Starting phenix.real_space_refine on Wed Jun 25 18:49:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jn2_36430/06_2025/8jn2_36430.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jn2_36430/06_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_36430/06_2025/8jn2_36430.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jn2_36430/06_2025/8jn2_36430.map" model { file = "/net/cci-nas-00/data/ceres_data/8jn2_36430/06_2025/8jn2_36430.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jn2_36430/06_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 16.39, per 1000 atoms: 0.55 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: 7.42 Conformation dependent library (CDL) restraints added in 3.6 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: 4.11 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: 11.05 Time building geometry restraints manager: 8.75 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: 0.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.000 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 64.270 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.180 ------------------------------------------------------------------------------- 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 : 3.346 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: 0.3902 time to fit residues: 717.9969 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 : 3.236 ------------------------------------------------------------------------------- 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 = 0.131748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.113556 restraints weight = 51220.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.116256 restraints weight = 28325.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.118043 restraints weight = 18226.563| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1751 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= 0.212 Angle : 0.744 11.576 41636 Z= 0.379 Chirality : 0.046 0.193 4862 Planarity : 0.004 0.047 5182 Dihedral : 11.057 89.046 4716 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.37 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 0.006 0.001 ARG A 284 Details of bonding type rmsd link_NAG-ASN : bond 0.00390 ( 12) link_NAG-ASN : angle 2.65388 ( 36) link_BETA1-4 : bond 0.00589 ( 20) link_BETA1-4 : angle 2.33062 ( 60) hydrogen bonds : bond 0.04996 ( 1098) hydrogen bonds : angle 6.64041 ( 3024) SS BOND : bond 0.00424 ( 28) SS BOND : angle 1.73177 ( 56) covalent geometry : bond 0.00483 (30596) covalent geometry : angle 0.73366 (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 1038 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 1028 time to evaluate : 3.402 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: 0.7966 (t0) REVERT: A 49 GLU cc_start: 0.8319 (mp0) cc_final: 0.7758 (mp0) REVERT: A 69 THR cc_start: 0.9161 (p) cc_final: 0.8512 (p) REVERT: A 71 ASP cc_start: 0.8207 (p0) cc_final: 0.7835 (t70) REVERT: A 76 THR cc_start: 0.8032 (p) cc_final: 0.7825 (p) REVERT: A 182 GLU cc_start: 0.7117 (mm-30) cc_final: 0.6687 (tp30) REVERT: A 190 ASP cc_start: 0.8558 (t0) cc_final: 0.7821 (t0) REVERT: A 195 ILE cc_start: 0.9035 (mt) cc_final: 0.8209 (tt) REVERT: A 453 MET cc_start: 0.8567 (tpp) cc_final: 0.8319 (tpp) REVERT: A 486 TYR cc_start: 0.8378 (t80) cc_final: 0.8134 (t80) REVERT: A 487 LEU cc_start: 0.8796 (tt) cc_final: 0.8525 (tp) REVERT: A 492 GLN cc_start: 0.8436 (mt0) cc_final: 0.7778 (tm-30) REVERT: C 1 MET cc_start: 0.8794 (mmp) cc_final: 0.7881 (mmm) REVERT: C 47 LYS cc_start: 0.8598 (mttp) cc_final: 0.8212 (pttt) REVERT: C 71 ASP cc_start: 0.8930 (t70) cc_final: 0.8639 (t0) REVERT: C 148 GLN cc_start: 0.8820 (tt0) cc_final: 0.8357 (tm-30) REVERT: C 193 GLU cc_start: 0.6342 (pm20) cc_final: 0.5407 (pm20) REVERT: C 199 MET cc_start: 0.9133 (ptm) cc_final: 0.8905 (ptm) REVERT: C 204 TRP cc_start: 0.9490 (m-90) cc_final: 0.8623 (m-90) REVERT: C 453 MET cc_start: 0.9041 (mmp) cc_final: 0.8758 (tpp) REVERT: D 14 THR cc_start: 0.8652 (p) cc_final: 0.8451 (p) REVERT: D 38 ARG cc_start: 0.8282 (ttp-170) cc_final: 0.8073 (ttp-170) REVERT: D 68 MET cc_start: 0.8535 (mmm) cc_final: 0.7585 (tmm) REVERT: E 132 TYR cc_start: 0.8622 (t80) cc_final: 0.8190 (t80) REVERT: E 239 LYS cc_start: 0.7626 (ttmt) cc_final: 0.7378 (ttpt) REVERT: E 247 GLU cc_start: 0.7604 (pm20) cc_final: 0.7332 (pm20) REVERT: E 399 MET cc_start: 0.7923 (tmm) cc_final: 0.7459 (tmm) REVERT: E 419 ASP cc_start: 0.7452 (m-30) cc_final: 0.7229 (m-30) REVERT: E 455 ILE cc_start: 0.9278 (tp) cc_final: 0.9012 (tp) REVERT: F 51 HIS cc_start: 0.7912 (t-90) cc_final: 0.7606 (t-90) REVERT: H 3 GLN cc_start: 0.7693 (pm20) cc_final: 0.7046 (pm20) REVERT: H 21 SER cc_start: 0.8544 (p) cc_final: 0.8298 (p) REVERT: H 29 PHE cc_start: 0.6377 (t80) cc_final: 0.6037 (t80) REVERT: H 36 TRP cc_start: 0.7460 (m100) cc_final: 0.6557 (m100) REVERT: H 43 GLN cc_start: 0.7278 (mm-40) cc_final: 0.6969 (mm-40) REVERT: H 81 MET cc_start: 0.7367 (ttt) cc_final: 0.5448 (ttt) REVERT: H 111 TYR cc_start: 0.7718 (m-80) cc_final: 0.7426 (m-80) REVERT: L 3 VAL cc_start: 0.6878 (p) cc_final: 0.6160 (m) REVERT: O 1 MET cc_start: 0.8419 (mmm) cc_final: 0.7857 (mmm) REVERT: O 42 ASP cc_start: 0.8195 (t0) cc_final: 0.7969 (t0) REVERT: O 49 GLU cc_start: 0.8347 (mp0) cc_final: 0.7761 (mp0) REVERT: O 69 THR cc_start: 0.9151 (p) cc_final: 0.8506 (p) REVERT: O 71 ASP cc_start: 0.8213 (p0) cc_final: 0.7818 (t70) REVERT: O 76 THR cc_start: 0.8056 (p) cc_final: 0.7813 (p) REVERT: O 182 GLU cc_start: 0.7113 (mm-30) cc_final: 0.6689 (tp30) REVERT: O 190 ASP cc_start: 0.8591 (t0) cc_final: 0.7887 (t0) REVERT: O 195 ILE cc_start: 0.9020 (mt) cc_final: 0.8366 (mp) REVERT: O 453 MET cc_start: 0.8566 (tpp) cc_final: 0.8307 (tpp) REVERT: O 486 TYR cc_start: 0.8373 (t80) cc_final: 0.8125 (t80) REVERT: O 487 LEU cc_start: 0.8788 (tt) cc_final: 0.8515 (tp) REVERT: O 492 GLN cc_start: 0.8436 (mt0) cc_final: 0.7763 (tm-30) REVERT: Q 1 MET cc_start: 0.8798 (mmp) cc_final: 0.7899 (mmm) REVERT: Q 47 LYS cc_start: 0.8637 (mttp) cc_final: 0.8046 (pttt) REVERT: Q 49 GLU cc_start: 0.7886 (mp0) cc_final: 0.7527 (mp0) REVERT: Q 71 ASP cc_start: 0.8946 (t70) cc_final: 0.8642 (t0) REVERT: Q 148 GLN cc_start: 0.8814 (tt0) cc_final: 0.8355 (tm-30) REVERT: Q 186 ARG cc_start: 0.8838 (mmm160) cc_final: 0.8530 (mmt180) REVERT: Q 193 GLU cc_start: 0.6367 (pm20) cc_final: 0.5398 (pm20) REVERT: Q 199 MET cc_start: 0.9148 (ptm) cc_final: 0.8929 (ptm) REVERT: Q 204 TRP cc_start: 0.9483 (m-90) cc_final: 0.8627 (m-90) REVERT: Q 453 MET cc_start: 0.9030 (mmp) cc_final: 0.8754 (tpp) REVERT: R 38 ARG cc_start: 0.8279 (ttp-170) cc_final: 0.8070 (ttp-170) REVERT: R 68 MET cc_start: 0.8547 (mmm) cc_final: 0.7579 (tmm) REVERT: S 132 TYR cc_start: 0.8620 (t80) cc_final: 0.8185 (t80) REVERT: S 239 LYS cc_start: 0.7628 (ttmt) cc_final: 0.7366 (ttpt) REVERT: S 247 GLU cc_start: 0.7613 (pm20) cc_final: 0.7331 (pm20) REVERT: S 328 ASP cc_start: 0.8442 (m-30) cc_final: 0.8220 (m-30) REVERT: S 399 MET cc_start: 0.7921 (tmm) cc_final: 0.7459 (tmm) REVERT: S 419 ASP cc_start: 0.7471 (m-30) cc_final: 0.7238 (m-30) REVERT: S 455 ILE cc_start: 0.9267 (tp) cc_final: 0.9004 (tp) REVERT: T 51 HIS cc_start: 0.7914 (t-90) cc_final: 0.7603 (t-90) REVERT: U 3 GLN cc_start: 0.7688 (pm20) cc_final: 0.7096 (pm20) REVERT: U 21 SER cc_start: 0.8538 (p) cc_final: 0.8295 (p) REVERT: U 27 TYR cc_start: 0.7991 (p90) cc_final: 0.7483 (p90) REVERT: U 29 PHE cc_start: 0.6387 (t80) cc_final: 0.5871 (t80) REVERT: U 36 TRP cc_start: 0.7459 (m100) cc_final: 0.6551 (m100) REVERT: U 43 GLN cc_start: 0.7275 (mm-40) cc_final: 0.6966 (mm-40) REVERT: U 81 MET cc_start: 0.7384 (ttt) cc_final: 0.5457 (ttt) REVERT: U 111 TYR cc_start: 0.7753 (m-80) cc_final: 0.7466 (m-80) REVERT: V 3 VAL cc_start: 0.6868 (p) cc_final: 0.6160 (m) outliers start: 10 outliers final: 3 residues processed: 1030 average time/residue: 0.4086 time to fit residues: 676.3691 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 : 3.452 ------------------------------------------------------------------------------- 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: 1.9990 chunk 333 optimal weight: 2.9990 chunk 106 optimal weight: 20.0000 chunk 105 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 159 optimal weight: 6.9990 chunk 343 optimal weight: 4.9990 chunk 193 optimal weight: 7.9990 chunk 123 optimal weight: 10.0000 chunk 7 optimal weight: 0.4980 overall best weight: 1.8988 ------------------------------------------------------------------------------- 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** B 59 GLN ** 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 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** P 59 GLN ** 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 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 = 0.3537 r_free = 0.3537 target = 0.135960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.118081 restraints weight = 50933.