Starting phenix.real_space_refine on Mon Apr 6 11:54:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x67_66617/04_2026/9x67_66617.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x67_66617/04_2026/9x67_66617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9x67_66617/04_2026/9x67_66617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x67_66617/04_2026/9x67_66617.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9x67_66617/04_2026/9x67_66617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x67_66617/04_2026/9x67_66617.map" } resolution = 1.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 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 30 5.16 5 C 10200 2.51 5 N 2940 2.21 5 O 5428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18598 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1113 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 156} Chain: "B" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1113 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 156} Chain: "C" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1113 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 156} Chain: "D" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1113 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 156} Chain: "E" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1113 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 156} Chain: "F" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1113 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 156} Chain: "G" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1113 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 156} Chain: "H" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1113 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 156} Chain: "I" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1113 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 156} Chain: "J" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1113 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 156} Chain: "K" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1113 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 156} Chain: "L" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1113 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 156} Chain: "M" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1113 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 156} Chain: "N" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1113 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 156} Chain: "O" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1113 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 156} Chain: "A" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 141 Classifications: {'water': 141} Link IDs: {None: 140} Chain: "B" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 149 Classifications: {'water': 149} Link IDs: {None: 148} Chain: "C" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 125 Classifications: {'water': 125} Link IDs: {None: 124} Chain: "D" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 123 Classifications: {'water': 123} Link IDs: {None: 122} Chain: "E" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 135 Classifications: {'water': 135} Link IDs: {None: 134} Chain: "F" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 117 Classifications: {'water': 117} Link IDs: {None: 116} Chain: "G" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} Chain: "H" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 122 Classifications: {'water': 122} Link IDs: {None: 121} Chain: "I" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "J" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 112 Classifications: {'water': 112} Link IDs: {None: 111} Chain: "K" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "L" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 114 Classifications: {'water': 114} Link IDs: {None: 113} Chain: "M" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 127 Classifications: {'water': 127} Link IDs: {None: 126} Chain: "N" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 148 Classifications: {'water': 148} Link IDs: {None: 147} Chain: "O" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 142 Classifications: {'water': 142} Link IDs: {None: 141} Time building chain proxies: 5.00, per 1000 atoms: 0.27 Number of scatterers: 18598 At special positions: 0 Unit cell: (86.108, 86.944, 152.988, 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 30 16.00 O 5428 8.00 N 2940 7.00 C 10200 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 61 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 61 " distance=2.03 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 61 " distance=2.03 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 61 " distance=2.03 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 61 " distance=2.04 Simple disulfide: pdb=" SG CYS F 21 " - pdb=" SG CYS F 61 " distance=2.04 Simple disulfide: pdb=" SG CYS G 21 " - pdb=" SG CYS G 61 " distance=2.03 Simple disulfide: pdb=" SG CYS H 21 " - pdb=" SG CYS H 61 " distance=2.03 Simple disulfide: pdb=" SG CYS I 21 " - pdb=" SG CYS I 61 " distance=2.03 Simple disulfide: pdb=" SG CYS J 21 " - pdb=" SG CYS J 61 " distance=2.04 Simple disulfide: pdb=" SG CYS K 21 " - pdb=" SG CYS K 61 " distance=2.03 Simple disulfide: pdb=" SG CYS L 21 " - pdb=" SG CYS L 61 " distance=2.03 Simple disulfide: pdb=" SG CYS M 21 " - pdb=" SG CYS M 61 " distance=2.03 Simple disulfide: pdb=" SG CYS N 21 " - pdb=" SG CYS N 61 " distance=2.03 Simple disulfide: pdb=" SG CYS O 21 " - pdb=" SG CYS O 61 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 834.3 milliseconds 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4290 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 57 sheets defined 4.7% alpha, 61.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 24 through 29 removed outlier: 4.647A pdb=" N ASP A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 42 Processing helix chain 'B' and resid 24 through 28 Processing helix chain 'B' and resid 40 through 43 removed outlier: 4.097A pdb=" N ALA B 43 " --> pdb=" O ALA B 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 40 through 43' Processing helix chain 'C' and resid 24 through 28 Processing helix chain 'C' and resid 40 through 42 No H-bonds generated for 'chain 'C' and resid 40 through 42' Processing helix chain 'D' and resid 24 through 28 Processing helix chain 'D' and resid 40 through 42 No H-bonds generated for 'chain 'D' and resid 40 through 42' Processing helix chain 'E' and resid 24 through 28 Processing helix chain 'E' and resid 40 through 42 No H-bonds generated for 'chain 'E' and resid 40 through 42' Processing helix chain 'F' and resid 24 through 28 Processing helix chain 'F' and resid 40 through 43 removed outlier: 4.147A pdb=" N ALA F 43 " --> pdb=" O ALA F 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 40 through 43' Processing helix chain 'G' and resid 24 through 28 Processing helix chain 'G' and resid 40 through 42 No H-bonds generated for 'chain 'G' and resid 40 through 42' Processing helix chain 'H' and resid 24 through 28 Processing helix chain 'H' and resid 40 through 43 removed outlier: 4.181A pdb=" N ALA H 43 " --> pdb=" O ALA H 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 40 through 43' Processing helix chain 'I' and resid 24 through 28 Processing helix chain 'I' and resid 40 through 43 removed outlier: 4.059A pdb=" N ALA I 43 " --> pdb=" O ALA I 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 40 through 43' Processing helix chain 'J' and resid 24 through 28 Processing helix chain 'J' and resid 40 through 42 No H-bonds generated for 'chain 'J' and resid 40 through 42' Processing helix chain 'L' and resid 24 through 28 Processing helix chain 'L' and resid 40 through 43 removed outlier: 4.157A pdb=" N ALA L 43 " --> pdb=" O ALA L 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 40 through 43' Processing helix chain 'M' and resid 40 through 43 removed outlier: 4.171A pdb=" N ALA M 43 " --> pdb=" O ALA M 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 40 through 43' Processing helix chain 'N' and resid 40 through 42 No H-bonds generated for 'chain 'N' and resid 40 through 42' Processing helix chain 'O' and resid 24 through 28 Processing helix chain 'O' and resid 40 through 43 removed outlier: 4.119A pdb=" N ALA O 43 " --> pdb=" O ALA O 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 40 through 43' Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 38 removed outlier: 8.657A pdb=" N GLN B 30 " --> pdb=" O GLY A 7 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR A 9 " --> pdb=" O GLN B 30 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL B 32 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N HIS A 11 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU B 34 " --> pdb=" O HIS A 11 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N LYS A 13 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLN B 36 " --> pdb=" O LYS A 13 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLU A 15 " --> pdb=" O GLN B 36 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ARG B 38 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N VAL A 17 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N PHE B 154 " --> pdb=" O GLY A 7 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N THR A 9 