Starting phenix.real_space_refine on Sun Jul 5 20:14:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xvc_67286/07_2026/9xvc_67286.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xvc_67286/07_2026/9xvc_67286.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xvc_67286/07_2026/9xvc_67286.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xvc_67286/07_2026/9xvc_67286.map" model { file = "/net/cci-nas-00/data/ceres_data/9xvc_67286/07_2026/9xvc_67286.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xvc_67286/07_2026/9xvc_67286.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.042 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: 5 Type Number sf(0) Gaussians P 32 5.49 5 S 88 5.16 5 C 18872 2.51 5 N 4816 2.21 5 O 5592 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29400 Number of models: 1 Model: "" Number of chains: 32 Chain: "C" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1459 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "D" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1459 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "H" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2163 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain: "G" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2163 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain: "F" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2163 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain: "E" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2163 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain: "A" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1459 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "B" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1459 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "K" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1459 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "L" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1459 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "P" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2163 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain: "O" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2163 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain: "N" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2163 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain: "M" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2163 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 10, 'TRANS': 253} Chain: "I" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1459 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "J" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1459 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'Y43': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'Y43': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Chain: "G" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Chain: "F" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'Y43': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'Y43': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'Y43': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'Y43': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Chain: "O" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Chain: "N" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna3p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna3p': 1} Chain: "M" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna3p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna3p': 1} Chain: "I" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'Y43': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'Y43': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.44, per 1000 atoms: 0.22 Number of scatterers: 29400 At special positions: 0 Unit cell: (156.88, 168.54, 126.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 88 16.00 P 32 15.00 O 5592 8.00 N 4816 7.00 C 18872 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.30 Conformation dependent library (CDL) restraints added in 995.8 milliseconds 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6672 Finding SS restraints... Secondary structure from input PDB file: 182 helices and 20 sheets defined 50.7% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'C' and resid 9 through 20 removed outlier: 3.814A pdb=" N ILE C 13 " --> pdb=" O ASN C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 58 removed outlier: 3.503A pdb=" N LEU C 45 " --> pdb=" O ASN C 41 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU C 56 " --> pdb=" O LYS C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 74 No H-bonds generated for 'chain 'C' and resid 72 through 74' Processing helix chain 'C' and resid 80 through 89 removed outlier: 3.771A pdb=" N PHE C 84 " --> pdb=" O LEU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 140 through 144 removed outlier: 4.053A pdb=" N CYS C 144 " --> pdb=" O GLN C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 161 through 166 removed outlier: 3.751A pdb=" N ILE C 165 " --> pdb=" O ARG C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 180 removed outlier: 3.515A pdb=" N LYS C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYS C 174 " --> pdb=" O LYS C 170 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE C 175 " --> pdb=" O ALA C 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 20 Processing helix chain 'D' and resid 41 through 57 Processing helix chain 'D' and resid 72 through 74 No H-bonds generated for 'chain 'D' and resid 72 through 74' Processing helix chain 'D' and resid 80 through 89 Processing helix chain 'D' and resid 90 through 93 Processing helix chain 'D' and resid 158 through 165 removed outlier: 3.796A pdb=" N ARG D 161 " --> pdb=" O MET D 158 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN D 163 " --> pdb=" O ASP D 160 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU D 164 " --> pdb=" O ARG D 161 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE D 165 " --> pdb=" O LYS D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 181 Processing helix chain 'H' and resid 2 through 9 removed outlier: 3.696A pdb=" N LYS H 9 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 24 removed outlier: 3.824A pdb=" N ASN H 24 " --> pdb=" O GLY H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 42 Processing helix chain 'H' and resid 55 through 63 removed outlier: 3.714A pdb=" N TYR H 61 " --> pdb=" O LEU H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 80 removed outlier: 3.566A pdb=" N HIS H 80 " --> pdb=" O ASP H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 98 Processing helix chain 'H' and resid 110 through 119 Processing helix chain 'H' and resid 129 through 135 Processing helix chain 'H' and resid 158 through 164 Processing helix chain 'H' and resid 170 through 180 Processing helix chain 'H' and resid 194 through 211 removed outlier: 3.941A pdb=" N GLN H 211 " --> pdb=" O LEU H 207 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 217 removed outlier: 3.862A pdb=" N GLN H 217 " --> pdb=" O GLU