Starting phenix.real_space_refine on Thu Sep 18 16:51:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vkv_65144/09_2025/9vkv_65144.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vkv_65144/09_2025/9vkv_65144.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vkv_65144/09_2025/9vkv_65144.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vkv_65144/09_2025/9vkv_65144.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vkv_65144/09_2025/9vkv_65144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vkv_65144/09_2025/9vkv_65144.map" } resolution = 2.09 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= 0.002 sd= 0.073 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 5169 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18339 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: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 146 Classifications: {'water': 146} Link IDs: {None: 145} Chain: "B" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 115 Classifications: {'water': 115} Link IDs: {None: 114} 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: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "E" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 95 Classifications: {'water': 95} Link IDs: {None: 94} Chain: "F" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 103 Classifications: {'water': 103} Link IDs: {None: 102} Chain: "G" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 103 Classifications: {'water': 103} Link IDs: {None: 102} Chain: "H" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 101 Classifications: {'water': 101} Link IDs: {None: 100} Chain: "I" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "J" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 100 Classifications: {'water': 100} Link IDs: {None: 99} Chain: "K" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "L" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 100 Classifications: {'water': 100} Link IDs: {None: 99} Chain: "M" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Chain: "N" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Chain: "O" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 137 Classifications: {'water': 137} Link IDs: {None: 136} Time building chain proxies: 4.79, per 1000 atoms: 0.26 Number of scatterers: 18339 At special positions: 0 Unit cell: (87.78, 85.272, 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 5169 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=2.03 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=2.03 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 817.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 23 helices and 52 sheets defined 4.0% alpha, 58.6% 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: 4.519A pdb=" N ASP A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 28 Processing helix chain 'B' and resid 40 through 42 No H-bonds generated for 'chain 'B' and resid 40 through 42' 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 40 through 42 No H-bonds generated for 'chain 'F' and resid 40 through 42' Processing helix chain 'G' and resid 24 through 28 Processing helix chain 'G' and resid 40 through 43 removed outlier: 4.166A pdb=" N ALA G 43 " --> pdb=" O ALA G 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 40 through 43' Processing helix chain 'H' and resid 24 through 28 Processing helix chain 'H' and resid 40 through 42 No H-bonds generated for 'chain 'H' and resid 40 through 42' Processing helix chain 'I' and resid 40 through 43 removed outlier: 4.155A 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 43 removed outlier: 4.122A pdb=" N ALA J 43 " --> pdb=" O ALA J 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 40 through 43' Processing helix chain 'K' and resid 40 through 42 No H-bonds generated for 'chain 'K' 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: 4.088A 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 24 through 28 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 40 through 43 removed outlier: 4.147A 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: 8.798A pdb=" N GLN B 30 " --> pdb=" O GLY A 7 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR A 9 " --> pdb=" O GLN B 30 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N VAL B 32 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N HIS A 11 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N LEU B 34 " --> pdb=" O HIS A 11 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N LYS A 13 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLN B 36 " --> pdb=" O LYS A 13 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLU A 15 " --> pdb=" O GLN B 36 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG B 38 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N VAL A 17 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE B 154 " --> pdb=" O GLY A 7 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N THR A 9 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA B 152 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N HIS A 11 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 6.594A 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: 8.798A pdb=" N GLN B 30 " --> pdb=" O GLY A 7 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR A 9 " --> pdb=" O GLN B 30 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N VAL B 32 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N HIS A 11 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N LEU B 34 " --> pdb=" O HIS A 11 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N LYS A 13 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLN B 36 " --> pdb=" O LYS A 13 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLU A 15 " --> pdb=" O GLN B 36 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG B 38 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 5.845A 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: 5.490A pdb=" N GLY A 53 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ALA A 135 " --> pdb=" O GLY A 53 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ASN A 55 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N PHE A 133 " --> pdb=" O ASN A 55 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N GLN A 57 " --> pdb=" O ILE A 131 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE A 131 " --> pdb=" O GLN A 57 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ASN A 59 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASN A 129 " --> pdb=" O ASN A 59 " (cutoff:3.500A) removed outlier: 6.848A 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: 8.332A 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: 8.710A pdb=" N GLN C 30 " --> pdb=" O GLY B 7 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N THR B 9 " --> pdb=" O GLN C 30 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N VAL C 32 " --> pdb=" O THR B 9 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N HIS B 11 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LEU C 34 " --> pdb=" O HIS B 11 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LYS B 13 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLN C 36 " --> pdb=" O LYS B 13 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLU B 15 " --> pdb=" O GLN C 36 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ARG C 38 " --> pdb=" O GLU B 15 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N VAL B 17 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N THR B 4 " --> pdb=" O TYR C 158 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N TYR C 158 " --> pdb=" O THR B 4 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ASN B 6 " --> pdb=" O VAL C 156 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N VAL C 156 " --> pdb=" O ASN B 6 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 29 through 38 removed outlier: 8.710A pdb=" N GLN C 30 " --> pdb=" O GLY B 7 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N THR B 9 " --> pdb=" O GLN C 30 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N VAL C 32 " --> pdb=" O THR B 9 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N HIS B 11 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LEU C 34 " --> pdb=" O HIS B 11 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LYS B 13 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLN C 36 " --> pdb=" O LYS B 13 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLU B 15 " --> pdb=" O GLN C 36 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ARG C 38 " --> pdb=" O GLU B 15 " (cutoff:3.500A) removed outlier: 5.852A 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: 3.602A 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) Processing sheet with id=AA9, first strand: chain 'D' and resid 29 through 38 removed outlier: 8.840A pdb=" N GLN D 30 " --> pdb=" O GLY C 7 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR C 9 " --> pdb=" O GLN D 30 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL D 32 " --> pdb=" O THR C 9 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N HIS C 11 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU D 34 " --> pdb=" O HIS C 11 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N LYS C 13 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLN D 36 " --> pdb=" O LYS C 13 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLU C 15 " --> pdb=" O GLN D 36 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ARG D 38 " --> pdb=" O GLU C 15 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N VAL C 17 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N PHE D 154 " --> pdb=" O GLY C 7 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR C 9 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA D 152 " --> pdb=" O THR C 9 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N HIS C 11 " --> pdb=" O ALA D 150 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA D 150 " --> pdb=" O HIS C 11 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 29 through 38 removed outlier: 8.840A pdb=" N GLN D 30 " --> pdb=" O GLY C 7 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR C 9 " --> pdb=" O GLN D 30 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL D 32 " --> pdb=" O THR C 9 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N HIS C 11 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU D 34 " --> pdb=" O HIS C 11 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N LYS C 13 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLN D 36 " --> pdb=" O LYS C 13 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLU C 15 " --> pdb=" O GLN D 36 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ARG D 38 " --> pdb=" O GLU C 15 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N VAL C 17 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 22 through 23 removed outlier: 5.353A pdb=" N GLY C 127 " --> pdb=" O ASP C 60 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASN C 98 " --> pdb=" O THR C 140 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 77 through 79 removed outlier: 8.386A pdb=" N VAL C 85 " --> pdb=" O ILE C 78 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 29 through 38 removed outlier: 8.828A pdb=" N GLN E 30 " --> pdb=" O GLY D 7 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR D 9 " --> pdb=" O GLN E 30 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL E 32 " --> pdb=" O THR D 9 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N HIS D 11 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU E 34 " --> pdb=" O HIS D 11 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N LYS D 13 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLN E 36 " --> pdb=" O LYS D 13 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLU D 15 " --> pdb=" O GLN E 36 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ARG E 38 " --> pdb=" O GLU D 15 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N VAL D 17 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N THR D 4 " --> pdb=" O TYR E 158 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N TYR E 158 " --> pdb=" O THR D 4 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ASN D 6 " --> pdb=" O VAL E 156 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N VAL E 156 " --> pdb=" O ASN D 6 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 29 through 38 removed outlier: 8.828A pdb=" N GLN E 30 " --> pdb=" O GLY D 7 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR D 9 " --> pdb=" O GLN E 30 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL E 32 " --> pdb=" O THR D 9 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N HIS D 11 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU E 34 " --> pdb=" O HIS D 11 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N LYS D 13 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLN E 36 " --> pdb=" O LYS D 13 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLU D 15 " --> pdb=" O GLN E 36 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ARG E 38 " --> pdb=" O GLU D 15 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N VAL D 17 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 22 through 23 removed outlier: 5.238A pdb=" N GLY D 127 " --> pdb=" O ASP D 60 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASN D 98 " --> pdb=" O THR D 140 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 77 through 79 removed outlier: 8.353A pdb=" N VAL D 85 " --> pdb=" O ILE D 78 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 29 through 38 removed outlier: 8.751A pdb=" N GLN F 30 " --> pdb=" O GLY E 7 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR E 9 " --> pdb=" O GLN F 30 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N VAL F 32 " --> pdb=" O THR E 9 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N HIS E 11 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LEU F 34 " --> pdb=" O HIS E 11 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LYS E 13 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLN F 36 " --> pdb=" O LYS E 13 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLU E 15 " --> pdb=" O GLN F 36 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ARG F 38 " --> pdb=" O GLU E 15 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N VAL E 17 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N THR E 4 " --> pdb=" O TYR F 158 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N TYR F 158 " --> pdb=" O THR E 4 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ASN E 6 " --> pdb=" O VAL F 156 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N VAL F 156 " --> pdb=" O ASN E 6 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 29 through 38 removed outlier: 8.751A pdb=" N GLN F 30 " --> pdb=" O GLY E 7 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR E 9 " --> pdb=" O GLN F 30 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N VAL F 32 " --> pdb=" O THR E 9 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N HIS E 11 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LEU F 34 " --> pdb=" O HIS E 11 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LYS E 13 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLN F 36 " --> pdb=" O LYS E 13 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLU E 15 " --> pdb=" O GLN F 36 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ARG F 38 " --> pdb=" O GLU E 15 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N VAL E 17 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 22 through 23 removed outlier: 3.613A pdb=" N ASP E 60 " --> pdb=" O GLY E 127 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N GLY E 127 " --> pdb=" O ASP E 60 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 29 through 38 removed outlier: 8.858A pdb=" N GLN G 30 " --> pdb=" O GLY F 7 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR F 9 " --> pdb=" O GLN G 30 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL G 32 " --> pdb=" O THR F 9 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N HIS F 11 " --> pdb=" O VAL G 32 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LEU G 34 " --> pdb=" O HIS F 11 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N LYS F 13 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLN G 36 " --> pdb=" O LYS F 13 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLU F 15 " --> pdb=" O GLN G 36 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ARG G 38 " --> pdb=" O GLU F 15 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N VAL F 17 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N THR F 4 " --> pdb=" O TYR G 158 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N TYR G 158 " --> pdb=" O THR F 4 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ASN F 6 " --> pdb=" O VAL G 156 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N VAL G 156 " --> pdb=" O ASN F 6 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 29 through 38 removed outlier: 8.858A pdb=" N GLN G 30 " --> pdb=" O GLY F 7 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR F 9 " --> pdb=" O GLN G 30 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL G 32 " --> pdb=" O THR F 9 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N HIS F 11 " --> pdb=" O VAL G 32 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LEU G 34 " --> pdb=" O HIS F 11 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N LYS F 13 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLN G 36 " --> pdb=" O LYS F 13 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLU F 15 " --> pdb=" O GLN G 36 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ARG G 38 " --> pdb=" O GLU F 15 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N VAL F 17 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 22 through 23 removed outlier: 3.616A pdb=" N ASP F 60 " --> pdb=" O GLY F 127 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N GLY F 127 " --> pdb=" O ASP F 60 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASN F 98 " --> pdb=" O THR F 140 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 77 through 79 removed outlier: 8.402A pdb=" N VAL F 85 " --> pdb=" O ILE F 78 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 29 through 38 removed outlier: 9.060A pdb=" N GLN H 30 " --> pdb=" O GLY G 7 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR G 9 " --> pdb=" O GLN H 30 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N VAL H 32 " --> pdb=" O THR G 9 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N HIS G 11 " --> pdb=" O