Starting phenix.real_space_refine on Tue May 27 18:19:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jn2_36430/05_2025/8jn2_36430.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jn2_36430/05_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_36430/05_2025/8jn2_36430.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jn2_36430/05_2025/8jn2_36430.map" model { file = "/net/cci-nas-00/data/ceres_data/8jn2_36430/05_2025/8jn2_36430.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jn2_36430/05_2025/8jn2_36430.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 17.32, per 1000 atoms: 0.58 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: 7.47 Conformation dependent library (CDL) restraints added in 3.5 seconds 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: 3.79 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: 10.70 Time building geometry restraints manager: 8.53 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: 0.01 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: 0.000 Normalize map: mean=0, sd=1: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.160 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 62.710 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.720 ------------------------------------------------------------------------------- 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 : 14.33 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.13), residues: 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 TRP 0.040 0.002 TRP E 451 HIS 0.006 0.001 HIS A 27 PHE 0.017 0.002 PHE C 304 TYR 0.014 0.002 TYR C 324 ARG 0.006 0.001 ARG Q 186 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 12) link_NAG-ASN : angle 2.63283 ( 36) link_BETA1-4 : bond 0.00676 ( 20) link_BETA1-4 : angle 1.97810 ( 60) hydrogen bonds : bond 0.21275 ( 1098) hydrogen bonds : angle 8.83837 ( 3024) SS BOND : bond 0.00449 ( 28) SS BOND : angle 1.13975 ( 56) covalent geometry : bond 0.00453 (30596) covalent geometry : angle 0.76010 (41484) *********************** 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 : 3.113 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: 0.3816 time to fit residues: 699.8067 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 : 3.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 320 optimal weight: 6.9990 chunk 288 optimal weight: 20.0000 chunk 159 optimal weight: 0.0470 chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 297 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 181 optimal weight: 6.9990 chunk 221 optimal weight: 5.9990 chunk 345 optimal weight: 10.0000 overall best weight: 4.8086 ------------------------------------------------------------------------------- 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 280 HIS ** 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 Q 209 GLN ** Q 353 ASN ** 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.131741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.113519 restraints weight = 51219.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.116247 restraints weight = 28410.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.118056 restraints weight = 18236.003| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 30656 Z= 0.213 Angle : 0.745 11.613 41636 Z= 0.380 Chirality : 0.046 0.194 4862 Planarity : 0.004 0.047 5182 Dihedral : 11.059 89.042 4716 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.31 % Allowed : 7.00 % Favored : 92.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.13), residues: 3838 helix: 0.74 (0.17), residues: 910 sheet: -1.11 (0.17), residues: 966 loop : -2.02 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP S 451 HIS 0.006 0.001 HIS P 7 PHE 0.018 0.002 PHE F 42 TYR 0.019 0.002 TYR T 52 ARG 0.009 0.001 ARG A 284 Details of bonding type rmsd link_NAG-ASN : bond 0.00384 ( 12) link_NAG-ASN : angle 2.65507 ( 36) link_BETA1-4 : bond 0.00730 ( 20) link_BETA1-4 : angle 2.32974 ( 60) hydrogen bonds : bond 0.04987 ( 1098) hydrogen bonds : angle 6.63821 ( 3024) SS BOND : bond 0.00408 ( 28) SS BOND : angle 1.71891 ( 56) covalent geometry : bond 0.00485 (30596) covalent geometry : angle 0.73399 (41484) *********************** 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 1039 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 1029 time to evaluate : 2.984 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 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: 0.8421 (mmm) cc_final: 0.7858 (mmm) REVERT: A 42 ASP cc_start: 0.8190 (t0) cc_final: 0.7963 (t0) REVERT: A 49 GLU cc_start: 0.8319 (mp0) cc_final: 0.7762 (mp0) REVERT: A 69 THR cc_start: 0.9162 (p) cc_final: 0.8513 (p) REVERT: A 71 ASP cc_start: 0.8207 (p0) cc_final: 0.7838 (t70) REVERT: A 76 THR cc_start: 0.8032 (p) cc_final: 0.7824 (p) REVERT: A 182 GLU cc_start: 0.7117 (mm-30) cc_final: 0.6685 (tp30) REVERT: A 190 ASP cc_start: 0.8562 (t0) cc_final: 0.7823 (t0) REVERT: A 195 ILE cc_start: 0.9030 (mt) cc_final: 0.8207 (tt) REVERT: A 453 MET cc_start: 0.8566 (tpp) cc_final: 0.8317 (tpp) REVERT: A 486 TYR cc_start: 0.8378 (t80) cc_final: 0.8134 (t80) REVERT: A 487 LEU cc_start: 0.8792 (tt) cc_final: 0.8524 (tp) REVERT: A 492 GLN cc_start: 0.8437 (mt0) cc_final: 0.7780 (tm-30) REVERT: C 1 MET cc_start: 0.8795 (mmp) cc_final: 0.7880 (mmm) REVERT: C 47 LYS cc_start: 0.8638 (mttp) cc_final: 0.8208 (pttt) REVERT: C 71 ASP cc_start: 0.8930 (t70) cc_final: 0.8640 (t0) REVERT: C 148 GLN cc_start: 0.8822 (tt0) cc_final: 0.8357 (tm-30) REVERT: C 193 GLU cc_start: 0.6343 (pm20) cc_final: 0.5407 (pm20) REVERT: C 199 MET cc_start: 0.9133 (ptm) cc_final: 0.8917 (ptm) REVERT: C 204 TRP cc_start: 0.9490 (m-90) cc_final: 0.8623 (m-90) REVERT: C 453 MET cc_start: 0.9044 (mmp) cc_final: 0.8759 (tpp) REVERT: D 14 THR cc_start: 0.8651 (p) cc_final: 0.8450 (p) REVERT: D 38 ARG cc_start: 0.8282 (ttp-170) cc_final: 0.8073 (ttp-170) REVERT: D 68 MET cc_start: 0.8536 (mmm) cc_final: 0.7588 (tmm) REVERT: E 132 TYR cc_start: 0.8624 (t80) cc_final: 0.8189 (t80) REVERT: E 239 LYS cc_start: 0.7628 (ttmt) cc_final: 0.7380 (ttpt) REVERT: E 247 GLU cc_start: 0.7606 (pm20) cc_final: 0.7334 (pm20) REVERT: E 399 MET cc_start: 0.7920 (tmm) cc_final: 0.7459 (tmm) REVERT: E 419 ASP cc_start: 0.7451 (m-30) cc_final: 0.7228 (m-30) REVERT: E 455 ILE cc_start: 0.9277 (tp) cc_final: 0.9011 (tp) REVERT: F 51 HIS cc_start: 0.7911 (t-90) cc_final: 0.7607 (t-90) REVERT: H 3 GLN cc_start: 0.7696 (pm20) cc_final: 0.7046 (pm20) REVERT: H 21 SER cc_start: 0.8541 (p) cc_final: 0.8296 (p) REVERT: H 29 PHE cc_start: 0.6376 (t80) cc_final: 0.6035 (t80) REVERT: H 36 TRP cc_start: 0.7458 (m100) cc_final: 0.6555 (m100) REVERT: H 43 GLN cc_start: 0.7269 (mm-40) cc_final: 0.6961 (mm-40) REVERT: H 81 MET cc_start: 0.7368 (ttt) cc_final: 0.5446 (ttt) REVERT: H 111 TYR cc_start: 0.7715 (m-80) cc_final: 0.7422 (m-80) REVERT: L 3 VAL cc_start: 0.6879 (p) cc_final: 0.6165 (m) REVERT: O 1 MET cc_start: 0.8421 (mmm) cc_final: 0.7856 (mmm) REVERT: O 42 ASP cc_start: 0.8192 (t0) cc_final: 0.7966 (t0) REVERT: O 49 GLU cc_start: 0.8347 (mp0) cc_final: 0.7762 (mp0) REVERT: O 69 THR cc_start: 0.9151 (p) cc_final: 0.8506 (p) REVERT: O 71 ASP cc_start: 0.8215 (p0) cc_final: 0.7820 (t70) REVERT: O 76 THR cc_start: 0.8056 (p) cc_final: 0.7815 (p) REVERT: O 182 GLU cc_start: 0.7114 (mm-30) cc_final: 0.6687 (tp30) REVERT: O 190 ASP cc_start: 0.8591 (t0) cc_final: 0.7888 (t0) REVERT: O 195 ILE cc_start: 0.9019 (mt) cc_final: 0.8364 (mp) REVERT: O 453 MET cc_start: 0.8565 (tpp) cc_final: 0.8306 (tpp) REVERT: O 486 TYR cc_start: 0.8374 (t80) cc_final: 0.8125 (t80) REVERT: O 487 LEU cc_start: 0.8786 (tt) cc_final: 0.8513 (tp) REVERT: O 492 GLN cc_start: 0.8437 (mt0) cc_final: 0.7762 (tm-30) REVERT: Q 1 MET cc_start: 0.8798 (mmp) cc_final: 0.7897 (mmm) REVERT: Q 47 LYS cc_start: 0.8636 (mttp) cc_final: 0.8215 (pttt) REVERT: Q 71 ASP cc_start: 0.8947 (t70) cc_final: 0.8643 (t0) REVERT: Q 148 GLN cc_start: 0.8816 (tt0) cc_final: 0.8358 (tm-30) REVERT: Q 186 ARG cc_start: 0.8839 (mmm160) cc_final: 0.8533 (mmt180) REVERT: Q 193 GLU cc_start: 0.6366 (pm20) cc_final: 0.5399 (pm20) REVERT: Q 199 MET cc_start: 0.9147 (ptm) cc_final: 0.8926 (ptm) REVERT: Q 204 TRP cc_start: 0.9483 (m-90) cc_final: 0.8626 (m-90) REVERT: Q 453 MET cc_start: 0.9031 (mmp) cc_final: 0.8756 (tpp) REVERT: R 38 ARG cc_start: 0.8280 (ttp-170) cc_final: 0.8071 (ttp-170) REVERT: R 68 MET cc_start: 0.8547 (mmm) cc_final: 0.7580 (tmm) REVERT: S 132 TYR cc_start: 0.8620 (t80) cc_final: 0.8183 (t80) REVERT: S 239 LYS cc_start: 0.7630 (ttmt) cc_final: 0.7365 (ttpt) REVERT: S 247 GLU cc_start: 0.7611 (pm20) cc_final: 0.7327 (pm20) REVERT: S 328 ASP cc_start: 0.8441 (m-30) cc_final: 0.8220 (m-30) REVERT: S 399 MET cc_start: 0.7920 (tmm) cc_final: 0.7457 (tmm) REVERT: S 419 ASP cc_start: 0.7472 (m-30) cc_final: 0.7239 (m-30) REVERT: S 455 ILE cc_start: 0.9265 (tp) cc_final: 0.9003 (tp) REVERT: T 51 HIS cc_start: 0.7914 (t-90) cc_final: 0.7603 (t-90) REVERT: U 3 GLN cc_start: 0.7691 (pm20) cc_final: 0.7096 (pm20) REVERT: U 21 SER cc_start: 0.8537 (p) cc_final: 0.8292 (p) REVERT: U 27 TYR cc_start: 0.7991 (p90) cc_final: 0.7484 (p90) REVERT: U 29 PHE cc_start: 0.6387 (t80) cc_final: 0.5871 (t80) REVERT: U 36 TRP cc_start: 0.7460 (m100) cc_final: 0.6555 (m100) REVERT: U 43 GLN cc_start: 0.7269 (mm-40) cc_final: 0.6957 (mm-40) REVERT: U 81 MET cc_start: 0.7387 (ttt) cc_final: 0.5490 (ttt) REVERT: U 111 TYR cc_start: 0.7751 (m-80) cc_final: 0.7464 (m-80) REVERT: V 3 VAL cc_start: 0.6869 (p) cc_final: 0.6165 (m) outliers start: 10 outliers final: 3 residues processed: 1031 average time/residue: 0.3882 time to fit residues: 638.6825 Evaluate side-chains 826 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 823 time to evaluate : 3.