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ALA B 152 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N HIS A 11 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA B 150 " --> pdb=" O HIS A 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 29 through 38 removed outlier: 8.657A pdb=" N GLN B 30 " --> pdb=" O GLY A 7 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR A 9 " --> pdb=" O GLN B 30 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL B 32 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N HIS A 11 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU B 34 " --> pdb=" O HIS A 11 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N LYS A 13 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLN B 36 " --> pdb=" O LYS A 13 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLU A 15 " --> pdb=" O GLN B 36 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ARG B 38 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N VAL A 17 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 22 through 23 removed outlier: 5.330A pdb=" N GLY A 127 " --> pdb=" O ASP A 60 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASN A 98 " --> pdb=" O THR A 140 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 123 Processing sheet with id=AA5, first strand: chain 'A' and resid 77 through 79 removed outlier: 8.297A pdb=" N VAL A 85 " --> pdb=" O ILE A 78 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 29 through 38 removed outlier: 8.630A pdb=" N GLN C 30 " --> pdb=" O GLY B 7 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR B 9 " --> pdb=" O GLN C 30 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL C 32 " --> pdb=" O THR B 9 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N HIS B 11 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU C 34 " --> pdb=" O HIS B 11 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LYS B 13 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLN C 36 " --> pdb=" O LYS B 13 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLU B 15 " --> pdb=" O GLN C 36 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ARG C 38 " --> pdb=" O GLU B 15 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N VAL B 17 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N PHE C 154 " --> pdb=" O GLY B 7 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N THR B 9 " --> pdb=" O ALA C 152 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA C 152 " --> pdb=" O THR B 9 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N HIS B 11 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA C 150 " --> pdb=" O HIS B 11 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 29 through 38 removed outlier: 8.630A pdb=" N GLN C 30 " --> pdb=" O GLY B 7 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR B 9 " --> pdb=" O GLN C 30 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL C 32 " --> pdb=" O THR B 9 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N HIS B 11 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU C 34 " --> pdb=" O HIS B 11 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LYS B 13 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLN C 36 " --> pdb=" O LYS B 13 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLU B 15 " --> pdb=" O GLN C 36 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ARG C 38 " --> pdb=" O GLU B 15 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N VAL B 17 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 22 through 23 removed outlier: 3.537A pdb=" N ASP B 60 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLY B 127 " --> pdb=" O ASP B 60 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASN B 98 " --> pdb=" O THR B 140 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 77 through 79 removed outlier: 8.323A pdb=" N VAL B 85 " --> pdb=" O ILE B 78 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 29 through 38 removed outlier: 8.622A pdb=" N GLN D 30 " --> pdb=" O GLY C 7 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR C 9 " --> pdb=" O GLN D 30 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL D 32 " --> pdb=" O THR C 9 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N HIS C 11 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU D 34 " --> pdb=" O HIS C 11 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LYS C 13 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLN D 36 " --> pdb=" O LYS C 13 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLU C 15 " --> pdb=" O GLN D 36 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ARG D 38 " --> pdb=" O GLU C 15 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N VAL C 17 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N THR C 4 " --> pdb=" O TYR D 158 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N TYR D 158 " --> pdb=" O THR C 4 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ASN C 6 " --> pdb=" O VAL D 156 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N VAL D 156 " --> pdb=" O ASN C 6 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 29 through 38 removed outlier: 8.622A pdb=" N GLN D 30 " --> pdb=" O GLY C 7 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR C 9 " --> pdb=" O GLN D 30 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL D 32 " --> pdb=" O THR C 9 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N HIS C 11 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU D 34 " --> pdb=" O HIS C 11 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LYS C 13 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLN D 36 " --> pdb=" O LYS C 13 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLU C 15 " --> pdb=" O GLN D 36 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ARG D 38 " --> pdb=" O GLU C 15 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N VAL C 17 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 22 through 23 removed outlier: 5.370A pdb=" N GLY C 127 " --> pdb=" O ASP C 60 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASN C 98 " --> pdb=" O THR C 140 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 77 through 79 removed outlier: 8.332A pdb=" N VAL C 85 " --> pdb=" O ILE C 78 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 29 through 38 removed outlier: 8.697A pdb=" N GLN E 30 " --> pdb=" O GLY D 7 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR D 9 " --> pdb=" O GLN E 30 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N VAL E 32 " --> pdb=" O THR D 9 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N HIS D 11 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU E 34 " --> pdb=" O HIS D 11 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LYS D 13 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLN E 36 " --> pdb=" O LYS D 13 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLU D 15 " --> pdb=" O GLN E 36 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ARG E 38 " --> pdb=" O GLU D 15 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N VAL D 17 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N PHE E 154 " --> pdb=" O GLY D 7 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N THR D 9 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA E 152 " --> pdb=" O THR D 9 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N HIS D 11 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA E 150 " --> pdb=" O HIS D 11 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 29 through 38 removed outlier: 8.697A pdb=" N GLN E 30 " --> pdb=" O GLY D 7 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR D 9 " --> pdb=" O GLN E 30 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N VAL E 32 " --> pdb=" O THR D 9 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N HIS D 11 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU E 34 " --> pdb=" O HIS D 11 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LYS D 13 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLN E 36 " --> pdb=" O LYS D 13 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLU D 15 " --> pdb=" O GLN E 36 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ARG E 38 " --> pdb=" O GLU D 15 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N VAL D 17 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 22 through 23 removed outlier: 5.415A pdb=" N GLY D 127 " --> pdb=" O ASP D 60 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ASN D 98 " --> pdb=" O THR D 140 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 77 through 79 removed outlier: 8.305A pdb=" N VAL D 85 " --> pdb=" O ILE D 78 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 29 through 38 removed outlier: 8.678A pdb=" N GLN F 30 " --> pdb=" O GLY E 7 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR E 9 " --> pdb=" O GLN F 30 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL F 32 " --> pdb=" O THR E 9 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N HIS E 11 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU F 34 " --> pdb=" O HIS E 11 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N LYS E 13 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLN F 36 " --> pdb=" O LYS E 13 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLU E 15 " --> pdb=" O GLN F 36 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ARG F 38 " --> pdb=" O GLU E 15 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL E 17 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N PHE F 