VAL H 32 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU H 34 " --> pdb=" O HIS G 11 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N LYS G 13 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLN H 36 " --> pdb=" O LYS G 13 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLU G 15 " --> pdb=" O GLN H 36 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ARG H 38 " --> pdb=" O GLU G 15 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N VAL G 17 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N THR G 4 " --> pdb=" O TYR H 158 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N TYR H 158 " --> pdb=" O THR G 4 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ASN G 6 " --> pdb=" O VAL H 156 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N VAL H 156 " --> pdb=" O ASN G 6 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 29 through 38 removed outlier: 9.060A pdb=" N GLN H 30 " --> pdb=" O GLY G 7 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR G 9 " --> pdb=" O GLN H 30 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N VAL H 32 " --> pdb=" O THR G 9 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N HIS G 11 " --> pdb=" O VAL H 32 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU H 34 " --> pdb=" O HIS G 11 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N LYS G 13 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLN H 36 " --> pdb=" O LYS G 13 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLU G 15 " --> pdb=" O GLN H 36 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ARG H 38 " --> pdb=" O GLU G 15 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N VAL G 17 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 22 through 23 removed outlier: 5.213A pdb=" N GLY G 127 " --> pdb=" O ASP G 60 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ASN G 98 " --> pdb=" O THR G 140 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ILE G 103 " --> pdb=" O ASN G 84 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ASN G 84 " --> pdb=" O ILE G 103 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N VAL G 85 " --> pdb=" O ILE G 78 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 29 through 38 removed outlier: 8.754A pdb=" N GLN I 30 " --> pdb=" O GLY H 7 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR H 9 " --> pdb=" O GLN I 30 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL I 32 " --> pdb=" O THR H 9 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N HIS H 11 " --> pdb=" O VAL I 32 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LEU I 34 " --> pdb=" O HIS H 11 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N LYS H 13 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLN I 36 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLU H 15 " --> pdb=" O GLN I 36 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ARG I 38 " --> pdb=" O GLU H 15 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL H 17 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N THR H 4 " --> pdb=" O TYR I 158 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N TYR I 158 " --> pdb=" O THR H 4 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ASN H 6 " --> pdb=" O VAL I 156 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N VAL I 156 " --> pdb=" O ASN H 6 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 29 through 38 removed outlier: 8.754A pdb=" N GLN I 30 " --> pdb=" O GLY H 7 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR H 9 " --> pdb=" O GLN I 30 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL I 32 " --> pdb=" O THR H 9 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N HIS H 11 " --> pdb=" O VAL I 32 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LEU I 34 " --> pdb=" O HIS H 11 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N LYS H 13 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLN I 36 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLU H 15 " --> pdb=" O GLN I 36 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ARG I 38 " --> pdb=" O GLU H 15 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL H 17 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 22 through 23 removed outlier: 3.675A pdb=" N ASP H 60 " --> pdb=" O GLY H 127 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N GLY H 127 " --> pdb=" O ASP H 60 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASN H 98 " --> pdb=" O THR H 140 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 77 through 79 removed outlier: 8.371A pdb=" N VAL H 85 " --> pdb=" O ILE H 78 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 29 through 38 removed outlier: 8.760A pdb=" N GLN J 30 " --> pdb=" O GLY I 7 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR I 9 " --> pdb=" O GLN J 30 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N VAL J 32 " --> pdb=" O THR I 9 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N HIS I 11 " --> pdb=" O VAL J 32 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU J 34 " --> pdb=" O HIS I 11 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N LYS I 13 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLN J 36 " --> pdb=" O LYS I 13 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLU I 15 " --> pdb=" O GLN J 36 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ARG J 38 " --> pdb=" O GLU I 15 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N VAL I 17 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N THR I 4 " --> pdb=" O TYR J 158 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N TYR J 158 " --> pdb=" O THR I 4 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ASN I 6 " --> pdb=" O VAL J 156 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N VAL J 156 " --> pdb=" O ASN I 6 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 29 through 38 removed outlier: 8.760A pdb=" N GLN J 30 " --> pdb=" O GLY I 7 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR I 9 " --> pdb=" O GLN J 30 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N VAL J 32 " --> pdb=" O THR I 9 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N HIS I 11 " --> pdb=" O VAL J 32 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU J 34 " --> pdb=" O HIS I 11 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N LYS I 13 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLN J 36 " --> pdb=" O LYS I 13 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLU I 15 " --> pdb=" O GLN J 36 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ARG J 38 " --> pdb=" O GLU I 15 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N VAL I 17 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 22 through 23 removed outlier: 3.617A pdb=" N ASP I 60 " --> pdb=" O GLY I 127 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N GLY I 127 " --> pdb=" O ASP I 60 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 77 through 79 removed outlier: 8.420A pdb=" N VAL I 85 " --> pdb=" O ILE I 78 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 29 through 38 removed outlier: 8.903A pdb=" N GLN K 30 " --> pdb=" O GLY J 7 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR J 9 " --> pdb=" O GLN K 30 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N VAL K 32 " --> pdb=" O THR J 9 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N HIS J 11 " --> pdb=" O VAL K 32 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LEU K 34 " --> pdb=" O HIS J 11 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LYS J 13 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN K 36 " --> pdb=" O LYS J 13 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLU J 15 " --> pdb=" O GLN K 36 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ARG K 38 " --> pdb=" O GLU J 15 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N VAL J 17 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N THR J 4 " --> pdb=" O TYR K 158 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N TYR K 158 " --> pdb=" O THR J 4 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ASN J 6 " --> pdb=" O VAL K 156 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N VAL K 156 " --> pdb=" O ASN J 6 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 29 through 38 removed outlier: 8.903A pdb=" N GLN K 30 " --> pdb=" O GLY J 7 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR J 9 " --> pdb=" O GLN K 30 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N VAL K 32 " --> pdb=" O THR J 9 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N HIS J 11 " --> pdb=" O VAL K 32 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LEU K 34 " --> pdb=" O HIS J 11 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LYS J 13 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN K 36 " --> pdb=" O LYS J 13 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLU J 15 " --> pdb=" O GLN K 36 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ARG K 38 " --> pdb=" O GLU J 15 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N VAL J 17 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 22 through 23 removed outlier: 5.227A pdb=" N GLY J 127 " --> pdb=" O ASP J 60 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASN J 98 " --> pdb=" O THR J 140 