm20) REVERT: Q 408 ARG cc_start: 0.8995 (tpp80) cc_final: 0.8717 (tpp80) REVERT: R 30 GLU cc_start: 0.8277 (tp30) cc_final: 0.7837 (tp30) REVERT: S 26 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8023 (mt-10) REVERT: S 61 ILE cc_start: 0.9250 (tp) cc_final: 0.8928 (tp) REVERT: S 281 LEU cc_start: 0.8849 (tp) cc_final: 0.8643 (tp) REVERT: S 399 MET cc_start: 0.8018 (tmm) cc_final: 0.7448 (tmm) REVERT: S 455 ILE cc_start: 0.9370 (tp) cc_final: 0.9077 (tp) REVERT: T 10 MET cc_start: 0.8178 (mmp) cc_final: 0.7914 (mmp) REVERT: T 43 THR cc_start: 0.9077 (m) cc_final: 0.8824 (m) REVERT: U 3 GLN cc_start: 0.7633 (pm20) cc_final: 0.7236 (pm20) REVERT: U 12 LYS cc_start: 0.6740 (mmtm) cc_final: 0.6478 (mmtt) REVERT: U 21 SER cc_start: 0.8427 (p) cc_final: 0.8223 (p) REVERT: U 27 TYR cc_start: 0.8553 (p90) cc_final: 0.7797 (p90) REVERT: U 36 TRP cc_start: 0.7737 (m100) cc_final: 0.7305 (m100) REVERT: U 38 ARG cc_start: 0.8221 (tmm-80) cc_final: 0.7970 (tmm-80) REVERT: U 50 TRP cc_start: 0.8287 (m-10) cc_final: 0.7936 (m-10) REVERT: U 61 HIS cc_start: 0.8712 (t-90) cc_final: 0.8094 (t-90) REVERT: V 3 VAL cc_start: 0.6837 (p) cc_final: 0.5991 (m) REVERT: V 28 ASN cc_start: 0.8751 (p0) cc_final: 0.8481 (p0) REVERT: V 47 LEU cc_start: 0.7370 (tt) cc_final: 0.7032 (tt) REVERT: V 88 TYR cc_start: 0.8325 (m-10) cc_final: 0.8069 (m-10) outliers start: 6 outliers final: 4 residues processed: 967 average time/residue: 0.1711 time to fit residues: 272.5096 Evaluate side-chains 827 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 823 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 225 optimal weight: 8.9990 chunk 136 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 241 optimal weight: 0.9990 chunk 278 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 chunk 265 optimal weight: 4.9990 chunk 197 optimal weight: 5.9990 chunk 177 optimal weight: 8.9990 chunk 95 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 ASN F 59 GLN ** H 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 16 GLN L 38 GLN L 53 ASN ** O 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 428 ASN T 59 GLN ** U 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 16 GLN V 38 GLN V 53 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.127851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.109446 restraints weight = 52785.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.112153 restraints weight = 29424.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.113959 restraints weight = 19152.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.115162 restraints weight = 13922.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.115900 restraints weight = 11051.168| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 30656 Z= 0.182 Angle : 0.742 12.002 41636 Z= 0.371 Chirality : 0.047 0.225 4862 Planarity : 0.004 0.045 5182 Dihedral : 6.381 52.848 4716 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.13), residues: 3838 helix: 0.66 (0.17), residues: 908 sheet: -1.10 (0.17), residues: 992 loop : -2.11 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 2 TYR 0.029 0.002 TYR P 52 PHE 0.027 0.002 PHE Q 304 TRP 0.022 0.002 TRP O 451 HIS 0.018 0.001 HIS O 207 