H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 229 through 238 removed outlier: 4.343A pdb=" N GLU H 233 " --> pdb=" O PRO H 229 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE H 234 " --> pdb=" O ILE H 230 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LEU H 235 " --> pdb=" O GLN H 231 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N TRP H 238 " --> pdb=" O ILE H 234 " (cutoff:3.500A) Processing helix chain 'H' and resid 249 through 263 removed outlier: 4.374A pdb=" N ASN H 260 " --> pdb=" O GLU H 256 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE H 261 " --> pdb=" O PHE H 257 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU H 263 " --> pdb=" O LYS H 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 11 removed outlier: 4.372A pdb=" N ALA G 6 " --> pdb=" O GLU G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 24 removed outlier: 3.505A pdb=" N ASN G 24 " --> pdb=" O VAL G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 42 Processing helix chain 'G' and resid 44 through 49 Processing helix chain 'G' and resid 53 through 65 removed outlier: 3.682A pdb=" N TYR G 61 " --> pdb=" O LEU G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 79 removed outlier: 3.523A pdb=" N TRP G 74 " --> pdb=" O PRO G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 98 Processing helix chain 'G' and resid 110 through 119 Processing helix chain 'G' and resid 128 through 135 removed outlier: 4.072A pdb=" N ALA G 133 " --> pdb=" O SER G 130 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE G 135 " --> pdb=" O ILE G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 167 removed outlier: 3.640A pdb=" N TYR G 162 " --> pdb=" O ASP G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 180 Processing helix chain 'G' and resid 194 through 211 removed outlier: 3.605A pdb=" N ARG G 198 " --> pdb=" O ASP G 194 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN G 211 " --> pdb=" O LEU G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 217 removed outlier: 3.548A pdb=" N GLN G 217 " --> pdb=" O GLU G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 238 removed outlier: 3.639A pdb=" N GLU G 233 " --> pdb=" O PRO G 229 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TRP G 238 " --> pdb=" O ILE G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 259 Processing helix chain 'F' and resid 2 through 10 removed outlier: 4.329A pdb=" N ALA F 6 " --> pdb=" O GLU F 2 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS F 10 " --> pdb=" O ALA F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 42 Processing helix chain 'F' and resid 44 through 50 removed outlier: 3.786A pdb=" N THR F 50 " --> pdb=" O ASP F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 66 removed outlier: 3.868A pdb=" N TYR F 61 " --> pdb=" O LEU F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 80 removed outlier: 3.562A pdb=" N TRP F 74 " --> pdb=" O PRO F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 88 removed outlier: 3.572A pdb=" N LYS F 88 " --> pdb=" O ASP F 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 85 through 88' Processing helix chain 'F' and resid 89 through 97 Processing helix chain 'F' and resid 110 through 120 Processing helix chain 'F' and resid 128 through 133 Processing helix chain 'F' and resid 158 through 166 removed outlier: 3.527A pdb=" N GLN F 164 " --> pdb=" O THR F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 180 Processing helix chain 'F' and resid 196 through 211 removed outlier: 3.656A pdb=" N TYR F 202 " --> pdb=" O ARG F 198 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN F 211 " --> pdb=" O LEU F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 217 Processing helix chain 'F' and resid 228 through 236 Processing helix chain 'F' and resid 249 through 260 removed outlier: 3.577A pdb=" N SER F 253 " --> pdb=" O ASN F 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 11 Processing helix chain 'E' and resid 29 through 42 removed outlier: 3.874A pdb=" N ASP E 35 " --> pdb=" O SER E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 49 removed outlier: 3.748A pdb=" N ARG E 49 " --> pdb=" O PRO E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 52 No H-bonds generated for 'chain 'E' and resid 50 through 52' Processing helix chain 'E' and resid 55 through 64 removed outlier: 3.935A pdb=" N TYR E 61 " --> pdb=" O LEU E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 79 Processing helix chain 'E' and resid 85 through 88 removed outlier: 3.590A pdb=" N LYS E 88 " --> pdb=" O ASP E 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 85 through 88' Processing helix chain 'E' and resid 89 through 98 Processing helix chain 'E' and resid 112 through 119 removed outlier: 3.565A pdb=" N TYR E 119 " --> pdb=" O ALA E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 135 Processing helix chain 'E' and resid 158 through 163 Processing helix chain 'E' and resid 170 through 180 removed outlier: 3.622A pdb=" N LYS E 175 " --> pdb=" O PRO E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 211 removed outlier: 3.968A pdb=" N ARG E 198 " --> pdb=" O ASP E 194 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLN E 211 " --> pdb=" O LEU E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 217 removed outlier: 3.567A pdb=" N GLN E 217 " --> pdb=" O GLU E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 238 removed outlier: 3.909A pdb=" N GLU E 233 " --> pdb=" O PRO E 229 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TRP E 238 " --> pdb=" O ILE E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 263 removed outlier: 3.530A pdb=" N SER E 253 " --> pdb=" O ASN E 249 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS E 259 " --> pdb=" O GLU E 255 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ASN E 260 " --> pdb=" O GLU E 256 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N PHE E 261 " --> pdb=" O PHE E 257 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU E 263 " --> pdb=" O LYS E 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 20 Processing helix chain 'A' and resid 41 through 58 removed outlier: 4.184A pdb=" N LEU A 56 " --> pdb=" O LYS A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 96 removed outlier: 8.155A pdb=" N ALA A 90 " --> pdb=" O ASP A 86 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N ASP A 91 " --> pdb=" O LYS A 87 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN A 95 " --> pdb=" O ASP A 91 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU A 96 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 144 removed outlier: 3.886A pdb=" N CYS A 144 " --> pdb=" O GLN A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 159 removed outlier: 4.045A pdb=" N GLY A 159 " --> pdb=" O PHE A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 165 removed outlier: 3.772A pdb=" N GLU A 164 " --> pdb=" O ARG A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 182 Processing helix chain 'B' and resid 9 through 20 Processing helix chain 'B' and resid 41 through 55 removed outlier: 3.760A pdb=" N LEU B 45 " --> pdb=" O ASN B 41 