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 29 through 38 removed outlier: 8.645A pdb=" N GLN L 30 " --> pdb=" O GLY K 7 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR K 9 " --> pdb=" O GLN L 30 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N VAL L 32 " --> pdb=" O THR K 9 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N HIS K 11 " --> pdb=" O VAL L 32 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LEU L 34 " --> pdb=" O HIS K 11 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N LYS K 13 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLN L 36 " --> pdb=" O LYS K 13 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLU K 15 " --> pdb=" O GLN L 36 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ARG L 38 " --> pdb=" O GLU K 15 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N VAL K 17 " --> pdb=" O ARG L 38 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N THR K 4 " --> pdb=" O TYR L 158 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N TYR L 158 " --> pdb=" O THR K 4 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ASN K 6 " --> pdb=" O VAL L 156 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N VAL L 156 " --> pdb=" O ASN K 6 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 29 through 38 removed outlier: 8.645A pdb=" N GLN L 30 " --> pdb=" O GLY K 7 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR K 9 " --> pdb=" O GLN L 30 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N VAL L 32 " --> pdb=" O THR K 9 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N HIS K 11 " --> pdb=" O VAL L 32 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LEU L 34 " --> pdb=" O HIS K 11 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N LYS K 13 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLN L 36 " --> pdb=" O LYS K 13 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLU K 15 " --> pdb=" O GLN L 36 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ARG L 38 " --> pdb=" O GLU K 15 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N VAL K 17 " --> pdb=" O ARG L 38 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 22 through 23 removed outlier: 3.592A pdb=" N ASP K 60 " --> pdb=" O GLY K 127 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N GLY K 127 " --> pdb=" O ASP K 60 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 77 through 79 removed outlier: 8.412A pdb=" N VAL K 85 " --> pdb=" O ILE K 78 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 29 through 38 removed outlier: 8.710A pdb=" N GLN M 30 " --> pdb=" O GLY L 7 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR L 9 " --> pdb=" O GLN M 30 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL M 32 " --> pdb=" O THR L 9 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N HIS L 11 " --> pdb=" O VAL M 32 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU M 34 " --> pdb=" O HIS L 11 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N LYS L 13 " --> pdb=" O LEU M 34 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLN M 36 " --> pdb=" O LYS L 13 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLU L 15 " --> pdb=" O GLN M 36 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ARG M 38 " --> pdb=" O GLU L 15 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N VAL L 17 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N PHE M 154 " --> pdb=" O GLY L 7 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N THR L 9 " --> pdb=" O ALA M 152 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ALA M 152 " --> pdb=" O THR L 9 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N HIS L 11 " --> pdb=" O ALA M 150 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA M 150 " --> pdb=" O HIS L 11 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 29 through 38 removed outlier: 8.710A pdb=" N GLN M 30 " --> pdb=" O GLY L 7 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR L 9 " --> pdb=" O GLN M 30 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL M 32 " --> pdb=" O THR L 9 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N HIS L 11 " --> pdb=" O VAL M 32 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU M 34 " --> pdb=" O HIS L 11 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N LYS L 13 " --> pdb=" O LEU M 34 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLN M 36 " --> pdb=" O LYS L 13 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLU L 15 " --> pdb=" O GLN M 36 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ARG M 38 " --> pdb=" O GLU L 15 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N VAL L 17 " --> pdb=" O ARG M 38 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 22 through 23 removed outlier: 5.361A pdb=" N GLY L 127 " --> pdb=" O ASP L 60 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'N' and resid 29 through 38 removed outlier: 8.791A pdb=" N GLN N 30 " --> pdb=" O GLY M 7 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR M 9 " --> pdb=" O GLN N 30 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N VAL N 32 " --> pdb=" O THR M 9 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N HIS M 11 " --> pdb=" O VAL N 32 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU N 34 " --> pdb=" O HIS M 11 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N LYS M 13 " --> pdb=" O LEU N 34 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLN N 36 " --> pdb=" O LYS M 13 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLU M 15 " --> pdb=" O GLN N 36 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ARG N 38 " --> pdb=" O GLU M 15 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N VAL M 17 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N THR M 4 " --> pdb=" O TYR N 158 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N TYR N 158 " --> pdb=" O THR M 4 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ASN M 6 " --> pdb=" O VAL N 156 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N VAL N 156 " --> pdb=" O ASN M 6 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 29 through 38 removed outlier: 8.791A pdb=" N GLN N 30 " --> pdb=" O GLY M 7 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR M 9 " --> pdb=" O GLN N 30 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N VAL N 32 " --> pdb=" O THR M 9 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N HIS M 11 " --> pdb=" O VAL N 32 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU N 34 " --> pdb=" O HIS M 11 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N LYS M 13 " --> pdb=" O LEU N 34 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLN N 36 " --> pdb=" O LYS M 13 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLU M 15 " --> pdb=" O GLN N 36 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ARG N 38 " --> pdb=" O GLU M 15 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N VAL M 17 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 22 through 23 removed outlier: 5.108A pdb=" N GLY M 127 " --> pdb=" O ASP M 60 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN M 98 " --> pdb=" O THR M 140 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'O' and resid 29 through 38 removed outlier: 8.722A pdb=" N GLN O 30 " --> pdb=" O GLY N 7 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR N 9 " --> pdb=" O GLN O 30 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N VAL O 32 " --> pdb=" O THR N 9 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N HIS N 11 " --> pdb=" O VAL O 32 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU O 34 " --> pdb=" O HIS N 11 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LYS N 13 " --> pdb=" O LEU O 34 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLN O 36 " --> pdb=" O LYS N 13 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLU N 15 " --> pdb=" O GLN O 36 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ARG O 38 " --> pdb=" O GLU N 15 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N VAL N 17 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N THR N 4 " --> pdb=" O TYR O 158 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N TYR O 158 " --> pdb=" O THR N 4 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ASN N 6 " --> pdb=" O VAL O 156 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL O 156 " --> pdb=" O ASN N 6 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'O' and resid 29 through 38 removed outlier: 8.722A pdb=" N GLN O 30 " --> pdb=" O GLY N 7 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR N 9 " --> pdb=" O GLN O 30 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N VAL O 32 " --> pdb=" O THR N 9 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N HIS N 11 " --> pdb=" O VAL O 32 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU O 34 " --> pdb=" O HIS N 11 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LYS N 13 " --> pdb=" O LEU O 34 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLN O 36 " --> pdb=" O LYS N 13 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLU N 15 " --> pdb=" O GLN O 36 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ARG O 38 " --> pdb=" O GLU N 15 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N VAL N 17 " --> pdb=" O ARG O 38 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 22 through 23 removed outlier: 3.531A pdb=" N ASP N 60 " --> pdb=" O GLY N 127 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N GLY N 127 " --> pdb=" O ASP N 60 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 77 through 79 removed outlier: 8.429A pdb=" N VAL N 85 " --> pdb=" O ILE N 78 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'O' and resid 22 through 23 removed outlier: 3.670A pdb=" N ASP O 60 " --> pdb=" O GLY O 127 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N GLY O 127 " --> pdb=" O ASP O 60 " (cutoff:3.500A) 500 hydrogen bonds defined for protein. 