Details of bonding type rmsd covalent geometry : bond 0.00426 (30596) covalent geometry : angle 0.73625 (41484) SS BOND : bond 0.00401 ( 28) SS BOND : angle 1.65371 ( 56) hydrogen bonds : bond 0.04153 ( 1098) hydrogen bonds : angle 5.68305 ( 3024) link_BETA1-4 : bond 0.00508 ( 20) link_BETA1-4 : angle 1.50672 ( 60) link_NAG-ASN : bond 0.00417 ( 12) link_NAG-ASN : angle 2.14930 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 967 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 967 time to evaluate : 1.166 Fit side-chains 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 D 72 " (corrupted residue). Skipping it. Corrupt residue: chain: D residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO R 72 " (corrupted residue). Skipping it. Corrupt residue: chain: R residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8185 (tpt) cc_final: 0.7592 (tmm) REVERT: A 71 ASP cc_start: 0.7232 (t70) cc_final: 0.7004 (t0) REVERT: A 209 GLN cc_start: 0.7556 (tm-30) cc_final: 0.7172 (tm-30) REVERT: A 323 GLU cc_start: 0.8359 (tp30) cc_final: 0.8081 (tp30) REVERT: A 353 ASN cc_start: 0.8396 (t0) cc_final: 0.8075 (t0) REVERT: A 453 MET cc_start: 0.8580 (tpp) cc_final: 0.8199 (tpp) REVERT: A 486 TYR cc_start: 0.8377 (t80) cc_final: 0.8091 (t80) REVERT: C 1 MET cc_start: 0.8422 (mmp) cc_final: 0.7335 (mmm) REVERT: C 62 GLU cc_start: 0.6526 (tt0) cc_final: 0.6279 (tt0) REVERT: C 71 ASP cc_start: 0.8791 (t70) cc_final: 0.8528 (t0) REVERT: C 101 TRP cc_start: 0.8572 (m-10) cc_final: 0.8117 (m-10) REVERT: C 193 GLU cc_start: 0.6171 (pm20) cc_final: 0.5089 (pm20) REVERT: C 204 TRP cc_start: 0.9258 (m-90) cc_final: 0.8681 (m-90) REVERT: C 233 GLU cc_start: 0.7507 (tm-30) cc_final: 0.7190 (tm-30) REVERT: C 286 LYS cc_start: 0.8152 (tttm) cc_final: 0.7778 (mtpp) REVERT: C 324 TYR cc_start: 0.8603 (t80) cc_final: 0.8322 (t80) REVERT: C 366 GLU cc_start: 0.7805 (pm20) cc_final: 0.7600 (pm20) REVERT: C 408 ARG cc_start: 0.8954 (tpp80) cc_final: 0.8680 (tpp80) REVERT: D 30 GLU cc_start: 0.8250 (tp30) cc_final: 0.7814 (tp30) REVERT: E 26 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7639 (mt-10) REVERT: E 41 LEU cc_start: 0.9086 (pt) cc_final: 0.8762 (pt) REVERT: E 61 ILE cc_start: 0.9270 (tp) cc_final: 0.8957 (tp) REVERT: E 186 ARG cc_start: 0.8470 (mmp-170) cc_final: 0.8125 (mmp-170) REVERT: E 399 MET cc_start: 0.7926 (tmm) cc_final: 0.7630 (tmm) REVERT: F 10 MET cc_start: 0.8130 (mmp) cc_final: 0.7919 (mmp) REVERT: F 28 GLN cc_start: 0.7367 (mm-40) cc_final: 0.7133 (mm-40) REVERT: F 43 THR cc_start: 0.9032 (m) cc_final: 0.8764 (m) REVERT: H 3 GLN cc_start: 0.7579 (pm20) cc_final: 0.7173 (pm20) REVERT: H 21 SER cc_start: 0.8423 (p) cc_final: 0.8171 (p) REVERT: H 27 TYR cc_start: 0.7977 (p90) cc_final: 0.7482 (p90) REVERT: H 29 PHE cc_start: 0.6595 (t80) cc_final: 0.6174 (t80) REVERT: H 36 TRP cc_start: 0.7583 (m100) cc_final: 0.7090 (m100) REVERT: H 50 TRP cc_start: 0.8156 (m-10) cc_final: 0.7877 (m-10) REVERT: H 61 HIS cc_start: 0.8635 (t-90) cc_final: 0.8166 (t-90) REVERT: L 3 VAL cc_start: 0.6761 (p) cc_final: 0.5925 (m) REVERT: L 28 ASN cc_start: 0.8574 (p0) cc_final: 0.8096 (p0) REVERT: O 71 ASP cc_start: 0.7250 (t70) cc_final: 0.7023 (t0) REVERT: O 