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.120824 restraints weight = 28161.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.122635 restraints weight = 18111.383| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30656 Z= 0.141 Angle : 0.682 10.109 41636 Z= 0.346 Chirality : 0.046 0.269 4862 Planarity : 0.004 0.081 5182 Dihedral : 9.114 81.420 4716 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.12 % Allowed : 4.56 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.13), residues: 3838 helix: 0.82 (0.17), residues: 910 sheet: -1.06 (0.17), residues: 954 loop : -1.97 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 451 HIS 0.008 0.001 HIS R 39 PHE 0.016 0.002 PHE Q 335 TYR 0.016 0.002 TYR P 52 ARG 0.006 0.001 ARG Q 99 Details of bonding type rmsd link_NAG-ASN : bond 0.00277 ( 12) link_NAG-ASN : angle 2.37156 ( 36) link_BETA1-4 : bond 0.00647 ( 20) link_BETA1-4 : angle 2.11107 ( 60) hydrogen bonds : bond 0.04315 ( 1098) hydrogen bonds : angle 6.13960 ( 3024) SS BOND : bond 0.00572 ( 28) SS BOND : angle 1.70502 ( 56) covalent geometry : bond 0.00320 (30596) covalent geometry : angle 0.67241 (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 1055 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1051 time to evaluate : 3.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO D 72 " (corrupted residue). Skipping it. Corrupt residue: chain: D residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO F 72 " (corrupted residue). Skipping it. Corrupt residue: chain: F residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO R 72 " (corrupted residue). Skipping it. Corrupt residue: chain: R residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO T 72 " (corrupted residue). Skipping it. Corrupt residue: chain: T residue: PRO 72 >>> skipping REVERT: A 42 ASP cc_start: 0.8127 (t0) cc_final: 0.7843 (t0) REVERT: A 49 GLU cc_start: 0.8551 (mp0) cc_final: 0.7978 (mp0) REVERT: A 69 THR cc_start: 0.9243 (p) cc_final: 0.8478 (p) REVERT: A 176 TYR cc_start: 0.8183 (m-10) cc_final: 0.7854 (m-10) REVERT: A 182 GLU cc_start: 0.7000 (mm-30) cc_final: 0.6631 (tp30) REVERT: A 195 ILE cc_start: 0.8889 (mt) cc_final: 0.8105 (tt) REVERT: A 453 MET cc_start: 0.8416 (tpp) cc_final: 0.7910 (tpp) REVERT: A 486 TYR cc_start: 0.8315 (t80) cc_final: 0.8107 (t80) REVERT: A 487 LEU cc_start: 0.8655 (tt) cc_final: 0.8436 (tp) REVERT: A 492 GLN cc_start: 0.8432 (mt0) cc_final: 0.7755 (tm-30) REVERT: B 60 LYS cc_start: 0.8381 (mttm) cc_final: 0.7997 (mmtm) REVERT: C 1 MET cc_start: 0.8826 (mmp) cc_final: 0.8069 (mmm) REVERT: C 34 MET cc_start: 0.8616 (ptp) cc_final: 0.8143 (ptp) REVERT: C 47 LYS cc_start: 0.8657 (mttp) cc_final: 0.8305 (pttt) REVERT: C 71 ASP cc_start: 0.8897 (t70) cc_final: 0.8615 (t0) REVERT: C 204 TRP cc_start: 0.9364 (m-90) cc_final: 0.8698 (m-90) REVERT: C 286 LYS cc_start: 0.8162 (tttm) cc_final: 0.7821 (mtpp) REVERT: C 324 TYR cc_start: 0.8762 (t80) cc_final: 0.8560 (t80) REVERT: C 389 TRP cc_start: 0.7227 (t60) cc_final: 0.6208 (t60) REVERT: C 390 TYR cc_start: 0.8512 (t80) cc_final: 0.8170 (t80) REVERT: C 433 MET cc_start: 0.7921 (tpp) cc_final: 0.7617 (tpp) REVERT: D 68 MET cc_start: 0.8631 (mmm) cc_final: 0.7491 (tmm) REVERT: E 26 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7933 (mt-10) REVERT: E 123 GLU cc_start: 0.8634 (tt0) cc_final: 0.8349 (tt0) REVERT: E 335 PHE cc_start: 0.8353 (t80) cc_final: 0.7993 (t80) REVERT: E 399 MET cc_start: 0.7844 (tmm) cc_final: 0.7390 (tmm) REVERT: E 455 ILE cc_start: 0.9351 (tp) cc_final: 0.9000 (tp) REVERT: F 43 THR cc_start: 0.8976 (m) cc_final: 0.8744 (m) REVERT: F 51 HIS cc_start: 0.7873 (t-90) cc_final: 0.7623 (t-90) REVERT: H 3 GLN cc_start: 0.7602 (pm20) cc_final: 0.7041 (pm20) REVERT: H 21 SER cc_start: 0.8385 (p) cc_final: 0.8121 (p) REVERT: H 27 TYR cc_start: 0.8246 (p90) cc_final: 0.7621 (p90) REVERT: H 29 PHE cc_start: 0.6564 (t80) cc_final: 0.6070 (t80) REVERT: H 36 TRP cc_start: 0.7454 (m100) cc_final: 0.6560 (m100) REVERT: H 81 MET cc_start: 0.7383 (ttt) cc_final: 0.5840 (ttt) REVERT: H 111 TYR cc_start: 0.7840 (m-80) cc_final: 0.7556 (m-80) REVERT: L 3 VAL cc_start: 0.6776 (p) cc_final: 0.5968 (m) REVERT: O 42 ASP cc_start: 0.8125 (t0) cc_final: 0.7822 (t0) REVERT: O 49 GLU cc_start: 0.8542 (mp0) cc_final: 0.8107 (mp0) REVERT: O 69 THR cc_start: 0.9232 (p) cc_final: 0.8471 (p) REVERT: O 76 THR cc_start: 0.8694 (p) cc_final: 0.8485 (p) REVERT: O 176 TYR cc_start: 0.8195 (m-10) cc_final: 0.7863 (m-10) REVERT: O 195 ILE cc_start: 0.8882 (mt) cc_final: 0.8247 (mp) REVERT: O 453 MET cc_start: 0.8406 (tpp) cc_final: 0.7946 (tpp) REVERT: O 486 TYR cc_start: 0.8313 (t80) cc_final: 0.8100 (t80) REVERT: O 487 LEU cc_start: 0.8652 (tt) cc_final: 0.8431 (tp) REVERT: O 492 GLN cc_start: 0.8426 (mt0) cc_final: 0.7759 (tm-30) REVERT: P 10 MET cc_start: 0.7399 (tpp) cc_final: 0.6907 (mmm) REVERT: P 60 LYS cc_start: 0.8340 (mttm) cc_final: 0.8004 (mmtm) REVERT: Q 1 MET cc_start: 0.8831 (mmp) cc_final: 0.8046 (mmm) REVERT: Q 47 LYS cc_start: 0.8598 (mttp) cc_final: 0.8117 (pttt) REVERT: Q 71 ASP cc_start: 0.8913 (t70) cc_final: 0.8638 (t0) REVERT: Q 148 GLN cc_start: 0.8805 (tt0) cc_final: 0.8322 (tm-30) REVERT: Q 186 ARG cc_start: 0.8770 (mmm160) cc_final: 0.8511 (mmt180) REVERT: Q 204 TRP cc_start: 0.9359 (m-90) cc_final: 0.8709 (m-90) REVERT: Q 286 LYS cc_start: 0.8148 (tttm) cc_final: 0.7817 (mtpp) REVERT: Q 324 TYR cc_start: 0.8752 (t80) cc_final: 0.7756 (t80) REVERT: Q 389 TRP cc_start: 0.7220 (t60) cc_final: 0.6232 (t60) REVERT: Q 390 TYR cc_start: 0.8500 (t80) cc_final: 0.8166 (t80) REVERT: Q 433 MET cc_start: 0.7927 (tpp) cc_final: 0.7628 (tpp) REVERT: R 68 MET cc_start: 0.8635 (mmm) cc_final: 0.7496 (tmm) REVERT: S 2 ARG cc_start: 0.7692 (ttt180) cc_final: 0.7417 (ttt180) REVERT: S 26 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7935 (mt-10) REVERT: S 123 GLU cc_start: 0.8633 (tt0) cc_final: 0.8354 (tt0) REVERT: S 335 PHE cc_start: 0.8360 (t80) cc_final: 0.8016 (t80) REVERT: S 399 MET cc_start: 0.7848 (tmm) cc_final: 0.7390 (tmm) REVERT: S 455 ILE cc_start: 0.9351 (tp) cc_final: 0.8999 (tp) REVERT: T 43 THR cc_start: 0.8964 (m) cc_final: 0.8732 (m) REVERT: T 51 HIS cc_start: 0.7883 (t-90) cc_final: 0.7625 (t-90) REVERT: U 3 GLN cc_start: 0.7607 (pm20) cc_final: 0.7047 (pm20) REVERT: U 21 SER cc_start: 0.8386 (p) cc_final: 0.8124 (p) REVERT: U 27 TYR cc_start: 0.8246 (p90) cc_final: 0.7609 (p90) REVERT: U 29 PHE cc_start: 0.6577 (t80) cc_final: 0.6069 (t80) REVERT: U 36 TRP cc_start: 0.7453 (m100) cc_final: 0.6543 (m100) REVERT: U 81 MET cc_start: 0.7392 (ttt) cc_final: 0.5841 (ttt) REVERT: U 111 TYR cc_start: 0.7897 (m-80) cc_final: 0.7563 (m-80) REVERT: V 3 VAL cc_start: 0.6780 (p) cc_final: 0.5968 (m) outliers start: 4 outliers final: 0 residues processed: 1053 average time/residue: 0.3893 time to fit residues: 664.5048 Evaluate side-chains 829 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 829 time to evaluate : 3.256 ------------------------------------------------------------------------------- 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: 2.9990 chunk 360 optimal weight: 40.0000 chunk 320 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 300 optimal weight: 7.9990 chunk 303 optimal weight: 7.9990 chunk 266 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN B 51 HIS C 209 GLN ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 17 GLN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN L 16 GLN L 38 GLN O 192 ASN P 51 HIS Q 209 GLN Q 280 HIS ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN ** S 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 59 GLN V 16 GLN V 38 GLN V 52 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.134136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.116126 restraints weight = 51624.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.118848 restraints weight = 28622.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.120640 restraints weight = 18505.728| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30656 Z= 0.171 Angle : 0.687 12.324 41636 Z= 0.346 Chirality : 0.046 0.191 4862 Planarity : 0.004 0.072 5182 Dihedral : 7.835 72.157 4716 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.06 % Allowed : 4.75 % Favored : 95.19 % 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: -1.56 (0.13), residues: 3838 helix: 0.86 (0.17), residues: 906 sheet: -1.10 (0.17), residues: 976 loop : -1.95 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 451 HIS 0.008 0.001 HIS A 207 PHE 0.016 0.002 PHE T 42 TYR 0.018 0.002 TYR S 297 ARG 0.007 0.001 ARG Q 57 Details of bonding type rmsd link_NAG-ASN : bond 0.00259 ( 12) link_NAG-ASN : angle 2.27851 ( 36) link_BETA1-4 : bond 0.00504 ( 20) link_BETA1-4 : angle 1.98315 ( 60) hydrogen bonds : bond 0.04181 ( 1098) hydrogen bonds : angle 5.93832 ( 3024) SS BOND : bond 0.00501 ( 28) SS BOND : angle 1.75949 ( 56) covalent geometry : bond 0.00392 (30596) covalent geometry : angle 0.67769 (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 1009 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1007 time to evaluate : 3.