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 237 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 333 optimal weight: 0.9990 chunk 106 optimal weight: 20.0000 chunk 105 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 159 optimal weight: 0.9980 chunk 343 optimal weight: 8.9990 chunk 193 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- 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** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 17 GLN ** D 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 HIS E 144 HIS ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 ASN L 16 GLN ** 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 ** R 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 27 HIS S 144 HIS ** T 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 ASN V 16 GLN ** V 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 38 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.133801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.115884 restraints weight = 51212.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.118571 restraints weight = 28513.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.120355 restraints weight = 18481.086| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 30656 Z= 0.175 Angle : 0.702 9.859 41636 Z= 0.357 Chirality : 0.046 0.270 4862 Planarity : 0.004 0.082 5182 Dihedral : 9.447 82.369 4716 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.12 % Allowed : 4.88 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.13), residues: 3838 helix: 0.79 (0.17), residues: 906 sheet: -1.09 (0.17), residues: 964 loop : -2.02 (0.13), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 451 HIS 0.007 0.001 HIS R 39 PHE 0.014 0.002 PHE C 335 TYR 0.017 0.002 TYR P 52 ARG 0.005 0.001 ARG Q 99 Details of bonding type rmsd link_NAG-ASN : bond 0.00295 ( 12) link_NAG-ASN : angle 2.45243 ( 36) link_BETA1-4 : bond 0.00735 ( 20) link_BETA1-4 : angle 2.14126 ( 60) hydrogen bonds : bond 0.04485 ( 1098) hydrogen bonds : angle 6.24298 ( 3024) SS BOND : bond 0.00508 ( 28) SS BOND : angle 1.77715 ( 56) covalent geometry : bond 0.00395 (30596) covalent geometry : angle 0.69204 (41484) *********************** 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 1020 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1016 time to evaluate : 3.085 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 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: 0.8351 (mmm) cc_final: 0.7430 (mmm) REVERT: A 42 ASP cc_start: 0.8165 (t0) cc_final: 0.7829 (t0) REVERT: A 49 GLU cc_start: 0.8381 (mp0) cc_final: 0.8116 (mp0) REVERT: A 76 THR cc_start: 0.8563 (p) cc_final: 0.8346 (p) REVERT: A 176 TYR cc_start: 0.8237 (m-10) cc_final: 0.7868 (m-10) REVERT: A 182 GLU cc_start: 0.7034 (mm-30) cc_final: 0.6652 (tp30) REVERT: A 190 ASP cc_start: 0.8466 (t0) cc_final: 0.8002 (t0) REVERT: A 195 ILE cc_start: 0.8924 (mt) cc_final: 0.8184 (tt) REVERT: A 453 MET cc_start: 0.8459 (tpp) cc_final: 0.8000 (tpp) REVERT: A 486 TYR cc_start: 0.8347 (t80) cc_final: 0.8130 (t80) REVERT: A 487 LEU cc_start: 0.8722 (tt) cc_final: 0.8506 (tp) REVERT: A 492 GLN cc_start: 0.8444 (mt0) cc_final: 0.7789 (tm-30) REVERT: B 10 MET cc_start: 0.7455 (tpp) cc_final: 0.7009 (mmm) REVERT: B 45 LEU cc_start: 0.9287 (tp) cc_final: 0.9085 (tp) REVERT: B 60 LYS cc_start: 0.8429 (mttm) cc_final: 0.8053 (mmtm) REVERT: C 1 MET cc_start: 0.8840 (mmp) cc_final: 0.7938 (mmm) REVERT: C 34 MET cc_start: 0.8598 (ptp) cc_final: 0.8129 (ptp) REVERT: C 47 LYS cc_start: 0.8686 (mttp) cc_final: 0.8303 (pttt) REVERT: C 71 ASP cc_start: 0.8881 (t70) cc_final: 0.8604 (t0) REVERT: C 156 GLN cc_start: 0.8779 (mt0) cc_final: 0.8485 (mt0) REVERT: C 186 ARG cc_start: 0.8835 (mmm160) cc_final: 0.8351 (mmt180) REVERT: C 193 GLU cc_start: 0.6398 (pm20) cc_final: 0.5324 (pm20) REVERT: C 204 TRP cc_start: 0.9381 (m-90) cc_final: 0.8714 (m-90) REVERT: C 286 LYS cc_start: 0.8225 (tttm) cc_final: 0.7866 (mtpp) REVERT: C 390 TYR cc_start: 0.8526 (t80) cc_final: 0.8249 (t80) REVERT: D 68 MET cc_start: 0.8631 (mmm) cc_final: 0.7534 (tmm) REVERT: E 399 MET cc_start: 0.7868 (tmm) cc_final: 0.7411 (tmm) REVERT: E 455 ILE cc_start: 0.9391 (tp) cc_final: 0.9048 (tp) REVERT: F 43 THR cc_start: 0.9007 (m) cc_final: 0.8776 (m) REVERT: F 47 LEU cc_start: 0.8270 (mt) cc_final: 0.8070 (mt) REVERT: F 51 HIS cc_start: 0.7878 (t-90) cc_final: 0.7606 (t-90) REVERT: H 3 GLN cc_start: 0.7643 (pm20) cc_final: 0.7088 (pm20) REVERT: H 21 SER cc_start: 0.8444 (p) cc_final: 0.8188 (p) REVERT: H 27 TYR cc_start: 0.8146 (p90) cc_final: 0.7550 (p90) REVERT: H 29 PHE cc_start: 0.6592 (t80) cc_final: 0.6102 (t80) REVERT: H 36 TRP cc_start: 0.7498 (m100) cc_final: 0.6620 (m100) REVERT: H 81 MET cc_start: 0.7481 (ttt) cc_final: 0.5897 (ttt) REVERT: H 111 TYR cc_start: 0.7887 (m-80) cc_final: 0.7623 (m-80) REVERT: L 3 VAL cc_start: 0.6820 (p) cc_final: 0.6019 (m) REVERT: O 1 MET cc_start: 0.8341 (mmm) cc_final: 0.7421 (mmm) REVERT: O 42 ASP cc_start: 0.8158 (t0) cc_final: 0.7829 (t0) REVERT: O 49 GLU cc_start: 0.8365 (mp0) cc_final: 0.8094 (mp0) REVERT: O 76 THR cc_start: 0.8590 (p) cc_final: 0.8353 (p) REVERT: O 176 TYR cc_start: 0.8247 (m-10) cc_final: 0.7879 (m-10) REVERT: O 190 ASP cc_start: 0.8469 (t0) cc_final: 0.8022 (t0) REVERT: O 195 ILE cc_start: 0.8914 (mt) cc_final: 0.8373 (mp) REVERT: O 453 MET cc_start: 0.8447 (tpp) cc_final: 0.7994 (tpp) REVERT: O 486 TYR cc_start: 0.8345 (t80) cc_final: 0.8125 (t80) REVERT: O 487 LEU cc_start: 0.8727 (tt) cc_final: 0.8503 (tp) REVERT: O 492 GLN cc_start: 0.8445 (mt0) cc_final: 0.7788 (tm-30) REVERT: P 10 MET cc_start: 0.7491 (tpp) cc_final: 0.6983 (mmm) REVERT: P 60 LYS cc_start: 0.8503 (mttm) cc_final: 0.8176 (mmtm) REVERT: Q 1 MET cc_start: 0.8844 (mmp) cc_final: 0.7935 (mmm) REVERT: Q 34 MET cc_start: 0.8607 (ptp) cc_final: 0.8155 (ptp) REVERT: Q 47 LYS cc_start: 0.8683 (mttp) cc_final: 0.8328 (pttt) REVERT: Q 71 ASP cc_start: 0.8974 (t70) cc_final: 0.8634 (t0) REVERT: Q 148 GLN cc_start: 0.8806 (tt0) cc_final: 0.8344 (tm-30) REVERT: Q 156 GLN cc_start: 0.8790 (mt0) cc_final: 0.8456 (mt0) REVERT: Q 186 ARG cc_start: 0.8830 (mmm160) cc_final: 0.8539 (mmt180) REVERT: Q 193 GLU cc_start: 0.6428 (pm20) cc_final: 0.5297 (pm20) REVERT: Q 204 TRP cc_start: 0.9379 (m-90) cc_final: 0.8721 (m-90) REVERT: Q 390 TYR cc_start: 0.8508 (t80) cc_final: 0.8239 (t80) REVERT: R 68 MET cc_start: 0.8630 (mmm) cc_final: 0.7533 (tmm) REVERT: S 399 MET cc_start: 0.7869 (tmm) cc_final: 0.7408 (tmm) REVERT: S 455 ILE cc_start: 0.9387 (tp) cc_final: 0.9046 (tp) REVERT: T 43 THR cc_start: 0.8993 (m) cc_final: 0.8767 (m) REVERT: T 51 HIS cc_start: 0.7891 (t-90) cc_final: 0.7613 (t-90) REVERT: U 3 GLN cc_start: 0.7653 (pm20) cc_final: 0.7094 (pm20) REVERT: U 21 SER cc_start: 0.8443 (p) cc_final: 0.8192 (p) REVERT: U 27 TYR cc_start: 0.8146 (p90) cc_final: 0.7535 (p90) REVERT: U 29 PHE cc_start: 0.6602 (t80) cc_final: 0.6108 (t80) REVERT: U 36 TRP cc_start: 0.7497 (m100) cc_final: 0.6605 (m100) REVERT: U 81 MET cc_start: 0.7490 (ttt) cc_final: 0.5880 (ttt) REVERT: U 111 TYR cc_start: 0.7944 (m-80) cc_final: 0.7626 (m-80) REVERT: V 3 VAL cc_start: 0.6830 (p) cc_final: 0.6026 (m) outliers start: 4 outliers final: 0 residues processed: 1018 average time/residue: 0.3837 time to fit residues: 631.6747 Evaluate side-chains 838 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 838 time to evaluate : 3.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 321 optimal weight: 6.9990 chunk 360 optimal weight: 10.0000 chunk 320 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 300 optimal weight: 8.9990 chunk 303 optimal weight: 10.0000 chunk 266 optimal weight: 0.7980 chunk 155 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- 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 C 149 HIS C 209 GLN ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 17 GLN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 GLN F 59 GLN L 16 GLN L 38 GLN O 192 ASN O 207 HIS P 51 HIS P 59 GLN Q 209 GLN Q 280 HIS ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN ** S 27 HIS ** 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: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.129740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.111385 restraints weight = 52124.