154 " --> pdb=" O GLY E 7 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N THR E 9 " --> pdb=" O ALA F 152 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ALA F 152 " --> pdb=" O THR E 9 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N HIS E 11 " --> pdb=" O ALA F 150 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ALA F 150 " --> pdb=" O HIS E 11 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 29 through 38 removed outlier: 8.678A pdb=" N GLN F 30 " --> pdb=" O GLY E 7 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR E 9 " --> pdb=" O GLN F 30 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL F 32 " --> pdb=" O THR E 9 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N HIS E 11 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU F 34 " --> pdb=" O HIS E 11 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N LYS E 13 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLN F 36 " --> pdb=" O LYS E 13 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLU E 15 " --> pdb=" O GLN F 36 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ARG F 38 " --> pdb=" O GLU E 15 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL E 17 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 22 through 23 removed outlier: 3.522A pdb=" N ASP E 60 " --> pdb=" O GLY E 127 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N GLY E 127 " --> pdb=" O ASP E 60 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASN E 98 " --> pdb=" O THR E 140 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 29 through 38 removed outlier: 8.677A pdb=" N GLN G 30 " --> pdb=" O GLY F 7 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR F 9 " --> pdb=" O GLN G 30 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL G 32 " --> pdb=" O THR F 9 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N HIS F 11 " --> pdb=" O VAL G 32 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU G 34 " --> pdb=" O HIS F 11 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LYS F 13 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLN G 36 " --> pdb=" O LYS F 13 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLU F 15 " --> pdb=" O GLN G 36 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ARG G 38 " --> pdb=" O GLU F 15 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N VAL F 17 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE G 154 " --> pdb=" O GLY F 7 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N THR F 9 " --> pdb=" O ALA G 152 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ALA G 152 " --> pdb=" O THR F 9 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N HIS F 11 " --> pdb=" O ALA G 150 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA G 150 " --> pdb=" O HIS F 11 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 29 through 38 removed outlier: 8.677A pdb=" N GLN G 30 " --> pdb=" O GLY F 7 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR F 9 " --> pdb=" O GLN G 30 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL G 32 " --> pdb=" O THR F 9 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N HIS F 11 " --> pdb=" O VAL G 32 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU G 34 " --> pdb=" O HIS F 11 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LYS F 13 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLN G 36 " --> pdb=" O LYS F 13 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLU F 15 " --> pdb=" O GLN G 36 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ARG G 38 " --> pdb=" O GLU F 15 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N VAL F 17 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 22 through 23 removed outlier: 5.290A pdb=" N GLY F 127 " --> pdb=" O ASP F 60 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ASN F 98 " --> pdb=" O THR F 140 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 77 through 79 removed outlier: 8.371A pdb=" N VAL F 85 " --> pdb=" O ILE F 78 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 29 through 38 removed outlier: 8.690A pdb=" N GLN H 30 " --> pdb=" O GLY G 7 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR G 9 " --> pdb=" O GLN H 30 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL H 32 " --> pdb=" O THR G 9 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N HIS G 11 " --> pdb=" O VAL H 32 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU H 34 " --> pdb=" O HIS G 11 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LYS G 13 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLN H 36 " --> pdb=" O LYS G 13 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLU G 15 " --> pdb=" O GLN H 36 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ARG H 38 " --> pdb=" O GLU G 15 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N VAL G 17 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N PHE H 154 " --> pdb=" O GLY G 7 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THR G 9 " --> pdb=" O ALA H 152 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA H 152 " --> pdb=" O THR G 9 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N HIS G 11 " --> pdb=" O ALA H 150 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ALA H 150 " --> pdb=" O HIS G 11 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 29 through 38 removed outlier: 8.690A pdb=" N GLN H 30 " --> pdb=" O GLY G 7 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR G 9 " --> pdb=" O GLN H 30 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL H 32 " --> pdb=" O THR G 9 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N HIS G 11 " --> pdb=" O VAL H 32 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU H 34 " --> pdb=" O HIS G 11 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LYS G 13 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLN H 36 " --> pdb=" O LYS G 13 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLU G 15 " --> pdb=" O GLN H 36 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ARG H 38 " --> pdb=" O GLU G 15 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N VAL G 17 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 22 through 23 removed outlier: 5.353A pdb=" N GLY G 127 " --> pdb=" O ASP G 60 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASN G 98 " --> pdb=" O THR G 140 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ILE G 103 " --> pdb=" O ASN G 84 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N ASN G 84 " --> pdb=" O ILE G 103 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N VAL G 85 " --> pdb=" O ILE G 78 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 29 through 38 removed outlier: 8.664A pdb=" N GLN I 30 " --> pdb=" O GLY H 7 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR H 9 " --> pdb=" O GLN I 30 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N VAL I 32 " --> pdb=" O THR H 9 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N HIS H 11 " --> pdb=" O VAL I 32 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU I 34 " --> pdb=" O HIS H 11 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LYS H 13 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLN I 36 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLU H 15 " --> pdb=" O GLN I 36 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ARG I 38 " --> pdb=" O GLU H 15 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N VAL H 17 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N PHE I 154 " --> pdb=" O GLY H 7 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N THR H 9 " --> pdb=" O ALA I 152 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA I 152 " --> pdb=" O THR H 9 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N HIS H 11 " --> pdb=" O ALA I 150 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA I 150 " --> pdb=" O HIS H 11 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 29 through 38 removed outlier: 8.664A pdb=" N GLN I 30 " --> pdb=" O GLY H 7 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR H 9 " --> pdb=" O GLN I 30 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N VAL I 32 " --> pdb=" O THR H 9 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N HIS H 11 " --> pdb=" O VAL I 32 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU I 34 " --> pdb=" O HIS H 11 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LYS H 13 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLN I 36 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLU H 15 " --> pdb=" O GLN I 36 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ARG I 38 " --> pdb=" O GLU H 15 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N VAL H 17 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 22 through 23 removed outlier: 5.295A pdb=" N GLY H 127 " --> pdb=" O ASP H 60 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ASN H 98 " --> pdb=" O THR H 140 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 77 through 79 removed outlier: 8.331A pdb=" N VAL H 85 " --> pdb=" O ILE H 78 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 29 through 38 removed outlier: 8.651A pdb=" N GLN J 30 " --> pdb=" O GLY I 7 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR I 9 " --> pdb=" O GLN J 30 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL J 32 " --> pdb=" O THR I 9 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N HIS I 11 " --> pdb=" O VAL J 32 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU J 34 " --> pdb=" O