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO D 72 " (corrupted residue). Skipping it. Corrupt residue: chain: D residue: PRO 72 >>> skipping revert: symmetry clash TARDY: cannot create tardy model for: "PRO F 72 " (corrupted residue). Skipping it. Corrupt residue: chain: F residue: PRO 72 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PRO R 72 " (corrupted residue). Skipping it. Corrupt residue: chain: R residue: PRO 72 >>> skipping revert: symmetry clash TARDY: cannot create tardy model for: "PRO T 72 " (corrupted residue). Skipping it. Corrupt residue: chain: T residue: PRO 72 >>> skipping revert: symmetry clash REVERT: A 1 MET cc_start: 0.8368 (mmm) cc_final: 0.7718 (mmm) REVERT: A 42 ASP cc_start: 0.8043 (t0) cc_final: 0.7663 (t0) REVERT: A 49 GLU cc_start: 0.8549 (mp0) cc_final: 0.8088 (mp0) REVERT: A 69 THR cc_start: 0.9267 (p) cc_final: 0.8682 (p) REVERT: A 190 ASP cc_start: 0.8486 (t0) cc_final: 0.8014 (t0) REVERT: A 262 LEU cc_start: 0.9292 (pt) cc_final: 0.8981 (pp) REVERT: A 312 GLU cc_start: 0.8675 (tp30) cc_final: 0.8451 (tp30) REVERT: A 453 MET cc_start: 0.8525 (tpp) cc_final: 0.8211 (tpp) REVERT: A 486 TYR cc_start: 0.8348 (t80) cc_final: 0.8094 (t80) REVERT: A 487 LEU cc_start: 0.8773 (tt) cc_final: 0.8559 (tp) REVERT: A 492 GLN cc_start: 0.8472 (mt0) cc_final: 0.7726 (tm-30) REVERT: B 60 LYS cc_start: 0.8461 (mttm) cc_final: 0.8055 (mmtm) REVERT: C 1 MET cc_start: 0.8465 (mmp) cc_final: 0.7507 (mmm) REVERT: C 47 LYS cc_start: 0.8563 (mttp) cc_final: 0.8352 (pttt) REVERT: C 71 ASP cc_start: 0.8877 (t70) cc_final: 0.8575 (t0) REVERT: C 148 GLN cc_start: 0.8782 (tt0) cc_final: 0.8314 (tm-30) REVERT: C 186 ARG cc_start: 0.8844 (mmm160) cc_final: 0.8586 (mmt180) REVERT: C 193 GLU cc_start: 0.6327 (pm20) cc_final: 0.5278 (pm20) REVERT: C 204 TRP cc_start: 0.9360 (m-90) cc_final: 0.8765 (m-90) REVERT: C 286 LYS cc_start: 0.8178 (tttm) cc_final: 0.7830 (mtpp) REVERT: C 389 TRP cc_start: 0.7215 (t60) cc_final: 0.6069 (t60) REVERT: C 390 TYR cc_start: 0.8324 (t80) cc_final: 0.8037 (t80) REVERT: E 26 GLU cc_start: 0.8398 (mt-10) cc_final: 0.7808 (mt-10) REVERT: E 335 PHE cc_start: 0.8383 (t80) cc_final: 0.8030 (t80) REVERT: E 399 MET cc_start: 0.7828 (tmm) cc_final: 0.7340 (tmm) REVERT: F 51 HIS cc_start: 0.7809 (t-90) cc_final: 0.7556 (t-90) REVERT: H 3 GLN cc_start: 0.7424 (pm20) cc_final: 0.7077 (pm20) REVERT: H 21 SER cc_start: 0.8348 (p) cc_final: 0.8124 (p) REVERT: H 27 TYR cc_start: 0.8253 (p90) cc_final: 0.7564 (p90) REVERT: H 29 PHE cc_start: 0.6632 (t80) cc_final: 0.6054 (t80) REVERT: H 46 GLU cc_start: 0.8976 (pm20) cc_final: 0.8373 (pm20) REVERT: H 118 VAL cc_start: 0.7918 (m) cc_final: 0.7692 (p) REVERT: L 3 VAL cc_start: 0.6830 (p) cc_final: 0.6041 (m) REVERT: L 28 ASN cc_start: 0.8386 (p0) cc_final: 0.7660 (p0) REVERT: L 87 TYR cc_start: 0.7837 (m-80) cc_final: 0.7178 (m-10) REVERT: O 1 MET cc_start: 0.8369 (mmm) cc_final: 0.7703 (mmm) REVERT: O 42 ASP cc_start: 0.8040 (t0) cc_final: 0.7668 (t0) REVERT: O 49 GLU cc_start: 0.8505 (mp0) cc_final: 0.7998 (mp0) REVERT: O 69 THR cc_start: 0.9256 (p) cc_final: 0.8684 (p) REVERT: O 76 THR cc_start: 0.8200 (p) cc_final: 0.7986 (p) REVERT: O 195 ILE cc_start: 0.8928 (mt) cc_final: 0.8244 (mp) REVERT: O 312 GLU cc_start: 0.8681 (tp30) cc_final: 0.8443 (tp30) REVERT: O 453 MET cc_start: 0.8543 (tpp) cc_final: 0.8244 (tpp) REVERT: O 486 TYR cc_start: 0.8329 (t80) cc_final: 0.8099 (t80) REVERT: O 487 LEU cc_start: 0.8767 (tt) cc_final: 0.8522 (tp) REVERT: O 492 GLN cc_start: 0.8491 (mt0) cc_final: 0.8222 (mt0) REVERT: P 10 MET cc_start: 0.7411 (tpp) cc_final: 0.7098 (mmm) REVERT: P 60 LYS cc_start: 0.8407 (mttm) cc_final: 0.8093 (mmtm) REVERT: Q 1 MET cc_start: 0.8466 (mmp) cc_final: 0.7523 (mmm) REVERT: Q 33 THR cc_start: 0.8437 (m) cc_final: 0.8152 (m) REVERT: Q 47 LYS cc_start: 0.8675 (mttp) cc_final: 0.8307 (pttt) REVERT: Q 71 ASP cc_start: 0.8926 (t70) cc_final: 0.8605 (t0) REVERT: Q 148 GLN cc_start: 0.8801 (tt0) cc_final: 0.8329 (tm-30) REVERT: Q 186 ARG cc_start: 0.8789 (mmm160) cc_final: 0.8545 (mmt180) REVERT: Q 193 GLU cc_start: 0.6315 (pm20) cc_final: 0.5239 (pm20) REVERT: Q 204 TRP cc_start: 0.9359 (m-90) cc_final: 0.8770 (m-90) REVERT: Q 286 LYS cc_start: 0.8202 (tttm) cc_final: 0.7836 (mtpp) REVERT: Q 389 TRP cc_start: 0.7225 (t60) cc_final: 0.6082 (t60) REVERT: Q 390 TYR cc_start: 0.8310 (t80) cc_final: 0.8022 (t80) REVERT: S 26 GLU cc_start: 0.8412 (mt-10) cc_final: 0.7850 (mt-10) REVERT: S 306 LEU cc_start: 0.9093 (tp) cc_final: 0.8886 (tp) REVERT: S 335 PHE cc_start: 0.8391 (t80) cc_final: 0.8045 (t80) REVERT: S 399 MET cc_start: 0.7827 (tmm) cc_final: 0.7335 (tmm) REVERT: T 51 HIS cc_start: 0.7806 (t-90) cc_final: 0.7552 (t-90) REVERT: U 3 GLN cc_start: 0.7440 (pm20) cc_final: 0.7082 (pm20) REVERT: U 21 SER cc_start: 0.8342 (p) cc_final: 0.8125 (p) REVERT: U 27 TYR cc_start: 0.8277 (p90) cc_final: 0.7554 (p90) REVERT: U 29 PHE cc_start: 0.6655 (t80) cc_final: 0.6067 (t80) REVERT: U 46 GLU cc_start: 0.8975 (pm20) cc_final: 0.8368 (pm20) REVERT: U 111 TYR cc_start: 0.7875 (m-80) cc_final: 0.7622 (m-80) REVERT: U 118 VAL cc_start: 0.7904 (m) cc_final: 0.7681 (p) REVERT: V 3 VAL cc_start: 0.6847 (p) cc_final: 0.6021 (m) REVERT: V 28 ASN cc_start: 0.8302 (p0) cc_final: 0.7956 (p0) REVERT: V 87 TYR cc_start: 0.7844 (m-80) cc_final: 0.7182 (m-10) outliers start: 2 outliers final: 0 residues processed: 1007 average time/residue: 0.3893 time to fit residues: 639.0063 Evaluate side-chains 842 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 842 time to evaluate : 3.146 ------------------------------------------------------------------------------- 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: 6.9990 chunk 2 optimal weight: 6.9990 chunk 205 optimal weight: 20.0000 chunk 272 optimal weight: 2.9990 chunk 242 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 290 optimal weight: 9.9990 chunk 378 optimal weight: 9.9990 chunk 131 optimal weight: 2.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 ** 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 53 ASN O 89 ASN O 192 ASN P 59 GLN ** 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 364 ASN T 59 GLN 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 = 0.3481 r_free = 0.3481 target = 0.131686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.113804 restraints weight = 51729.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.116456 restraints weight = 28896.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.118223 restraints weight = 18824.248| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2665 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= 0.215 Angle : 0.725 12.676 41636 Z= 0.365 Chirality : 0.047 0.220 4862 Planarity : 0.004 0.065 5182 Dihedral : 7.167 61.548 4716 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.19 % Allowed : 4.00 % Favored : 95.81 % 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: -1.57 (0.13), residues: 3838 helix: 0.73 (0.17), residues: 908 sheet: -1.01 (0.17), residues: 934 loop : -1.95 (0.13), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP S 451 HIS 0.006 0.001 HIS A 207 PHE 0.020 0.002 PHE F 42 TYR 0.022 0.002 TYR B 52 ARG 0.008 0.001 ARG O 348 Details of bonding type rmsd link_NAG-ASN : bond 0.00407 ( 12) link_NAG-ASN : angle 2.26528 ( 36) link_BETA1-4 : bond 0.00425 ( 20) link_BETA1-4 : angle 1.78804 ( 60) hydrogen bonds : bond 0.04222 ( 1098) hydrogen bonds : angle 5.89673 ( 3024) SS BOND : bond 0.00518 ( 28) SS BOND : angle 1.77153 ( 56) covalent geometry : bond 0.00495 (30596) covalent geometry : angle 0.71748 (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 998 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 992 time to evaluate : 3.194 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 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 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 1 MET cc_start: 0.8390 (mmm) cc_final: 0.7764 (mmm) REVERT: A 42 ASP cc_start: 0.8008 (t0) cc_final: 0.7566 (t0) REVERT: A 47 LYS cc_start: 0.9343 (pttm) cc_final: 0.8191 (pttm) REVERT: A 49 GLU cc_start: 0.8593 (mp0) cc_final: 0.7485 (mp0) REVERT: A 69 THR cc_start: 0.9204 (p) cc_final: 0.8633 (p) REVERT: A 176 TYR cc_start: 0.8280 (m-10) cc_final: 0.7962 (m-10) REVERT: A 209 GLN cc_start: 0.7269 (tm-30) cc_final: 0.6795 (tm-30) REVERT: A 262 LEU cc_start: 0.9328 (pt) cc_final: 0.9068 (pp) REVERT: A 312 GLU cc_start: 0.8496 (tp30) cc_final: 0.7888 (tp30) REVERT: A 323 GLU cc_start: 0.8419 (tp30) cc_final: 0.8147 (tp30) REVERT: A 453 MET cc_start: 0.8603 (tpp) cc_final: 0.8317 (tpp) REVERT: A 486 TYR cc_start: 0.8382 (t80) cc_final: 0.8085 (t80) REVERT: A 487 LEU cc_start: 0.8685 (tt) cc_final: 0.8450 (tp) REVERT: A 492 GLN cc_start: 0.8499 (mt0) cc_final: 0.7760 (tm-30) REVERT: B 68 MET cc_start: 0.8496 (tpp) cc_final: 0.7421 (ttp) REVERT: B 70 VAL cc_start: 0.8488 (t) cc_final: 0.8203 (t) REVERT: C 1 MET cc_start: 0.8455 (mmp) cc_final: 0.7364 (mmm) REVERT: C 47 LYS cc_start: 0.8721 (mttp) cc_final: 0.8243 (pttt) REVERT: C 204 TRP cc_start: 0.9354 (m-90) cc_final: 0.8787 (m-90) REVERT: C 286 LYS cc_start: 0.8186 (tttm) cc_final: 0.7875 (mtpp) REVERT: C 366 GLU cc_start: 0.7728 (pm20) cc_final: 0.7524 (pm20) REVERT: C 389 TRP cc_start: 0.7425 (t60) cc_final: 0.5451 (t60) REVERT: C 390 TYR cc_start: 0.8327 (t80) cc_final: 0.7992 (t80) REVERT: C 408 ARG cc_start: 0.8968 (tpp80) cc_final: 0.8737 (tpp80) REVERT: E 96 TYR cc_start: 0.8918 (m-10) cc_final: 0.8678 (m-80) REVERT: E 281 LEU cc_start: 0.8792 (tp) cc_final: 0.8243 (tt) REVERT: E 399 MET cc_start: 0.7855 (tmm) cc_final: 0.7378 (tmm) REVERT: E 455 ILE cc_start: 0.9371 (tp) cc_final: 0.9068 (tp) REVERT: F 10 MET cc_start: 0.8284 (mmp) cc_final: 0.8040 (mmp) REVERT: H 3 GLN cc_start: 0.7466 (pm20) cc_final: 0.7134 (pm20) REVERT: H 21 SER cc_start: 0.8418 (p) cc_final: 0.8155 (p) REVERT: H 27 TYR cc_start: 0.8193 (p90) cc_final: 0.7600 (p90) REVERT: H 29 PHE cc_start: 0.6542 (t80) cc_final: 0.6081 (t80) REVERT: H 36 TRP cc_start: 0.7627 (m100) cc_final: 0.6765 (m100) REVERT: H 46 GLU cc_start: 0.9122 (pm20) cc_final: 0.8687 (pm20) REVERT: L 3 VAL cc_start: 0.6825 (p) cc_final: 0.6001 (m) REVERT: L 28 ASN cc_start: 0.8485 (p0) cc_final: 0.8075 (p0) REVERT: O 1 MET cc_start: 0.8381 (mmm) cc_final: 0.7732 (mmm) REVERT: O 42 ASP cc_start: 0.7991 (t0) cc_final: 0.7528 (t0) REVERT: O 47 LYS cc_start: 0.9326 (pttm) cc_final: 0.8679 (pttm) REVERT: O 49 GLU cc_start: 0.8585 (mp0) cc_final: 0.7846 (mp0) REVERT: O 69 THR cc_start: 0.9188 (p) cc_final: 0.8640 (p) REVERT: O 176 TYR cc_start: 0.8282 (m-10) cc_final: 0.7976 (m-10) REVERT: O 209 GLN cc_start: 0.7541 (tm-30) cc_final: 0.6966 (tm-30) REVERT: O 262 LEU cc_start: 0.9308 (pt) cc_final: 0.9051 (pp) REVERT: O 312 GLU cc_start: 0.8510 (tp30) cc_final: 0.7887 (tp30) REVERT: O 323 GLU cc_start: 0.8426 (tp30) cc_final: 0.8167 (tp30) REVERT: O 353 ASN cc_start: 0.8486 (t0) cc_final: 0.8052 (t0) REVERT: O 453 MET cc_start: 0.8615 (tpp) cc_final: 0.8322 (tpp) REVERT: O 486 TYR cc_start: 0.8360 (t80) cc_final: 0.8079 (t80) REVERT: O 487 LEU cc_start: 0.8685 (tt) cc_final: 0.8434 (tp) REVERT: O 492 GLN cc_start: 0.8499 (mt0) cc_final: 0.8272 (mt0) REVERT: P 60 LYS cc_start: 0.8331 (mttm) cc_final: 0.7979 (mttt) REVERT: P 70 VAL cc_start: 0.8471 (t) cc_final: 0.8221 (t) REVERT: Q 1 MET cc_start: 0.8284 (mmp) cc_final: 0.7062 (mmm) REVERT: Q 47 LYS cc_start: 0.8743 (mttp) cc_final: 0.8355 (tttt) REVERT: Q 71 ASP cc_start: 0.8977 (t70) cc_final: 0.8696 (t0) REVERT: Q 204 TRP cc_start: 0.9352 (m-90) cc_final: 0.8800 (m-90) REVERT: Q 286 LYS cc_start: 0.8170 (tttm) cc_final: 0.7861 (mtpp) REVERT: Q 366 GLU cc_start: 0.7706 (pm20) cc_final: 0.7501 (pm20) REVERT: Q 389 TRP cc_start: 0.7430 (t60) cc_final: 0.5466 (t60) REVERT: Q 390 TYR cc_start: 0.8313 (t80) cc_final: 0.7985 (t80) REVERT: S 96 TYR cc_start: 0.8920 (m-10) cc_final: 0.8679 (m-80) REVERT: S 247 GLU cc_start: 0.7472 (pm20) cc_final: 0.7254 (pm20) REVERT: S 281 LEU cc_start: 0.8812 (tp) cc_final: 0.8264 (tt) REVERT: S 399 MET cc_start: 0.7854 (tmm) cc_final: 0.7370 (tmm) REVERT: S 455 ILE cc_start: 0.9369 (tp) cc_final: 0.9072 (tp) REVERT: T 10 MET cc_start: 0.8301 (mmp) cc_final: 0.8052 (mmp) REVERT: U 3 GLN cc_start: 0.7468 (pm20) cc_final: 0.7147 (pm20) REVERT: U 21 SER cc_start: 0.8405 (p) cc_final: 0.8154 (p) REVERT: U 27 TYR cc_start: 0.8186 (p90) cc_final: 0.7687 (p90) REVERT: U 29 PHE cc_start: 0.6542 (t80) cc_final: 0.6083 (t80) REVERT: U 36 TRP cc_start: 0.7441 (m100) cc_final: 0.6483 (m100) REVERT: U 46 GLU cc_start: 0.9120 (pm20) cc_final: 0.8680 (pm20) REVERT: U 98 ARG cc_start: 0.6789 (ttp-170) cc_final: 0.6128 (ttp-110) REVERT: U 111 TYR cc_start: 0.7894 (m-80) cc_final: 0.7450 (m-80) REVERT: V 3 VAL cc_start: 0.6819 (p) cc_final: 0.6008 (m) REVERT: V 28 ASN cc_start: 0.8365 (p0) cc_final: 0.8143 (p0) outliers start: 6 outliers final: 0 residues processed: 996 average time/residue: 0.3907 time to fit residues: 634.8107 Evaluate side-chains 823 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 823 time to evaluate : 3.236 ------------------------------------------------------------------------------- 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: 3.9990 chunk 109 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 149 optimal weight: 10.0000 chunk 245 optimal weight: 3.9990 chunk 271 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 70 optimal weight: 9.9990 chunk 300 optimal weight: 6.9990 chunk 174 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 HIS C 209 GLN ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 17 GLN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 364 ASN F 59 GLN L 16 GLN L 38 GLN L 53 ASN O 192 ASN O 207 HIS P 51 HIS Q 77 GLN Q 149 HIS Q 209 GLN Q 353 ASN 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.132078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.114105 restraints weight = 52116.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.116806 restraints weight = 29161.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.118598 restraints weight = 18924.123| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2880 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= 0.176 Angle : 0.694 12.850 41636 Z= 0.351 Chirality : 0.046 0.181 4862 Planarity : 0.004 0.058 5182 Dihedral : 6.709 53.127 4716 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.22 % Allowed : 3.09 % Favored : 96.69 % 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: -1.51 (0.13), residues: 3838 helix: 0.81 (0.17), residues: 908 sheet: -0.95 (0.17), residues: 926 loop : -1.93 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP S 451 HIS 0.016 0.001 HIS Q 149 PHE 0.017 0.002 PHE Q 335 TYR 0.014 0.002 TYR A 90 ARG 0.005 0.001 ARG Q 405 Details of bonding type rmsd link_NAG-ASN : bond 0.00290 ( 12) link_NAG-ASN : angle 2.16930 ( 36) link_BETA1-4 : bond 0.00453 ( 20) link_BETA1-4 : angle 1.63113 ( 60) hydrogen bonds : bond 0.04073 ( 1098) hydrogen bonds : angle 5.71698 ( 3024) SS BOND : bond 0.00424 ( 28) SS BOND : angle 1.65300 ( 56) covalent geometry : bond 0.00405 (30596) covalent geometry : angle 0.68708 (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 1003 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 996 time to evaluate : 3.686 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 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: 0.7723 (t0) cc_final: 0.7297 (t0) REVERT: A 69 THR cc_start: 0.9199 (p) cc_final: 0.8579 (p) REVERT: A 176 TYR cc_start: 0.8247 (m-10) cc_final: 0.7953 (m-10) REVERT: A 262 LEU cc_start: 0.9246 (pt) cc_final: 0.8995 (pp) REVERT: A 312 GLU cc_start: 0.8414 (tp30) cc_final: 0.7642 (tp30) REVERT: A 453 MET cc_start: 0.8582 (tpp) cc_final: 0.8303 (tpp) REVERT: A 486 TYR cc_start: 0.8343 (t80) cc_final: 0.8063 (t80) REVERT: A 487 LEU cc_start: 0.8618 (tt) cc_final: 0.8401 (tp) REVERT: A 492 GLN cc_start: 0.8485 (mt0) cc_final: 0.7808 (tm-30) REVERT: C 1 MET cc_start: 0.8206 (mmp) cc_final: 0.7494 (mmm) REVERT: C 22 ASP cc_start: 0.7772 (m-30) cc_final: 0.7330 (m-30) REVERT: C 47 LYS cc_start: 0.8709 (mttp) cc_final: 0.8223 (pttt) REVERT: C 57 ARG cc_start: 0.9234 (tpp80) cc_final: 0.8852 (tpp80) REVERT: C 204 TRP cc_start: 0.9343 (m-90) cc_final: 0.8830 (m-90) REVERT: C 286 LYS cc_start: 0.8157 (tttm) cc_final: 0.7839 (mtpp) REVERT: C 389 TRP cc_start: 0.7338 (t60) cc_final: 0.5411 (t60) REVERT: C 390 TYR cc_start: 0.8331 (t80) cc_final: 0.7982 (t80) REVERT: C 433 MET cc_start: 0.7878 (tpp) cc_final: 0.7457 (tpp) REVERT: D 14 THR cc_start: 0.8531 (p) cc_final: 0.8328 (p) REVERT: D 30 GLU cc_start: 0.8264 (tp30) cc_final: 0.7925 (tp30) REVERT: D 68 MET cc_start: 0.8477 (mmm) cc_final: 0.7259 (tmm) REVERT: E 96 TYR cc_start: 0.8767 (m-10) cc_final: 0.8553 (m-80) REVERT: E 399 MET cc_start: 0.7829 (tmm) cc_final: 0.7365 (tmm) REVERT: E 455 ILE cc_start: 0.9363 (tp) cc_final: 0.9060 (tp) REVERT: F 10 MET cc_start: 0.8207 (mmp) cc_final: 0.7902 (mmt) REVERT: F 15 ARG cc_start: 0.8559 (mmm-85) cc_final: 0.8328 (mmt180) REVERT: F 28 GLN cc_start: 0.7360 (mm-40) cc_final: 0.7112 (mm-40) REVERT: F 43 THR cc_start: 0.9098 (m) cc_final: 0.8898 (m) REVERT: H 3 GLN cc_start: 0.7314 (pm20) cc_final: 0.6976 (pm20) REVERT: H 21 SER cc_start: 0.8360 (p) cc_final: 0.8154 (p) REVERT: H 27 TYR cc_start: 0.8126 (p90) cc_final: 0.7601 (p90) REVERT: H 29 PHE cc_start: 0.6520 (t80) cc_final: 0.6069 (t80) REVERT: H 46 GLU cc_start: 0.9148 (pm20) cc_final: 0.8514 (pm20) REVERT: L 3 VAL cc_start: 0.6730 (p) cc_final: 0.5898 (m) REVERT: L 28 ASN cc_start: 0.8503 (p0) cc_final: 0.8013 (p0) REVERT: O 42 ASP cc_start: 0.7696 (t0) cc_final: 0.7247 (t0) REVERT: O 49 GLU cc_start: 0.8468 (mp0) cc_final: 0.8172 (mp0) REVERT: O 69 THR cc_start: 0.9165 (p) cc_final: 0.8552 (p) REVERT: O 176 TYR cc_start: 0.8248 (m-10) cc_final: 0.7952 (m-10) REVERT: O 209 GLN cc_start: 0.7430 (tm-30) cc_final: 0.6561 (tm-30) REVERT: O 262 LEU cc_start: 0.9243 (pt) cc_final: 0.8989 (pp) REVERT: O 312 GLU cc_start: 0.8413 (tp30) cc_final: 0.7646 (tp30) REVERT: O 453 MET cc_start: 0.8585 (tpp) cc_final: 0.8300 (tpp) REVERT: O 486 TYR cc_start: 0.8342 (t80) cc_final: 0.8060 (t80) REVERT: O 487 LEU cc_start: 0.8631 (tt) cc_final: 0.8404 (tp) REVERT: O 492 GLN cc_start: 0.8483 (mt0) cc_final: 0.7805 (tm-30) REVERT: P 60 LYS cc_start: 0.8243 (mttm) cc_final: 0.7920 (mttt) REVERT: Q 1 MET cc_start: 0.8198 (mmp) cc_final: 0.7486 (mmm) REVERT: Q 47 LYS cc_start: 0.8685 (mttp) cc_final: 0.8219 (tttt) REVERT: Q 71 ASP cc_start: 0.8946 (t70) cc_final: 0.8653 (t0) REVERT: Q 101 TRP cc_start: 0.8622 (m-10) cc_final: 0.8156 (m-10) REVERT: Q 204 TRP cc_start: 0.9307 (m-90) cc_final: 0.8755 (m-90) REVERT: Q 205 MET cc_start: 0.8894 (ptp) cc_final: 0.8690 (ptp) REVERT: Q 286 LYS cc_start: 0.8151 (tttm) cc_final: 0.7824 (mtpp) REVERT: Q 389 TRP cc_start: 0.7346 (t60) cc_final: 0.5415 (t60) REVERT: Q 390 TYR cc_start: 0.8314 (t80) cc_final: 0.7974 (t80) REVERT: Q 433 MET cc_start: 0.7899 (tpp) cc_final: 0.7472 (tpp) REVERT: R 14 THR cc_start: 0.8548 (p) cc_final: 0.8346 (p) REVERT: R 30 GLU cc_start: 0.8268 (tp30) cc_final: 0.7939 (tp30) REVERT: R 68 MET cc_start: 0.8473 (mmm) cc_final: 0.7259 (tmm) REVERT: S 1 MET cc_start: 0.8068 (mmt) cc_final: 0.7723 (mmm) REVERT: S 96 TYR cc_start: 0.8771 (m-10) cc_final: 0.8560 (m-80) REVERT: S 247 GLU cc_start: 0.7377 (pm20) cc_final: 0.7139 (pm20) REVERT: S 281 LEU cc_start: 0.8827 (tp) cc_final: 0.8622 (tp) REVERT: S 399 MET cc_start: 0.7819 (tmm) cc_final: 0.7357 (tmm) REVERT: S 455 ILE cc_start: 0.9358 (tp) cc_final: 0.9043 (tp) REVERT: T 10 MET cc_start: 0.8220 (mmp) cc_final: 0.7908 (mmp) REVERT: T 28 GLN cc_start: 0.7368 (mm-40) cc_final: 0.7108 (mm-40) REVERT: T 43 THR cc_start: 0.9096 (m) cc_final: 0.8890 (m) REVERT: U 3 GLN cc_start: 0.7314 (pm20) cc_final: 0.6980 (pm20) REVERT: U 27 TYR cc_start: 0.8109 (p90) cc_final: 0.7494 (p90) REVERT: U 29 PHE cc_start: 0.6540 (t80) cc_final: 0.6096 (t80) REVERT: U 46 GLU cc_start: 0.9140 (pm20) cc_final: 0.8500 (pm20) REVERT: U 111 TYR cc_start: 0.7831 (m-80) cc_final: 0.7465 (m-80) REVERT: V 3 VAL cc_start: 0.6754 (p) cc_final: 0.5914 (m) REVERT: V 28 ASN cc_start: 0.8653 (p0) cc_final: 0.8422 (p0) outliers start: 7 outliers final: 3 residues processed: 1000 average time/residue: 0.4424 time to fit residues: 728.9555 Evaluate side-chains 855 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 852 time to evaluate : 3.636 ------------------------------------------------------------------------------- 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: 9.9990 chunk 7 optimal weight: 0.9980 chunk 129 optimal weight: 8.9990 chunk 121 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 99 optimal weight: 20.0000 chunk 273 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 379 optimal weight: 5.9990 chunk 320 optimal weight: 9.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 GLN C 353 ASN D 17 GLN ** E 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 L 53 ASN ** O 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 467 ASN R 17 GLN ** S 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 207 HIS S 364 ASN T 59 GLN ** U 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 16 GLN V 38 GLN V 53 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.125626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.107939 restraints weight = 52944.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.110394 restraints weight = 30860.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.112033 restraints weight = 20697.465| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 30656 Z= 0.249 Angle : 0.766 10.991 41636 Z= 0.386 Chirality : 0.048 0.268 4862 Planarity : 0.005 0.061 5182 Dihedral : 6.660 52.403 4716 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 0.12 % Allowed : 2.25 % Favored : 97.62 % 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: -1.62 (0.13), residues: 3838 helix: 0.68 (0.17), residues: 906 sheet: -0.94 (0.18), residues: 908 loop : -2.02 (0.12), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP U 50 HIS 0.009 0.001 HIS Q 280 PHE 0.021 0.002 PHE T 42 TYR 0.026 0.002 TYR P 52 ARG 0.010 0.001 ARG S 186 Details of bonding type rmsd link_NAG-ASN : bond 0.00540 ( 12) link_NAG-ASN : angle 2.28090 ( 36) link_BETA1-4 : bond 0.00440 ( 20) link_BETA1-4 : angle 1.61560 ( 60) hydrogen bonds : bond 0.04353 ( 1098) hydrogen bonds : angle 5.84813 ( 3024) SS BOND : bond 0.00467 ( 28) SS BOND : angle 1.64422 ( 56) covalent geometry : bond 0.00578 (30596) covalent geometry : angle 0.75972 (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 991 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 987 time to evaluate : 3.910 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: 0.8353 (mmm) cc_final: 0.7990 (mmm) REVERT: A 42 ASP cc_start: 0.7680 (t0) cc_final: 0.7219 (t0) REVERT: A 47 LYS cc_start: 0.9326 (pttm) cc_final: 0.9047 (pttm) REVERT: A 69 THR cc_start: 0.9249 (p) cc_final: 0.8673 (p) REVERT: A 71 ASP cc_start: 0.7349 (t70) cc_final: 0.7093 (t0) REVERT: A 176 TYR cc_start: 0.8333 (m-10) cc_final: 0.7893 (m-10) REVERT: A 209 GLN cc_start: 0.7787 (tm-30) cc_final: 0.7469 (tm-30) REVERT: A 312 GLU cc_start: 0.8481 (tp30) cc_final: 0.7675 (tp30) REVERT: A 323 GLU cc_start: 0.8454 (tp30) cc_final: 0.8126 (tp30) REVERT: A 453 MET cc_start: 0.8657 (tpp) cc_final: 0.8351 (tpt) REVERT: A 486 TYR cc_start: 0.8392 (t80) cc_final: 0.8098 (t80) REVERT: A 487 LEU cc_start: 0.8763 (tt) cc_final: 0.8505 (tp) REVERT: A 492 GLN cc_start: 0.8496 (mt0) cc_final: 0.8282 (mt0) REVERT: B 70 VAL cc_start: 0.8489 (t) cc_final: 0.8289 (t) REVERT: C 1 MET cc_start: 0.8298 (mmp) cc_final: 0.7122 (mmm) REVERT: C 47 LYS cc_start: 0.8738 (mttp) cc_final: 0.8244 (tttt) REVERT: C 57 ARG cc_start: 0.9285 (tpp80) cc_final: 0.9049 (tpp80) REVERT: C 193 GLU cc_start: 0.6279 (pm20) cc_final: 0.5081 (pm20) REVERT: C 204 TRP cc_start: 0.9371 (m-90) cc_final: 0.8820 (m-90) REVERT: C 233 GLU cc_start: 0.7488 (tm-30) cc_final: 0.7228 (tm-30) REVERT: C 286 LYS cc_start: 0.8187 (tttm) cc_final: 0.7846 (mtpp) REVERT: C 324 TYR cc_start: 0.8690 (t80) cc_final: 0.8258 (t80) REVERT: C 389 TRP cc_start: 0.7559 (t60) cc_final: 0.5564 (t60) REVERT: C 433 MET cc_start: 0.7926 (tpp) cc_final: 0.7468 (tpp) REVERT: D 30 GLU cc_start: 0.8240 (tp30) cc_final: 0.7828 (tp30) REVERT: E 26 GLU cc_start: 0.8491 (mt-10) cc_final: 0.7941 (mt-10) REVERT: E 281 LEU cc_start: 0.8831 (tp) cc_final: 0.8614 (tp) REVERT: E 399 MET cc_start: 0.7820 (tmm) cc_final: 0.7421 (tmm) REVERT: E 455 ILE cc_start: 0.9416 (tp) cc_final: 0.9099 (tp) REVERT: F 10 MET cc_start: 0.8244 (mmp) cc_final: 0.8026 (mmp) REVERT: F 28 GLN cc_start: 0.7519 (mm-40) cc_final: 0.7275 (mm-40) REVERT: H 3 GLN cc_start: 0.7574 (pm20) cc_final: 0.7201 (pm20) REVERT: H 12 LYS cc_start: 0.6720 (mmtm) cc_final: 0.6464 (mmtt) REVERT: H 21 SER cc_start: 0.8438 (p) cc_final: 0.8214 (p) REVERT: H 27 TYR cc_start: 0.8139 (p90) cc_final: 0.7347 (p90) REVERT: H 29 PHE cc_start: 0.6585 (t80) cc_final: 0.6174 (t80) REVERT: H 46 GLU cc_start: 0.9219 (pm20) cc_final: 0.9004 (pm20) REVERT: H 50 TRP cc_start: 0.8173 (m-10) cc_final: 0.7951 (m-10) REVERT: H 61 HIS cc_start: 0.8890 (t-90) cc_final: 0.8221 (t-90) REVERT: L 3 VAL cc_start: 0.6841 (p) cc_final: 0.6043 (m) REVERT: L 28 ASN cc_start: 0.8550 (p0) cc_final: 0.8116 (p0) REVERT: L 47 LEU cc_start: 0.7226 (tt) cc_final: 0.6977 (tt) REVERT: O 1 MET cc_start: 0.8367 (mmm) cc_final: 0.7972 (mmm) REVERT: O 42 ASP cc_start: 0.7690 (t0) cc_final: 0.7203 (t0) REVERT: O 47 LYS cc_start: 0.9266 (pttm) cc_final: 0.9024 (pttm) REVERT: O 69 THR cc_start: 0.9250 (p) cc_final: 0.8677 (p) REVERT: O 71 ASP cc_start: 0.7329 (t70) cc_final: 0.7063 (t0) REVERT: O 176 TYR cc_start: 0.8362 (m-10) cc_final: 0.7944 (m-10) REVERT: O 209 GLN cc_start: 0.7575 (tm-30) cc_final: 0.7181 (tm-30) REVERT: O 312 GLU cc_start: 0.8477 (tp30) cc_final: 0.7632 (tp30) REVERT: O 323 GLU cc_start: 0.8450 (tp30) cc_final: 0.8154 (tp30) REVERT: O 353 ASN cc_start: 0.8475 (t0) cc_final: 0.8082 (t0) REVERT: O 453 MET cc_start: 0.8660 (tpp) cc_final: 0.8378 (tpp) REVERT: O 486 TYR cc_start: 0.8396 (t80) cc_final: 0.8089 (t80) REVERT: O 487 LEU cc_start: 0.8768 (tt) cc_final: 0.8529 (tp) REVERT: O 492 GLN cc_start: 0.8488 (mt0) cc_final: 0.8177 (mt0) REVERT: P 60 LYS cc_start: 0.8223 (mttm) cc_final: 0.7932 (mtpt) REVERT: Q 1 MET cc_start: 0.8318 (mmp) cc_final: 0.7131 (mmm) REVERT: Q 71 ASP cc_start: 0.8985 (t70) cc_final: 0.8684 (t0) REVERT: Q 101 TRP cc_start: 0.8645 (m-10) cc_final: 0.8213 (m-10) REVERT: Q 204 TRP cc_start: 0.9285 (m-90) cc_final: 0.8811 (m-90) REVERT: Q 233 GLU cc_start: 0.7501 (tm-30) cc_final: 0.7244 (tm-30) REVERT: Q 286 LYS cc_start: 0.8222 (tttm) cc_final: 0.7845 (mtpp) REVERT: Q 324 TYR cc_start: 0.8665 (t80) cc_final: 0.8266 (t80) REVERT: Q 389 TRP cc_start: 0.7552 (t60) cc_final: 0.5586 (t60) REVERT: Q 433 MET cc_start: 0.7954 (tpp) cc_final: 0.7503 (tpp) REVERT: R 30 GLU cc_start: 0.8256 (tp30) cc_final: 0.7836 (tp30) REVERT: S 26 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7668 (mt-10) REVERT: S 281 LEU cc_start: 0.8844 (tp) cc_final: 0.8640 (tp) REVERT: S 399 MET cc_start: 0.7946 (tmm) cc_final: 0.7399 (tmm) REVERT: S 455 ILE cc_start: 0.9413 (tp) cc_final: 0.9089 (tp) REVERT: T 10 MET cc_start: 0.8236 (mmp) cc_final: 0.8006 (mmp) REVERT: T 28 GLN cc_start: 0.7513 (mm-40) cc_final: 0.7267 (mm-40) REVERT: U 3 GLN cc_start: 0.7569 (pm20) cc_final: 0.7199 (pm20) REVERT: U 12 LYS cc_start: 0.6711 (mmtm) cc_final: 0.6461 (mmtt) REVERT: U 21 SER cc_start: 0.8416 (p) cc_final: 0.8203 (p) REVERT: U 27 TYR cc_start: 0.8028 (p90) cc_final: 0.7551 (p90) REVERT: U 29 PHE cc_start: 0.6558 (t80) cc_final: 0.6119 (t80) REVERT: U 46 GLU cc_start: 0.9173 (pm20) cc_final: 0.8535 (pm20) REVERT: U 61 HIS cc_start: 0.8896 (t-90) cc_final: 0.8229 (t-90) REVERT: U 98 ARG cc_start: 0.7184 (ttp-110) cc_final: 0.6623 (ttp-110) REVERT: V 3 VAL cc_start: 0.6866 (p) cc_final: 0.6042 (m) REVERT: V 28 ASN cc_start: 0.8808 (p0) cc_final: 0.8542 (p0) REVERT: V 47 LEU cc_start: 0.7212 (tt) cc_final: 0.7009 (tt) outliers start: 4 outliers final: 1 residues processed: 990 average time/residue: 0.3856 time to fit residues: 625.2347 Evaluate side-chains 812 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 811 time to evaluate : 3.276 ------------------------------------------------------------------------------- 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: 4.9990 chunk 203 optimal weight: 0.9990 chunk 196 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 149 optimal weight: 9.9990 chunk 222 optimal weight: 7.9990 chunk 141 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 275 optimal weight: 5.9990 chunk 219 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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** B 51 HIS C 149 HIS C 209 GLN C 353 ASN D 17 GLN E 27 HIS ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN E 364 ASN F 59 GLN ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 16 GLN L 38 GLN L 53 ASN ** O 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 HIS Q 209 GLN ** Q 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 467 ASN R 17 GLN S 27 HIS ** S 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 246 GLN 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: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.129097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.110632 restraints weight = 52824.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.113387 restraints weight = 29506.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.115203 restraints weight = 19121.242| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3138 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= 0.152 Angle : 0.708 12.271 41636 Z= 0.356 Chirality : 0.046 0.211 4862 Planarity : 0.004 0.050 5182 Dihedral : 6.281 53.819 4716 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.19 % Allowed : 1.81 % Favored : 98.00 % 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: -1.51 (0.13), residues: 3838 helix: 0.78 (0.17), residues: 908 sheet: -0.84 (0.18), residues: 896 loop : -1.97 (0.12), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 451 HIS 0.016 0.001 HIS C 149 PHE 0.041 0.002 PHE C 304 TYR 0.015 0.002 TYR C 486 ARG 0.006 0.001 ARG Q 405 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 12) link_NAG-ASN : angle 2.06554 ( 36) link_BETA1-4 : bond 0.00477 ( 20) link_BETA1-4 : angle 1.52652 ( 60) hydrogen bonds : bond 0.03929 ( 1098) hydrogen bonds : angle 5.59731 ( 3024) SS BOND : bond 0.00588 ( 28) SS BOND : angle 1.64910 ( 56) covalent geometry : bond 0.00351 (30596) covalent geometry : angle 0.70200 (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 1012 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1006 time to evaluate : 4.643 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: symmetry clash REVERT: A 1 MET cc_start: 0.8229 (mmm) cc_final: 0.7760 (mmm) REVERT: A 47 LYS cc_start: 0.9285 (pttm) cc_final: 0.8972 (pttm) REVERT: A 69 THR cc_start: 0.9212 (p) cc_final: 0.8535 (p) REVERT: A 71 ASP cc_start: 0.7272 (t70) cc_final: 0.7030 (t0) REVERT: A 209 GLN cc_start: 0.7524 (tm-30) cc_final: 0.7258 (tm-30) REVERT: A 312 GLU cc_start: 0.8387 (tp30) cc_final: 0.7656 (tp30) REVERT: A 323 GLU cc_start: 0.8436 (tp30) cc_final: 0.8140 (tp30) REVERT: A 453 MET cc_start: 0.8583 (tpp) cc_final: 0.8318 (tpt) REVERT: A 486 TYR cc_start: 0.8327 (t80) cc_final: 0.8041 (t80) REVERT: A 487 LEU cc_start: 0.8738 (tt) cc_final: 0.8493 (tp) REVERT: A 492 GLN cc_start: 0.8488 (mt0) cc_final: 0.7771 (tm-30) REVERT: B 60 LYS cc_start: 0.8232 (mttm) cc_final: 0.7943 (mtpt) REVERT: B 68 MET cc_start: 0.8463 (tpp) cc_final: 0.7394 (ttp) REVERT: C 1 MET cc_start: 0.8310 (mmp) cc_final: 0.5881 (mmm) REVERT: C 47 LYS cc_start: 0.8457 (mttp) cc_final: 0.7258 (pttt) REVERT: C 49 GLU cc_start: 0.7263 (mp0) cc_final: 0.6809 (mp0) REVERT: C 101 TRP cc_start: 0.8651 (m-10) cc_final: 0.8168 (m-10) REVERT: C 150 GLN cc_start: 0.8115 (tt0) cc_final: 0.6763 (tt0) REVERT: C 204 TRP cc_start: 0.9338 (m-90) cc_final: 0.8823 (m-90) REVERT: C 233 GLU cc_start: 0.7471 (tm-30) cc_final: 0.7225 (tm-30) REVERT: C 286 LYS cc_start: 0.8211 (tttm) cc_final: 0.7982 (mtpp) REVERT: C 366 GLU cc_start: 0.7537 (pm20) cc_final: 0.7252 (pm20) REVERT: C 433 MET cc_start: 0.7923 (tpp) cc_final: 0.7465 (tpp) REVERT: D 30 GLU cc_start: 0.8244 (tp30) cc_final: 0.7837 (tp30) REVERT: E 26 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8118 (mt-10) REVERT: E 41 LEU cc_start: 0.8928 (pt) cc_final: 0.8462 (pt) REVERT: E 399 MET cc_start: 0.8076 (tmm) cc_final: 0.7658 (tmm) REVERT: E 455 ILE cc_start: 0.9348 (tp) cc_final: 0.9039 (tp) REVERT: F 15 ARG cc_start: 0.8569 (mmm-85) cc_final: 0.7855 (mmm-85) REVERT: F 43 THR cc_start: 0.9106 (m) cc_final: 0.8829 (m) REVERT: F 64 PHE cc_start: 0.8760 (t80) cc_final: 0.8506 (t80) REVERT: H 3 GLN cc_start: 0.7491 (pm20) cc_final: 0.7187 (pm20) REVERT: H 12 LYS cc_start: 0.6682 (mmtm) cc_final: 0.6396 (mmtt) REVERT: H 21 SER cc_start: 0.8346 (p) cc_final: 0.8072 (p) REVERT: H 27 TYR cc_start: 0.8097 (p90) cc_final: 0.7488 (p90) REVERT: H 29 PHE cc_start: 0.6485 (t80) cc_final: 0.6059 (t80) REVERT: H 36 TRP cc_start: 0.7681 (m100) cc_final: 0.6608 (m100) REVERT: H 61 HIS cc_start: 0.8534 (t-90) cc_final: 0.8159 (t-90) REVERT: L 3 VAL cc_start: 0.6770 (p) cc_final: 0.5966 (m) REVERT: L 28 ASN cc_start: 0.8521 (p0) cc_final: 0.8069 (p0) REVERT: L 46 LYS cc_start: 0.7802 (ttpp) cc_final: 0.7201 (mmtp) REVERT: O 1 MET cc_start: 0.8218 (mmm) cc_final: 0.7745 (mmm) REVERT: O 47 LYS cc_start: 0.9196 (pttm) cc_final: 0.8989 (pttm) REVERT: O 69 THR cc_start: 0.9194 (p) cc_final: 0.8548 (p) REVERT: O 176 TYR cc_start: 0.8217 (m-10) cc_final: 0.7873 (m-10) REVERT: O 209 GLN cc_start: 0.7419 (tm-30) cc_final: 0.7117 (tm-30) REVERT: O 312 GLU cc_start: 0.8388 (tp30) cc_final: 0.7686 (tp30) REVERT: O 323 GLU cc_start: 0.8436 (tp30) cc_final: 0.8159 (tp30) REVERT: O 453 MET cc_start: 0.8587 (tpp) cc_final: 0.8297 (tpp) REVERT: O 486 TYR cc_start: 0.8321 (t80) cc_final: 0.8044 (t80) REVERT: O 487 LEU cc_start: 0.8761 (tt) cc_final: 0.8501 (tp) REVERT: O 492 GLN cc_start: 0.8500 (mt0) cc_final: 0.7796 (tm-30) REVERT: P 60 LYS cc_start: 0.8189 (mttm) cc_final: 0.7888 (mtpt) REVERT: Q 1 MET cc_start: 0.8398 (mmp) cc_final: 0.5914 (mmm) REVERT: Q 71 ASP cc_start: 0.8921 (t70) cc_final: 0.8689 (t0) REVERT: Q 101 TRP cc_start: 0.8638 (m-10) cc_final: 0.8235 (m-10) REVERT: Q 150 GLN cc_start: 0.8199 (tt0) cc_final: 0.6807 (tt0) REVERT: Q 204 TRP cc_start: 0.9245 (m-90) cc_final: 0.8812 (m-90) REVERT: Q 233 GLU cc_start: 0.7470 (tm-30) cc_final: 0.7235 (tm-30) REVERT: Q 286 LYS cc_start: 0.8022 (tttm) cc_final: 0.7748 (mtpp) REVERT: Q 324 TYR cc_start: 0.8524 (t80) cc_final: 0.8295 (t80) REVERT: Q 366 GLU cc_start: 0.7547 (pm20) cc_final: 0.7251 (pm20) REVERT: Q 433 MET cc_start: 0.7926 (tpp) cc_final: 0.7466 (tpp) REVERT: R 30 GLU cc_start: 0.8246 (tp30) cc_final: 0.7827 (tp30) REVERT: S 26 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7878 (mt-10) REVERT: S 41 LEU cc_start: 0.9060 (pt) cc_final: 0.8693 (pt) REVERT: S 399 MET cc_start: 0.8070 (tmm) cc_final: 0.7649 (tmm) REVERT: S 455 ILE cc_start: 0.9340 (tp) cc_final: 0.9038 (tp) REVERT: T 43 THR cc_start: 0.9099 (m) cc_final: 0.8841 (m) REVERT: T 64 PHE cc_start: 0.8742 (t80) cc_final: 0.8498 (t80) REVERT: U 3 GLN cc_start: 0.7470 (pm20) cc_final: 0.7185 (pm20) REVERT: U 12 LYS cc_start: 0.6743 (mmtm) cc_final: 0.6480 (mmtt) REVERT: U 21 SER cc_start: 0.8347 (p) cc_final: 0.8088 (p) REVERT: U 27 TYR cc_start: 0.8070 (p90) cc_final: 0.7501 (p90) REVERT: U 29 PHE cc_start: 0.6477 (t80) cc_final: 0.6063 (t80) REVERT: U 36 TRP cc_start: 0.7641 (m100) cc_final: 0.6596 (m100) REVERT: U 46 GLU cc_start: 0.9166 (pm20) cc_final: 0.8633 (pm20) REVERT: U 61 HIS cc_start: 0.8595 (t-90) cc_final: 0.8169 (t-90) REVERT: V 3 VAL cc_start: 0.6764 (p) cc_final: 0.5929 (m) REVERT: V 28 ASN cc_start: 0.8715 (p0) cc_final: 0.8512 (p0) REVERT: V 46 LYS cc_start: 0.7779 (ttpp) cc_final: 0.7219 (mmtp) outliers start: 6 outliers final: 3 residues processed: 1009 average time/residue: 0.3959 time to fit residues: 650.8808 Evaluate side-chains 832 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 829 time to evaluate : 3.194 ------------------------------------------------------------------------------- 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: 0.0060 chunk 127 optimal weight: 9.9990 chunk 248 optimal weight: 8.9990 chunk 304 optimal weight: 3.9990 chunk 157 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 262 optimal weight: 10.0000 chunk 229 optimal weight: 5.9990 chunk 191 optimal weight: 9.9990 chunk 291 optimal weight: 5.9990 overall best weight: 4.