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.114104 restraints weight = 28901.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.115907 restraints weight = 18710.503| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 30656 Z= 0.192 Angle : 0.706 13.079 41636 Z= 0.358 Chirality : 0.047 0.231 4862 Planarity : 0.004 0.072 5182 Dihedral : 8.030 72.387 4716 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 0.12 % Allowed : 5.25 % Favored : 94.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.13), residues: 3838 helix: 0.76 (0.17), residues: 906 sheet: -1.12 (0.17), residues: 964 loop : -2.01 (0.13), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 451 HIS 0.009 0.001 HIS C 149 PHE 0.020 0.002 PHE F 42 TYR 0.018 0.002 TYR S 297 ARG 0.006 0.001 ARG E 2 Details of bonding type rmsd link_NAG-ASN : bond 0.00336 ( 12) link_NAG-ASN : angle 2.30239 ( 36) link_BETA1-4 : bond 0.00511 ( 20) link_BETA1-4 : angle 1.98002 ( 60) hydrogen bonds : bond 0.04290 ( 1098) hydrogen bonds : angle 5.98898 ( 3024) SS BOND : bond 0.00450 ( 28) SS BOND : angle 1.70588 ( 56) covalent geometry : bond 0.00441 (30596) covalent geometry : angle 0.69766 (41484) *********************** 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 999 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 995 time to evaluate : 3.352 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 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 TARDY: cannot create tardy model for: "PRO R 72 " (corrupted residue). Skipping it. Corrupt residue: chain: R residue: PRO 72 >>> skipping 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 42 ASP cc_start: 0.8004 (t0) cc_final: 0.7656 (t0) REVERT: A 47 LYS cc_start: 0.9248 (pttm) cc_final: 0.8923 (pttm) REVERT: A 69 THR cc_start: 0.9184 (p) cc_final: 0.8601 (p) REVERT: A 190 ASP cc_start: 0.8512 (t0) cc_final: 0.8107 (t0) REVERT: A 195 ILE cc_start: 0.8973 (mt) cc_final: 0.8289 (mp) REVERT: A 262 LEU cc_start: 0.9290 (pt) cc_final: 0.9011 (pp) REVERT: A 312 GLU cc_start: 0.8670 (tp30) cc_final: 0.8188 (tp30) REVERT: A 453 MET cc_start: 0.8588 (tpp) cc_final: 0.8276 (tpp) REVERT: A 486 TYR cc_start: 0.8372 (t80) cc_final: 0.8086 (t80) REVERT: A 487 LEU cc_start: 0.8794 (tt) cc_final: 0.8571 (tp) REVERT: A 492 GLN cc_start: 0.8485 (mt0) cc_final: 0.8258 (mt0) REVERT: B 60 LYS cc_start: 0.8472 (mttm) cc_final: 0.8040 (mmtm) REVERT: C 1 MET cc_start: 0.8452 (mmp) cc_final: 0.7441 (mmm) REVERT: C 47 LYS cc_start: 0.8558 (mttp) cc_final: 0.8229 (pttt) REVERT: C 71 ASP cc_start: 0.8945 (t70) cc_final: 0.8665 (t0) REVERT: C 193 GLU cc_start: 0.6467 (pm20) cc_final: 0.5437 (pm20) REVERT: C 204 TRP cc_start: 0.9379 (m-90) cc_final: 0.8728 (m-90) REVERT: C 286 LYS cc_start: 0.8208 (tttm) cc_final: 0.7870 (mtpp) REVERT: C 324 TYR cc_start: 0.8731 (t80) cc_final: 0.7802 (t80) REVERT: E 61 ILE cc_start: 0.9237 (tp) cc_final: 0.9009 (tp) REVERT: E 399 MET cc_start: 0.7862 (tmm) cc_final: 0.7374 (tmm) REVERT: F 43 THR cc_start: 0.9010 (m) cc_final: 0.8808 (m) REVERT: H 3 GLN cc_start: 0.7513 (pm20) cc_final: 0.7126 (pm20) REVERT: H 21 SER cc_start: 0.8404 (p) cc_final: 0.8142 (p) REVERT: H 27 TYR cc_start: 0.8111 (p90) cc_final: 0.7422 (p90) REVERT: H 29 PHE cc_start: 0.6555 (t80) cc_final: 0.6026 (t80) REVERT: H 36 TRP cc_start: 0.7519 (m100) cc_final: 0.6653 (m100) REVERT: H 46 GLU cc_start: 0.8965 (pm20) cc_final: 0.8355 (pm20) REVERT: H 81 MET cc_start: 0.7838 (ttt) cc_final: 0.6502 (ttt) REVERT: L 3 VAL cc_start: 0.6886 (p) cc_final: 0.6098 (m) REVERT: L 28 ASN cc_start: 0.8383 (p0) cc_final: 0.7716 (p0) REVERT: L 87 TYR cc_start: 0.7921 (m-80) cc_final: 0.7265 (m-10) REVERT: O 42 ASP cc_start: 0.8013 (t0) cc_final: 0.7658 (t0) REVERT: O 47 LYS cc_start: 0.9215 (pttm) cc_final: 0.8903 (pttm) REVERT: O 69 THR cc_start: 0.9173 (p) cc_final: 0.8606 (p) REVERT: O 76 THR cc_start: 0.8078 (p) cc_final: 0.7852 (p) REVERT: O 190 ASP cc_start: 0.8520 (t0) cc_final: 0.8068 (t0) REVERT: O 195 ILE cc_start: 0.8956 (mt) cc_final: 0.8304 (mp) REVERT: O 210 TRP cc_start: 0.9220 (t60) cc_final: 0.8830 (t60) REVERT: O 262 LEU cc_start: 0.9277 (pt) cc_final: 0.8964 (pp) REVERT: O 312 GLU cc_start: 0.8712 (tp30) cc_final: 0.8193 (tp30) REVERT: O 453 MET cc_start: 0.8589 (tpp) cc_final: 0.8255 (tpp) REVERT: O 486 TYR cc_start: 0.8367 (t80) cc_final: 0.8089 (t80) REVERT: O 487 LEU cc_start: 0.8794 (tt) cc_final: 0.8565 (tp) REVERT: O 492 GLN cc_start: 0.8505 (mt0) cc_final: 0.8264 (mt0) REVERT: P 59 GLN cc_start: 0.7796 (mt0) cc_final: 0.7578 (mt0) REVERT: P 60 LYS cc_start: 0.8529 (mttm) cc_final: 0.8162 (mmtm) REVERT: Q 1 MET cc_start: 0.8480 (mmp) cc_final: 0.7487 (mmm) REVERT: Q 47 LYS cc_start: 0.8555 (mttp) cc_final: 0.8223 (pttt) REVERT: Q 71 ASP cc_start: 0.8967 (t70) cc_final: 0.8667 (t0) REVERT: Q 193 GLU cc_start: 0.6422 (pm20) cc_final: 0.5391 (pm20) REVERT: Q 204 TRP cc_start: 0.9372 (m-90) cc_final: 0.8726 (m-90) REVERT: Q 286 LYS cc_start: 0.8213 (tttm) cc_final: 0.7860 (mtpp) REVERT: Q 324 TYR cc_start: 0.8746 (t80) cc_final: 0.7772 (t80) REVERT: S 61 ILE cc_start: 0.9239 (tp) cc_final: 0.9009 (tp) REVERT: S 399 MET cc_start: 0.7857 (tmm) cc_final: 0.7371 (tmm) REVERT: T 43 THR cc_start: 0.9002 (m) cc_final: 0.8801 (m) REVERT: U 3 GLN cc_start: 0.7532 (pm20) cc_final: 0.7128 (pm20) REVERT: U 21 SER cc_start: 0.8409 (p) cc_final: 0.8142 (p) REVERT: U 27 TYR cc_start: 0.8129 (p90) cc_final: 0.7401 (p90) REVERT: U 29 PHE cc_start: 0.6564 (t80) cc_final: 0.6016 (t80) REVERT: U 36 TRP cc_start: 0.7569 (m100) cc_final: 0.7051 (m100) REVERT: U 46 GLU cc_start: 0.8963 (pm20) cc_final: 0.8345 (pm20) REVERT: U 81 MET cc_start: 0.7748 (ttt) cc_final: 0.6509 (ttt) REVERT: U 111 TYR cc_start: 0.7866 (m-80) cc_final: 0.7644 (m-80) REVERT: V 3 VAL cc_start: 0.6889 (p) cc_final: 0.6079 (m) REVERT: V 28 ASN cc_start: 0.8324 (p0) cc_final: 0.8036 (p0) REVERT: V 87 TYR cc_start: 0.7924 (m-80) cc_final: 0.7254 (m-10) outliers start: 4 outliers final: 2 residues processed: 997 average time/residue: 0.3786 time to fit residues: 612.6317 Evaluate side-chains 822 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 820 time to evaluate : 3.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 182 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 205 optimal weight: 9.9990 chunk 272 optimal weight: 9.9990 chunk 242 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 290 optimal weight: 2.9990 chunk 378 optimal weight: 20.0000 chunk 131 optimal weight: 2.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 192 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 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 364 ASN F 59 GLN L 16 GLN L 38 GLN O 192 ASN Q 149 HIS ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 467 ASN R 17 GLN ** S 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 207 HIS S 364 ASN T 59 GLN ** U 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 16 GLN V 38 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.130301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.112184 restraints weight = 51912.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.114844 restraints weight = 29305.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.116593 restraints weight = 19119.823| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 30656 Z= 0.226 Angle : 0.736 10.194 41636 Z= 0.372 Chirality : 0.047 0.235 4862 Planarity : 0.004 0.061 5182 Dihedral : 7.405 63.118 4716 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 0.12 % Allowed : 3.69 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.13), residues: 3838 helix: 0.70 (0.17), residues: 908 sheet: -1.14 (0.17), residues: 948 loop : -2.02 (0.13), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 451 HIS 0.016 0.001 HIS Q 149 PHE 0.017 0.002 PHE P 42 TYR 0.021 0.002 TYR B 52 ARG 0.010 0.001 ARG S 186 Details of bonding type rmsd link_NAG-ASN : bond 0.00427 ( 12) link_NAG-ASN : angle 2.32004 ( 36) link_BETA1-4 : bond 0.00494 ( 20) link_BETA1-4 : angle 1.84644 ( 60) hydrogen bonds : bond 0.04330 ( 1098) hydrogen bonds : angle 5.95179 ( 3024) SS BOND : bond 0.00497 ( 28) SS BOND : angle 1.73965 ( 56) covalent geometry : bond 0.00523 (30596) covalent geometry : angle 0.72761 (41484) *********************** 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 1004 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1000 time to evaluate : 2.