HIS I 11 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LYS I 13 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLN J 36 " --> pdb=" O LYS I 13 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLU I 15 " --> pdb=" O GLN J 36 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ARG J 38 " --> pdb=" O GLU I 15 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N VAL I 17 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N THR I 4 " --> pdb=" O TYR J 158 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N TYR J 158 " --> pdb=" O THR I 4 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ASN I 6 " --> pdb=" O VAL J 156 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL J 156 " --> pdb=" O ASN I 6 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 29 through 38 removed outlier: 8.651A pdb=" N GLN J 30 " --> pdb=" O GLY I 7 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR I 9 " --> pdb=" O GLN J 30 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL J 32 " --> pdb=" O THR I 9 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N HIS I 11 " --> pdb=" O VAL J 32 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU J 34 " --> pdb=" O HIS I 11 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LYS I 13 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLN J 36 " --> pdb=" O LYS I 13 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLU I 15 " --> pdb=" O GLN J 36 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ARG J 38 " --> pdb=" O GLU I 15 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N VAL I 17 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 22 through 23 removed outlier: 5.399A pdb=" N GLY I 127 " --> pdb=" O ASP I 60 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASN I 98 " --> pdb=" O THR I 140 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 77 through 79 removed outlier: 8.390A pdb=" N VAL I 85 " --> pdb=" O ILE I 78 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 29 through 38 removed outlier: 8.666A pdb=" N GLN K 30 " --> pdb=" O GLY J 7 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR J 9 " --> pdb=" O GLN K 30 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N VAL K 32 " --> pdb=" O THR J 9 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N HIS J 11 " --> pdb=" O VAL K 32 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU K 34 " --> pdb=" O HIS J 11 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LYS J 13 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLN K 36 " --> pdb=" O LYS J 13 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLU J 15 " --> pdb=" O GLN K 36 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ARG K 38 " --> pdb=" O GLU J 15 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N VAL J 17 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N THR J 4 " --> pdb=" O TYR K 158 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N TYR K 158 " --> pdb=" O THR J 4 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ASN J 6 " --> pdb=" O VAL K 156 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N VAL K 156 " --> pdb=" O ASN J 6 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 29 through 38 removed outlier: 8.666A pdb=" N GLN K 30 " --> pdb=" O GLY J 7 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR J 9 " --> pdb=" O GLN K 30 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N VAL K 32 " --> pdb=" O THR J 9 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N HIS J 11 " --> pdb=" O VAL K 32 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU K 34 " --> pdb=" O HIS J 11 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LYS J 13 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLN K 36 " --> pdb=" O LYS J 13 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLU J 15 " --> pdb=" O GLN K 36 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ARG K 38 " --> pdb=" O GLU J 15 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N VAL J 17 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 22 through 23 removed outlier: 3.515A pdb=" N ASP J 60 " --> pdb=" O GLY J 127 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N GLY J 127 " --> pdb=" O ASP J 60 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN J 98 " --> pdb=" O THR J 140 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 77 through 79 removed outlier: 8.335A pdb=" N VAL J 85 " --> pdb=" O ILE J 78 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 29 through 38 removed outlier: 8.669A pdb=" N GLN L 30 " --> pdb=" O GLY K 7 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR K 9 " --> pdb=" O GLN L 30 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N VAL L 32 " --> pdb=" O THR K 9 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N HIS K 11 " --> pdb=" O VAL L 32 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU L 34 " --> pdb=" O HIS K 11 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LYS K 13 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLN L 36 " --> pdb=" O LYS K 13 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLU K 15 " --> pdb=" O GLN L 36 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ARG L 38 " --> pdb=" O GLU K 15 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N VAL K 17 " --> pdb=" O ARG L 38 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N PHE L 154 " --> pdb=" O GLY K 7 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N THR K 9 " --> pdb=" O ALA L 152 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA L 152 " --> pdb=" O THR K 9 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N HIS K 11 " --> pdb=" O ALA L 150 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA L 150 " --> pdb=" O HIS K 11 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 29 through 38 removed outlier: 8.669A pdb=" N GLN L 30 " --> pdb=" O GLY K 7 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR K 9 " --> pdb=" O GLN L 30 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N VAL L 32 " --> pdb=" O THR K 9 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N HIS K 11 " --> pdb=" O VAL L 32 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU L 34 " --> pdb=" O HIS K 11 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LYS K 13 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLN L 36 " --> pdb=" O LYS K 13 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLU K 15 " --> pdb=" O GLN L 36 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ARG L 38 " --> pdb=" O GLU K 15 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N VAL K 17 " --> pdb=" O ARG L 38 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 22 through 23 removed outlier: 3.508A pdb=" N ASP K 60 " --> pdb=" O GLY K 127 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N GLY K 127 " --> pdb=" O ASP K 60 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASN K 98 " --> pdb=" O THR K 140 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 77 through 79 removed outlier: 8.344A pdb=" N VAL K 85 " --> pdb=" O ILE K 78 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 29 through 38 removed outlier: 8.557A pdb=" N GLN M 30 " --> pdb=" O GLY L 7 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR L 9 " --> pdb=" O GLN M 30 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL M 32 " --> pdb=" O THR L 9 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N HIS L 11 " --> pdb=" O VAL M 32 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU M 34 " --> pdb=" O HIS L 11 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LYS L 13 " --> pdb=" O LEU M 34 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN M 36 " --> pdb=" O LYS L 13 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLU L 15 " --> pdb=" O GLN M 36 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ARG M 38 " --> pdb=" O GLU L 15 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N VAL L 17 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N THR L 4 " --> pdb=" O TYR M 158 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N TYR M 158 " --> pdb=" O THR L 4 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ASN L 6 " --> pdb=" O VAL M 156 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N VAL M 156 " --> pdb=" O ASN L 6 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 29 through 38 removed outlier: 8.557A pdb=" N GLN M 30 " --> pdb=" O GLY L 7 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR L 9 " --> pdb=" O GLN M 30 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL M 32 " --> pdb=" O THR L 9 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N HIS L 11 " --> pdb=" O VAL M 32 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU M 34 " --> pdb=" O HIS L 11 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LYS L 13 " --> pdb=" O LEU M 34 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN M 36 " --> pdb=" O LYS L 13 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLU L 15 " --> pdb=" O GLN M 36 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ARG M 38 " --> pdb=" O GLU L 15 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N VAL L 17 " --> pdb=" O ARG M 38 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 22 through 23 removed outlier: 5.376A pdb=" N GLY L 127 " --> pdb=" O ASP L 60 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN L 98 " --> pdb=" O THR L 140 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 77 through 79 removed outlier: 8.369A pdb=" N VAL L 85 " --> pdb=" O ILE L 78 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 29 through 38 removed outlier: 8.703A pdb=" N GLN N 30 " --> pdb=" O GLY M 7 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N THR M 9 " --> pdb=" O GLN N 30 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N VAL N 32 " --> pdb=" O THR M 9 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N HIS M 11 " --> pdb=" O VAL N 32 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LEU N 34 " --> pdb=" O HIS M 11 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N LYS M 13 " --> pdb=" O LEU N 34 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLN N 36 " --> pdb=" O LYS M 13 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLU M 15 " --> pdb=" O GLN N 36 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ARG N 38 " --> pdb=" O GLU M 15 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N VAL M 17 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N THR M 4 " --> pdb=" O TYR N 158 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N TYR N 158 " --> pdb=" O THR M 4 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ASN M 6 " --> pdb=" O VAL N 156 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N VAL N 156 " --> pdb=" O ASN M 6 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 29 through 38 removed outlier: 8.703A pdb=" N GLN N 30 " --> pdb=" O GLY M 7 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N THR M 9 " --> pdb=" O GLN N 30 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N VAL N 32 " --> pdb=" O THR M 9 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N HIS M 11 " --> pdb=" O VAL N 32 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LEU N 34 " --> pdb=" O HIS M 11 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N LYS M 13 " --> pdb=" O LEU N 34 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLN N 36 " --> pdb=" O LYS M 13 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLU M 15 " --> pdb=" O GLN N 36 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ARG N 38 " --> pdb=" O GLU M 15 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N VAL M 17 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 22 through 23 removed outlier: 5.326A pdb=" N GLY M 127 " --> pdb=" O ASP M 60 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ASN M 98 " --> pdb=" O THR M 140 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 77 through 79 removed outlier: 8.341A pdb=" N VAL M 85 " --> pdb=" O ILE M 78 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'O' and resid 29 through 38 removed outlier: 8.772A pdb=" N GLN O 30 " --> pdb=" O GLY N 7 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR N 9 " --> pdb=" O GLN O 30 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL O 32 " --> pdb=" O THR N 9 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N HIS N 11 " --> pdb=" O VAL O 32 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LEU O 34 " --> pdb=" O HIS N 11 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N LYS N 13 " --> pdb=" O LEU O 34 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN O 36 " --> pdb=" O LYS N 13 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLU N 15 " --> pdb=" O GLN O 36 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ARG O 38 " --> pdb=" O GLU N 15 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N VAL N 17 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N PHE O 154 " --> pdb=" O GLY N 7 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N THR N 9 " --> pdb=" O ALA O 152 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA O 152 " --> pdb=" O THR N 9 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N HIS N 11 " --> pdb=" O ALA O 150 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA O 150 " --> pdb=" O HIS N 11 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'O' and resid 29 through 38 removed outlier: 8.772A pdb=" N GLN O 30 " --> pdb=" O GLY N 7 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR N 9 " --> pdb=" O GLN O 30 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL O 32 " --> pdb=" O THR N 9 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N HIS N 11 " --> pdb=" O VAL O 32 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LEU O 34 " --> pdb=" O HIS N 11 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N LYS N 13 " --> pdb=" O LEU O 34 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN O 36 " --> pdb=" O LYS N 13 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLU N 15 " --> pdb=" O GLN O 36 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ARG O 38 " --> pdb=" O GLU N 15 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N VAL N 17 " --> pdb=" O ARG O 38 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'N' and resid 22 through 23 removed outlier: 3.581A pdb=" N ASP N 60 " --> pdb=" O GLY N 127 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N GLY N 127 " --> pdb=" O ASP N 60 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASN N 98 " --> pdb=" O THR N 140 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'N' and resid 77 through 79 removed outlier: 8.324A pdb=" N VAL N 85 " --> pdb=" O ILE N 78 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'O' and resid 22 through 23 removed outlier: 5.390A pdb=" N GLY O 127 " --> pdb=" O ASP O 60 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'O' and resid 77 through 79 removed outlier: 8.345A pdb=" N VAL O 85 " --> pdb=" O ILE O 78 " (cutoff:3.500A) 517 hydrogen bonds defined for protein. 1323 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: 3.43 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5897 1.33 - 1.45: 2243 1.45 - 1.57: 8705 1.57 - 1.69: 0 1.69 - 1.80: 30 Bond restraints: 16875 Sorted by residual: bond pdb=" CA THR M 144 " pdb=" CB THR M 144 " ideal model delta sigma weight residual 1.534 1.475 0.059 1.30e-02 5.92e+03 2.04e+01 bond pdb=" CB VAL J 99 " pdb=" CG2 VAL J 99 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.95e+00 bond pdb=" CB GLN K 102 " pdb=" CG GLN K 102 " ideal model delta sigma weight residual 1.520 1.470 0.050 3.00e-02 1.11e+03 2.79e+00 bond pdb=" CB VAL M 99 " pdb=" CG2 VAL M 99 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.76e+00 bond pdb=" CB GLN D 102 " pdb=" CG GLN D 102 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.67e+00 ... (remaining 16870 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 22717 1.94 - 3.88: 318 3.88 - 5.82: 18 5.82 - 7.76: 11 7.76 - 9.70: 6 Bond angle restraints: 23070 Sorted by residual: angle pdb=" CA LEU E 86 " pdb=" CB LEU E 86 " pdb=" CG LEU E 86 " ideal model delta sigma weight residual 116.30 126.00 -9.70 3.50e+00 8.16e-02 7.68e+00 angle pdb=" N GLY K 141 " pdb=" CA GLY K 141 " pdb=" C GLY K 141 " ideal model delta sigma weight residual 113.18 107.15 6.03 2.37e+00 1.78e-01 6.47e+00 angle pdb=" N GLY H 141 " pdb=" CA GLY H 141 " pdb=" C GLY H 141 " ideal model delta sigma weight residual 113.18 107.21 5.97 2.37e+00 1.78e-01 6.35e+00 angle pdb=" N GLY B 141 " pdb=" CA GLY B 141 " pdb=" C GLY B 141 " ideal model delta sigma weight residual 113.18 107.35 5.83 2.37e+00 1.78e-01 6.06e+00 angle pdb=" CA LEU N 86 " pdb=" CB LEU N 86 " pdb=" CG LEU N 86 " ideal model delta sigma weight residual 116.30 124.72 -8.42 3.50e+00 8.16e-02 5.79e+00 ... (remaining 23065 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 9115 17.97 - 35.94: 517 35.94 - 53.91: 122 53.91 - 71.88: 69 71.88 - 89.85: 32 Dihedral angle restraints: 9855 sinusoidal: 3165 harmonic: 6690 Sorted by residual: dihedral pdb=" CA GLN B 89 " pdb=" C GLN B 89 " pdb=" N SER B 90 " pdb=" CA SER B 90 " ideal model delta harmonic sigma weight residual 180.00 155.49 24.51 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA GLN H 89 " pdb=" C GLN H 89 " pdb=" N SER H 90 " pdb=" CA SER H 90 " ideal model delta harmonic sigma weight residual 180.00 156.04 23.96 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA GLN K 89 " pdb=" C GLN K 89 " pdb=" N SER K 90 " pdb=" CA SER K 90 " ideal model delta harmonic sigma weight residual 180.00 156.49 23.51 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 9852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1743 0.037 - 0.075: 840 0.075 - 0.112: 241 0.112 - 0.150: 52 0.150 - 0.187: 4 Chirality restraints: 2880 Sorted by residual: chirality pdb=" CA THR M 144 " pdb=" N THR M 144 " pdb=" C THR M 144 " pdb=" CB THR M 144 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.79e-01 chirality pdb=" CB VAL C 99 " pdb=" CA VAL C 99 " pdb=" CG1 VAL C 99 " pdb=" CG2 VAL C 99 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.27e-01 chirality pdb=" CB VAL F 99 " pdb=" CA VAL F 99 " pdb=" CG1 VAL F 99 " pdb=" CG2 VAL F 99 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.06e-01 ... (remaining 2877 not shown) Planarity restraints: 3105 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN I 89 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.35e+00 pdb=" C GLN I 89 " 0.032 2.00e-02 2.50e+03 pdb=" O GLN I 89 " -0.012 2.00e-02 2.50e+03 pdb=" N SER I 90 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN L 89 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" C GLN L 89 " 0.029 2.00e-02 2.50e+03 pdb=" O GLN L 89 " -0.011 2.00e-02 2.50e+03 pdb=" N SER L 90 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 89 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.61e+00 pdb=" C GLN B 89 " 0.028 2.00e-02 2.50e+03 pdb=" O GLN B 89 " -0.010 2.00e-02 2.50e+03 pdb=" N SER B 90 " -0.009 2.00e-02 2.50e+03 ... (remaining 3102 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2666 2.74 - 3.28: 19443 3.28 - 3.82: 38245 3.82 - 4.36: 45972 4.36 - 4.90: 76033 Nonbonded interactions: 182359 Sorted by model distance: nonbonded pdb=" OE2 GLU L 121 " pdb=" NE2 GLN L 159 " model vdw 2.198 3.120 nonbonded pdb=" OG1 THR D 97 " pdb=" OG1 THR D 144 " model vdw 2.208 3.040 nonbonded pdb=" OG1 THR L 97 " pdb=" OG1 THR L 144 " model vdw 2.208 3.040 nonbonded pdb=" O SER D 27 " pdb=" O HOH D 201 " model vdw 2.228 3.040 nonbonded pdb=" O HOH D 283 " pdb=" O HOH G 216 " model vdw 2.241 3.040 ... (remaining 182354 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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 individual isotropic 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: 1.150 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 18.740 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 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:6.