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS B 47 " --> pdb=" O HIS B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 89 Processing helix chain 'B' and resid 89 through 97 removed outlier: 3.839A pdb=" N PHE B 93 " --> pdb=" O GLN B 89 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N SER B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N GLN B 95 " --> pdb=" O ASP B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 144 removed outlier: 4.279A pdb=" N CYS B 144 " --> pdb=" O GLN B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 165 removed outlier: 3.828A pdb=" N ASN B 163 " --> pdb=" O ASP B 160 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU B 164 " --> pdb=" O ARG B 161 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE B 165 " --> pdb=" O LYS B 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 160 through 165' Processing helix chain 'B' and resid 166 through 182 Processing helix chain 'K' and resid 9 through 20 Processing helix chain 'K' and resid 41 through 58 removed outlier: 3.921A pdb=" N LEU K 56 " --> pdb=" O LYS K 52 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL K 57 " --> pdb=" O ALA K 53 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY K 58 " --> pdb=" O PHE K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 74 No H-bonds generated for 'chain 'K' and resid 72 through 74' Processing helix chain 'K' and resid 80 through 89 removed outlier: 3.902A pdb=" N PHE K 84 " --> pdb=" O LEU K 80 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN K 89 " --> pdb=" O TRP K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 97 removed outlier: 3.631A pdb=" N LEU K 96 " --> pdb=" O LYS K 92 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 144 removed outlier: 3.631A pdb=" N ASP K 143 " --> pdb=" O PHE K 140 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N CYS K 144 " --> pdb=" O GLN K 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 140 through 144' Processing helix chain 'K' and resid 154 through 160 removed outlier: 3.821A pdb=" N GLY K 159 " --> pdb=" O ALA K 156 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASP K 160 " --> pdb=" O GLU K 157 " (cutoff:3.500A) Processing helix chain 'K' and resid 161 through 166 removed outlier: 4.148A pdb=" N ILE K 165 " --> pdb=" O ARG K 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 180 removed outlier: 4.433A pdb=" N LYS K 174 " --> pdb=" O LYS K 170 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE K 175 " --> pdb=" O ALA K 171 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 20 Processing helix chain 'L' and resid 41 through 55 Processing helix chain 'L' and resid 72 through 74 No H-bonds generated for 'chain 'L' and resid 72 through 74' Processing helix chain 'L' and resid 80 through 89 Processing helix chain 'L' and resid 90 through 93 Processing helix chain 'L' and resid 140 through 144 removed outlier: 4.394A pdb=" N CYS L 144 " --> pdb=" O GLN L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 158 through 165 removed outlier: 3.775A pdb=" N ARG L 161 " --> pdb=" O MET L 158 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASN L 163 " --> pdb=" O ASP L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 166 through 181 removed outlier: 3.566A pdb=" N LYS L 170 " --> pdb=" O SER L 166 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 11 removed outlier: 3.625A pdb=" N LYS P 10 " --> pdb=" O ALA P 6 " (cutoff:3.500A) Processing helix chain 'P' and resid 18 through 24 removed outlier: 3.992A pdb=" N SER P 22 " --> pdb=" O GLY P 18 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN P 24 " --> pdb=" O GLY P 20 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 42 Processing helix chain 'P' and resid 44 through 50 removed outlier: 3.689A pdb=" N ARG P 49 " --> pdb=" O PRO P 45 " (cutoff:3.500A) Processing helix chain 'P' and resid 55 through 63 removed outlier: 3.694A pdb=" N TYR P 61 " --> pdb=" O LEU P 57 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 79 Processing helix chain 'P' and resid 89 through 98 Processing helix chain 'P' and resid 110 through 119 Processing helix chain 'P' and resid 131 through 135 Processing helix chain 'P' and resid 158 through 166 removed outlier: 3.566A pdb=" N TYR P 162 " --> pdb=" O ASP P 158 " (cutoff:3.500A) Processing helix chain 'P' and resid 170 through 180 removed outlier: 3.514A pdb=" N SER P 178 " --> pdb=" O ILE P 174 " (cutoff:3.500A) Processing helix chain 'P' and resid 194 through 211 removed outlier: 3.564A pdb=" N TYR P 202 " --> pdb=" O ARG P 198 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN P 211 " --> pdb=" O LEU P 207 " (cutoff:3.500A) Processing helix chain 'P' and resid 213 through 217 removed outlier: 3.749A pdb=" N GLN P 217 " --> pdb=" O GLU P 214 " (cutoff:3.500A) Processing helix chain 'P' and resid 229 through 237 removed outlier: 4.370A pdb=" N GLU P 233 " --> pdb=" O PRO P 229 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ILE P 234 " --> pdb=" O ILE P 230 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU P 235 " --> pdb=" O GLN P 231 " (cutoff:3.500A) Processing helix chain 'P' and resid 249 through 263 removed outlier: 4.240A pdb=" N ASN P 260 " --> pdb=" O GLU P 256 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N PHE P 261 " --> pdb=" O PHE P 257 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU P 263 " --> pdb=" O LYS P 259 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 11 removed outlier: 4.317A pdb=" N ALA O 6 " --> pdb=" O GLU O 2 " (cutoff:3.500A) Processing helix chain 'O' and resid 20 through 24 removed outlier: 3.810A pdb=" N ASN O 24 " --> pdb=" O VAL O 21 " (cutoff:3.500A) Processing helix chain 'O' and resid 29 through 42 Processing helix chain 'O' and resid 44 through 49 Processing helix chain 'O' and resid 53 through 66 removed outlier: 3.824A pdb=" N TYR O 61 " --> pdb=" O LEU O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 68 through 80 removed outlier: 3.601A pdb=" N TRP O 74 " --> pdb=" O PRO O 70 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 88 removed outlier: 3.677A pdb=" N LYS O 88 " --> pdb=" O ASP O 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 85 through 88' Processing helix chain 'O' and resid 89 through 98 Processing helix chain 'O' and resid 110 through 119 Processing helix chain 'O' and resid 128 through 135 removed outlier: 3.974A pdb=" N ALA O 133 " --> pdb=" O SER O 130 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE O 135 " --> pdb=" O ILE O 132 " (cutoff:3.500A) Processing helix chain 'O' and resid 159 through 167 Processing helix chain 'O' and resid 170 through 180 Processing helix chain 'O' and resid 194 through 211 removed outlier: 3.622A pdb=" N ARG O 198 " --> pdb=" O ASP O 194 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN O 211 " --> pdb=" O LEU O 207 " (cutoff:3.500A) Processing helix chain 'O' and resid 213 through 217 Processing helix chain 'O' and resid 228 through 238 removed outlier: 3.695A pdb=" N TRP O 238 " --> pdb=" O ILE O 234 " (cutoff:3.500A) Processing helix chain 'O' and resid 249 through 259 Processing