1278 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: 3.67 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5791 1.33 - 1.45: 2098 1.45 - 1.57: 8956 1.57 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 16875 Sorted by residual: bond pdb=" C GLN E 89 " pdb=" N SER E 90 " ideal model delta sigma weight residual 1.332 1.303 0.030 1.40e-02 5.10e+03 4.50e+00 bond pdb=" CA HIS J 82 " pdb=" CB HIS J 82 " ideal model delta sigma weight residual 1.528 1.501 0.027 1.49e-02 4.50e+03 3.21e+00 bond pdb=" CB VAL J 99 " pdb=" CG2 VAL J 99 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.20e+00 bond pdb=" CB VAL K 99 " pdb=" CG2 VAL K 99 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.93e+00 bond pdb=" CB VAL H 99 " pdb=" CG2 VAL H 99 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.85e+00 ... (remaining 16870 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 22627 1.83 - 3.66: 401 3.66 - 5.49: 18 5.49 - 7.31: 15 7.31 - 9.14: 9 Bond angle restraints: 23070 Sorted by residual: angle pdb=" N GLY N 141 " pdb=" CA GLY N 141 " pdb=" C GLY N 141 " ideal model delta sigma weight residual 113.18 104.16 9.02 2.37e+00 1.78e-01 1.45e+01 angle pdb=" CA GLN L 44 " pdb=" CB GLN L 44 " pdb=" CG GLN L 44 " ideal model delta sigma weight residual 114.10 120.63 -6.53 2.00e+00 2.50e-01 1.07e+01 angle pdb=" C THR M 140 " pdb=" N GLY M 141 " pdb=" CA GLY M 141 " ideal model delta sigma weight residual 120.51 124.12 -3.61 1.22e+00 6.72e-01 8.77e+00 angle pdb=" CA SER D 90 " pdb=" C SER D 90 " pdb=" N SER D 91 " ideal model delta sigma weight residual 119.71 116.56 3.15 1.17e+00 7.31e-01 7.25e+00 angle pdb=" N LEU N 42 " pdb=" CA LEU N 42 " pdb=" C LEU N 42 " ideal model delta sigma weight residual 110.44 107.24 3.20 1.20e+00 6.94e-01 7.13e+00 ... (remaining 23065 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 9068 17.96 - 35.92: 549 35.92 - 53.88: 149 53.88 - 71.84: 62 71.84 - 89.81: 27 Dihedral angle restraints: 9855 sinusoidal: 3165 harmonic: 6690 Sorted by residual: dihedral pdb=" CA GLN M 89 " pdb=" C GLN M 89 " pdb=" N SER M 90 " pdb=" CA SER M 90 " ideal model delta harmonic sigma weight residual 180.00 156.77 23.23 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA GLN D 89 " pdb=" C GLN D 89 " pdb=" N SER D 90 " pdb=" CA SER D 90 " ideal model delta harmonic sigma weight residual 180.00 156.90 23.10 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA GLN J 89 " pdb=" C GLN J 89 " pdb=" N SER J 90 " pdb=" CA SER J 90 " ideal model delta harmonic sigma weight residual 180.00 157.84 22.16 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 9852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1629 0.037 - 0.073: 845 0.073 - 0.110: 326 0.110 - 0.146: 66 0.146 - 0.182: 14 Chirality restraints: 2880 Sorted by residual: chirality pdb=" CB VAL H 99 " pdb=" CA VAL H 99 " pdb=" CG1 VAL H 99 " pdb=" CG2 VAL H 99 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.33e-01 chirality pdb=" CB VAL J 99 " pdb=" CA VAL J 99 " pdb=" CG1 VAL J 99 " pdb=" CG2 VAL J 99 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.89e-01 chirality pdb=" CB VAL K 99 " pdb=" CA VAL K 99 " pdb=" CG1 VAL K 99 " pdb=" CG2 VAL K 99 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.17 2.00e-01 2.50e+01 7.63e-01 ... (remaining 2877 not shown) Planarity restraints: 3105 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 89 " -0.010 2.00e-02 2.50e+03 2.00e-02 3.98e+00 pdb=" C GLN A 89 " 0.035 2.00e-02 2.50e+03 pdb=" O GLN A 89 " -0.013 2.00e-02 2.50e+03 pdb=" N SER A 90 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 144 " -0.029 5.00e-02 4.00e+02 4.37e-02 3.05e+00 pdb=" N PRO B 145 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 145 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 145 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR O 144 " -0.028 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO O 145 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO O 145 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO O 145 " -0.024 5.00e-02 4.00e+02 ... (remaining 3102 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3221 2.76 - 3.29: 17852 3.29 - 3.83: 36420 3.83 - 4.36: 44758 4.36 - 4.90: 70761 Nonbonded interactions: 173012 Sorted by model distance: nonbonded pdb=" ND1 HIS A 11 " pdb=" OD2 ASP B 151 " model vdw 2.219 3.120 nonbonded pdb=" ND1 HIS N 11 " pdb=" OD1 ASP O 151 " model vdw 2.227 3.120 nonbonded pdb=" ND1 HIS C 11 " pdb=" OD1 ASP D 151 " model vdw 2.247 3.120 nonbonded pdb=" OD2 ASP M 24 " pdb=" O HOH M 201 " model vdw 2.258 3.040 nonbonded pdb=" OD1 ASP C 24 " pdb=" ND2 ASN C 59 " model vdw 2.266 3.120 ... (remaining 173007 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: 1.200 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 18.850 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 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 : 0.007 0.059 16890 Z= 0.350 Angle : 0.676 9.142 23100 Z= 0.378 Chirality : 0.049 0.182 2880 Planarity : 0.005 0.044 3105 Dihedral : 15.245 89.805 5520 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.61 % Allowed : 10.95 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.15), residues: 2355 helix: None (None), residues: 0 sheet: 1.12 (0.16), residues: 660 loop : 0.07 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 136 TYR 0.015 0.003 TYR C 137 PHE 0.022 0.003 PHE C 118 HIS 0.010 0.002 HIS M 11 Details of bonding type rmsd covalent geometry : bond 0.00741 (16875) covalent geometry : angle 0.67623 (23070) SS BOND : bond 0.00192 ( 15) SS BOND : angle 0.65198 ( 30) hydrogen bonds : bond 0.12466 ( 500) hydrogen bonds : angle 8.61844 ( 1278) *********************** 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 193 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 0.679 Fit side-chains REVERT: A 90 SER cc_start: 0.8652 (t) cc_final: 0.8259 (p) REVERT: C 68 LYS cc_start: 0.8770 (mttt) cc_final: 0.8466 (mttp) REVERT: F 121 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8168 (mt-10) REVERT: G 44 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8177 (pm20) REVERT: J 45 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7579 (tp30) REVERT: L 44 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8470 (pm20) REVERT: M 68 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8421 (mmtt) REVERT: O 44 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8530 (pm20) REVERT: O 45 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7754 (tp30) outliers start: 27 outliers final: 18 residues processed: 184 average time/residue: 0.6215 time to fit residues: 129.3167 Evaluate side-chains 188 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain G residue 44 GLN 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 K residue 3 THR Chi-restraints excluded: chain K residue 41 SER Chi-restraints excluded: chain L residue 44 GLN Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain M residue 68 LYS Chi-restraints excluded: chain M residue 153 THR Chi-restraints excluded: chain N residue 3 THR Chi-restraints excluded: chain N residue 41 SER Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 44 GLN Chi-restraints excluded: chain O residue 45 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 9.9990 chunk 212 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN E 89 GLN E 125 ASN H 134 GLN I 64 ASN I 125 ASN J 30 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.104300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.091102 restraints weight = 19914.372| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.13 r_work: 0.3005 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 16890 Z= 0.101 Angle : 0.430 4.407 23100 Z= 0.249 Chirality : 0.041 0.145 2880 Planarity : 0.003 0.032 3105 Dihedral : 6.281 79.158 2497 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.61 % Allowed : 11.01 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.15), residues: 2355 helix: None (None), residues: 0 sheet: 1.56 (0.17), residues: 660 loop : 0.10 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 106 TYR 0.008 0.001 TYR D 137 PHE 0.013 0.002 PHE J 54 HIS 0.003 0.001 HIS A 11 Details of bonding type rmsd covalent geometry : bond 0.00197 (16875) covalent geometry : angle 0.43018 (23070) SS BOND : bond 0.00093 ( 15) SS BOND : angle 0.43658 ( 30) hydrogen bonds : bond 0.03617 ( 500) hydrogen bonds : angle 6.42794 ( 1278) *********************** 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 215 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 0.739 Fit side-chains REVERT: A 90 SER cc_start: 0.8078 (t) cc_final: 0.7777 (p) REVERT: C 68 LYS cc_start: 0.8678 (mttt) cc_final: 0.8448 (mttm) REVERT: F 