209 GLN cc_start: 0.7363 (tm-30) cc_final: 0.7044 (tm-30) REVERT: O 323 GLU cc_start: 0.8365 (tp30) cc_final: 0.8075 (tp30) REVERT: O 353 ASN cc_start: 0.8414 (t0) cc_final: 0.8092 (t0) REVERT: O 453 MET cc_start: 0.8614 (tpp) cc_final: 0.8341 (tpp) REVERT: O 486 TYR cc_start: 0.8328 (t80) cc_final: 0.8036 (t80) REVERT: O 492 GLN cc_start: 0.8557 (mt0) cc_final: 0.8304 (mt0) REVERT: P 60 LYS cc_start: 0.8219 (mttm) cc_final: 0.7950 (mtpt) REVERT: Q 1 MET cc_start: 0.8252 (mmp) cc_final: 0.7117 (mmm) REVERT: Q 62 GLU cc_start: 0.6518 (tt0) cc_final: 0.6276 (tt0) REVERT: Q 71 ASP cc_start: 0.8886 (t70) cc_final: 0.8609 (t0) REVERT: Q 101 TRP cc_start: 0.8531 (m-10) cc_final: 0.8148 (m-10) REVERT: Q 193 GLU cc_start: 0.6207 (pm20) cc_final: 0.5102 (pm20) REVERT: Q 204 TRP cc_start: 0.9245 (m-90) cc_final: 0.8681 (m-90) REVERT: Q 233 GLU cc_start: 0.7491 (tm-30) cc_final: 0.7213 (tm-30) REVERT: Q 286 LYS cc_start: 0.8166 (tttm) cc_final: 0.7794 (mtpp) REVERT: Q 408 ARG cc_start: 0.8975 (tpp80) cc_final: 0.8688 (tpp80) REVERT: R 30 GLU cc_start: 0.8244 (tp30) cc_final: 0.7812 (tp30) REVERT: S 26 GLU cc_start: 0.8434 (mt-10) cc_final: 0.7990 (mt-10) REVERT: S 41 LEU cc_start: 0.9060 (pt) cc_final: 0.8699 (pt) REVERT: S 61 ILE cc_start: 0.9252 (tp) cc_final: 0.8929 (tp) REVERT: S 399 MET cc_start: 0.7940 (tmm) cc_final: 0.7632 (tmm) REVERT: T 10 MET cc_start: 0.8120 (mmp) cc_final: 0.7908 (mmp) REVERT: T 28 GLN cc_start: 0.7219 (mm-40) cc_final: 0.6922 (mm-40) REVERT: T 43 THR cc_start: 0.9097 (m) cc_final: 0.8866 (m) REVERT: U 3 GLN cc_start: 0.7569 (pm20) cc_final: 0.7163 (pm20) REVERT: U 21 SER cc_start: 0.8418 (p) cc_final: 0.8178 (p) REVERT: U 27 TYR cc_start: 0.8485 (p90) cc_final: 0.7682 (p90) REVERT: U 36 TRP cc_start: 0.7596 (m100) cc_final: 0.6995 (m100) REVERT: U 50 TRP cc_start: 0.8254 (m-10) cc_final: 0.7961 (m-10) REVERT: U 61 HIS cc_start: 0.8653 (t-90) cc_final: 0.8185 (t-90) REVERT: V 3 VAL cc_start: 0.6774 (p) cc_final: 0.5920 (m) REVERT: V 28 ASN cc_start: 0.8703 (p0) cc_final: 0.8476 (p0) REVERT: V 46 LYS cc_start: 0.7570 (ttpp) cc_final: 0.6984 (mmtp) outliers start: 0 outliers final: 0 residues processed: 967 average time/residue: 0.1699 time to fit residues: 271.9526 Evaluate side-chains 820 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 820 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 362 optimal weight: 0.9990 chunk 310 optimal weight: 8.9990 chunk 338 optimal weight: 0.0270 chunk 375 optimal weight: 4.9990 chunk 331 optimal weight: 6.9990 chunk 174 optimal weight: 9.9990 chunk 379 optimal weight: 0.0060 chunk 234 optimal weight: 10.0000 chunk 343 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 109 optimal weight: 0.8980 overall best weight: 1.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 HIS C 94 HIS C 209 GLN ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 ASN E 27 HIS ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN H 108 GLN L 16 GLN L 38 GLN L 52 ASN L 53 ASN O 144 HIS ** O 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 HIS Q 77 GLN Q 209 GLN ** Q 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 353 ASN S 27 HIS ** S 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 428 ASN T 59 GLN V 16 GLN V 35 ASN V 38 GLN V 52 ASN V 53 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.134176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.116215 restraints weight = 51516.