helix chain 'N' and resid 3 through 11 Processing helix chain 'N' and resid 29 through 42 Processing helix chain 'N' and resid 44 through 50 removed outlier: 3.985A pdb=" N THR N 50 " --> pdb=" O ASP N 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 66 removed outlier: 3.881A pdb=" N TYR N 61 " --> pdb=" O LEU N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 68 through 79 Processing helix chain 'N' and resid 85 through 88 removed outlier: 3.564A pdb=" N LYS N 88 " --> pdb=" O ASP N 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 85 through 88' Processing helix chain 'N' and resid 89 through 97 Processing helix chain 'N' and resid 110 through 120 Processing helix chain 'N' and resid 128 through 133 Processing helix chain 'N' and resid 158 through 166 Processing helix chain 'N' and resid 170 through 180 removed outlier: 3.615A pdb=" N SER N 178 " --> pdb=" O ILE N 174 " (cutoff:3.500A) Processing helix chain 'N' and resid 194 through 211 removed outlier: 3.669A pdb=" N ARG N 198 " --> pdb=" O ASP N 194 " (cutoff:3.500A) Processing helix chain 'N' and resid 213 through 217 removed outlier: 3.642A pdb=" N GLN N 217 " --> pdb=" O GLU N 214 " (cutoff:3.500A) Processing helix chain 'N' and resid 228 through 238 removed outlier: 3.560A pdb=" N ILE N 234 " --> pdb=" O ILE N 230 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN N 237 " --> pdb=" O GLU N 233 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N TRP N 238 " --> pdb=" O ILE N 234 " (cutoff:3.500A) Processing helix chain 'N' and resid 249 through 260 removed outlier: 3.573A pdb=" N SER N 253 " --> pdb=" O ASN N 249 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 11 removed outlier: 3.542A pdb=" N LYS M 10 " --> pdb=" O ALA M 6 " (cutoff:3.500A) Processing helix chain 'M' and resid 21 through 26 removed outlier: 3.929A pdb=" N LEU M 25 " --> pdb=" O VAL M 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 42 removed outlier: 3.776A pdb=" N ASP M 35 " --> pdb=" O SER M 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 47 through 52 removed outlier: 3.545A pdb=" N PHE M 51 " --> pdb=" O TYR M 48 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY M 52 " --> pdb=" O ARG M 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 64 removed outlier: 3.993A pdb=" N TYR M 61 " --> pdb=" O LEU M 57 " (cutoff:3.500A) Processing helix chain 'M' and resid 68 through 80 removed outlier: 3.699A pdb=" N HIS M 80 " --> pdb=" O ASP M 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 98 Processing helix chain 'M' and resid 112 through 119 Processing helix chain 'M' and resid 131 through 135 removed outlier: 3.519A pdb=" N ILE M 135 " --> pdb=" O ILE M 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 158 through 166 removed outlier: 3.851A pdb=" N GLN M 164 " --> pdb=" O THR M 160 " (cutoff:3.500A) Processing helix chain 'M' and resid 170 through 180 removed outlier: 3.613A pdb=" N LYS M 175 " --> pdb=" O PRO M 171 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 211 removed outlier: 3.959A pdb=" N ARG M 198 " --> pdb=" O ASP M 194 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN M 211 " --> pdb=" O LEU M 207 " (cutoff:3.500A) Processing helix chain 'M' and resid 213 through 217 Processing helix chain 'M' and resid 228 through 238 removed outlier: 3.815A pdb=" N GLU M 233 " --> pdb=" O PRO M 229 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TRP M 238 " --> pdb=" O ILE M 234 " (cutoff:3.500A) Processing helix chain 'M' and resid 249 through 258 Processing helix chain 'I' and resid 9 through 20 Processing helix chain 'I' and resid 41 through 58 removed outlier: 4.549A pdb=" N LEU I 56 " --> pdb=" O LYS I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 98 removed outlier: 7.969A pdb=" N ALA I 90 " --> pdb=" O ASP I 86 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N ASP I 91 " --> pdb=" O LYS I 87 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS I 92 " --> pdb=" O LEU I 88 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN I 95 " --> pdb=" O ASP I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 144 removed outlier: 4.194A pdb=" N CYS I 144 " --> pdb=" O GLN I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 154 through 159 Processing helix chain 'I' and resid 160 through 164 removed outlier: 3.582A pdb=" N ASN I 163 " --> pdb=" O ASP I 160 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU I 164 " --> pdb=" O ARG I 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 160 through 164' Processing helix chain 'I' and resid 166 through 182 Processing helix chain 'J' and resid 9 through 20 removed outlier: 3.547A pdb=" N ILE J 13 " --> pdb=" O ASN J 9 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 58 removed outlier: 4.380A pdb=" N LYS J 47 " --> pdb=" O HIS J 43 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU J 56 " --> pdb=" O LYS J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 89 Processing helix chain 'J' and resid 140 through 144 removed outlier: 4.302A pdb=" N CYS J 144 " --> pdb=" O GLN J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 154 through 159 removed outlier: 3.786A pdb=" N GLY J 159 " --> pdb=" O ALA J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 165 removed outlier: 3.639A pdb=" N GLU J 164 " --> pdb=" O ARG J 161 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 182 removed outlier: 3.652A pdb=" N LYS J 170 " --> pdb=" O SER J 166 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 26 through 31 removed outlier: 6.570A pdb=" N ILE C 3 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N SER C 30 " --> pdb=" O ILE C 3 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE C 5 " --> pdb=" O SER C 30 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N PHE C 62 " --> pdb=" O ASN C 2 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ARG C 4 " --> pdb=" O PHE C 62 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N GLU C 64 " --> pdb=" O ARG C 4 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ILE C 6 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 10.245A pdb=" N THR C 66 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL C 61 " --> pdb=" O CYS C 114 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N CYS C 114 " --> pdb=" O VAL C 61 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA C 107 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR C 126 " --> pdb=" O ALA C 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 26 through 30 removed outlier: 6.909A pdb=" N ILE D 3 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N SER D 30 " --> pdb=" O ILE D 3 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N PHE D 5 " --> pdb=" O SER D 30 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N PHE D 62 " --> pdb=" O ASN D 2 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ARG D 4 " --> pdb=" O PHE D 62 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N GLU D 64 " --> pdb=" O ARG D 4 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE D 6 " --> pdb=" O GLU D 64 " (cutoff:3.500A) removed outlier: 10.339A pdb=" N THR D 66 