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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 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 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 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: 0.7971 (t0) cc_final: 0.7614 (t0) REVERT: A 47 LYS cc_start: 0.9363 (pttm) cc_final: 0.9115 (pttm) REVERT: A 69 THR cc_start: 0.9253 (p) cc_final: 0.8681 (p) REVERT: A 176 TYR cc_start: 0.8321 (m-10) cc_final: 0.8019 (m-10) REVERT: A 195 ILE cc_start: 0.8892 (mt) cc_final: 0.8263 (mt) REVERT: A 209 GLN cc_start: 0.7283 (tm-30) cc_final: 0.6667 (tm-30) REVERT: A 262 LEU cc_start: 0.9340 (pt) cc_final: 0.9099 (pp) REVERT: A 312 GLU cc_start: 0.8555 (tp30) cc_final: 0.7889 (tp30) REVERT: A 353 ASN cc_start: 0.8499 (t0) cc_final: 0.8084 (t0) REVERT: A 453 MET cc_start: 0.8620 (tpp) cc_final: 0.8326 (tpp) REVERT: A 486 TYR cc_start: 0.8365 (t80) cc_final: 0.8111 (t80) REVERT: A 487 LEU cc_start: 0.8698 (tt) cc_final: 0.8474 (tp) REVERT: A 492 GLN cc_start: 0.8499 (mt0) cc_final: 0.7789 (tm-30) REVERT: B 60 LYS cc_start: 0.8317 (mttm) cc_final: 0.8042 (mttt) REVERT: B 68 MET cc_start: 0.8520 (tpp) cc_final: 0.7410 (ttp) REVERT: B 70 VAL cc_start: 0.8493 (t) cc_final: 0.8219 (t) REVERT: C 1 MET cc_start: 0.8627 (mmp) cc_final: 0.7814 (mmm) REVERT: C 47 LYS cc_start: 0.8702 (mttp) cc_final: 0.8289 (tttt) REVERT: C 71 ASP cc_start: 0.8875 (t70) cc_final: 0.8658 (t0) REVERT: C 204 TRP cc_start: 0.9360 (m-90) cc_final: 0.8767 (m-90) REVERT: C 408 ARG cc_start: 0.8893 (tpp80) cc_final: 0.8684 (tpp80) REVERT: C 433 MET cc_start: 0.7912 (tpp) cc_final: 0.7486 (tpp) REVERT: D 30 GLU cc_start: 0.8246 (tp30) cc_final: 0.7824 (tp30) REVERT: E 61 ILE cc_start: 0.9244 (tp) cc_final: 0.8973 (tp) REVERT: E 399 MET cc_start: 0.7939 (tmm) cc_final: 0.7438 (tmm) REVERT: E 455 ILE cc_start: 0.9365 (tp) cc_final: 0.9061 (tp) REVERT: F 10 MET cc_start: 0.8290 (mmp) cc_final: 0.8053 (mmp) REVERT: F 15 ARG cc_start: 0.8019 (mmt180) cc_final: 0.7743 (mmt90) REVERT: H 3 GLN cc_start: 0.7529 (pm20) cc_final: 0.7182 (pm20) REVERT: H 21 SER cc_start: 0.8452 (p) cc_final: 0.8163 (p) REVERT: H 27 TYR cc_start: 0.8080 (p90) cc_final: 0.7537 (p90) REVERT: H 29 PHE cc_start: 0.6715 (t80) cc_final: 0.6221 (t80) REVERT: H 36 TRP cc_start: 0.7471 (m100) cc_final: 0.6944 (m100) REVERT: H 81 MET cc_start: 0.7894 (ttt) cc_final: 0.6652 (ttt) REVERT: L 3 VAL cc_start: 0.6865 (p) cc_final: 0.6008 (m) REVERT: L 28 ASN cc_start: 0.8575 (p0) cc_final: 0.8027 (p0) REVERT: O 42 ASP cc_start: 0.7955 (t0) cc_final: 0.7603 (t0) REVERT: O 47 LYS cc_start: 0.9331 (pttm) cc_final: 0.9104 (pttm) REVERT: O 69 THR cc_start: 0.9231 (p) cc_final: 0.8676 (p) REVERT: O 176 TYR cc_start: 0.8327 (m-10) cc_final: 0.8016 (m-10) REVERT: O 195 ILE cc_start: 0.8889 (mt) cc_final: 0.8277 (mt) REVERT: O 209 GLN cc_start: 0.7465 (tm-30) cc_final: 0.6663 (tm-30) REVERT: O 210 TRP cc_start: 0.9093 (t60) cc_final: 0.8735 (t60) REVERT: O 262 LEU cc_start: 0.9319 (pt) cc_final: 0.9027 (pp) REVERT: O 312 GLU cc_start: 0.8618 (tp30) cc_final: 0.8081 (tp30) REVERT: O 453 MET cc_start: 0.8613 (tpp) cc_final: 0.8316 (tpp) REVERT: O 486 TYR cc_start: 0.8368 (t80) cc_final: 0.8101 (t80) REVERT: O 487 LEU cc_start: 0.8691 (tt) cc_final: 0.8477 (tp) REVERT: O 492 GLN cc_start: 0.8503 (mt0) cc_final: 0.7778 (tm-30) REVERT: P 60 LYS cc_start: 0.8356 (mttm) cc_final: 0.8025 (mttt) REVERT: P 68 MET cc_start: 0.8511 (tpp) cc_final: 0.7373 (ttp) REVERT: P 70 VAL cc_start: 0.8491 (t) cc_final: 0.8261 (t) REVERT: Q 1 MET cc_start: 0.8476 (mmp) cc_final: 0.7792 (mmm) REVERT: Q 47 LYS cc_start: 0.8706 (mttp) cc_final: 0.8298 (tttt) REVERT: Q 71 ASP cc_start: 0.8973 (t70) cc_final: 0.8689 (t0) REVERT: Q 204 TRP cc_start: 0.9353 (m-90) cc_final: 0.8772 (m-90) REVERT: Q 286 LYS cc_start: 0.8278 (tttm) cc_final: 0.7869 (mtpp) REVERT: Q 433 MET cc_start: 0.8026 (tpp) cc_final: 0.7712 (tpp) REVERT: R 30 GLU cc_start: 0.8246 (tp30) cc_final: 0.7813 (tp30) REVERT: S 26 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8075 (mt-10) REVERT: S 61 ILE cc_start: 0.9237 (tp) cc_final: 0.8964 (tp) REVERT: S 399 MET cc_start: 0.7934 (tmm) cc_final: 0.7418 (tmm) REVERT: S 455 ILE cc_start: 0.9364 (tp) cc_final: 0.9061 (tp) REVERT: T 10 MET cc_start: 0.8282 (mmp) cc_final: 0.8027 (mmp) REVERT: U 3 GLN cc_start: 0.7522 (pm20) cc_final: 0.7187 (pm20) REVERT: U 21 SER cc_start: 0.8481 (p) cc_final: 0.8196 (p) REVERT: U 27 TYR cc_start: 0.8059 (p90) cc_final: 0.7615 (p90) REVERT: U 29 PHE cc_start: 0.6704 (t80) cc_final: 0.6186 (t80) REVERT: U 36 TRP cc_start: 0.7476 (m100) cc_final: 0.6948 (m100) REVERT: U 81 MET cc_start: 0.7870 (ttt) cc_final: 0.6639 (ttt) REVERT: U 98 ARG cc_start: 0.6834 (ttp-170) cc_final: 0.6197 (ttp-110) REVERT: U 111 TYR cc_start: 0.7934 (m-80) cc_final: 0.7526 (m-80) REVERT: U 118 VAL cc_start: 0.8085 (m) cc_final: 0.7861 (p) REVERT: V 3 VAL cc_start: 0.6856 (p) cc_final: 0.6022 (m) REVERT: V 28 ASN cc_start: 0.8508 (p0) cc_final: 0.8299 (p0) outliers start: 4 outliers final: 0 residues processed: 1004 average time/residue: 0.3826 time to fit residues: 625.2103 Evaluate side-chains 816 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 816 time to evaluate : 3.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 90 optimal weight: 30.0000 chunk 109 optimal weight: 4.9990 chunk 129 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 149 optimal weight: 10.0000 chunk 245 optimal weight: 5.9990 chunk 271 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 chunk 300 optimal weight: 6.9990 chunk 174 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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** B 51 HIS C 209 GLN ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 17 GLN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 364 ASN F 59 GLN L 16 GLN L 38 GLN O 192 ASN P 51 HIS Q 77 GLN Q 209 GLN ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN ** S 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 364 ASN T 59 GLN V 16 GLN V 38 GLN V 52 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.129893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.111639 restraints weight = 52459.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.114305 restraints weight = 29321.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.116107 restraints weight = 19105.971| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 30656 Z= 0.184 Angle : 0.706 12.769 41636 Z= 0.356 Chirality : 0.046 0.185 4862 Planarity : 0.004 0.057 5182 Dihedral : 6.856 53.033 4716 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.25 % Allowed : 3.72 % Favored : 96.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.13), residues: 3838 helix: 0.77 (0.17), residues: 908 sheet: -1.06 (0.17), residues: 972 loop : -2.00 (0.13), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP S 451 HIS 0.007 0.001 HIS P 51 PHE 0.020 0.002 PHE T 42 TYR 0.016 0.002 TYR C 442 ARG 0.006 0.001 ARG C 405 Details of bonding type rmsd link_NAG-ASN : bond 0.00304 ( 12) link_NAG-ASN : angle 2.18269 ( 36) link_BETA1-4 : bond 0.00478 ( 20) link_BETA1-4 : angle 1.65334 ( 60) hydrogen bonds : bond 0.04116 ( 1098) hydrogen bonds : angle 5.77575 ( 3024) SS BOND : bond 0.00479 ( 28) SS BOND : angle 1.60369 ( 56) covalent geometry : bond 0.00426 (30596) covalent geometry : angle 0.69893 (41484) *********************** 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 1005 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 997 time to evaluate : 3.265 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 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: symmetry clash REVERT: A 42 ASP cc_start: 0.7701 (t0) cc_final: 0.7325 (t0) REVERT: A 47 LYS cc_start: 0.9370 (pttm) cc_final: 0.9070 (pttm) REVERT: A 69 THR cc_start: 0.9256 (p) cc_final: 0.8622 (p) REVERT: A 176 TYR cc_start: 0.8323 (m-10) cc_final: 0.7978 (m-10) REVERT: A 209 GLN cc_start: 0.7571 (tm-30) cc_final: 0.7044 (tm-30) REVERT: A 262 LEU cc_start: 0.9277 (pt) cc_final: 0.9038 (pp) REVERT: A 312 GLU cc_start: 0.8494 (tp30) cc_final: 0.7630 (tp30) REVERT: A 323 GLU cc_start: 0.8470 (tp30) cc_final: 0.8148 (tp30) REVERT: A 453 MET cc_start: 0.8620 (tpp) cc_final: 0.8347 (tpp) REVERT: A 486 TYR cc_start: 0.8342 (t80) cc_final: 0.8085 (t80) REVERT: A 487 LEU cc_start: 0.8667 (tt) cc_final: 0.8448 (tp) REVERT: A 492 GLN cc_start: 0.8517 (mt0) cc_final: 0.7837 (tm-30) REVERT: B 60 LYS cc_start: 0.8208 (mttm) cc_final: 0.7969 (mmtm) REVERT: C 1 MET cc_start: 0.8420 (mmp) cc_final: 0.7223 (mmm) REVERT: C 47 LYS cc_start: 0.8695 (mttp) cc_final: 0.8171 (tttt) REVERT: C 57 ARG cc_start: 0.9278 (tpp80) cc_final: 0.8897 (tpp80) REVERT: C 71 ASP cc_start: 0.8950 (t70) cc_final: 0.8668 (t0) REVERT: C 101 TRP cc_start: 0.8658 (m-10) cc_final: 0.8208 (m-10) REVERT: C 193 GLU cc_start: 0.6139 (pm20) cc_final: 0.5167 (pm20) REVERT: C 204 TRP cc_start: 0.9364 (m-90) cc_final: 0.8795 (m-90) REVERT: C 286 LYS cc_start: 0.8193 (tttm) cc_final: 0.7830 (mtpp) REVERT: C 408 ARG cc_start: 0.8949 (tpp80) cc_final: 0.8689 (tpp80) REVERT: D 30 GLU cc_start: 0.8269 (tp30) cc_final: 0.7815 (tp30) REVERT: E 26 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8083 (mt-10) REVERT: E 61 ILE cc_start: 0.9241 (tp) cc_final: 0.8994 (tp) REVERT: E 399 MET cc_start: 0.7902 (tmm) cc_final: 0.7427 (tmm) REVERT: E 455 ILE cc_start: 0.9368 (tp) cc_final: 0.9073 (tp) REVERT: F 10 MET cc_start: 0.8199 (mmp) cc_final: 0.7903 (mmt) REVERT: F 28 GLN cc_start: 0.7438 (mm-40) cc_final: 0.7156 (mm-40) REVERT: F 43 THR cc_start: 0.9001 (m) cc_final: 0.8790 (m) REVERT: H 3 GLN cc_start: 0.7535 (pm20) cc_final: 0.7157 (pm20) REVERT: H 21 SER cc_start: 0.8396 (p) cc_final: 0.8119 (p) REVERT: H 27 TYR cc_start: 0.8024 (p90) cc_final: 0.7539 (p90) REVERT: H 29 PHE cc_start: 0.6597 (t80) cc_final: 0.6193 (t80) REVERT: H 36 TRP cc_start: 0.7551 (m100) cc_final: 0.6980 (m100) REVERT: H 81 MET cc_start: 0.7519 (ttt) cc_final: 0.6477 (ttt) REVERT: L 3 VAL cc_start: 0.6794 (p) cc_final: 0.5937 (m) REVERT: L 28 ASN cc_start: 0.8431 (p0) cc_final: 0.7939 (p0) REVERT: O 42 ASP cc_start: 0.7701 (t0) cc_final: 0.7325 (t0) REVERT: O 47 LYS cc_start: 0.9348 (pttm) cc_final: 0.9056 (pttm) REVERT: O 69 THR cc_start: 0.9232 (p) cc_final: 0.8604 (p) REVERT: O 176 TYR cc_start: 0.8333 (m-10) cc_final: 0.7987 (m-10) REVERT: O 209 GLN cc_start: 0.7398 (tm-30) cc_final: 0.6535 (tm-30) REVERT: O 262 LEU cc_start: 0.9260 (pt) cc_final: 0.9014 (pp) REVERT: O 312 GLU cc_start: 0.8608 (tp30) cc_final: 0.7787 (tp30) REVERT: O 323 GLU cc_start: 0.8490 (tp30) cc_final: 0.8168 (tp30) REVERT: O 453 MET cc_start: 0.8612 (tpp) cc_final: 0.8344 (tpp) REVERT: O 486 TYR cc_start: 0.8345 (t80) cc_final: 0.8082 (t80) REVERT: O 487 LEU cc_start: 0.8667 (tt) cc_final: 0.8449 (tp) REVERT: O 492 GLN cc_start: 0.8502 (mt0) cc_final: 0.7816 (tm-30) REVERT: Q 1 MET cc_start: 0.8414 (mmp) cc_final: 0.7415 (mmm) REVERT: Q 47 LYS cc_start: 0.8698 (mttp) cc_final: 0.8188 (tttt) REVERT: Q 57 ARG cc_start: 0.9273 (tpp80) cc_final: 0.8893 (tpp80) REVERT: Q 71 ASP cc_start: 0.8966 (t70) cc_final: 0.8663 (t0) REVERT: Q 101 TRP cc_start: 0.8648 (m-10) cc_final: 0.8198 (m-10) REVERT: Q 204 TRP cc_start: 0.9356 (m-90) cc_final: 0.8795 (m-90) REVERT: Q 286 LYS cc_start: 0.8182 (tttm) cc_final: 0.7849 (mtpp) REVERT: Q 433 MET cc_start: 0.8051 (tpp) cc_final: 0.7724 (tpp) REVERT: R 30 GLU cc_start: 0.8261 (tp30) cc_final: 0.7809 (tp30) REVERT: S 2 ARG cc_start: 0.7872 (ttt180) cc_final: 0.7397 (ttt180) REVERT: S 61 ILE cc_start: 0.9240 (tp) cc_final: 0.8948 (tp) REVERT: S 399 MET cc_start: 0.7909 (tmm) cc_final: 0.7431 (tmm) REVERT: S 455 ILE cc_start: 0.9362 (tp) cc_final: 0.9067 (tp) REVERT: T 10 MET cc_start: 0.8162 (mmp) cc_final: 0.7909 (mmt) REVERT: T 15 ARG cc_start: 0.7991 (mmt180) cc_final: 0.7735 (mmt90) REVERT: T 28 GLN cc_start: 0.7440 (mm-40) cc_final: 0.7156 (mm-40) REVERT: T 43 THR cc_start: 0.8998 (m) cc_final: 0.8792 (m) REVERT: U 3 GLN cc_start: 0.7526 (pm20) cc_final: 0.7161 (pm20) REVERT: U 21 SER cc_start: 0.8399 (p) cc_final: 0.8107 (p) REVERT: U 27 TYR cc_start: 0.8025 (p90) cc_final: 0.7449 (p90) REVERT: U 29 PHE cc_start: 0.6594 (t80) cc_final: 0.6192 (t80) REVERT: U 36 TRP cc_start: 0.7559 (m100) cc_final: 0.6888 (m100) REVERT: U 81 MET cc_start: 0.7587 (ttt) cc_final: 0.6697 (ttt) REVERT: U 111 TYR cc_start: 0.7544 (m-80) cc_final: 0.7246 (m-80) REVERT: V 3 VAL cc_start: 0.6804 (p) cc_final: 0.5924 (m) REVERT: V 28 ASN cc_start: 0.8655 (p0) cc_final: 0.8382 (p0) outliers start: 8 outliers final: 3 residues processed: 1001 average time/residue: 0.3812 time to fit residues: 617.3451 Evaluate side-chains 843 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 840 time to evaluate : 3.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 148 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 273 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 379 optimal weight: 3.9990 chunk 320 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 17 GLN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 364 ASN F 59 GLN L 16 GLN L 38 GLN ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN O 89 ASN ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN ** S 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 364 ASN T 59 GLN V 16 GLN V 38 GLN V 53 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.129364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.111258 restraints weight = 52376.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.113946 restraints weight = 29255.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.115701 restraints weight = 19024.578| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 30656 Z= 0.228 Angle : 0.747 10.716 41636 Z= 0.377 Chirality : 0.047 0.238 4862 Planarity : 0.005 0.060 5182 Dihedral : 6.688 52.405 4716 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 0.06 % Allowed : 2.53 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.13), residues: 3838 helix: 0.69 (0.17), residues: 908 sheet: -1.02 (0.17), residues: 976 loop : -2.08 (0.13), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 218 HIS 0.010 0.001 HIS Q 280 PHE 0.028 0.002 PHE F 42 TYR 0.027 0.002 TYR P 52 ARG 0.007 0.001 ARG A 2 Details of bonding type rmsd link_NAG-ASN : bond 0.00469 ( 12) link_NAG-ASN : angle 2.23855 ( 36) link_BETA1-4 : bond 0.00493 ( 20) link_BETA1-4 : angle 1.59606 ( 60) hydrogen bonds : bond 0.04287 ( 1098) hydrogen bonds : angle 5.82131 ( 3024) SS BOND : bond 0.00546 ( 28) SS BOND : angle 1.73792 ( 56) covalent geometry : bond 0.00529 (30596) covalent geometry : angle 0.74038 (41484) *********************** 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 994 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 992 time to evaluate : 3.677 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 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: 0.7702 (t0) cc_final: 0.7274 (t0) REVERT: A 47 LYS cc_start: 0.9377 (pttm) cc_final: 0.9099 (pttm) REVERT: A 69 THR cc_start: 0.9281 (p) cc_final: 0.8664 (p) REVERT: A 71 ASP cc_start: 0.7312 (t70) cc_final: 0.7017 (t0) REVERT: A 176 TYR cc_start: 0.8365 (m-10) cc_final: 0.7960 (m-10) REVERT: A 209 GLN cc_start: 0.7655 (tm-30) cc_final: 0.7285 (tm-30) REVERT: A 210 TRP cc_start: 0.9165 (t60) cc_final: 0.8765 (t60) REVERT: A 312 GLU cc_start: 0.8660 (tp30) cc_final: 0.8003 (tp30) REVERT: A 357 THR cc_start: 0.8330 (p) cc_final: 0.8123 (p) REVERT: A 453 MET cc_start: 0.8667 (tpp) cc_final: 0.8394 (tpp) REVERT: A 486 TYR cc_start: 0.8368 (t80) cc_final: 0.8081 (t80) REVERT: A 487 LEU cc_start: 0.8713 (tt) cc_final: 0.8485 (tp) REVERT: A 492 GLN cc_start: 0.8537 (mt0) cc_final: 0.8313 (mt0) REVERT: B 70 VAL cc_start: 0.8489 (t) cc_final: 0.8272 (t) REVERT: C 1 MET cc_start: 0.8447 (mmp) cc_final: 0.7222 (mmm) REVERT: C 47 LYS cc_start: 0.8743 (mttp) cc_final: 0.8144 (tttt) REVERT: C 57 ARG cc_start: 0.9283 (tpp80) cc_final: 0.9062 (tpp80) REVERT: C 71 ASP cc_start: 0.8977 (t70) cc_final: 0.8639 (t0) REVERT: C 101 TRP cc_start: 0.8691 (m-10) cc_final: 0.8183 (m-10) REVERT: C 193 GLU cc_start: 0.6288 (pm20) cc_final: 0.5112 (pm20) REVERT: C 204 TRP cc_start: 0.9359 (m-90) cc_final: 0.8778 (m-90) REVERT: C 233 GLU cc_start: 0.7525 (tm-30) cc_final: 0.7252 (tm-30) REVERT: C 286 LYS cc_start: 0.8180 (tttm) cc_final: 0.7843 (mtpp) REVERT: C 324 TYR cc_start: 0.8678 (t80) cc_final: 0.8008 (t80) REVERT: D 30 GLU cc_start: 0.8298 (tp30) cc_final: 0.7861 (tp30) REVERT: E 61 ILE cc_start: 0.9312 (tp) cc_final: 0.9100 (tp) REVERT: E 399 MET cc_start: 0.8044 (tmm) cc_final: 0.7498 (tmm) REVERT: E 455 ILE cc_start: 0.9378 (tp) cc_final: 0.9075 (tp) REVERT: F 28 GLN cc_start: 0.7411 (mm-40) cc_final: 0.7091 (mm-40) REVERT: F 43 THR cc_start: 0.9092 (m) cc_final: 0.8850 (m) REVERT: H 3 GLN cc_start: 0.7433 (pm20) cc_final: 0.7020 (pm20) REVERT: H 21 SER cc_start: 0.8434 (p) cc_final: 0.8192 (p) REVERT: H 27 TYR cc_start: 0.8090 (p90) cc_final: 0.7353 (p90) REVERT: H 29 PHE cc_start: 0.6581 (t80) cc_final: 0.6247 (t80) REVERT: H 36 TRP cc_start: 0.7676 (m100) cc_final: 0.7295 (m100) REVERT: H 38 ARG cc_start: 0.8162 (tmm-80) cc_final: 0.7783 (tmm-80) REVERT: H 50 TRP cc_start: 0.8190 (m-10) cc_final: 0.7950 (m-10) REVERT: H 69 THR cc_start: 0.8418 (p) cc_final: 0.8103 (p) REVERT: H 81 MET cc_start: 0.7552 (ttt) cc_final: 0.6544 (tmm) REVERT: L 3 VAL cc_start: 0.6842 (p) cc_final: 0.6052 (m) REVERT: L 28 ASN cc_start: 0.8540 (p0) cc_final: 0.8070 (p0) REVERT: O 42 ASP cc_start: 0.7717 (t0) cc_final: 0.7285 (t0) REVERT: O 47 LYS cc_start: 0.9355 (pttm) cc_final: 0.9082 (pttm) REVERT: O 69 THR cc_start: 0.9256 (p) cc_final: 0.8651 (p) REVERT: O 71 ASP cc_start: 0.7321 (t70) cc_final: 0.7037 (t0) REVERT: O 176 TYR cc_start: 0.8385 (m-10) cc_final: 0.7966 (m-10) REVERT: O 209 GLN cc_start: 0.7623 (tm-30) cc_final: 0.7112 (tm-30) REVERT: O 312 GLU cc_start: 0.8571 (tp30) cc_final: 0.7959 (tp30) REVERT: O 357 THR cc_start: 0.8340 (p) cc_final: 0.8130 (p) REVERT: O 453 MET cc_start: 0.8662 (tpp) cc_final: 0.8380 (tpp) REVERT: O 486 TYR cc_start: 0.8373 (t80) cc_final: 0.8082 (t80) REVERT: O 487 LEU cc_start: 0.8712 (tt) cc_final: 0.8485 (tp) REVERT: O 492 GLN cc_start: 0.8540 (mt0) cc_final: 0.8310 (mt0) REVERT: P 60 LYS cc_start: 0.8240 (mttm) cc_final: 0.7932 (mtpt) REVERT: Q 1 MET cc_start: 0.8447 (mmp) cc_final: 0.7242 (mmm) REVERT: Q 47 LYS cc_start: 0.8721 (mttp) cc_final: 0.8134 (tttt) REVERT: Q 57 ARG cc_start: 0.9280 (tpp80) cc_final: 0.9062 (tpp80) REVERT: Q 71 ASP cc_start: 0.9007 (t70) cc_final: 0.8677 (t0) REVERT: Q 101 