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.118932 restraints weight = 28680.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.120699 restraints weight = 18556.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.121925 restraints weight = 13516.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.122720 restraints weight = 10680.592| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30656 Z= 0.133 Angle : 0.706 12.254 41636 Z= 0.350 Chirality : 0.045 0.185 4862 Planarity : 0.004 0.047 5182 Dihedral : 5.961 53.941 4716 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.22 % Allowed : 0.84 % Favored : 98.94 % 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: -1.58 (0.13), residues: 3838 helix: 0.79 (0.17), residues: 912 sheet: -0.99 (0.17), residues: 970 loop : -2.01 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG O 2 TYR 0.014 0.001 TYR Q 324 PHE 0.018 0.001 PHE B 42 TRP 0.024 0.002 TRP S 451 HIS 0.014 0.001 HIS O 207 Details of bonding type rmsd covalent geometry : bond 0.00301 (30596) covalent geometry : angle 0.69980 (41484) SS BOND : bond 0.00434 ( 28) SS BOND : angle 1.56773 ( 56) hydrogen bonds : bond 0.03805 ( 1098) hydrogen bonds : angle 5.45705 ( 3024) link_BETA1-4 : bond 0.00510 ( 20) link_BETA1-4 : angle 1.47160 ( 60) link_NAG-ASN : bond 0.00251 ( 12) link_NAG-ASN : angle 2.02848 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 989 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 982 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO D 72 " (corrupted residue). Skipping it. Corrupt residue: chain: D 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 R 72 " (corrupted residue). Skipping it. Corrupt residue: chain: R residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8369 (mp0) cc_final: 0.7968 (mp0) REVERT: A 170 GLU cc_start: 0.7705 (pp20) cc_final: 0.7433 (pp20) REVERT: A 323 GLU cc_start: 0.8297 (tp30) cc_final: 0.8054 (tp30) REVERT: A 453 MET cc_start: 0.8453 (tpp) cc_final: 0.8072 (tpp) REVERT: A 471 THR cc_start: 0.7983 (m) cc_final: 0.7764 (t) REVERT: A 486 TYR cc_start: 0.8319 (t80) cc_final: 0.8052 (t80) REVERT: C 1 MET cc_start: 0.8194 (mmp) cc_final: 0.7550 (mmm) REVERT: C 62 GLU cc_start: 0.6721 (tt0) cc_final: 0.6490 (tt0) REVERT: C 71 ASP cc_start: 0.8709 (t70) cc_final: 0.8461 (t0) REVERT: C 101 TRP cc_start: 0.8549 (m-10) cc_final: 0.8116 (m-10) REVERT: C 193 GLU cc_start: 0.6082 (pm20) cc_final: 0.5116 (pm20) REVERT: C 204 TRP cc_start: 0.9195 (m-90) cc_final: 0.8715 (m-90) REVERT: C 286 LYS cc_start: 0.8166 (tttm) cc_final: 0.7926 (mtpp) REVERT: C 324 TYR cc_start: 0.8591 (t80) cc_final: 0.8290 (t80) REVERT: C 366 GLU cc_start: 0.7801 (pm20) cc_final: 0.7505 (pm20) REVERT: C 408 ARG cc_start: 0.8982 (tpp80) cc_final: 0.8720 (tpp80) REVERT: D 30 GLU cc_start: 0.8279 (tp30) cc_final: 0.7899 (tp30) REVERT: D 31 LYS cc_start: 0.9169 (ttpt) cc_final: 0.8961 (ttpt) REVERT: E 26 GLU cc_start: 0.8412 (mt-10) cc_final: 0.7977 (mt-10) REVERT: E 41 LEU cc_start: 0.9044 (pt) cc_final: 