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL D 106 " --> pdb=" O TYR D 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 123 through 126 removed outlier: 5.930A pdb=" N ILE H 124 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LYS H 144 " --> pdb=" O ILE H 124 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ILE H 126 " --> pdb=" O LYS H 144 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL H 13 " --> pdb=" O ILE H 102 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N TYR H 104 " --> pdb=" O VAL H 13 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU H 15 " --> pdb=" O TYR H 104 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ILE H 14 " --> pdb=" O LEU H 186 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE H 188 " --> pdb=" O ILE H 14 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N PHE H 16 " --> pdb=" O ILE H 188 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER H 220 " --> pdb=" O GLY H 241 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ILE H 243 " --> pdb=" O SER H 220 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE H 222 " --> pdb=" O ILE H 243 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 141 through 144 removed outlier: 6.896A pdb=" N VAL G 13 " --> pdb=" O ILE G 102 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N TYR G 104 " --> pdb=" O VAL G 13 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N LEU G 15 " --> pdb=" O TYR G 104 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE G 14 " --> pdb=" O LEU G 186 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE G 188 " --> pdb=" O ILE G 14 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N PHE G 16 " --> pdb=" O ILE G 188 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N SER G 220 " --> pdb=" O GLY G 241 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ILE G 243 " --> pdb=" O SER G 220 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ILE G 222 " --> pdb=" O ILE G 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 123 through 126 removed outlier: 5.933A pdb=" N ILE F 124 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LYS F 144 " --> pdb=" O ILE F 124 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE F 126 " --> pdb=" O LYS F 144 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ILE F 102 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE F 14 " --> pdb=" O LEU F 186 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ILE F 188 " --> pdb=" O ILE F 14 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N PHE F 16 " --> pdb=" O ILE F 188 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N VAL F 185 " --> pdb=" O TYR F 221 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N PHE F 223 " --> pdb=" O VAL F 185 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N PHE F 187 " --> pdb=" O PHE F 223 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N SER F 220 " --> pdb=" O GLY F 241 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 125 through 126 removed outlier: 7.151A pdb=" N ILE E 126 " --> pdb=" O LYS E 144 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL E 13 " --> pdb=" O ILE E 102 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N TYR E 104 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N LEU E 15 " --> pdb=" O TYR E 104 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE E 188 " --> pdb=" O PHE E 16 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL E 185 " --> pdb=" O TYR E 221 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N PHE E 223 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N PHE E 187 " --> pdb=" O PHE E 223 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N SER E 220 " --> pdb=" O GLY E 241 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 26 through 30 removed outlier: 6.387A pdb=" N ILE A 3 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N SER A 30 " --> pdb=" O ILE A 3 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N PHE A 5 " --> pdb=" O SER A 30 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N PHE A 62 " --> pdb=" O ASN A 2 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ARG A 4 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N GLU A 64 " --> pdb=" O ARG A 4 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ILE A 6 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 10.336A pdb=" N THR A 66 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY A 124 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 26 through 31 removed outlier: 8.352A pdb=" N PHE B 62 " --> pdb=" O ASN B 2 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ARG B 4 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N GLU B 64 " --> pdb=" O ARG B 4 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ILE B 6 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 9.913A pdb=" N THR B 66 " --> pdb=" O ILE B 6 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 26 through 31 removed outlier: 8.352A pdb=" N PHE B 62 " --> pdb=" O ASN B 2 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ARG B 4 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N GLU B 64 " --> pdb=" O ARG B 4 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ILE B 6 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 9.913A pdb=" N THR B 66 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR B 126 " --> pdb=" O ALA B 107 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 2 through 7 removed outlier: 6.990A pdb=" N ILE K 3 " --> pdb=" O LEU K 28 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N SER K 30 " --> pdb=" O ILE K 3 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N PHE K 5 " --> pdb=" O SER K 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'K' and resid 61 through 70 Processing sheet with id=AB3, first strand: chain 'L' and resid 26 through 31 removed outlier: 3.672A pdb=" N LEU L 28 " --> pdb=" O ILE L 3 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE L 5 " --> pdb=" O LEU L 28 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N PHE L 62 " --> pdb=" O ASN L 2 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG L 4 " --> pdb=" O PHE L 62 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N GLU L 64 " --> pdb=" O ARG L 4 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ILE L 6 " --> pdb=" O GLU L 64 " (cutoff:3.500A) removed outlier: 10.350A pdb=" N THR L 66 " --> pdb=" O ILE L 6 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 26 through 31 removed outlier: 3.672A pdb=" N LEU L 28 " --> pdb=" O ILE L 3 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE L 5 " --> pdb=" O LEU L 28 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N PHE L 62 " --> pdb=" O ASN L 2 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARG L 4 " --> pdb=" O PHE L 62 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N GLU L 64 " --> pdb=" O ARG L 4 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ILE L 6 " --> pdb=" O GLU L 64 " (cutoff:3.500A) removed outlier: 10.350A pdb=" N THR L 66 " --> pdb=" O ILE L 6 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'P' and resid 123 through 126 removed outlier: 