TRP cc_start: 0.8644 (m-10) cc_final: 0.8203 (m-10) REVERT: Q 193 GLU cc_start: 0.6343 (pm20) cc_final: 0.5117 (pm20) REVERT: Q 204 TRP cc_start: 0.9357 (m-90) cc_final: 0.8776 (m-90) REVERT: Q 233 GLU cc_start: 0.7519 (tm-30) cc_final: 0.7245 (tm-30) REVERT: Q 286 LYS cc_start: 0.8197 (tttm) cc_final: 0.7834 (mtpp) REVERT: Q 408 ARG cc_start: 0.8945 (tpp80) cc_final: 0.8745 (tpp80) REVERT: Q 433 MET cc_start: 0.8046 (tpp) cc_final: 0.7801 (tpp) REVERT: R 30 GLU cc_start: 0.8299 (tp30) cc_final: 0.7852 (tp30) REVERT: S 2 ARG cc_start: 0.7896 (ttt180) cc_final: 0.7517 (ttt180) REVERT: S 26 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8131 (mt-10) REVERT: S 399 MET cc_start: 0.8041 (tmm) cc_final: 0.7480 (tmm) REVERT: S 455 ILE cc_start: 0.9382 (tp) cc_final: 0.9070 (tp) REVERT: T 28 GLN cc_start: 0.7412 (mm-40) cc_final: 0.7100 (mm-40) REVERT: T 43 THR cc_start: 0.9087 (m) cc_final: 0.8849 (m) REVERT: U 3 GLN cc_start: 0.7413 (pm20) cc_final: 0.7022 (pm20) REVERT: U 21 SER cc_start: 0.8439 (p) cc_final: 0.8178 (p) REVERT: U 27 TYR cc_start: 0.8006 (p90) cc_final: 0.7575 (p90) REVERT: U 29 PHE cc_start: 0.6576 (t80) cc_final: 0.6220 (t80) REVERT: U 36 TRP cc_start: 0.7682 (m100) cc_final: 0.7010 (m100) REVERT: U 38 ARG cc_start: 0.8151 (tmm-80) cc_final: 0.7801 (tmm-80) REVERT: U 81 MET cc_start: 0.7578 (ttt) cc_final: 0.5522 (ttt) REVERT: U 98 ARG cc_start: 0.7193 (ttp-110) cc_final: 0.6677 (ttp-110) REVERT: V 3 VAL cc_start: 0.6866 (p) cc_final: 0.6058 (m) REVERT: V 28 ASN cc_start: 0.8768 (p0) cc_final: 0.8533 (p0) outliers start: 2 outliers final: 0 residues processed: 994 average time/residue: 0.3842 time to fit residues: 620.0146 Evaluate side-chains 839 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 839 time to evaluate : 3.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 347 optimal weight: 6.9990 chunk 203 optimal weight: 0.9990 chunk 196 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 chunk 222 optimal weight: 4.9990 chunk 141 optimal weight: 0.3980 chunk 215 optimal weight: 8.9990 chunk 275 optimal weight: 0.5980 chunk 219 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 HIS A 207 HIS B 51 HIS C 77 GLN C 94 HIS C 207 HIS C 209 GLN ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 17 GLN E 27 HIS ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 364 ASN F 59 GLN L 16 GLN ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN L 53 ASN O 144 HIS P 51 HIS Q 77 GLN Q 209 GLN ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN S 27 HIS ** S 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 364 ASN T 59 GLN V 16 GLN V 38 GLN V 52 ASN V 53 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.135229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.117118 restraints weight = 52130.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.119893 restraints weight = 28915.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.121734 restraints weight = 18664.188| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30656 Z= 0.128 Angle : 0.698 12.805 41636 Z= 0.347 Chirality : 0.045 0.202 4862 Planarity : 0.004 0.047 5182 Dihedral : 6.103 55.018 4716 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.22 % Allowed : 1.19 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.13), residues: 3838 helix: 0.83 (0.17), residues: 904 sheet: -1.00 (0.17), residues: 962 loop : -1.94 (0.13), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP U 50 HIS 0.008 0.001 HIS P 51 PHE 0.021 0.001 PHE C 335 TYR 0.015 0.001 TYR Q 486 ARG 0.009 0.001 ARG A 2 Details of bonding type rmsd link_NAG-ASN : bond 0.00209 ( 12) link_NAG-ASN : angle 2.01672 ( 36) link_BETA1-4 : bond 0.00502 ( 20) link_BETA1-4 : angle 1.54033 ( 60) hydrogen bonds : bond 0.03807 ( 1098) hydrogen bonds : angle 5.47821 ( 3024) SS BOND : bond 0.00443 ( 28) SS BOND : angle 1.61872 ( 56) covalent geometry : bond 0.00286 (30596) covalent geometry : angle 0.69170 (41484) *********************** 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 1056 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 1049 time to evaluate : 3.082 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 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: symmetry clash REVERT: A 49 GLU cc_start: 0.8369 (mp0) cc_final: 0.8138 (mp0) REVERT: A 69 THR cc_start: 0.9236 (p) cc_final: 0.8484 (p) REVERT: A 312 GLU cc_start: 0.8326 (tp30) cc_final: 0.7399 (tp30) REVERT: A 453 MET cc_start: 0.8496 (tpp) cc_final: 0.8210 (tpp) REVERT: A 486 TYR cc_start: 0.8278 (t80) cc_final: 0.7967 (t80) REVERT: A 487 LEU cc_start: 0.8693 (tt) cc_final: 0.8430 (tp) REVERT: A 492 GLN cc_start: 0.8511 (mt0) cc_final: 0.7802 (tm-30) REVERT: B 45 LEU cc_start: 0.9149 (tp) cc_final: 0.8829 (tp) REVERT: B 60 LYS cc_start: 0.8222 (mttm) cc_final: 0.7926 (mtpt) REVERT: B 68 MET cc_start: 0.8406 (tpp) cc_final: 0.7421 (ttp) REVERT: C 1 MET cc_start: 0.8223 (mmp) cc_final: 0.7792 (mmm) REVERT: C 47 LYS cc_start: 0.8465 (mttp) cc_final: 0.8128 (pttt) REVERT: C 71 ASP cc_start: 0.8819 (t70) cc_final: 0.8578 (t0) REVERT: C 101 TRP cc_start: 0.8785 (m-10) cc_final: 0.8390 (m-10) REVERT: C 204 TRP cc_start: 0.9208 (m-90) cc_final: 0.8766 (m-90) REVERT: C 233 GLU cc_start: 0.7399 (tm-30) cc_final: 0.7173 (tm-30) REVERT: C 286 LYS cc_start: 0.8170 (tttm) cc_final: 0.7962 (mtpp) REVERT: C 324 TYR cc_start: 0.8437 (t80) cc_final: 0.8023 (t80) REVERT: C 408 ARG cc_start: 0.8909 (tpp80) cc_final: 0.8444 (tpt170) REVERT: C 433 MET cc_start: 0.8029 (tpp) cc_final: 0.7755 (tpp) REVERT: D 30 GLU cc_start: 0.8295 (tp30) cc_final: 0.7941 (tp30) REVERT: D 68 MET cc_start: 0.8397 (mmm) cc_final: 0.6999 (tmm) REVERT: E 1 MET cc_start: 0.8165 (mmm) cc_final: 0.7927 (mmm) REVERT: E 26 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7697 (tt0) REVERT: E 41 LEU cc_start: 0.8993 (pt) cc_final: 0.8729 (pt) REVERT: E 116 CYS cc_start: 0.5878 (m) cc_final: 0.5472 (m) REVERT: E 399 MET cc_start: 0.8170 (tmm) cc_final: 0.7691 (tmm) REVERT: E 455 ILE cc_start: 0.9329 (tp) cc_final: 0.9027 (tp) REVERT: F 10 MET cc_start: 0.8211 (mmp) cc_final: 0.8010 (mmp) REVERT: F 15 ARG cc_start: 0.7851 (mmt180) cc_final: 0.7439 (mmt90) REVERT: F 33 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6171 (mt-10) REVERT: F 43 THR cc_start: 0.9125 (m) cc_final: 0.8838 (m) REVERT: H 3 GLN cc_start: 0.7571 (pm20) cc_final: 0.7208 (pm20) REVERT: H 21 SER cc_start: 0.8298 (p) cc_final: 0.8048 (p) REVERT: H 27 TYR cc_start: 0.8031 (p90) cc_final: 0.7393 (p90) REVERT: H 29 PHE cc_start: 0.6538 (t80) cc_final: 0.6003 (t80) REVERT: H 61 HIS cc_start: 0.8487 (t-90) cc_final: 0.8150 (t-90) REVERT: L 3 VAL cc_start: 0.6758 (p) cc_final: 0.5914 (m) REVERT: L 28 ASN cc_start: 0.8526 (p0) cc_final: 0.8085 (p0) REVERT: L 46 LYS cc_start: 0.7736 (ttpp) cc_final: 0.7138 (mmtp) REVERT: O 49 GLU cc_start: 0.8408 (mp0) cc_final: 0.8193 (mp0) REVERT: O 69 THR cc_start: 0.9218 (p) cc_final: 0.8472 (p) REVERT: O 312 GLU cc_start: 0.8391 (tp30) cc_final: 0.7414 (tp30) REVERT: O 453 MET cc_start: 0.8500 (tpp) cc_final: 0.8183 (tpp) REVERT: O 486 TYR cc_start: 0.8272 (t80) cc_final: 0.7959 (t80) REVERT: O 487 LEU cc_start: 0.8706 (tt) cc_final: 0.8447 (tp) REVERT: O 492 GLN cc_start: 0.8522 (mt0) cc_final: 0.7790 (tm-30) REVERT: P 45 LEU cc_start: 0.9180 (tp) cc_final: 0.8902 (tp) REVERT: P 60 LYS cc_start: 0.8201 (mttm) cc_final: 0.7905 (mtpt) REVERT: P 67 LEU cc_start: 0.9338 (tp) cc_final: 0.9128 (tp) REVERT: P 68 MET cc_start: 0.8380 (tpp) cc_final: 0.7351 (ttp) REVERT: Q 1 MET cc_start: 0.8223 (mmp) cc_final: 0.7784 (mmm) REVERT: Q 20 TRP cc_start: 0.8282 (p-90) cc_final: 0.8057 (p-90) REVERT: Q 22 ASP cc_start: 0.7617 (m-30) cc_final: 0.7183 (m-30) REVERT: Q 47 LYS cc_start: 0.8456 (mttp) cc_final: 0.8121 (pttt) REVERT: Q 71 ASP cc_start: 0.8855 (t70) cc_final: 0.8584 (t0) REVERT: Q 101 TRP cc_start: 0.8784 (m-10) cc_final: 0.8437 (m-10) REVERT: Q 193 GLU cc_start: 0.6192 (pm20) cc_final: 0.5048 (pm20) REVERT: Q 204 TRP cc_start: 0.9205 (m-90) cc_final: 0.8781 (m-90) REVERT: Q 233 GLU cc_start: 0.7370 (tm-30) cc_final: 0.7130 (tm-30) REVERT: Q 408 ARG cc_start: 0.8942 (tpp80) cc_final: 0.8665 (tpp80) REVERT: Q 433 MET cc_start: 0.8085 (tpp) cc_final: 0.7735 (tpp) REVERT: R 30 GLU cc_start: 0.8286 (tp30) cc_final: 0.7933 (tp30) REVERT: R 68 MET cc_start: 0.8401 (mmm) cc_final: 0.6997 (tmm) REVERT: S 26 GLU cc_start: 0.8316 (mt-10) cc_final: 0.8077 (mt-10) REVERT: S 41 LEU cc_start: 0.8996 (pt) cc_final: 0.8731 (pt) REVERT: S 116 CYS cc_start: 0.5854 (m) cc_final: 0.5467 (m) REVERT: S 399 MET cc_start: 0.8177 (tmm) cc_final: 0.7681 (tmm) REVERT: S 426 VAL cc_start: 0.8032 (m) cc_final: 0.7768 (t) REVERT: S 455 ILE cc_start: 0.9325 (tp) cc_final: 0.9029 (tp) REVERT: T 10 MET cc_start: 0.8221 (mmp) cc_final: 0.8003 (mmp) REVERT: T 28 GLN cc_start: 0.7129 (mm-40) cc_final: 0.6893 (mm-40) REVERT: T 33 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6181 (mt-10) REVERT: T 43 THR cc_start: 0.9117 (m) cc_final: 0.8831 (m) REVERT: U 3 GLN cc_start: 0.7557 (pm20) cc_final: 0.7193 (pm20) REVERT: U 21 SER cc_start: 0.8311 (p) cc_final: 0.8018 (p) REVERT: U 27 TYR cc_start: 0.8003 (p90) cc_final: 0.7401 (p90) REVERT: U 29 PHE cc_start: 0.6567 (t80) cc_final: 0.6086 (t80) REVERT: U 36 TRP cc_start: 0.7429 (m100) cc_final: 0.6758 (m100) REVERT: U 48 MET cc_start: 0.7460 (mtm) cc_final: 0.6991 (mtm) REVERT: U 50 TRP cc_start: 0.8382 (m-10) cc_final: 0.7875 (m-10) REVERT: U 61 HIS cc_start: 0.8460 (t-90) cc_final: 0.8063 (t-90) REVERT: U 81 MET cc_start: 0.7462 (ttt) cc_final: 0.6634 (ttt) REVERT: U 98 ARG cc_start: 0.6883 (ttp-110) cc_final: 0.6301 (ttp-110) REVERT: V 3 VAL cc_start: 0.6889 (p) cc_final: 0.6096 (m) REVERT: V 28 ASN cc_start: 0.8769 (p0) cc_final: 0.8520 (p0) REVERT: V 46 LYS cc_start: 0.7726 (ttpp) cc_final: 0.7101 (mmtp) outliers start: 7 outliers final: 3 residues processed: 1052 average time/residue: 0.3789 time to fit residues: 640.0900 Evaluate side-chains 845 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 842 time to evaluate : 3.