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9224 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 : 0.006 0.059 16890 Z= 0.320 Angle : 0.652 9.698 23100 Z= 0.364 Chirality : 0.046 0.187 2880 Planarity : 0.004 0.033 3105 Dihedral : 15.005 89.848 5520 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.71 % Allowed : 7.86 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.15), residues: 2355 helix: None (None), residues: 0 sheet: 0.90 (0.16), residues: 660 loop : 0.34 (0.13), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 38 TYR 0.019 0.003 TYR M 137 PHE 0.025 0.003 PHE H 118 HIS 0.006 0.002 HIS E 11 Details of bonding type rmsd covalent geometry : bond 0.00639 (16875) covalent geometry : angle 0.65187 (23070) SS BOND : bond 0.00337 ( 15) SS BOND : angle 0.85633 ( 30) hydrogen bonds : bond 0.12553 ( 517) hydrogen bonds : angle 9.58947 ( 1323) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 195 time to evaluate : 0.614 Fit side-chains REVERT: A 63 THR cc_start: 0.8666 (m) cc_final: 0.8271 (p) REVERT: B 45 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8044 (tp30) REVERT: D 45 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.7941 (tp30) REVERT: D 63 THR cc_start: 0.8671 (m) cc_final: 0.8229 (p) REVERT: E 45 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.7924 (tp30) REVERT: F 45 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8371 (tp30) REVERT: G 63 THR cc_start: 0.8830 (m) cc_final: 0.8572 (p) REVERT: K 45 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.7746 (tp30) REVERT: L 45 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8344 (tm-30) REVERT: O 121 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8641 (mt-10) outliers start: 12 outliers final: 6 residues processed: 199 average time/residue: 0.6241 time to fit residues: 139.3653 Evaluate side-chains 205 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 194 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain L residue 3 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 7.9990 chunk 212 optimal weight: 1.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN D 18 ASN I 18 ASN K 125 ASN N 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.104760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.090500 restraints weight = 15675.512| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 0.84 r_work: 0.2915 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 1.92 restraints_weight: 0.2500 r_work: 0.2585 rms_B_bonded: 4.64 restraints_weight: 0.1250 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9197 moved from start: 0.0579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16890 Z= 0.221 Angle : 0.558 8.549 23100 Z= 0.314 Chirality : 0.043 0.147 2880 Planarity : 0.003 0.031 3105 Dihedral : 6.085 39.385 2483 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.48 % Allowed : 7.44 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.15), residues: 2355 helix: None (None), residues: 0 sheet: 1.05 (0.16), residues: 660 loop : 0.32 (0.13), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 136 TYR 0.012 0.002 TYR C 137 PHE 0.019 0.003 PHE B 54 HIS 0.003 0.001 HIS I 82 Details of bonding type rmsd covalent geometry : bond 0.00433 (16875) covalent geometry : angle 0.55779 (23070) SS BOND : bond 0.00122 ( 15) SS BOND : angle 0.64701 ( 30) hydrogen bonds : bond 0.04823 ( 517) hydrogen bonds : angle 7.89063 ( 1323) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 206 time to evaluate : 0.615 Fit side-chains REVERT: A 63 THR cc_start: 0.8572 (m) cc_final: 0.8202 (p) REVERT: D 63 THR cc_start: 0.8598 (m) cc_final: 0.8212 (p) REVERT: J 24 ASP cc_start: 0.9247 (t70) cc_final: 0.9025 (t70) REVERT: L 45 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8311 (tm-30) REVERT: N 45 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8002 (tp30) REVERT: N 114 ASP cc_start: 0.9389 (p0) cc_final: 0.9165 (p0) REVERT: O 121 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8573 (mt-10) outliers start: 8 outliers final: 3 residues processed: 211 average time/residue: 0.5911 time to fit residues: 140.8404 Evaluate side-chains 203 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 199 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain N residue 45 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 16 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 146 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 191 optimal weight: 9.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN I 18 ASN K 125 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.103694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.089311 restraints weight = 15814.101| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 0.84 r_work: 0.2895 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 1.92 restraints_weight: 0.2500 r_work: 0.2565 rms_B_bonded: 4.63 restraints_weight: 0.1250 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9210 moved from start: 0.0519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16890 Z= 0.270 Angle : 0.604 9.782 23100 Z= 0.338 Chirality : 0.045 0.150 2880 Planarity : 0.004 0.032 3105 Dihedral : 5.747 35.597 2462 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.77 % Allowed : 7.44 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.15), residues: 2355 helix: None (None), residues: 0 sheet: 1.00 (0.16), residues: 660 loop : 0.32 (0.13), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 136 TYR 0.014 0.003 TYR C 137 PHE 0.021 0.003 PHE E 118 HIS 0.003 0.001 HIS I 82 Details of bonding type rmsd covalent geometry : bond 0.00532 (16875) covalent geometry : angle 0.60326 (23070) SS BOND : bond 0.00155 ( 15) SS BOND : angle 0.81601 ( 30) hydrogen bonds : bond 0.05125 ( 517) hydrogen bonds : angle 8.03499 ( 1323) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 201 time to evaluate : 0.585 Fit side-chains REVERT: A 63 THR cc_start: 0.8587 (m) cc_final: 0.8265 (p) REVERT: B 45 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8165 (tp30) REVERT: D 63 THR cc_start: 0.8633 (m) cc_final: 0.8218 (p) REVERT: E 45 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.7893 (tp30) REVERT: J 42 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8510 (mt) REVERT: N 45 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8038 (tp30) REVERT: N 114 ASP cc_start: 0.9414 (p0) cc_final: 0.9179 (p0) REVERT: O 121 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8567 (mt-10) outliers start: 13 outliers final: 5 residues processed: 208 average time/residue: 0.5915 time to fit residues: 138.7457 Evaluate side-chains 203 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 194 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain M residue 95 SER Chi-restraints excluded: chain N residue 45 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 8 optimal weight: 8.9990 chunk 179 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 173 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 117 optimal weight: 7.9990 chunk 151 optimal weight: 9.9990 chunk 193 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 207 optimal weight: 10.0000 chunk 216 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN I 18 ASN K 125 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.102577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.088111 restraints weight = 15815.606| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 0.84 r_work: 0.2874 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 1.93 restraints_weight: 0.2500 r_work: 0.2544 rms_B_bonded: 4.65 restraints_weight: 0.1250 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9234 moved from start: 0.0512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 16890 Z= 0.367 Angle : 0.689 11.197 23100 Z= 0.385 Chirality : 0.048 0.187 2880 Planarity : 0.004 0.037 3105 Dihedral : 6.012 37.803 2462 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.13 % Allowed : 7.02 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.15), residues: 2355 helix: None (None), residues: 0 sheet: 0.85 (0.16), residues: 660 loop : 0.26 (0.13), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 38 TYR 0.016 0.003 TYR C 137 PHE 0.028 0.004 PHE E 118 HIS 0.005 0.002 HIS E 11 Details of bonding type rmsd covalent geometry : bond 0.00730 (16875) covalent geometry : angle 0.68819 (23070) SS BOND : bond 0.00293 ( 15) SS BOND : angle 1.04400 ( 30) hydrogen bonds : bond 0.05784 ( 517) hydrogen bonds : angle 8.31596 ( 1323) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 201 time to evaluate : 0.643 Fit side-chains REVERT: A 63 THR cc_start: 0.8722 (m) cc_final: 0.8429 (p) REVERT: B 45 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.8195 (tp30) REVERT: D 63 THR cc_start: 0.8711 (OUTLIER) cc_final: 0.8261 (p) REVERT: E 45 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.7981 (tp30) REVERT: K 45 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.7762 (tp30) REVERT: N 45 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8119 (tp30) REVERT: O 121 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8614 (mt-10) outliers start: 19 outliers final: 9 residues processed: 210 average time/residue: 0.6064 time to fit residues: 143.4874 Evaluate side-chains 207 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 193 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain N residue 45 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 148 optimal weight: 4.9990 chunk 208 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 136 optimal weight: 20.0000 chunk 58 optimal weight: 0.7980 chunk 142 optimal weight: 9.9990 chunk 84 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 chunk 104 optimal weight: 8.