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 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 L 16 GLN L 38 GLN L 52 ASN L 53 ASN ** O 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 46 GLN ** Q 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 39 HIS ** 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 364 ASN T 59 GLN V 16 GLN V 38 GLN V 53 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.131084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.112924 restraints weight = 52327.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.115613 restraints weight = 29518.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.117391 restraints weight = 19268.046| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 30656 Z= 0.196 Angle : 0.741 11.640 41636 Z= 0.372 Chirality : 0.047 0.238 4862 Planarity : 0.005 0.055 5182 Dihedral : 6.223 52.693 4716 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.12 % Allowed : 0.88 % Favored : 99.00 % 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: -1.53 (0.13), residues: 3838 helix: 0.75 (0.17), residues: 910 sheet: -0.90 (0.17), residues: 956 loop : -1.97 (0.13), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP H 47 HIS 0.016 0.001 HIS C 149 PHE 0.031 0.002 PHE Q 304 TYR 0.028 0.002 TYR P 52 ARG 0.011 0.001 ARG C 99 Details of bonding type rmsd link_NAG-ASN : bond 0.00434 ( 12) link_NAG-ASN : angle 2.18872 ( 36) link_BETA1-4 : bond 0.00462 ( 20) link_BETA1-4 : angle 1.51736 ( 60) hydrogen bonds : bond 0.04107 ( 1098) hydrogen bonds : angle 5.64834 ( 3024) SS BOND : bond 0.00523 ( 28) SS BOND : angle 1.74997 ( 56) covalent geometry : bond 0.00458 (30596) covalent geometry : angle 0.73472 (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 945 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 941 time to evaluate : 3.441 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 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 1 MET cc_start: 0.8233 (mmm) cc_final: 0.7978 (mmm) REVERT: A 47 LYS cc_start: 0.9301 (pttm) cc_final: 0.8993 (pttm) REVERT: A 71 ASP cc_start: 0.7252 (t70) cc_final: 0.7050 (t0) REVERT: A 312 GLU cc_start: 0.8407 (tp30) cc_final: 0.7742 (tp30) REVERT: A 453 MET cc_start: 0.8601 (tpp) cc_final: 0.8296 (tpt) REVERT: A 471 THR cc_start: 0.8009 (m) cc_final: 0.7806 (t) REVERT: A 486 TYR cc_start: 0.8346 (t80) cc_final: 0.8061 (t80) REVERT: A 487 LEU cc_start: 0.8866 (tt) cc_final: 0.8566 (tp) REVERT: A 492 GLN cc_start: 0.8575 (mt0) cc_final: 0.8274 (mt0) REVERT: B 60 LYS cc_start: 0.8226 (mttm) cc_final: 0.7940 (mtpt) REVERT: C 1 MET cc_start: 0.8277 (mmp) cc_final: 0.5691 (mmm) REVERT: C 47 LYS cc_start: 0.8482 (mttp) cc_final: 0.7297 (pttt) REVERT: C 49 GLU cc_start: 0.7349 (mp0) cc_final: 0.6863 (mp0) REVERT: C 101 TRP cc_start: 0.8645 (m-10) cc_final: 0.8175 (m-10) REVERT: C 150 GLN cc_start: 0.8162 (tt0) cc_final: 0.6778 (tt0) REVERT: C 193 GLU cc_start: 0.6256 (pm20) cc_final: 0.5109 (pm20) REVERT: C 204 TRP cc_start: 0.9324 (m-90) cc_final: 0.8871 (m-90) REVERT: C 233 GLU cc_start: 0.7405 (tm-30) cc_final: 0.7199 (tm-30) REVERT: C 286 LYS cc_start: 0.8155 (tttm) cc_final: 0.7835 (mtpp) REVERT: C 324 TYR cc_start: 0.8515 (t80) cc_final: 0.7927 (t80) REVERT: C 366 GLU cc_start: 0.7730 (pm20) cc_final: 0.7393 (pm20) REVERT: C 433 MET cc_start: 0.7938 (tpp) cc_final: 0.7475 (tpp) REVERT: C 453 MET cc_start: 0.8732 (mtm) cc_final: 0.8527 (mtm) REVERT: D 30 GLU cc_start: 0.8242 (tp30) cc_final: 0.7833 (tp30) REVERT: E 26 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8136 (mt-10) REVERT: E 399 MET cc_start: 0.8030 (tmm) cc_final: 0.7700 (tmm) REVERT: E 455 ILE cc_start: 0.9383 (tp) cc_final: 0.9068 (tp) REVERT: F 15 ARG cc_start: 0.8580 (mmm-85) cc_final: 0.7844 (mmm-85) REVERT: F 43 THR cc_start: 0.9117 (m) cc_final: 0.8885 (m) REVERT: H 3 GLN cc_start: 0.7501 (pm20) cc_final: 0.7245 (pm20) REVERT: H 21 SER cc_start: 0.8322 (p) cc_final: 0.8023 (p) REVERT: H 27 TYR cc_start: 0.8186 (p90) cc_final: 0.7341 (p90) REVERT: H 29 PHE cc_start: 0.6562 (t80) cc_final: 0.6060 (t80) REVERT: H 50 TRP cc_start: 0.8522 (m-10) cc_final: 0.7997 (m-10) REVERT: H 61 HIS cc_start: 0.8506 (t-90) cc_final: 0.8137 (t-90) REVERT: L 3 VAL cc_start: 0.6803 (p) cc_final: 0.5837 (m) REVERT: L 28 ASN cc_start: 0.8564 (p0) cc_final: 0.8298 (p0) REVERT: L 46 LYS cc_start: 0.7790 (ttpp) cc_final: 0.7193 (mmtp) REVERT: L 91 THR cc_start: 0.9038 (t) cc_final: 0.8793 (m) REVERT: L 100 LEU cc_start: 0.7889 (tp) cc_final: 0.7331 (tp) REVERT: O 47 LYS cc_start: 0.9232 (pttm) cc_final: 0.9002 (pttm) REVERT: O 71 ASP cc_start: 0.7270 (t70) cc_final: 0.7046 (t0) REVERT: O 176 TYR cc_start: 0.8249 (m-10) cc_final: 0.7866 (m-10) REVERT: O 209 GLN cc_start: 0.7339 (tm-30) cc_final: 0.7069 (tm-30) REVERT: O 312 GLU cc_start: 0.8399 (tp30) cc_final: 0.7701 (tp30) REVERT: O 353 ASN cc_start: 0.8412 (t0) cc_final: 0.8085 (t0) REVERT: O 453 MET cc_start: 0.8613 (tpp) cc_final: 0.8345 (tpp) REVERT: O 471 THR cc_start: 0.7985 (m) cc_final: 0.7780 (t) REVERT: O 486 TYR cc_start: 0.8341 (t80) cc_final: 0.8051 (t80) REVERT: O 487 LEU cc_start: 0.8846 (tt) cc_final: 0.8569 (tp) REVERT: P 12 LEU cc_start: 0.8581 (tt) cc_final: 0.8095 (tt) REVERT: P 60 LYS cc_start: 0.8191 (mttm) cc_final: 0.7916 (mtpt) REVERT: Q 1 MET cc_start: 0.8235 (mmp) cc_final: 0.5673 (mmm) REVERT: Q 46 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8386 (pm20) REVERT: Q 71 ASP cc_start: 0.8933 (t70) cc_final: 0.8722 (t0) REVERT: Q 101 TRP cc_start: 0.8661 (m-10) cc_final: 0.8210 (m-10) REVERT: Q 150 GLN cc_start: 0.8133 (tt0) cc_final: 0.6782 (tt0) REVERT: Q 204 TRP cc_start: 0.9259 (m-90) cc_final: 0.8844 (m-90) REVERT: Q 233 GLU cc_start: 0.7420 (tm-30) cc_final: 0.7218 (tm-30) REVERT: Q 286 LYS cc_start: 0.8086 (tttm) cc_final: 0.7792 (mtpp) REVERT: Q 324 TYR cc_start: 0.8579 (t80) cc_final: 0.8308 (t80) REVERT: Q 366 GLU cc_start: 0.7575 (pm20) cc_final: 0.7289 (pm20) REVERT: Q 453 MET cc_start: 0.8738 (mtm) cc_final: 0.8535 (mtm) REVERT: R 14 THR cc_start: 0.8546 (p) cc_final: 0.8340 (p) REVERT: R 30 GLU cc_start: 0.8241 (tp30) cc_final: 0.7820 (tp30) REVERT: S 26 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7616 (mt-10) REVERT: S 399 MET cc_start: 0.8055 (tmm) cc_final: 0.7693 (tmm) REVERT: S 455 ILE cc_start: 0.9383 (tp) cc_final: 0.9067 (tp) REVERT: T 43 THR cc_start: 0.9106 (m) cc_final: 0.8874 (m) REVERT: U 3 GLN cc_start: 0.7506 (pm20) cc_final: 0.7233 (pm20) REVERT: U 21 SER cc_start: 0.8321 (p) cc_final: 0.8036 (p) REVERT: U 27 TYR cc_start: 0.8151 (p90) cc_final: 0.7373 (p90) REVERT: U 29 PHE cc_start: 0.6558 (t80) cc_final: 0.6086 (t80) REVERT: U 46 GLU cc_start: 0.9201 (pm20) cc_final: 0.8619 (pm20) REVERT: U 61 HIS cc_start: 0.8615 (t-90) cc_final: 0.8162 (t-90) REVERT: V 3 VAL cc_start: 0.6723 (p) cc_final: 0.5897 (m) REVERT: V 46 LYS cc_start: 0.7779 (ttpp) cc_final: 0.7206 (mmtp) REVERT: V 91 THR cc_start: 0.8795 (t) cc_final: 0.8393 (m) outliers start: 4 outliers final: 1 residues processed: 945 average time/residue: 0.4040 time to fit residues: 627.7208 Evaluate side-chains 814 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 812 time to evaluate : 4.070 ------------------------------------------------------------------------------- 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: 5.9990 chunk 311 optimal weight: 6.9990 chunk 346 optimal weight: 2.9990 chunk 315 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 170 optimal weight: 6.9990 chunk 211 optimal weight: 0.3980 chunk 343 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 260 optimal weight: 7.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 HIS C 77 GLN 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 ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 16 GLN L 38 GLN L 53 ASN ** O 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 HIS Q 209 GLN ** Q 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 27 HIS ** S 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 246 GLN 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.131834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.113611 restraints weight = 52500.