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 115 optimal weight: 6.9990 chunk 127 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 304 optimal weight: 1.9990 chunk 157 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 262 optimal weight: 9.9990 chunk 229 optimal weight: 9.9990 chunk 191 optimal weight: 9.9990 chunk 291 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 HIS ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 GLN ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 364 ASN F 59 GLN ** H 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 16 GLN L 38 GLN ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN ** P 59 GLN ** 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 77 GLN ** S 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 207 HIS S 364 ASN T 59 GLN V 16 GLN V 38 GLN V 53 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.123583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.105007 restraints weight = 53855.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.107589 restraints weight = 30684.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.109322 restraints weight = 20241.944| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 30656 Z= 0.278 Angle : 0.798 10.870 41636 Z= 0.404 Chirality : 0.049 0.265 4862 Planarity : 0.005 0.104 5182 Dihedral : 6.343 51.866 4716 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 0.06 % Allowed : 0.84 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.13), residues: 3838 helix: 0.65 (0.17), residues: 908 sheet: -1.02 (0.17), residues: 964 loop : -2.07 (0.13), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 50 HIS 0.012 0.002 HIS Q 280 PHE 0.032 0.002 PHE C 304 TYR 0.036 0.002 TYR P 52 ARG 0.013 0.001 ARG A 2 Details of bonding type rmsd link_NAG-ASN : bond 0.00611 ( 12) link_NAG-ASN : angle 2.27736 ( 36) link_BETA1-4 : bond 0.00475 ( 20) link_BETA1-4 : angle 1.58787 ( 60) hydrogen bonds : bond 0.04365 ( 1098) hydrogen bonds : angle 5.76644 ( 3024) SS BOND : bond 0.00510 ( 28) SS BOND : angle 1.69088 ( 56) covalent geometry : bond 0.00648 (30596) covalent geometry : angle 0.79222 (41484) *********************** 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 955 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 953 time to evaluate : 3.185 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: symmetry clash REVERT: A 47 LYS cc_start: 0.9307 (pttm) cc_final: 0.9088 (pttm) REVERT: A 49 GLU cc_start: 0.8565 (mp0) cc_final: 0.8171 (mp0) REVERT: A 71 ASP cc_start: 0.7360 (t70) cc_final: 0.7113 (t0) REVERT: A 312 GLU cc_start: 0.8710 (tp30) cc_final: 0.8020 (tp30) REVERT: A 357 THR cc_start: 0.8286 (p) cc_final: 0.8086 (p) REVERT: A 453 MET cc_start: 0.8652 (tpp) cc_final: 0.8428 (tpp) REVERT: A 486 TYR cc_start: 0.8450 (t80) cc_final: 0.8197 (t80) REVERT: A 487 LEU cc_start: 0.8778 (tt) cc_final: 0.8566 (tp) REVERT: A 492 GLN cc_start: 0.8675 (mt0) cc_final: 0.8355 (mt0) REVERT: B 60 LYS cc_start: 0.8272 (mttm) cc_final: 0.8002 (mtpt) REVERT: C 1 MET cc_start: 0.8395 (mmp) cc_final: 0.7146 (mmm) REVERT: C 47 LYS cc_start: 0.8646 (mttp) cc_final: 0.8105 (tttt) REVERT: C 71 ASP cc_start: 0.8944 (t70) cc_final: 0.8679 (t0) REVERT: C 101 TRP cc_start: 0.8729 (m-10) cc_final: 0.8228 (m-10) REVERT: C 193 GLU cc_start: 0.6268 (pm20) cc_final: 0.5141 (pm20) REVERT: C 204 TRP cc_start: 0.9360 (m-90) cc_final: 0.8830 (m-90) REVERT: C 205 MET cc_start: 0.8684 (ptp) cc_final: 0.8438 (ptp) REVERT: C 233 GLU cc_start: 0.7476 (tm-30) cc_final: 0.7266 (tm-30) REVERT: C 286 LYS cc_start: 0.8183 (tttm) cc_final: 0.7825 (mtpp) REVERT: C 324 TYR cc_start: 0.8674 (t80) cc_final: 0.8244 (t80) REVERT: D 30 GLU cc_start: 0.8280 (tp30) cc_final: 0.7900 (tp30) REVERT: E 1 MET cc_start: 0.8095 (mmm) cc_final: 0.7753 (mmm) REVERT: E 26 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7851 (mt-10) REVERT: E 399 MET cc_start: 0.8053 (tmm) cc_final: 0.7700 (tmm) REVERT: E 455 ILE cc_start: 0.9409 (tp) cc_final: 0.9102 (tp) REVERT: F 47 LEU cc_start: 0.8571 (mt) cc_final: 0.8300 (mt) REVERT: H 3 GLN cc_start: 0.7579 (pm20) cc_final: 0.7224 (pm20) REVERT: H 10 GLU cc_start: 0.6739 (pp20) cc_final: 0.6305 (pp20) REVERT: H 21 SER cc_start: 0.8425 (p) cc_final: 0.8147 (p) REVERT: H 27 TYR cc_start: 0.8230 (p90) cc_final: 0.7425 (p90) REVERT: H 29 PHE cc_start: 0.6462 (t80) cc_final: 0.6040 (t80) REVERT: H 36 TRP cc_start: 0.7570 (m100) cc_final: 0.7126 (m100) REVERT: H 50 TRP cc_start: 0.8505 (m-10) cc_final: 0.8101 (m-10) REVERT: H 61 HIS cc_start: 0.8620 (t-90) cc_final: 0.8180 (t-90) REVERT: L 3 VAL cc_start: 0.6839 (p) cc_final: 0.5993 (m) REVERT: L 28 ASN cc_start: 0.8726 (p0) cc_final: 0.8405 (p0) REVERT: L 91 THR cc_start: 0.8953 (t) cc_final: 0.8640 (m) REVERT: O 34 MET cc_start: 0.6973 (ttp) cc_final: 0.6684 (ttp) REVERT: O 49 GLU cc_start: 0.8566 (mp0) cc_final: 0.8187 (mp0) REVERT: O 71 ASP cc_start: 0.7345 (t70) cc_final: 0.7111 (t0) REVERT: O 312 GLU cc_start: 0.8651 (tp30) cc_final: 0.8098 (tp30) REVERT: O 453 MET cc_start: 0.8653 (tpp) cc_final: 0.8411 (tpp) REVERT: O 486 TYR cc_start: 0.8417 (t80) cc_final: 0.8174 (t80) REVERT: O 487 LEU cc_start: 0.8796 (tt) cc_final: 0.8580 (tp) REVERT: O 492 GLN cc_start: 0.8705 (mt0) cc_final: 0.8367 (mt0) REVERT: P 60 LYS cc_start: 0.8226 (mttm) cc_final: 0.7956 (mtpt) REVERT: Q 1 MET cc_start: 0.8391 (mmp) cc_final: 0.7185 (mmm) REVERT: Q 20 TRP cc_start: 0.8623 (p-90) cc_final: 0.7844 (p-90) REVERT: Q 47 LYS cc_start: 0.8625 (mttp) cc_final: 0.8066 (tttt) REVERT: Q 71 ASP cc_start: 0.8859 (t70) cc_final: 0.8623 (t0) REVERT: Q 101 TRP cc_start: 0.8761 (m-10) cc_final: 0.8263 (m-10) REVERT: Q 193 GLU cc_start: 0.6395 (pm20) cc_final: 0.5202 (pm20) REVERT: Q 204 TRP cc_start: 0.9358 (m-90) cc_final: 0.8823 (m-90) REVERT: Q 205 MET cc_start: 0.8696 (ptp) cc_final: 0.8422 (ptp) REVERT: Q 324 TYR cc_start: 0.8764 (t80) cc_final: 0.8267 (t80) REVERT: Q 408 ARG cc_start: 0.8996 (tpp80) cc_final: 0.8727 (tpp80) REVERT: R 30 GLU cc_start: 0.8290 (tp30) cc_final: 0.7900 (tp30) REVERT: S 26 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8130 (mt-10) REVERT: S 399 MET cc_start: 0.8066 (tmm) cc_final: 0.7709 (tmm) REVERT: S 455 ILE cc_start: 0.9406 (tp) cc_final: 0.9102 (tp) REVERT: T 28 GLN cc_start: 0.7473 (mm-40) cc_final: 0.7138 (mm-40) REVERT: T 33 GLU cc_start: 0.7449 (mm-30) cc_final: 0.6442 (mt-10) REVERT: T 47 LEU cc_start: 0.8559 (mt) cc_final: 0.8297 (mt) REVERT: U 3 GLN cc_start: 0.7614 (pm20) cc_final: 0.7258 (pm20) REVERT: U 12 LYS cc_start: 0.6663 (mmtm) cc_final: 0.6437 (mmtt) REVERT: U 21 SER cc_start: 0.8419 (p) cc_final: 0.8142 (p) REVERT: U 27 TYR cc_start: 0.8014 (p90) cc_final: 0.7538 (p90) REVERT: U 29 PHE cc_start: 0.6582 (t80) cc_final: 0.6129 (t80) REVERT: U 36 TRP cc_start: 0.7700 (m100) cc_final: 0.7304 (m100) REVERT: U 50 TRP cc_start: 0.8306 (m-10) cc_final: 0.7804 (m-10) REVERT: U 61 HIS cc_start: 0.8620 (t-90) cc_final: 0.8173 (t-90) REVERT: U 98 ARG cc_start: 0.7041 (ttp-110) cc_final: 0.6480 (ttp-110) REVERT: V 3 VAL cc_start: 0.6855 (p) cc_final: 0.5991 (m) REVERT: V 91 THR cc_start: 0.8954 (t) cc_final: 0.8636 (m) outliers start: 2 outliers final: 0 residues processed: 955 average time/residue: 0.3785 time to fit residues: 591.8595 Evaluate side-chains 818 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 818 time to evaluate : 3.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 103 optimal weight: 7.9990 chunk 362 optimal weight: 0.0770 chunk 311 optimal weight: 5.9990 chunk 346 optimal weight: 0.4980 chunk 315 optimal weight: 7.9990 chunk 68 optimal weight: 0.3980 chunk 170 optimal weight: 6.9990 chunk 211 optimal weight: 4.9990 chunk 343 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 260 optimal weight: 9.9990 overall best weight: 2.