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN I 18 ASN K 125 ASN N 82 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.105264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.091044 restraints weight = 15710.620| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 0.84 r_work: 0.2924 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 1.92 restraints_weight: 0.2500 r_work: 0.2596 rms_B_bonded: 4.64 restraints_weight: 0.1250 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9190 moved from start: 0.0726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16890 Z= 0.196 Angle : 0.536 7.887 23100 Z= 0.303 Chirality : 0.043 0.149 2880 Planarity : 0.003 0.033 3105 Dihedral : 5.488 35.985 2462 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.77 % Allowed : 7.56 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.15), residues: 2355 helix: None (None), residues: 0 sheet: 1.06 (0.16), residues: 660 loop : 0.30 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 38 TYR 0.012 0.002 TYR C 137 PHE 0.018 0.002 PHE B 54 HIS 0.002 0.001 HIS I 82 Details of bonding type rmsd covalent geometry : bond 0.00382 (16875) covalent geometry : angle 0.53622 (23070) SS BOND : bond 0.00111 ( 15) SS BOND : angle 0.70231 ( 30) hydrogen bonds : bond 0.04489 ( 517) hydrogen bonds : angle 7.64721 ( 1323) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 205 time to evaluate : 0.635 Fit side-chains REVERT: A 63 THR cc_start: 0.8582 (m) cc_final: 0.8308 (p) REVERT: B 45 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8173 (tp30) REVERT: D 63 THR cc_start: 0.8577 (m) cc_final: 0.8193 (p) REVERT: E 45 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.7888 (tp30) REVERT: G 41 SER cc_start: 0.9107 (m) cc_final: 0.8905 (p) REVERT: J 42 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8396 (mt) REVERT: K 45 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.7702 (tp30) REVERT: N 45 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.7999 (tp30) REVERT: N 114 ASP cc_start: 0.9353 (p0) cc_final: 0.9118 (p0) REVERT: O 121 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8547 (mt-10) outliers start: 13 outliers final: 6 residues processed: 212 average time/residue: 0.6066 time to fit residues: 144.6687 Evaluate side-chains 209 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 198 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain M residue 95 SER Chi-restraints excluded: chain N residue 45 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 188 optimal weight: 10.0000 chunk 206 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 150 optimal weight: 20.0000 chunk 114 optimal weight: 0.0070 chunk 102 optimal weight: 5.9990 chunk 180 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 105 optimal weight: 20.0000 chunk 41 optimal weight: 9.9990 chunk 197 optimal weight: 9.9990 overall best weight: 6.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN I 18 ASN K 125 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.102761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.088365 restraints weight = 15628.208| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 0.84 r_work: 0.2880 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 1.91 restraints_weight: 0.2500 r_work: 0.2549 rms_B_bonded: 4.59 restraints_weight: 0.1250 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9219 moved from start: 0.0558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 16890 Z= 0.340 Angle : 0.666 11.122 23100 Z= 0.372 Chirality : 0.047 0.180 2880 Planarity : 0.004 0.036 3105 Dihedral : 5.961 38.098 2462 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.83 % Allowed : 7.20 % Favored : 91.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.15), residues: 2355 helix: None (None), residues: 0 sheet: 0.86 (0.16), residues: 660 loop : 0.28 (0.13), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 38 TYR 0.016 0.003 TYR C 137 PHE 0.026 0.004 PHE E 118 HIS 0.004 0.001 HIS I 82 Details of bonding type rmsd covalent geometry : bond 0.00673 (16875) covalent geometry : angle 0.66564 (23070) SS BOND : bond 0.00248 ( 15) SS BOND : angle 0.93853 ( 30) hydrogen bonds : bond 0.05545 ( 517) hydrogen bonds : angle 8.20835 ( 1323) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 199 time to evaluate : 0.658 Fit side-chains REVERT: A 63 THR cc_start: 0.8678 (m) cc_final: 0.8380 (p) REVERT: B 45 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8154 (tp30) REVERT: D 45 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.7912 (tp30) REVERT: D 63 THR cc_start: 0.8636 (OUTLIER) cc_final: 0.8187 (p) REVERT: E 45 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.7883 (tp30) REVERT: K 45 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.7661 (tp30) REVERT: N 45 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8038 (tp30) REVERT: N 114 ASP cc_start: 0.9415 (p0) cc_final: 0.9175 (p0) REVERT: O 121 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8552 (mt-10) outliers start: 14 outliers final: 7 residues processed: 204 average time/residue: 0.6224 time to fit residues: 142.7656 Evaluate side-chains 206 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 193 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain N residue 45 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 85 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 chunk 124 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 193 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN I 18 ASN K 125 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.102483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.088017 restraints weight = 15784.439| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 0.84 r_work: 0.2873 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 1.92 restraints_weight: 0.2500 r_work: 0.2543 rms_B_bonded: 4.63 restraints_weight: 0.1250 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9235 moved from start: 0.0534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 16890 Z= 0.391 Angle : 0.705 10.899 23100 Z= 0.394 Chirality : 0.049 0.181 2880 Planarity : 0.005 0.038 3105 Dihedral : 6.037 38.253 2462 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.95 % Allowed : 7.26 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.15), residues: 2355 helix: None (None), residues: 0 sheet: 0.81 (0.16), residues: 660 loop : 0.22 (0.13), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 38 TYR 0.017 0.004 TYR C 137 PHE 0.027 0.004 PHE E 118 HIS 0.005 0.002 HIS I 82 Details of bonding type rmsd covalent geometry : bond 0.00775 (16875) covalent geometry : angle 0.70411 (23070) SS BOND : bond 0.00347 ( 15) SS BOND : angle 1.06822 ( 30) hydrogen bonds : bond 0.05913 ( 517) hydrogen bonds : angle 8.32700 ( 1323) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 195 time to evaluate : 0.584 Fit side-chains REVERT: A 63 THR cc_start: 0.8720 (m) cc_final: 0.8446 (p) REVERT: B 45 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8227 (tp30) REVERT: D 63 THR cc_start: 0.8724 (OUTLIER) cc_final: 0.8272 (p) REVERT: E 45 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.7975 (tp30) REVERT: K 45 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.7741 (tp30) REVERT: N 45 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8114 (tp30) REVERT: N 114 ASP cc_start: 0.9449 (p0) cc_final: 0.9193 (p0) REVERT: O 121 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8596 (mt-10) outliers start: 16 outliers final: 8 residues processed: 202 average time/residue: 0.6103 time to fit residues: 138.5039 Evaluate side-chains 205 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 192 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain N residue 45 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 26 optimal weight: 10.0000 chunk 134 optimal weight: 0.9980 chunk 29 optimal weight: 7.9990 chunk 223 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 186 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 146 optimal weight: 7.9990 chunk 191 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN E 125 ASN I 18 ASN K 125 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.107871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.093877 