6.107A pdb=" N ILE P 124 " --> pdb=" O ILE P 142 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LYS P 144 " --> pdb=" O ILE P 124 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE P 126 " --> pdb=" O LYS P 144 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL P 13 " --> pdb=" O ILE P 102 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N TYR P 104 " --> pdb=" O VAL P 13 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LEU P 15 " --> pdb=" O TYR P 104 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE P 188 " --> pdb=" O PHE P 16 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N VAL P 185 " --> pdb=" O TYR P 221 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N PHE P 223 " --> pdb=" O VAL P 185 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N PHE P 187 " --> pdb=" O PHE P 223 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 123 through 126 removed outlier: 6.858A pdb=" N VAL O 13 " --> pdb=" O ILE O 102 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N TYR O 104 " --> pdb=" O VAL O 13 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N LEU O 15 " --> pdb=" O TYR O 104 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE O 14 " --> pdb=" O LEU O 186 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE O 188 " --> pdb=" O ILE O 14 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N PHE O 16 " --> pdb=" O ILE O 188 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER O 220 " --> pdb=" O GLY O 241 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 123 through 126 removed outlier: 7.243A pdb=" N VAL N 13 " --> pdb=" O ILE N 102 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N TYR N 104 " --> pdb=" O VAL N 13 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LEU N 15 " --> pdb=" O TYR N 104 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N VAL N 185 " --> pdb=" O TYR N 221 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N PHE N 223 " --> pdb=" O VAL N 185 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N PHE N 187 " --> pdb=" O PHE N 223 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N SER N 220 " --> pdb=" O GLY N 241 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 123 through 126 removed outlier: 5.885A pdb=" N ILE M 124 " --> pdb=" O ILE M 142 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LYS M 144 " --> pdb=" O ILE M 124 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ILE M 126 " --> pdb=" O LYS M 144 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL M 13 " --> pdb=" O ILE M 102 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N TYR M 104 " --> pdb=" O VAL M 13 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N LEU M 15 " --> pdb=" O TYR M 104 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE M 14 " --> pdb=" O LEU M 186 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ILE M 188 " --> pdb=" O ILE M 14 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N PHE M 16 " --> pdb=" O ILE M 188 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N SER M 220 " --> pdb=" O GLY M 241 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ILE M 243 " --> pdb=" O SER M 220 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE M 222 " --> pdb=" O ILE M 243 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 26 through 31 removed outlier: 6.601A pdb=" N ILE I 3 " --> pdb=" O LEU I 28 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N SER I 30 " --> pdb=" O ILE I 3 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N PHE I 5 " --> pdb=" O SER I 30 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N PHE I 62 " --> pdb=" O ASN I 2 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ARG I 4 " --> pdb=" O PHE I 62 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N GLU I 64 " --> pdb=" O ARG I 4 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ILE I 6 " --> pdb=" O GLU I 64 " (cutoff:3.500A) removed outlier: 9.676A pdb=" N THR I 66 " --> pdb=" O ILE I 6 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 26 through 31 removed outlier: 6.601A pdb=" N ILE I 3 " --> pdb=" O LEU I 28 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N SER I 30 " --> pdb=" O ILE I 3 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N PHE I 5 " --> pdb=" O SER I 30 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N PHE I 62 " --> pdb=" O ASN I 2 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ARG I 4 " --> pdb=" O PHE I 62 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N GLU I 64 " --> pdb=" O ARG I 4 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ILE I 6 " --> pdb=" O GLU I 64 " (cutoff:3.500A) removed outlier: 9.676A pdb=" N THR I 66 " --> pdb=" O ILE I 6 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA I 107 " --> pdb=" O THR I 126 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR I 126 " --> pdb=" O ALA I 107 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 26 through 31 removed outlier: 6.275A pdb=" N ILE J 3 " --> pdb=" O LEU J 28 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N SER J 30 " --> pdb=" O ILE J 3 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N PHE J 5 " --> pdb=" O SER J 30 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N PHE J 62 " --> pdb=" O ASN J 2 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ARG J 4 " --> pdb=" O PHE J 62 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N GLU J 64 " --> pdb=" O ARG J 4 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ILE J 6 " --> pdb=" O GLU J 64 " (cutoff:3.500A) removed outlier: 10.025A pdb=" N THR J 66 " --> pdb=" O ILE J 6 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR J 126 " --> pdb=" O ALA J 107 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY J 124 " --> pdb=" O THR J 109 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE J 122 " --> pdb=" O ILE J 111 " (cutoff:3.500A) 1216 hydrogen bonds defined for protein. 3465 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.72 Time building geometry restraints manager: 3.03 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: 6641 1.33 - 1.45: 6699 1.45 - 1.58: 16523 1.58 - 1.70: 57 1.70 - 1.82: 160 Bond restraints: 30080 Sorted by residual: bond pdb=" CAB Y43 A1001 " pdb=" CAC Y43 A1001 " ideal model delta sigma weight residual 1.524 1.222 0.302 2.00e-02 2.50e+03 2.28e+02 bond pdb=" CAB Y43 J1001 " pdb=" CAC Y43 J1001 " ideal model delta sigma weight residual 1.524 1.222 0.302 2.00e-02 2.50e+03 2.28e+02 bond pdb=" CAB Y43 I1001 " pdb=" CAC Y43 I1001 " ideal model delta sigma weight residual 1.524 1.224 0.300 2.00e-02 2.50e+03 2.26e+02 bond pdb=" CAB Y43 D1001 " pdb=" CAC Y43 D1001 " ideal model delta sigma weight residual 1.524 1.224 0.300 2.00e-02 2.50e+03 2.25e+02 bond pdb=" CAB Y43 B1001 " pdb=" CAC Y43 B1001 " ideal model delta sigma weight residual 1.524 1.224 0.300 2.00e-02 2.50e+03 2.25e+02 ... (remaining 30075 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.26: 40013 4.26 - 8.52: 599 8.52 - 12.78: 47 12.78 - 17.04: 4 17.04 - 21.30: 1 Bond angle restraints: 40664 Sorted by residual: angle pdb=" N GLU H 167 " pdb=" CA GLU H 167 " pdb=" C