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 HIS C 209 GLN ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 HIS ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 364 ASN F 59 GLN L 16 GLN L 38 GLN L 53 ASN O 134 ASN ** O 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 HIS ** P 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 27 HIS ** S 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 364 ASN T 59 GLN V 16 GLN V 38 GLN ** V 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.127433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.109023 restraints weight = 53541.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.111654 restraints weight = 30166.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.113399 restraints weight = 19783.855| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 30656 Z= 0.154 Angle : 0.740 12.511 41636 Z= 0.370 Chirality : 0.047 0.274 4862 Planarity : 0.005 0.089 5182 Dihedral : 6.101 53.728 4716 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.19 % Allowed : 0.75 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.13), residues: 3838 helix: 0.73 (0.17), residues: 908 sheet: -1.00 (0.17), residues: 958 loop : -2.04 (0.13), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP H 50 HIS 0.018 0.001 HIS A 207 PHE 0.027 0.002 PHE Q 304 TYR 0.030 0.002 TYR B 52 ARG 0.008 0.001 ARG C 99 Details of bonding type rmsd link_NAG-ASN : bond 0.00375 ( 12) link_NAG-ASN : angle 2.09436 ( 36) link_BETA1-4 : bond 0.00495 ( 20) link_BETA1-4 : angle 1.48993 ( 60) hydrogen bonds : bond 0.03920 ( 1098) hydrogen bonds : angle 5.56451 ( 3024) SS BOND : bond 0.00398 ( 28) SS BOND : angle 1.59781 ( 56) covalent geometry : bond 0.00360 (30596) covalent geometry : angle 0.73466 (41484) ********************** 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 978 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 972 time to evaluate : 3.310 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: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8354 (mp0) cc_final: 0.7813 (mp0) REVERT: A 71 ASP cc_start: 0.7229 (t70) cc_final: 0.7013 (t0) REVERT: A 312 GLU cc_start: 0.8443 (tp30) cc_final: 0.7689 (tp30) REVERT: A 453 MET cc_start: 0.8555 (tpp) cc_final: 0.8281 (tpt) REVERT: A 486 TYR cc_start: 0.8314 (t80) cc_final: 0.8042 (t80) REVERT: A 487 LEU cc_start: 0.8749 (tt) cc_final: 0.8511 (tp) REVERT: B 60 LYS cc_start: 0.8242 (mttm) cc_final: 0.7969 (mtpt) REVERT: C 1 MET cc_start: 0.8423 (mmp) cc_final: 0.7786 (mmm) REVERT: C 47 LYS cc_start: 0.8560 (mttp) cc_final: 0.8061 (tttt) REVERT: C 62 GLU cc_start: 0.6703 (tt0) cc_final: 0.6296 (tt0) REVERT: C 71 ASP cc_start: 0.8883 (t70) cc_final: 0.8633 (t0) REVERT: C 101 TRP cc_start: 0.8852 (m-10) cc_final: 0.8443 (m-10) REVERT: C 193 GLU cc_start: 0.6198 (pm20) cc_final: 0.5172 (pm20) REVERT: C 204 TRP cc_start: 0.9251 (m-90) cc_final: 0.8788 (m-90) REVERT: C 286 LYS cc_start: 0.8190 (tttm) cc_final: 0.7950 (mtpp) REVERT: C 324 TYR cc_start: 0.8579 (t80) cc_final: 0.8078 (t80) REVERT: C 366 GLU cc_start: 0.7857 (pm20) cc_final: 0.7592 (pm20) REVERT: C 408 ARG cc_start: 0.8987 (tpp80) cc_final: 0.8669 (tpp80) REVERT: D 30 GLU cc_start: 0.8234 (tp30) cc_final: 0.7829 (tp30) REVERT: D 38 ARG cc_start: 0.8256 (ttp80) cc_final: 0.7946 (ttp-170) REVERT: E 1 MET cc_start: 0.8364 (mmm) cc_final: 0.8033 (mmm) REVERT: E 41 LEU cc_start: 0.9041 (pt) cc_final: 0.8734 (pt) REVERT: E 116 CYS cc_start: 0.5838 (m) cc_final: 0.5281 (m) REVERT: E 199 MET cc_start: 0.8626 (mmt) cc_final: 0.8384 (mmm) REVERT: E 399 MET cc_start: 0.7941 (tmm) cc_final: 0.7624 (tmm) REVERT: E 455 ILE cc_start: 0.9355 (tp) cc_final: 0.9062 (tp) REVERT: F 10 MET cc_start: 0.8020 (mmp) cc_final: 0.7773 (mmp) REVERT: F 33 GLU cc_start: 0.7386 (mm-30) cc_final: 0.6542 (mt-10) REVERT: H 3 GLN cc_start: 0.7645 (pm20) cc_final: 0.7334 (pm20) REVERT: H 10 GLU cc_start: 0.6680 (pp20) cc_final: 0.6239 (pp20) REVERT: H 21 SER cc_start: 0.8350 (p) cc_final: 0.8077 (p) REVERT: H 27 TYR cc_start: 0.8454 (p90) cc_final: 0.7608 (p90) REVERT: H 29 PHE cc_start: 0.6446 (t80) cc_final: 0.5973 (t80) REVERT: H 36 TRP cc_start: 0.7647 (m100) cc_final: 0.7351 (m100) REVERT: H 50 TRP cc_start: 0.8429 (m-10) cc_final: 0.7769 (m-10) REVERT: H 61 HIS cc_start: 0.8434 (t-90) cc_final: 0.7857 (t-90) REVERT: L 3 VAL cc_start: 0.6752 (p) cc_final: 0.5900 (m) REVERT: L 28 ASN cc_start: 0.8687 (p0) cc_final: 0.8233 (p0) REVERT: O 49 GLU cc_start: 0.8522 (mp0) cc_final: 0.8088 (mp0) REVERT: O 357 THR cc_start: 0.8247 (p) cc_final: 0.8045 (p) REVERT: O 453 MET cc_start: 0.8549 (tpp) cc_final: 0.8283 (tpp) REVERT: O 486 TYR cc_start: 0.8319 (t80) cc_final: 0.8033 (t80) REVERT: O 487 LEU cc_start: 0.8762 (tt) cc_final: 0.8555 (tp) REVERT: P 12 LEU cc_start: 0.8669 (tt) cc_final: 0.8293 (tt) REVERT: Q 1 MET cc_start: 0.8409 (mmp) cc_final: 0.7800 (mmm) REVERT: Q 20 TRP cc_start: 0.8469 (p-90) cc_final: 0.8113 (p-90) REVERT: Q 47 LYS cc_start: 0.8505 (mttp) cc_final: 0.7958 (pttt) REVERT: Q 62 GLU cc_start: 0.6703 (tt0) cc_final: 0.6285 (tt0) REVERT: Q 71 ASP cc_start: 0.8851 (t70) cc_final: 0.8614 (t0) REVERT: Q 101 TRP cc_start: 0.8722 (m-10) cc_final: 0.8265 (m-10) REVERT: Q 193 GLU cc_start: 0.6200 (pm20) cc_final: 0.5124 (pm20) REVERT: Q 204 TRP cc_start: 0.9248 (m-90) cc_final: 0.8787 (m-90) REVERT: Q 324 TYR cc_start: 0.8717 (t80) cc_final: 0.8074 (t80) REVERT: Q 408 ARG cc_start: 0.8988 (tpp80) cc_final: 0.8748 (tpp80) REVERT: Q 433 MET cc_start: 0.7975 (tpp) cc_final: 0.7732 (tpp) REVERT: R 30 GLU cc_start: 0.8239 (tp30) cc_final: 0.7833 (tp30) REVERT: R 38 ARG cc_start: 0.8239 (ttp80) cc_final: 0.7938 (ttp-170) REVERT: S 26 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8220 (mt-10) REVERT: S 41 LEU cc_start: 0.9021 (pt) cc_final: 0.8707 (pt) REVERT: S 116 CYS cc_start: 0.5863 (m) cc_final: 0.5315 (m) REVERT: S 399 MET cc_start: 0.7955 (tmm) cc_final: 0.7632 (tmm) REVERT: S 455 ILE cc_start: 0.9345 (tp) cc_final: 0.9057 (tp) REVERT: T 10 MET cc_start: 0.8021 (mmp) cc_final: 0.7769 (mmp) REVERT: T 28 GLN cc_start: 0.7337 (mm-40) cc_final: 0.7089 (mm-40) REVERT: T 33 GLU cc_start: 0.7392 (mm-30) cc_final: 0.6552 (mt-10) REVERT: U 3 GLN cc_start: 0.7674 (pm20) cc_final: 0.7340 (pm20) REVERT: U 12 LYS cc_start: 0.6730 (mmtm) cc_final: 0.6447 (mmtt) REVERT: U 21 SER cc_start: 0.8374 (p) cc_final: 0.8142 (p) REVERT: U 27 TYR cc_start: 0.8043 (p90) cc_final: 0.7406 (p90) REVERT: U 29 PHE cc_start: 0.6506 (t80) cc_final: 0.6018 (t80) REVERT: U 50 TRP cc_start: 0.8329 (m-10) cc_final: 0.7744 (m-10) REVERT: U 61 HIS cc_start: 0.8417 (t-90) cc_final: 0.8070 (t-90) REVERT: U 81 MET cc_start: 0.7493 (tmm) cc_final: 0.7125 (tmm) REVERT: V 3 VAL cc_start: 0.6897 (p) cc_final: 0.5858 (m) REVERT: V 91 THR cc_start: 0.8890 (t) cc_final: 0.8442 (m) outliers start: 6 outliers final: 2 residues processed: 974 average time/residue: 0.3833 time to fit residues: 616.0811 Evaluate side-chains 810 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 808 time to evaluate : 3.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 40 optimal weight: 20.0000 chunk 340 optimal weight: 9.9990 chunk 320 optimal weight: 9.9990 chunk 347 optimal weight: 3.9990 chunk 329 optimal weight: 20.0000 chunk 122 optimal weight: 3.9990 chunk 248 optimal weight: 6.9990 chunk 249 optimal weight: 8.9990 chunk 310 optimal weight: 10.0000 chunk 224 optimal weight: 20.0000 chunk 267 optimal weight: 0.0980 overall best weight: 4.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN ** 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 364 ASN F 59 GLN L 16 GLN L 38 GLN L 53 ASN O 492 GLN ** 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 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 59 GLN V 16 GLN V 38 GLN ** V 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.125168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.106710 restraints weight = 53779.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.109285 restraints weight = 30467.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.110975 restraints weight = 20062.717| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 30656 Z= 0.208 Angle : 0.760 11.838 41636 Z= 0.381 Chirality : 0.047 0.268 4862 Planarity : 0.005 0.082 5182 Dihedral : 6.133 52.373 4716 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 0.03 % Allowed : 0.53 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.13), residues: 3838 helix: 0.68 (0.17), residues: 902 sheet: -1.02 (0.17), residues: 920 loop : -2.05 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 50 HIS 0.014 0.001 HIS Q 280 PHE 0.016 0.002 PHE B 42 TYR 0.017 0.002 TYR C 486 ARG 0.009 0.001 ARG C 99 Details of bonding type rmsd link_NAG-ASN : bond 0.00527 ( 12) link_NAG-ASN : angle 2.18674 ( 36) link_BETA1-4 : bond 0.00476 ( 20) link_BETA1-4 : angle 1.48773 ( 60) hydrogen bonds : bond 0.04165 ( 1098) hydrogen bonds : angle 5.63272 ( 3024) SS BOND : bond 0.00536 ( 28) SS BOND : angle 1.63509 ( 56) covalent geometry : bond 0.00486 (30596) covalent geometry : angle 0.75457 (41484) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11879.04 seconds wall clock time: 208 minutes 6.91 seconds (12486.91 seconds total)