62 ASP cc_start: 0.8952 (t0) cc_final: 0.8692 (t70) REVERT: F 121 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8200 (mt-10) REVERT: G 44 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.8140 (pm20) REVERT: I 104 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8808 (mt) REVERT: L 44 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8462 (pm20) REVERT: L 121 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7988 (mm-30) REVERT: N 41 SER cc_start: 0.8705 (t) cc_final: 0.8502 (t) REVERT: O 44 GLN cc_start: 0.8610 (pm20) cc_final: 0.8378 (pm20) REVERT: O 45 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7513 (tp30) outliers start: 27 outliers final: 10 residues processed: 205 average time/residue: 0.5888 time to fit residues: 137.3615 Evaluate side-chains 188 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 174 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain G residue 44 GLN Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain L residue 44 GLN Chi-restraints excluded: chain M residue 153 THR Chi-restraints excluded: chain N residue 3 THR Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 45 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 187 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 220 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 172 optimal weight: 20.0000 chunk 6 optimal weight: 0.0000 chunk 66 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 209 optimal weight: 8.9990 overall best weight: 3.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN E 125 ASN I 64 ASN J 64 ASN O 64 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.099924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.086427 restraints weight = 20186.455| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.14 r_work: 0.2930 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.0683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16890 Z= 0.218 Angle : 0.541 7.328 23100 Z= 0.304 Chirality : 0.044 0.141 2880 Planarity : 0.003 0.031 3105 Dihedral : 6.519 76.730 2476 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.96 % Allowed : 10.42 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.15), residues: 2355 helix: None (None), residues: 0 sheet: 1.41 (0.17), residues: 660 loop : 0.11 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 136 TYR 0.009 0.002 TYR L 137 PHE 0.015 0.002 PHE J 54 HIS 0.005 0.001 HIS M 11 Details of bonding type rmsd covalent geometry : bond 0.00450 (16875) covalent geometry : angle 0.54146 (23070) SS BOND : bond 0.00102 ( 15) SS BOND : angle 0.50996 ( 30) hydrogen bonds : bond 0.04429 ( 500) hydrogen bonds : angle 6.86242 ( 1278) *********************** 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 205 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 172 time to evaluate : 0.720 Fit side-chains REVERT: A 90 SER cc_start: 0.8523 (t) cc_final: 0.8126 (p) REVERT: C 68 LYS cc_start: 0.8754 (mttt) cc_final: 0.8500 (mttp) REVERT: F 62 ASP cc_start: 0.8988 (t0) cc_final: 0.8732 (t70) REVERT: F 121 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8203 (mt-10) REVERT: G 44 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.8070 (pm20) REVERT: G 45 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.7480 (tp30) REVERT: H 68 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8782 (mttm) REVERT: J 44 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.7664 (pm20) REVERT: J 45 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.7575 (tp30) REVERT: K 121 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7818 (mt-10) REVERT: L 121 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7986 (mm-30) REVERT: O 44 GLN cc_start: 0.8674 (pm20) cc_final: 0.8422 (pm20) REVERT: O 45 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7582 (tp30) outliers start: 33 outliers final: 15 residues processed: 191 average time/residue: 0.6083 time to fit residues: 131.7008 Evaluate side-chains 185 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain G residue 44 GLN Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain J residue 44 GLN Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 41 SER Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 121 GLU Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain M residue 153 THR Chi-restraints excluded: chain N residue 3 THR Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 45 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 167 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 82 optimal weight: 9.9990 chunk 86 optimal weight: 0.7980 chunk 172 optimal weight: 20.0000 chunk 193 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN E 125 ASN I 64 ASN J 64 ASN L 44 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.101326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.087878 restraints weight = 20022.014| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.13 r_work: 0.2954 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.0859 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= 0.159 Angle : 0.486 6.033 23100 Z= 0.275 Chirality : 0.042 0.141 2880 Planarity : 0.003 0.029 3105 Dihedral : 6.198 74.333 2473 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.73 % Allowed : 10.95 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.15), residues: 2355 helix: None (None), residues: 0 sheet: 1.44 (0.17), residues: 660 loop : 0.11 (0.13), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 136 TYR 0.008 0.001 TYR L 137 PHE 0.014 0.002 PHE J 54 HIS 0.003 0.001 HIS M 11 Details of bonding type rmsd covalent geometry : bond 0.00325 (16875) covalent geometry : angle 0.48630 (23070) SS BOND : bond 0.00074 ( 15) SS BOND : angle 0.41923 ( 30) hydrogen bonds : bond 0.03943 ( 500) hydrogen bonds : angle 6.56764 ( 1278) *********************** 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 200 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.688 Fit side-chains REVERT: A 90 SER cc_start: 0.8375 (t) cc_final: 0.8009 (p) REVERT: C 68 LYS cc_start: 0.8758 (mttt) cc_final: 0.8518 (mttp) REVERT: F 62 ASP cc_start: 0.8989 (t0) cc_final: 0.8723 (t70) REVERT: F 121 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8197 (mt-10) REVERT: G 44 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8062 (pm20) REVERT: H 68 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8784 (mttm) REVERT: J 44 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.7572 (pm20) REVERT: J 45 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7541 (tp30) REVERT: K 121 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7803 (mt-10) REVERT: L 121 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7987 (mm-30) REVERT: O 44 GLN cc_start: 0.8653 (pm20) cc_final: 0.8403 (pm20) REVERT: O 45 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7529 (tp30) outliers start: 29 outliers final: 13 residues processed: 186 average time/residue: 0.5981 time to fit residues: 125.7272 Evaluate side-chains 187 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain G residue 44 GLN Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain J residue 44 GLN Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 121 GLU Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain M residue 153 THR Chi-restraints excluded: chain N residue 3 THR Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 45 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 1 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 164 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 64 optimal weight: 20.0000 chunk 148 optimal weight: 10.0000 chunk 178 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 212 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 111 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN E 125 ASN I 64 ASN J 64 ASN O 64 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.099505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.085933 restraints weight = 19949.258| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.13 r_work: 0.2922 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.0661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16890 Z= 0.243 Angle : 0.564 7.833 23100 Z= 0.315 Chirality : 0.044 0.143 2880 Planarity : 0.003 0.031 3105 Dihedral : 6.575 71.186 2473 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.85 % Allowed : 10.48 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.15), residues: 2355 helix: None (None), residues: 0 sheet: 1.33 (0.16), residues: 660 loop : 0.10 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 106 TYR 0.011 0.002 TYR L 137 PHE 0.016 0.002 PHE C 118 HIS 0.005 0.001 HIS M 11 Details of bonding type rmsd covalent geometry : bond 0.00508 (16875) covalent geometry : angle 0.56371 (23070) SS BOND : bond 0.00115 ( 15) SS BOND : angle 0.59708 ( 30) hydrogen bonds : bond 0.04501 ( 500) hydrogen bonds : angle 6.90941 ( 1278) *********************** 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 198 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 0.725 Fit side-chains REVERT: A 90 SER cc_start: 0.8575 (t) cc_final: 0.8169 (p) REVERT: C 68 LYS cc_start: 0.8752 (mttt) cc_final: 0.8507 (mttp) REVERT: F 121 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8201 (mt-10) REVERT: G 44 GLN cc_start: 