GLU H 167 " ideal model delta sigma weight residual 107.23 85.93 21.30 1.67e+00 3.59e-01 1.63e+02 angle pdb=" N GLU L 181 " pdb=" CA GLU L 181 " pdb=" C GLU L 181 " ideal model delta sigma weight residual 112.38 102.69 9.69 1.22e+00 6.72e-01 6.31e+01 angle pdb=" N LYS P 90 " pdb=" CA LYS P 90 " pdb=" C LYS P 90 " ideal model delta sigma weight residual 112.23 104.68 7.55 1.26e+00 6.30e-01 3.59e+01 angle pdb=" N ASN P 249 " pdb=" CA ASN P 249 " pdb=" CB ASN P 249 " ideal model delta sigma weight residual 110.37 120.82 -10.45 1.78e+00 3.16e-01 3.44e+01 angle pdb=" N ILE A 145 " pdb=" CA ILE A 145 " pdb=" C ILE A 145 " ideal model delta sigma weight residual 113.47 107.71 5.76 1.01e+00 9.80e-01 3.26e+01 ... (remaining 40659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.15: 17561 34.15 - 68.30: 559 68.30 - 102.45: 42 102.45 - 136.60: 8 136.60 - 170.76: 6 Dihedral angle restraints: 18176 sinusoidal: 7808 harmonic: 10368 Sorted by residual: dihedral pdb=" C5' AMP O 301 " pdb=" O5' AMP O 301 " pdb=" P AMP O 301 " pdb=" O3P AMP O 301 " ideal model delta sinusoidal sigma weight residual -60.00 72.75 -132.75 1 2.00e+01 2.50e-03 4.03e+01 dihedral pdb=" C5' AMP H 301 " pdb=" O5' AMP H 301 " pdb=" P AMP H 301 " pdb=" O3P AMP H 301 " ideal model delta sinusoidal sigma weight residual -60.00 -173.18 113.18 1 2.00e+01 2.50e-03 3.34e+01 dihedral pdb=" C5' AMP G 301 " pdb=" O5' AMP G 301 " pdb=" P AMP G 301 " pdb=" O3P AMP G 301 " ideal model delta sinusoidal sigma weight residual -60.00 52.72 -112.72 1 2.00e+01 2.50e-03 3.33e+01 ... (remaining 18173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 4058 0.107 - 0.215: 308 0.215 - 0.322: 18 0.322 - 0.429: 5 0.429 - 0.536: 3 Chirality restraints: 4392 Sorted by residual: chirality pdb=" CB ILE B 147 " pdb=" CA ILE B 147 " pdb=" CG1 ILE B 147 " pdb=" CG2 ILE B 147 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.54 2.00e-01 2.50e+01 7.19e+00 chirality pdb=" CB ILE P 68 " pdb=" CA ILE P 68 " pdb=" CG1 ILE P 68 " pdb=" CG2 ILE P 68 " both_signs ideal model delta sigma weight residual False 2.64 2.12 0.53 2.00e-01 2.50e+01 7.00e+00 chirality pdb=" CB THR D 154 " pdb=" CA THR D 154 " pdb=" OG1 THR D 154 " pdb=" CG2 THR D 154 " both_signs ideal model delta sigma weight residual False 2.55 2.11 0.44 2.00e-01 2.50e+01 4.95e+00 ... (remaining 4389 not shown) Planarity restraints: 5104 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU H 166 " -0.026 2.00e-02 2.50e+03 5.45e-02 2.97e+01 pdb=" C LEU H 166 " 0.094 2.00e-02 2.50e+03 pdb=" O LEU H 166 " -0.035 2.00e-02 2.50e+03 pdb=" N GLU H 167 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU L 179 " 0.023 2.00e-02 2.50e+03 4.50e-02 2.02e+01 pdb=" C LEU L 179 " -0.078 2.00e-02 2.50e+03 pdb=" O LEU L 179 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU L 180 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN H 247 " -0.022 2.00e-02 2.50e+03 4.47e-02 2.00e+01 pdb=" C ASN H 247 " 0.077 2.00e-02 2.50e+03 pdb=" O ASN H 247 " -0.029 2.00e-02 2.50e+03 pdb=" N ASP H 248 " -0.026 2.00e-02 2.50e+03 ... (remaining 5101 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 8647 2.82 - 3.34: 26070 3.34 - 3.86: 49682 3.86 - 4.38: 57995 4.38 - 4.90: 99484 Nonbonded interactions: 241878 Sorted by model distance: nonbonded pdb=" OH TYR G 108 " pdb=" O VAL G 156 " model vdw 2.303 3.040 nonbonded pdb=" OG1 THR B 129 " pdb=" O ILE B 147 " model vdw 2.306 3.040 nonbonded pdb=" OH TYR E 48 " pdb=" O LEU E 57 " model vdw 2.306 3.040 nonbonded pdb=" OH TYR G 190 " pdb=" OD2 ASP G 194 " model vdw 2.310 3.040 nonbonded pdb=" OG SER N 128 " pdb=" OD1 ASP N 131 " model vdw 2.315 3.040 ... (remaining 241873 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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: 4.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 26.010 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 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 : 0.009 0.302 30080 Z= 0.456 Angle : 1.246 21.305 40664 Z= 0.689 Chirality : 0.061 0.536 4392 Planarity : 0.009 0.106 5104 Dihedral : 16.634 170.756 11504 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.71 % Favored : 94.09 % Rotamer: Outliers : 0.12 % Allowed : 0.59 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.13), residues: 3536 helix: -1.79 (0.11), residues: 1488 sheet: -1.73 (0.22), residues: 544 loop : -2.01 (0.15), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG L 4 TYR 0.027 0.002 TYR C 120 PHE 0.037 0.002 PHE B 155 TRP 0.064 0.003 TRP A 85 HIS 0.014 0.002 HIS K 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00888 / 0.46 (30080) covalent geometry : angle 1.24603 / 0.69 (40664) hydrogen bonds : bond 0.20604 / 13.70 ( 1180) hydrogen bonds : angle 7.76014 / 5.35 ( 3465) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 607 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 ASN cc_start: 0.8502 (t0) cc_final: 0.8259 (t0) REVERT: C 74 ASN cc_start: 0.8174 (t0) cc_final: 0.7833 (t0) REVERT: C 158 MET cc_start: 0.5405 (mtt) cc_final: 0.5170 (mtt) REVERT: D 2 ASN cc_start: 0.8634 (m-40) cc_final: 0.8389 (m-40) REVERT: D 158 MET cc_start: 0.8676 (tmm) cc_final: 0.8457 (tmm) REVERT: G 226 ARG cc_start: 0.8235 (ttm-80) cc_final: 0.8006 (ttm-80) REVERT: A 10 ARG cc_start: 0.8589 (mtm-85) cc_final: 0.8255 (mtm180) REVERT: A 94 SER cc_start: 0.8441 (p) cc_final: 0.7918 (t) REVERT: A 158 MET cc_start: 0.7243 (tpp) cc_final: 0.6160 (tpp) REVERT: A 161 ARG cc_start: 0.8149 (ttp-110) cc_final: 0.7746 (ttp-110) REVERT: B 9 ASN cc_start: 0.7439 (t0) cc_final: 0.7169 (t0) REVERT: B 26 VAL cc_start: 0.8797 (t) cc_final: 0.8588 (p) REVERT: B 85 TRP cc_start: 0.8222 (t-100) cc_final: 0.7710 (t-100) REVERT: B 141 GLN cc_start: 0.9128 (mm-40) cc_final: 0.8799 (mm110) REVERT: B 143 ASP cc_start: 0.7426 (m-30) cc_final: 0.6539 (p0) REVERT: B 163 ASN cc_start: 0.8419 (m110) cc_final: 0.8167 (m-40) REVERT: L 149 ASP cc_start: 0.7594 (m-30) cc_final: 0.7364 (m-30) REVERT: L 163 ASN cc_start: 0.7837 (p0) cc_final: 0.7404 (p0) REVERT: O 23 MET cc_start: 0.8210 (ttt) cc_final: 0.7960 (mtp) REVERT: O 209 LYS cc_start: 0.8432 (mttp) cc_final: 0.8072 (mptt) REVERT: M 49 ARG cc_start: 0.8256 (mtm-85) cc_final: 0.8036 (mtm-85) REVERT: I 109 THR cc_start: 0.8860 (m) cc_final: 0.8609 (m) REVERT: I 178 TYR cc_start: 0.8735 (t80) cc_final: 0.8473 (t80) REVERT: J 48 ASP cc_start: 0.8527 (t70) cc_final: 0.8208 (t0) REVERT: J 82 GLN cc_start: 0.7258 (tt0) cc_final: 0.7001 (tt0) outliers start: 4 outliers final: 1 residues processed: 609 average time/residue: 0.1971 time to fit residues: 188.6345 Evaluate side-chains 465 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 464 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 248 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.0270 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.0070 chunk 298 optimal weight: 9.9990 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 164 GLN G 24 ASN G 231 GLN F 24 ASN ** F 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 HIS L 102 ASN O 107 ASN M 92 HIS I 74 ASN J 32 