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.116332 restraints weight = 29429.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.118140 restraints weight = 19153.888| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3333 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= 0.163 Angle : 0.722 12.169 41636 Z= 0.362 Chirality : 0.046 0.187 4862 Planarity : 0.004 0.058 5182 Dihedral : 6.059 53.510 4716 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.16 % Allowed : 0.72 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.13), residues: 3838 helix: 0.80 (0.17), residues: 908 sheet: -0.88 (0.17), residues: 942 loop : -1.95 (0.13), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP H 47 HIS 0.026 0.001 HIS C 149 PHE 0.022 0.002 PHE Q 304 TYR 0.015 0.002 TYR Q 486 ARG 0.010 0.001 ARG O 2 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 12) link_NAG-ASN : angle 2.07073 ( 36) link_BETA1-4 : bond 0.00490 ( 20) link_BETA1-4 : angle 1.46493 ( 60) hydrogen bonds : bond 0.03936 ( 1098) hydrogen bonds : angle 5.55379 ( 3024) SS BOND : bond 0.00491 ( 28) SS BOND : angle 1.68990 ( 56) covalent geometry : bond 0.00382 (30596) covalent geometry : angle 0.71581 (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 939 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 934 time to evaluate : 3.148 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 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 47 LYS cc_start: 0.9269 (pttm) cc_final: 0.8975 (pttm) REVERT: A 71 ASP cc_start: 0.7219 (t70) cc_final: 0.6996 (t0) REVERT: A 194 MET cc_start: 0.8019 (mmm) cc_final: 0.7729 (mmt) REVERT: A 312 GLU cc_start: 0.8395 (tp30) cc_final: 0.7721 (tp30) REVERT: A 323 GLU cc_start: 0.8306 (tp30) cc_final: 0.8069 (tp30) REVERT: A 423 VAL cc_start: 0.8236 (m) cc_final: 0.8018 (p) REVERT: A 453 MET cc_start: 0.8568 (tpp) cc_final: 0.8296 (tpt) REVERT: A 471 THR cc_start: 0.8011 (m) cc_final: 0.7792 (t) REVERT: A 486 TYR cc_start: 0.8315 (t80) cc_final: 0.8055 (t80) REVERT: A 487 LEU cc_start: 0.8812 (tt) cc_final: 0.8530 (tp) REVERT: B 60 LYS cc_start: 0.8241 (mttm) cc_final: 0.7956 (mtpt) REVERT: C 1 MET cc_start: 0.8181 (mmp) cc_final: 0.7380 (mmm) REVERT: C 47 LYS cc_start: 0.8474 (mttp) cc_final: 0.7308 (pttt) REVERT: C 49 GLU cc_start: 0.7346 (mp0) cc_final: 0.6870 (mp0) REVERT: C 101 TRP cc_start: 0.8775 (m-10) cc_final: 0.8403 (m-10) REVERT: C 193 GLU cc_start: 0.6206 (pm20) cc_final: 0.5080 (pm20) REVERT: C 204 TRP cc_start: 0.9311 (m-90) cc_final: 0.8891 (m-90) REVERT: C 286 LYS cc_start: 0.8054 (tttm) cc_final: 0.7790 (mtpp) REVERT: C 324 TYR cc_start: 0.8566 (t80) cc_final: 0.7867 (t80) REVERT: C 366 GLU cc_start: 0.7763 (pm20) cc_final: 0.7438 (pm20) REVERT: C 433 MET cc_start: 0.7899 (tpp) cc_final: 0.7457 (tpp) REVERT: D 30 GLU cc_start: 0.8236 (tp30) cc_final: 0.7833 (tp30) REVERT: E 26 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8101 (mt-10) REVERT: E 41 LEU cc_start: 0.8995 (pt) cc_final: 0.8621 (pt) REVERT: E 116 CYS cc_start: 0.5674 (m) cc_final: 0.5273 (m) REVERT: E 399 MET cc_start: 0.7935 (tmm) cc_final: 0.7644 (tmm) REVERT: E 455 ILE cc_start: 0.9367 (tp) cc_final: 0.9057 (tp) REVERT: F 10 MET cc_start: 0.8187 (mmp) cc_final: 0.7972 (mmp) REVERT: F 15 ARG cc_start: 0.8576 (mmm-85) cc_final: 0.7837 (mmm-85) REVERT: F 33 GLU cc_start: 0.7412 (mm-30) cc_final: 0.6552 (mt-10) REVERT: F 43 THR cc_start: 0.9071 (m) cc_final: 0.8834 (m) REVERT: F 64 PHE cc_start: 0.8802 (t80) cc_final: 0.8535 (t80) REVERT: H 3 GLN cc_start: 0.7478 (pm20) cc_final: 0.7187 (pm20) REVERT: H 27 TYR cc_start: 0.8458 (p90) cc_final: 0.7580 (p90) REVERT: H 29 PHE cc_start: 0.6571 (t80) cc_final: 0.6053 (t80) REVERT: H 48 MET cc_start: 0.8173 (mtm) cc_final: 0.7804 (mtm) REVERT: H 50 TRP cc_start: 0.8308 (m-10) cc_final: 0.8031 (m-10) REVERT: H 61 HIS cc_start: 0.8463 (t-90) cc_final: 0.8071 (t-90) REVERT: H 81 MET cc_start: 0.6764 (ttt) cc_final: 0.5944 (ttt) REVERT: L 3 VAL cc_start: 0.6743 (p) cc_final: 0.5911 (m) REVERT: L 28 ASN cc_start: 0.8567 (p0) cc_final: 0.7638 (p0) REVERT: L 32 ASN cc_start: 0.7827 (m-40) cc_final: 0.7171 (p0) REVERT: L 46 LYS cc_start: 0.7745 (ttpp) cc_final: 0.7186 (mmtp) REVERT: O 69 THR cc_start: 0.9161 (p) cc_final: 0.8557 (p) REVERT: O 205 MET cc_start: 0.8493 (ttm) cc_final: 0.8140 (ttm) REVERT: O 312 GLU cc_start: 0.8396 (tp30) cc_final: 0.7711 (tp30) REVERT: O 323 GLU cc_start: 0.8311 (tp30) cc_final: 0.8106 (tp30) REVERT: O 353 ASN cc_start: 0.8390 (t0) cc_final: 0.8057 (t0) REVERT: O 453 MET cc_start: 0.8588 (tpp) cc_final: 0.8318 (tpp) REVERT: O 471 THR cc_start: 0.8008 (m) cc_final: 0.7765 (t) REVERT: O 486 TYR cc_start: 0.8328 (t80) cc_final: 0.8017 (t80) REVERT: O 487 LEU cc_start: 0.8765 (tt) cc_final: 0.8524 (tp) REVERT: P 60 LYS cc_start: 0.8197 (mttm) cc_final: 0.7938 (mtpt) REVERT: Q 1 MET cc_start: 0.8218 (mmp) cc_final: 0.5805 (mmm) REVERT: Q 101 TRP cc_start: 0.8651 (m-10) cc_final: 0.8241 (m-10) REVERT: Q 150 GLN cc_start: 0.8091 (tt0) cc_final: 0.6752 (tt0) REVERT: Q 193 GLU cc_start: 0.6175 (pm20) cc_final: 0.5119 (pm20) REVERT: Q 204 TRP cc_start: 0.9191 (m-90) cc_final: 0.8784 (m-90) REVERT: Q 286 LYS cc_start: 0.8044 (tttm) cc_final: 0.7753 (mtpp) REVERT: Q 324 TYR cc_start: 0.8501 (t80) cc_final: 0.8057 (t80) REVERT: Q 366 GLU cc_start: 0.7525 (pm20) cc_final: 0.7247 (pm20) REVERT: R 30 GLU cc_start: 0.8232 (tp30) cc_final: 0.7824 (tp30) REVERT: S 26 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7651 (mt-10) REVERT: S 399 MET cc_start: 0.7943 (tmm) cc_final: 0.7643 (tmm) REVERT: S 455 ILE cc_start: 0.9374 (tp) cc_final: 0.9058 (tp) REVERT: T 10 MET cc_start: 0.8196 (mmp) cc_final: 0.7966 (mmp) REVERT: T 33 GLU cc_start: 0.7390 (mm-30) cc_final: 0.6527 (mt-10) REVERT: T 43 THR cc_start: 0.9042 (m) cc_final: 0.8832 (m) REVERT: U 3 GLN cc_start: 0.7463 (pm20) cc_final: 0.7182 (pm20) REVERT: U 21 SER cc_start: 0.8213 (p) cc_final: 0.7990 (p) REVERT: U 27 TYR cc_start: 0.8135 (p90) cc_final: 0.7293 (p90) REVERT: U 29 PHE cc_start: 0.6552 (t80) cc_final: 0.6121 (t80) REVERT: U 36 TRP cc_start: 0.7632 (m100) cc_final: 0.6462 (m100) REVERT: U 46 GLU cc_start: 0.9213 (pm20) cc_final: 0.8931 (pm20) REVERT: U 48 MET cc_start: 0.7940 (mtm) cc_final: 0.7706 (mtm) REVERT: U 50 TRP cc_start: 0.8017 (m-10) cc_final: 0.7805 (m-10) REVERT: U 61 HIS cc_start: 0.8491 (t-90) cc_final: 0.8074 (t-90) REVERT: U 81 MET cc_start: 0.7041 (ttt) cc_final: 0.4080 (ttt) REVERT: V 3 VAL cc_start: 0.6804 (p) cc_final: 0.6038 (m) REVERT: V 46 LYS cc_start: 0.7756 (ttpp) cc_final: 0.7209 (mmtp) outliers start: 5 outliers final: 3 residues processed: 937 average time/residue: 0.3905 time to fit residues: 604.8205 Evaluate side-chains 812 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 809 time to evaluate : 3.196 ------------------------------------------------------------------------------- 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: 6.9990 chunk 340 optimal weight: 6.9990 chunk 320 optimal weight: 4.9990 chunk 347 optimal weight: 6.9990 chunk 329 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 chunk 248 optimal weight: 7.9990 chunk 249 optimal weight: 5.9990 chunk 310 optimal weight: 7.9990 chunk 224 optimal weight: 40.0000 chunk 267 optimal weight: 0.7980 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 364 ASN F 59 GLN L 16 GLN L 38 GLN L 52 ASN L 53 ASN ** O 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 492 GLN ** Q 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 39 HIS ** 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 246 GLN 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 = 0.3471 r_free = 0.3471 target = 0.130551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.113115 restraints weight = 52586.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.115583 restraints weight = 30576.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.117226 restraints weight = 20417.356| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 30656 Z= 0.184 Angle : 0.733 11.803 41636 Z= 0.368 Chirality : 0.046 0.204 4862 Planarity : 0.005 0.058 5182 Dihedral : 6.012 52.900 4716 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.09 % Allowed : 0.62 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.51 (0.13), residues: 3838 helix: 0.80 (0.17), residues: 900 sheet: -0.87 (0.18), residues: 920 loop : -1.97 (0.13), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 47 HIS 0.015 0.001 HIS C 149 PHE 0.014 0.002 PHE B 42 TYR 0.017 0.002 TYR Q 486 ARG 0.008 0.001 ARG C 99 Details of bonding type rmsd link_NAG-ASN : bond 0.00420 ( 12) link_NAG-ASN : angle 2.13159 ( 36) link_BETA1-4 : bond 0.00478 ( 20) link_BETA1-4 : angle 1.45533 ( 60) hydrogen bonds : bond 0.04012 ( 1098) hydrogen bonds : angle 5.57815 ( 3024) SS BOND : bond 0.00428 ( 28) SS BOND : angle 1.67621 ( 56) covalent geometry : bond 0.00430 (30596) covalent geometry : angle 0.72684 (41484) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12785.90 seconds wall clock time: 222 minutes 9.11 seconds (13329.11 seconds total)