restraints weight = 15762.793| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 0.84 r_work: 0.2971 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 1.93 restraints_weight: 0.2500 r_work: 0.2645 rms_B_bonded: 4.69 restraints_weight: 0.1250 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9157 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16890 Z= 0.132 Angle : 0.475 5.624 23100 Z= 0.272 Chirality : 0.042 0.147 2880 Planarity : 0.003 0.032 3105 Dihedral : 5.077 33.654 2462 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.54 % Allowed : 7.98 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.15), residues: 2355 helix: None (None), residues: 0 sheet: 1.21 (0.17), residues: 660 loop : 0.31 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 136 TYR 0.010 0.002 TYR C 137 PHE 0.015 0.002 PHE B 54 HIS 0.002 0.001 HIS I 82 Details of bonding type rmsd covalent geometry : bond 0.00257 (16875) covalent geometry : angle 0.47530 (23070) SS BOND : bond 0.00142 ( 15) SS BOND : angle 0.60776 ( 30) hydrogen bonds : bond 0.03770 ( 517) hydrogen bonds : angle 7.19639 ( 1323) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 214 time to evaluate : 0.544 Fit side-chains REVERT: A 63 THR cc_start: 0.8527 (m) cc_final: 0.8275 (p) REVERT: B 45 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8182 (tp30) REVERT: D 63 THR cc_start: 0.8534 (m) cc_final: 0.8185 (p) REVERT: E 45 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.7858 (tp30) REVERT: N 45 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.7960 (tp30) REVERT: O 121 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8520 (mt-10) outliers start: 9 outliers final: 3 residues processed: 218 average time/residue: 0.5853 time to fit residues: 143.9591 Evaluate side-chains 207 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 201 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain M residue 95 SER Chi-restraints excluded: chain N residue 45 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 185 optimal weight: 9.9990 chunk 148 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 144 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 217 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 chunk 117 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN C 18 ASN E 125 ASN I 18 ASN J 64 ASN K 125 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.102281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.087804 restraints weight = 15719.793| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 0.84 r_work: 0.2869 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 1.92 restraints_weight: 0.2500 r_work: 0.2539 rms_B_bonded: 4.62 restraints_weight: 0.1250 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9238 moved from start: 0.0557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 16890 Z= 0.422 Angle : 0.731 11.323 23100 Z= 0.407 Chirality : 0.050 0.209 2880 Planarity : 0.005 0.038 3105 Dihedral : 6.057 37.918 2461 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.77 % Allowed : 7.50 % Favored : 91.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.15), residues: 2355 helix: None (None), residues: 0 sheet: 0.85 (0.16), residues: 660 loop : 0.28 (0.13), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 38 TYR 0.016 0.004 TYR C 137 PHE 0.029 0.004 PHE E 118 HIS 0.005 0.002 HIS I 82 Details of bonding type rmsd covalent geometry : bond 0.00841 (16875) covalent geometry : angle 0.73011 (23070) SS BOND : bond 0.00414 ( 15) SS BOND : angle 1.03572 ( 30) hydrogen bonds : bond 0.05975 ( 517) hydrogen bonds : angle 8.36860 ( 1323) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 200 time to evaluate : 0.715 Fit side-chains REVERT: A 45 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.7985 (tp30) REVERT: A 63 THR cc_start: 0.8725 (m) cc_final: 0.8447 (p) REVERT: B 45 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8215 (tp30) REVERT: D 45 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.7978 (tp30) REVERT: D 63 THR cc_start: 0.8716 (m) cc_final: 0.8247 (p) REVERT: E 45 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.7989 (tp30) REVERT: K 45 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.7795 (tp30) REVERT: N 45 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8115 (tp30) REVERT: N 114 ASP cc_start: 0.9431 (p0) cc_final: 0.9191 (p0) REVERT: O 121 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8607 (mt-10) outliers start: 13 outliers final: 5 residues processed: 204 average time/residue: 0.6355 time to fit residues: 145.5552 Evaluate side-chains 203 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 192 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain N residue 45 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 189 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 chunk 218 optimal weight: 0.7980 chunk 117 optimal weight: 7.9990 chunk 210 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 168 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 133 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 overall best weight: 1.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 82 HIS E 125 ASN I 18 ASN J 64 ASN O 18 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.106517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.092407 restraints weight = 15646.456| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 0.83 r_work: 0.2947 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 1.92 restraints_weight: 0.2500 r_work: 0.2619 rms_B_bonded: 4.64 restraints_weight: 0.1250 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9174 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16890 Z= 0.162 Angle : 0.510 6.803 23100 Z= 0.290 Chirality : 0.042 0.147 2880 Planarity : 0.003 0.034 3105 Dihedral : 5.279 34.401 2461 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.42 % Allowed : 8.04 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.15), residues: 2355 helix: None (None), residues: 0 sheet: 1.16 (0.17), residues: 660 loop : 0.31 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 38 TYR 0.011 0.002 TYR C 137 PHE 0.016 0.002 PHE H 54 HIS 0.002 0.001 HIS L 82 Details of bonding type rmsd covalent geometry : bond 0.00314 (16875) covalent geometry : angle 0.50965 (23070) SS BOND : bond 0.00114 ( 15) SS BOND : angle 0.68542 ( 30) hydrogen bonds : bond 0.04111 ( 517) hydrogen bonds : angle 7.41476 ( 1323) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4710 Ramachandran restraints generated. 2355 Oldfield, 0 Emsley, 2355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 206 time to evaluate : 0.668 Fit side-chains REVERT: A 63 THR cc_start: 0.8593 (m) cc_final: 0.8339 (p) REVERT: B 45 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8131 (tp30) REVERT: D 63 THR cc_start: 0.8548 (m) cc_final: 0.8189 (p) REVERT: E 45 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.7880 (tp30) REVERT: K 45 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.7594 (tp30) REVERT: N 45 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.7987 (tp30) REVERT: N 114 ASP cc_start: 0.9340 (p0) cc_final: 0.9118 (p0) REVERT: O 121 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8519 (mt-10) outliers start: 7 outliers final: 2 residues processed: 207 average time/residue: 0.6121 time to fit residues: 142.7442 Evaluate side-chains 208 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 202 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain J residue 120 SER Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain N residue 45 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 134 optimal weight: 0.7980 chunk 94 optimal weight: 10.0000 chunk 127 optimal weight: 20.0000 chunk 111 optimal weight: 4.9990 chunk 186 optimal weight: 0.9980 chunk 97 optimal weight: 20.0000 chunk 196 optimal weight: 3.9990 chunk 150 optimal weight: 20.0000 chunk 76 optimal weight: 3.9990 chunk 182 optimal weight: 0.6980 chunk 129 optimal weight: 0.9980 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN E 125 ASN I 18 ASN J 64 ASN O 18 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.108017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.093938 restraints weight = 15836.552| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 0.84 r_work: 0.2972 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 1.94 restraints_weight: 0.2500 r_work: 0.2645 rms_B_bonded: 4.71 restraints_weight: 0.1250 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9157 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16890 Z= 0.140 Angle : 0.479 6.109 23100 Z= 0.273 Chirality : 0.042 0.145 2880 Planarity : 0.003 0.033 3105 Dihedral : 4.982 30.631 2461 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.42 % Allowed : 7.86 % Favored : 91.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.15), residues: 2355 helix: None (None), residues: 0 sheet: 1.23 (0.17), residues: 660 loop : 0.33 (0.13), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG M 106 TYR 0.009 0.002 TYR C 137 PHE 0.015 0.002 PHE B 54 HIS 0.002 0.001 HIS L 82 Details of bonding type rmsd covalent geometry : bond 0.00274 (16875) covalent geometry : angle 0.47907 (23070) SS BOND : bond 0.00092 ( 15) SS BOND : angle 0.62073 ( 30) hydrogen bonds : bond 0.03765 ( 517) hydrogen bonds : angle 7.10658 ( 1323) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7220.12 seconds wall clock time: 123 minutes 33.76 seconds (7413.76 seconds total)