0.8655 (pt) REVERT: E 61 ILE cc_start: 0.9249 (tp) cc_final: 0.8942 (tp) REVERT: E 116 CYS cc_start: 0.5875 (m) cc_final: 0.5560 (m) REVERT: E 309 GLU cc_start: 0.8365 (tp30) cc_final: 0.8116 (tp30) REVERT: E 399 MET cc_start: 0.7922 (tmm) cc_final: 0.7607 (tmm) REVERT: E 453 MET cc_start: 0.8165 (tpp) cc_final: 0.7896 (tpp) REVERT: F 10 MET cc_start: 0.8069 (mmp) cc_final: 0.7842 (mmp) REVERT: F 33 GLU cc_start: 0.7371 (mm-30) cc_final: 0.6388 (mt-10) REVERT: F 43 THR cc_start: 0.9050 (m) cc_final: 0.8837 (m) REVERT: H 3 GLN cc_start: 0.7575 (pm20) cc_final: 0.7308 (pm20) REVERT: H 27 TYR cc_start: 0.7994 (p90) cc_final: 0.7265 (p90) REVERT: H 29 PHE cc_start: 0.6721 (t80) cc_final: 0.6144 (t80) REVERT: H 48 MET cc_start: 0.7563 (mtm) cc_final: 0.7315 (mtm) REVERT: H 50 TRP cc_start: 0.8260 (m-10) cc_final: 0.8040 (m-10) REVERT: H 61 HIS cc_start: 0.8360 (t-90) cc_final: 0.7825 (t-90) REVERT: L 3 VAL cc_start: 0.6768 (p) cc_final: 0.5964 (m) REVERT: L 28 ASN cc_start: 0.8584 (p0) cc_final: 0.8079 (p0) REVERT: L 46 LYS cc_start: 0.7647 (ttpp) cc_final: 0.7170 (mmtp) REVERT: L 88 TYR cc_start: 0.8302 (m-10) cc_final: 0.8037 (m-10) REVERT: O 1 MET cc_start: 0.8181 (ttt) cc_final: 0.7787 (tpp) REVERT: O 143 VAL cc_start: 0.8818 (m) cc_final: 0.8523 (m) REVERT: O 170 GLU cc_start: 0.7710 (pp20) cc_final: 0.7426 (pp20) REVERT: O 209 GLN cc_start: 0.7346 (tm-30) cc_final: 0.7070 (tm-30) REVERT: O 323 GLU cc_start: 0.8318 (tp30) cc_final: 0.8087 (tp30) REVERT: O 453 MET cc_start: 0.8518 (tpp) cc_final: 0.8251 (tpp) REVERT: O 471 THR cc_start: 0.7977 (m) cc_final: 0.7749 (t) REVERT: O 486 TYR cc_start: 0.8252 (t80) cc_final: 0.7990 (t80) REVERT: P 55 THR cc_start: 0.7385 (p) cc_final: 0.7184 (p) REVERT: P 60 LYS cc_start: 0.8220 (mttm) cc_final: 0.7924 (mtpt) REVERT: Q 71 ASP cc_start: 0.8822 (t70) cc_final: 0.8559 (t0) REVERT: Q 101 TRP cc_start: 0.8486 (m-10) cc_final: 0.8120 (m-10) REVERT: Q 193 GLU cc_start: 0.6129 (pm20) cc_final: 0.5101 (pm20) REVERT: Q 204 TRP cc_start: 0.9185 (m-90) cc_final: 0.8710 (m-90) REVERT: Q 233 GLU cc_start: 0.7322 (tm-30) cc_final: 0.7114 (tm-30) REVERT: Q 286 LYS cc_start: 0.8184 (tttm) cc_final: 0.7932 (mtpp) REVERT: Q 291 GLU cc_start: 0.8189 (tt0) cc_final: 0.7979 (tm-30) REVERT: Q 324 TYR cc_start: 0.8626 (t80) cc_final: 0.7891 (t80) REVERT: Q 408 ARG cc_start: 0.8945 (tpp80) cc_final: 0.8692 (tpp80) REVERT: R 30 GLU cc_start: 0.8269 (tp30) cc_final: 0.7910 (tp30) REVERT: R 31 LYS cc_start: 0.9166 (ttpt) cc_final: 0.8965 (ttpt) REVERT: S 26 GLU cc_start: 0.8391 (mt-10) cc_final: 0.7682 (tt0) REVERT: S 41 LEU cc_start: 0.8981 (pt) cc_final: 0.8653 (pt) REVERT: S 61 ILE cc_start: 0.9220 (tp) cc_final: 0.8910 (tp) REVERT: S 116 CYS cc_start: 0.5866 (m) cc_final: 0.5522 (m) REVERT: S 399 MET cc_start: 0.7933 (tmm) cc_final: 0.7609 (tmm) REVERT: S 453 MET cc_start: 0.8169 (tpp) cc_final: 0.7873 (tpp) REVERT: T 10 MET cc_start: 0.8060 (mmp) cc_final: 0.7830 (mmp) REVERT: T 33 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6231 (mt-10) REVERT: T 43 THR cc_start: 0.9045 (m) cc_final: 0.8824 (m) REVERT: U 3 GLN cc_start: 0.7559 (pm20) cc_final: 0.7311 (pm20) REVERT: U 21 SER cc_start: 0.8318 (p) cc_final: 0.8084 (p) REVERT: U 27 TYR cc_start: 0.8349 (p90) cc_final: 0.7700 (p90) REVERT: U 48 MET cc_start: 0.7257 (mtm) cc_final: 0.7035 (mtm) REVERT: U 61 HIS cc_start: 0.8387 (t-90) cc_final: 0.7837 (t-90) REVERT: V 3 VAL cc_start: 0.6808 (p) cc_final: 0.5853 (m) REVERT: V 28 ASN cc_start: 0.8717 (p0) cc_final: 0.8497 (p0) REVERT: V 46 LYS cc_start: 0.7636 (ttpp) cc_final: 0.7158 (mmtp) REVERT: V 100 LEU cc_start: 0.7603 (tp) cc_final: 0.7012 (tp) outliers start: 7 outliers final: 6 residues processed: 985 average time/residue: 0.1765 time to fit residues: 287.3206 Evaluate side-chains 846 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 840 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 33 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 286 optimal weight: 20.0000 chunk 345 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 338 optimal weight: 9.9990 chunk 49 optimal weight: 0.0070 chunk 218 optimal weight: 9.9990 chunk 268 optimal weight: 0.9980 chunk 364 optimal weight: 20.0000 overall best weight: 5.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 HIS ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 ASN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 GLN ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN H 108 GLN L 16 GLN L 38 GLN L 53 ASN ** O 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 492 GLN ** Q 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 353 ASN ** S 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 77 GLN ** S 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 428 ASN T 59 GLN V 16 GLN V 38 GLN V 53 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.125208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.106839 restraints weight = 53850.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.109495 restraints weight = 30337.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.111256 restraints weight = 19843.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.112425 restraints weight = 14490.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.113245 restraints weight = 11542.705| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 30656 Z= 0.208 Angle : 0.745 10.868 41636 Z= 0.371 Chirality : 0.047 0.192 4862 Planarity : 0.004 0.051 5182 Dihedral : 6.056 52.199 4716 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.09 % Allowed : 0.69 % Favored : 99.22 % 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: -1.65 (0.13), residues: 3838 helix: 0.77 (0.17), residues: 908 sheet: -1.06 (0.17), residues: 948 loop : -2.05 (0.13), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 405 TYR 0.014 0.002 TYR C 442 PHE 0.015 0.002 PHE B 48 TRP 0.025 0.002 TRP A 218 HIS 0.015 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00489 (30596) covalent geometry : angle 0.73898 (41484) SS BOND : bond 0.00516 ( 28) SS BOND : angle 1.53386 ( 56) hydrogen bonds : bond 0.04105 ( 1098) hydrogen bonds : angle 5.57575 ( 3024) link_BETA1-4 : bond 0.00509 ( 20) link_BETA1-4 : angle 1.44681 ( 60) link_NAG-ASN : bond 0.00465 ( 12) link_NAG-ASN : angle 2.19473 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5978.19 seconds wall clock time: 103 minutes 57.79 seconds (6237.79 seconds total)