0.8413 (pm20) cc_final: 0.8071 (pm20) REVERT: H 68 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8781 (mttm) REVERT: J 44 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.7663 (pm20) REVERT: J 45 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7540 (tp30) REVERT: K 121 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7813 (mt-10) REVERT: L 121 GLU cc_start: 0.8223 (mt-10) cc_final: 0.8005 (mm-30) REVERT: M 68 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8488 (mmtt) REVERT: O 44 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8386 (pm20) REVERT: O 45 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7616 (tp30) outliers start: 31 outliers final: 17 residues processed: 185 average time/residue: 0.5869 time to fit residues: 122.6518 Evaluate side-chains 185 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 44 GLN Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 121 GLU Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain M residue 68 LYS Chi-restraints excluded: chain M residue 153 THR Chi-restraints excluded: chain N residue 3 THR Chi-restraints excluded: chain N residue 41 SER Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 44 GLN Chi-restraints excluded: chain O residue 45 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 147 optimal weight: 1.9990 chunk 160 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 218 optimal weight: 0.8980 chunk 64 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 116 optimal weight: 3.9990 chunk 27 optimal weight: 0.2980 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN E 125 ASN I 64 ASN J 64 ASN O 64 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.100927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.087464 restraints weight = 19898.584| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.13 r_work: 0.2946 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 16890 Z= 0.171 Angle : 0.499 6.194 23100 Z= 0.282 Chirality : 0.042 0.141 2880 Planarity : 0.003 0.030 3105 Dihedral : 6.030 58.345 2470 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.02 % Allowed : 10.42 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.15), residues: 2355 helix: None (None), residues: 0 sheet: 1.39 (0.17), residues: 660 loop : 0.10 (0.13), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 136 TYR 0.009 0.001 TYR L 137 PHE 0.014 0.002 PHE B 54 HIS 0.004 0.001 HIS M 11 Details of bonding type rmsd covalent geometry : bond 0.00350 (16875) covalent geometry : angle 0.49867 (23070) SS BOND : bond 0.00072 ( 15) SS BOND : angle 0.46041 ( 30) hydrogen bonds : bond 0.04003 ( 500) hydrogen bonds : angle 6.62683 ( 1278) *********************** 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 200 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 166 time to evaluate : 0.644 Fit side-chains REVERT: A 90 SER cc_start: 0.8407 (t) cc_final: 0.8034 (p) REVERT: C 68 LYS cc_start: 0.8737 (mttt) cc_final: 0.8497 (mttp) REVERT: F 62 ASP cc_start: 0.8974 (t0) cc_final: 0.8729 (t70) REVERT: F 121 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8220 (mt-10) REVERT: G 44 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8042 (pm20) REVERT: H 68 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8768 (mttm) REVERT: I 104 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.8873 (mt) REVERT: J 44 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.7580 (pm20) REVERT: J 45 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.7520 (tp30) REVERT: K 121 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7805 (mt-10) REVERT: L 121 GLU cc_start: 0.8236 (mt-10) cc_final: 0.8021 (mm-30) REVERT: M 68 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8488 (mmtt) REVERT: O 44 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8350 (pm20) REVERT: O 45 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7512 (tp30) outliers start: 34 outliers final: 17 residues processed: 186 average time/residue: 0.5801 time to fit residues: 121.7054 Evaluate side-chains 189 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain G residue 44 GLN Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain J residue 44 GLN Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 121 GLU Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain M residue 68 LYS Chi-restraints excluded: chain M residue 153 THR Chi-restraints excluded: chain N residue 3 THR Chi-restraints excluded: chain N residue 41 SER Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 44 GLN Chi-restraints excluded: chain O residue 45 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 80 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 222 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 112 optimal weight: 20.0000 chunk 130 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 160 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN E 125 ASN I 64 ASN J 64 ASN O 64 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.097961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.084367 restraints weight = 20213.253| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.13 r_work: 0.2896 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.0545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 16890 Z= 0.382 Angle : 0.681 9.456 23100 Z= 0.379 Chirality : 0.050 0.206 2880 Planarity : 0.004 0.037 3105 Dihedral : 6.788 59.972 2470 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.67 % Allowed : 10.77 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.15), residues: 2355 helix: None (None), residues: 0 sheet: 1.14 (0.16), residues: 660 loop : 0.04 (0.13), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 106 TYR 0.015 0.003 TYR L 137 PHE 0.023 0.003 PHE C 118 HIS 0.009 0.002 HIS M 11 Details of bonding type rmsd covalent geometry : bond 0.00809 (16875) covalent geometry : angle 0.68088 (23070) SS BOND : bond 0.00229 ( 15) SS BOND : angle 0.81335 ( 30) hydrogen bonds : bond 0.05171 ( 500) hydrogen bonds : angle 7.31624 ( 1278) *********************** 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 195 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 0.758 Fit side-chains REVERT: A 90 SER cc_start: 0.8669 (t) cc_final: 0.8263 (p) REVERT: C 68 LYS cc_start: 0.8769 (mttt) cc_final: 0.8514 (mttp) REVERT: F 62 ASP cc_start: 0.9006 (t0) cc_final: 0.8771 (t70) REVERT: F 121 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8201 (mt-10) REVERT: G 44 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8139 (pm20) REVERT: H 68 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8779 (mttm) REVERT: J 45 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.7555 (tp30) REVERT: K 121 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7828 (mt-10) REVERT: M 68 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8467 (mmtt) REVERT: O 44 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8432 (pm20) REVERT: O 45 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7724 (tp30) outliers start: 28 outliers final: 19 residues processed: 184 average time/residue: 0.6144 time to fit residues: 127.5412 Evaluate side-chains 189 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain G residue 44 GLN Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 41 SER Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain K residue 121 GLU Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain M residue 68 LYS Chi-restraints excluded: chain M residue 153 THR Chi-restraints excluded: chain N residue 3 THR Chi-restraints excluded: chain N residue 41 SER Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 44 GLN Chi-restraints excluded: chain O residue 45 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 142 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 160 optimal weight: 7.9990 chunk 150 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 143 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN E 64 ASN E 125 ASN I 64 ASN J 64 ASN K 89 GLN N 134 GLN O 64 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.100024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.086544 restraints weight = 19988.959| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.13 r_work: 0.2932 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.0743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16890 Z= 0.202 Angle : 0.535 6.750 23100 Z= 0.302 Chirality : 0.044 0.145 2880 Planarity : 0.003 0.033 3105 Dihedral : 6.328 59.307 2470 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.61 % Allowed : 10.95 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.15), residues: 2355 helix: None (None), residues: 0 sheet: 1.28 (0.16), residues: 660 loop : 0.05 (0.13), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 106 TYR 0.011 0.002 TYR L 137 PHE 0.016 0.002 PHE B 54 HIS 0.005 0.001 HIS M 11 Details of bonding type rmsd covalent geometry : bond 0.00419 (16875) covalent geometry : angle 0.53499 (23070) SS BOND : bond 0.00092 ( 15) SS BOND : angle 0.53095 ( 30) hydrogen bonds : bond 0.04297 ( 500) hydrogen bonds : angle 6.84032 ( 1278) *********************** 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 195 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.548 Fit side-chains REVERT: A 90 SER cc_start: 0.8490 (t) cc_final: 0.8095 (p) REVERT: C 68 LYS cc_start: 0.8743 (mttt) cc_final: 0.8509 (mttp) REVERT: F 62 ASP cc_start: 0.8991 (t0) cc_final: 0.8752 (t70) REVERT: F 121 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8193 (mt-10) REVERT: G 44 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8149 (pm20) REVERT: H 68 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8783 (mttm) REVERT: J 45 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.7553 (tp30) REVERT: K 121 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7787 (mt-10) REVERT: L 121 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7988 (mm-30) REVERT: M 68 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8485 (mmtt) REVERT: O 44 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8396 (pm20) REVERT: O 45 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7570 (tp30) outliers start: 27 outliers final: 17 residues processed: 182 average time/residue: 0.6150 time to fit residues: 126.1345 Evaluate side-chains 187 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain G residue 44 GLN Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 121 GLU Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain M residue 68 LYS Chi-restraints excluded: chain M residue 153 THR Chi-restraints excluded: chain N residue 3 THR Chi-restraints excluded: chain N residue 41 SER Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 44 GLN Chi-restraints excluded: chain O residue 45 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 11 optimal weight: 4.9990 chunk 137 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 216 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 223 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN E 64 ASN E 125 ASN I 64 ASN J 64 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.100849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.087416 restraints weight = 19906.982| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.13 r_work: 0.2945 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16890 Z= 0.170 Angle : 0.502 6.264 23100 Z= 0.284 Chirality : 0.042 0.142 2880 Planarity : 0.003 0.031 3105 Dihedral : 6.057 57.863 2470 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.49 % Allowed : 11.19 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.15), residues: 2355 helix: None (None), residues: 0 sheet: 1.36 (0.16), residues: 660 loop : 0.10 (0.13), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 136 TYR 0.009 0.002 TYR L 137 PHE 0.014 0.002 PHE J 54 HIS 0.004 0.001 HIS M 11 Details of bonding type rmsd covalent geometry : bond 0.00350 (16875) covalent geometry : angle 0.50182 (23070) SS BOND : bond 0.00076 ( 15) SS BOND : angle 0.50259 ( 30) hydrogen bonds : bond 0.04009 ( 500) hydrogen bonds : angle 6.63311 ( 1278) *********************** 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 192 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 0.726 Fit side-chains REVERT: A 90 SER cc_start: 0.8390 (t) cc_final: 0.8022 (p) REVERT: C 68 LYS cc_start: 0.8744 (mttt) cc_final: 0.8518 (mttp) REVERT: F 62 ASP cc_start: 0.8988 (t0) cc_final: 0.8744 (t70) REVERT: F 121 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8214 (mt-10) REVERT: G 44 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.8119 (pm20) REVERT: H 68 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8778 (mttm) REVERT: J 45 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7510 (tp30) REVERT: K 121 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7792 (mt-10) REVERT: L 121 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7992 (mm-30) REVERT: M 68 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8491 (mmtt) REVERT: O 44 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8345 (pm20) REVERT: O 45 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7550 (tp30) outliers start: 25 outliers final: 17 residues processed: 180 average time/residue: 0.5882 time to fit residues: 119.4293 Evaluate side-chains 186 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain G residue 44 GLN Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 121 GLU Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain M residue 68 LYS Chi-restraints excluded: chain M residue 153 THR Chi-restraints excluded: chain N residue 3 THR Chi-restraints excluded: chain N residue 41 SER Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 44 GLN Chi-restraints excluded: chain O residue 45 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 106 optimal weight: 10.0000 chunk 135 optimal weight: 20.0000 chunk 204 optimal weight: 8.9990 chunk 214 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 213 optimal weight: 0.6980 chunk 50 optimal weight: 20.0000 chunk 63 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN E 64 ASN E 125 ASN I 64 ASN J 64 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.100000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.086495 restraints weight = 20046.693| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.13 r_work: 0.2930 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.0772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16890 Z= 0.209 Angle : 0.543 7.201 23100 Z= 0.305 Chirality : 0.044 0.144 2880 Planarity : 0.003 0.031 3105 Dihedral : 6.236 56.737 2470 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.67 % Allowed : 11.25 % Favored : 87.08 % 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 aren not related in a simple way. whole: 0.63 (0.15), residues: 2355 helix: None (None), residues: 0 sheet: 1.31 (0.16), residues: 660 loop : 0.09 (0.13), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 136 TYR 0.011 0.002 TYR L 137 PHE 0.015 0.002 PHE B 54 HIS 0.004 0.001 HIS M 11 Details of bonding type rmsd covalent geometry : bond 0.00432 (16875) covalent geometry : angle 0.54307 (23070) SS BOND : bond 0.00098 ( 15) SS BOND : angle 0.57063 ( 30) hydrogen bonds : bond 0.04298 ( 500) hydrogen bonds : angle 6.79829 ( 1278) ********************** 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 191 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.692 Fit side-chains REVERT: A 90 SER cc_start: 0.8493 (t) cc_final: 0.8097 (p) REVERT: C 68 LYS cc_start: 0.8750 (mttt) cc_final: 0.8529 (mttp) REVERT: F 62 ASP cc_start: 0.8989 (t0) cc_final: 0.8748 (t70) REVERT: F 121 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8206 (mt-10) REVERT: G 44 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.8050 (pm20) REVERT: H 68 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8779 (mttm) REVERT: J 45 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7530 (tp30) REVERT: K 121 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7812 (mt-10) REVERT: L 121 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7999 (mm-30) REVERT: M 68 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8493 (mmtt) REVERT: O 44 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8372 (pm20) REVERT: O 45 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7596 (tp30) outliers start: 28 outliers final: 18 residues processed: 177 average time/residue: 0.5873 time to fit residues: 117.2211 Evaluate side-chains 186 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain D residue 3 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain G residue 44 GLN Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 68 LYS Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 121 GLU Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain M residue 68 LYS Chi-restraints excluded: chain M residue 153 THR Chi-restraints excluded: chain N residue 3 THR Chi-restraints excluded: chain N residue 41 SER Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain O residue 44 GLN Chi-restraints excluded: chain O residue 45 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 195 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 187 optimal weight: 20.0000 chunk 98 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 214 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN E 64 ASN E 125 ASN I 64 ASN J 64 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.101520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.088053 restraints weight = 19996.604| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.14 r_work: 0.2955 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16890 Z= 0.152 Angle : 0.486 6.069 23100 Z= 0.276 Chirality : 0.042 0.141 2880 Planarity : 0.003 0.031 3105 Dihedral : 5.879 55.050 2470 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.49 % Allowed : 11.55 % Favored : 86.96 % 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 aren not related in a simple way. whole: 0.70 (0.15), residues: 2355 helix: None (None), residues: 0 sheet: 1.41 (0.17), residues: 660 loop : 0.12 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG O 38 TYR 0.008 0.001 TYR L 137 PHE 0.014 0.002 PHE J 54 HIS 0.003 0.001 HIS N 11 Details of bonding type rmsd covalent geometry : bond 0.00310 (16875) covalent geometry : angle 0.48615 (23070) SS BOND : bond 0.00076 ( 15) SS BOND : angle 0.47308 ( 30) hydrogen bonds : bond 0.03850 ( 500) hydrogen bonds : angle 6.50980 ( 1278) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5690.09 seconds wall clock time: 98 minutes 0.14 seconds (5880.14 seconds total)