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.111324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.081532 restraints weight = 59369.071| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.79 r_work: 0.3045 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30080 Z= 0.123 Angle : 0.626 8.251 40664 Z= 0.311 Chirality : 0.046 0.218 4392 Planarity : 0.005 0.065 5104 Dihedral : 11.981 173.934 4202 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.36 % Favored : 95.56 % Rotamer: Outliers : 1.00 % Allowed : 9.16 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.13), residues: 3536 helix: -0.81 (0.13), residues: 1496 sheet: -1.26 (0.23), residues: 528 loop : -1.60 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 59 TYR 0.020 0.001 TYR J 69 PHE 0.026 0.001 PHE I 93 TRP 0.018 0.001 TRP L 85 HIS 0.008 0.001 HIS K 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (30080) covalent geometry : angle 0.62623 / 0.31 (40664) hydrogen bonds : bond 0.03870 / 2.59 ( 1180) hydrogen bonds : angle 5.07347 / 3.47 ( 3465) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 524 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 ASN cc_start: 0.8290 (t0) cc_final: 0.8025 (t0) REVERT: C 74 ASN cc_start: 0.8420 (t0) cc_final: 0.7834 (t0) REVERT: C 158 MET cc_start: 0.6066 (mtt) cc_final: 0.5849 (mtt) REVERT: D 1 MET cc_start: 0.7444 (tpt) cc_final: 0.7218 (tpt) REVERT: D 2 ASN cc_start: 0.8798 (m-40) cc_final: 0.8356 (m-40) REVERT: D 158 MET cc_start: 0.8446 (tmm) cc_final: 0.8162 (tmm) REVERT: E 56 GLU cc_start: 0.8457 (mp0) cc_final: 0.8228 (mp0) REVERT: E 151 ASP cc_start: 0.7819 (m-30) cc_final: 0.7292 (m-30) REVERT: A 94 SER cc_start: 0.8470 (p) cc_final: 0.8219 (t) REVERT: A 158 MET cc_start: 0.7719 (tpp) cc_final: 0.6499 (tpp) REVERT: A 161 ARG cc_start: 0.8355 (ttp-110) cc_final: 0.7849 (ttp-110) REVERT: B 19 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8764 (mp) REVERT: B 85 TRP cc_start: 0.7957 (t-100) cc_final: 0.7744 (t-100) REVERT: B 138 ARG cc_start: 0.7816 (mtt90) cc_final: 0.7385 (mtt90) REVERT: B 143 ASP cc_start: 0.7780 (m-30) cc_final: 0.6852 (p0) REVERT: K 173 ASP cc_start: 0.8741 (m-30) cc_final: 0.8482 (m-30) REVERT: P 226 ARG cc_start: 0.8263 (ttm170) cc_final: 0.8001 (mmt90) REVERT: P 256 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8425 (mm-30) REVERT: O 3 GLN cc_start: 0.7338 (tp-100) cc_final: 0.7123 (tp40) REVERT: O 209 LYS cc_start: 0.8717 (mttp) cc_final: 0.8422 (mptt) REVERT: N 164 GLN cc_start: 0.8874 (mt0) cc_final: 0.8655 (mt0) REVERT: I 109 THR cc_start: 0.8950 (m) cc_final: 0.8723 (m) REVERT: I 149 ASP cc_start: 0.7942 (t70) cc_final: 0.7560 (t0) REVERT: I 178 TYR cc_start: 0.8623 (t80) cc_final: 0.8421 (t80) REVERT: J 38 GLN cc_start: 0.8751 (mt0) cc_final: 0.8469 (mt0) REVERT: J 48 ASP cc_start: 0.8819 (t70) cc_final: 0.8508 (t0) REVERT: J 173 ASP cc_start: 0.8270 (m-30) cc_final: 0.7998 (m-30) outliers start: 32 outliers final: 18 residues processed: 536 average time/residue: 0.2037 time to fit residues: 171.7478 Evaluate side-chains 462 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 443 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain F residue 24 ASN Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 205 SER Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 85 TRP Chi-restraints excluded: chain B residue 11 HIS Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain P residue 46 ASP Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain J residue 133 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 220 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 283 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 334 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 345 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 131 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 32 HIS D 17 ASN H 164 GLN O 211 GLN O 237 GLN ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 127 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.109677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.078967 restraints weight = 58460.490| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.92 r_work: 0.2994 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30080 Z= 0.133 Angle : 0.594 8.033 40664 Z= 0.293 Chirality : 0.045 0.197 4392 Planarity : 0.005 0.061 5104 Dihedral : 11.307 174.621 4200 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.50 % Favored : 95.42 % Rotamer: Outliers : 1.28 % Allowed : 12.78 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.14), residues: 3536 helix: -0.36 (0.13), residues: 1512 sheet: -0.89 (0.22), residues: 584 loop : -1.50 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 168 TYR 0.016 0.001 TYR J 69 PHE 0.019 0.001 PHE A 172 TRP 0.015 0.001 TRP H 74 HIS 0.012 0.001 HIS B 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (30080) covalent geometry : angle 0.59404 / 0.29 (40664) hydrogen bonds : bond 0.03477 / 2.35 ( 1180) hydrogen bonds : angle 4.58834 / 3.14 ( 3465) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 480 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 ASN cc_start: 0.8168 (t0) cc_final: 0.7864 (t0) REVERT: C 143 ASP cc_start: 0.7710 (m-30) cc_final: 0.7386 (m-30) REVERT: D 1 MET cc_start: 0.7360 (tpt) cc_final: 0.7127 (tpt) REVERT: D 2 ASN cc_start: 0.8959 (m-40) cc_final: 0.8366 (m-40) REVERT: D 95 GLN cc_start: 0.8176 (pm20) cc_final: 0.7922 (mp10) REVERT: H 23 MET cc_start: 0.8240 (mtp) cc_final: 0.8007 (mtm) REVERT: H 169 GLU cc_start: 0.8363 (tp30) cc_final: 0.7969 (tp30) REVERT: G 167 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7878 (mm-30) REVERT: G 210 GLU cc_start: 0.8956 (tp30) cc_final: 0.8748 (tp30) REVERT: G 211 GLN cc_start: 0.8650 (mp10) cc_final: 0.8437 (mp10) REVERT: F 136 ASP cc_start: 0.8365 (t0) cc_final: 0.8101 (t0) REVERT: F 200 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8534 (tt) REVERT: F 237 GLN cc_start: 0.8943 (mm110) cc_final: 0.8575 (mt0) REVERT: E 56 GLU cc_start: 0.8527 (mp0) cc_final: 0.8150 (mp0) REVERT: E 151 ASP cc_start: 0.7839 (m-30) cc_final: 0.7266 (m-30) REVERT: E 173 ASP cc_start: 0.8939 (m-30) cc_final: 0.8636 (m-30) REVERT: A 94 SER cc_start: 0.8533 (p) cc_final: 0.8194 (t) REVERT: A 158 MET cc_start: 0.7896 (tpp) cc_final: 0.6697 (tpp) REVERT: A 161 ARG cc_start: 0.8346 (ttp-110) cc_final: 0.7869 (ttp-110) REVERT: A 177 GLU cc_start: 0.9047 (tp30) cc_final: 0.8750 (tm-30) REVERT: B 1 MET cc_start: 0.6738 (tpt) cc_final: 0.6497 (tpt) REVERT: B 138 ARG cc_start: 0.7813 (mtt90) cc_final: 0.7431 (mtt90) REVERT: B 143 ASP cc_start: 0.8120 (m-30) cc_final: 0.7184 (p0) REVERT: K 83 ILE cc_start: 0.8065 (mm) cc_final: 0.7826 (mm) REVERT: L 11 HIS cc_start: 0.8069 (m-70) cc_final: 0.7663 (m170) REVERT: L 71 GLU cc_start: 0.8623 (tt0) cc_final: 0.8415 (pt0) REVERT: P 226 ARG cc_start: 0.8170 (ttm170) cc_final: 0.7912 (mmt90) REVERT: P 256 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8329 (mm-30) REVERT: O 3 GLN cc_start: 0.7685 (tp-100) cc_final: 0.7322 (tp40) REVERT: O 173 ASP cc_start: 0.8668 (m-30) cc_final: 0.8312 (m-30) REVERT: O 209 LYS cc_start: 0.8600 (mttp) cc_final: 0.8270 (mttp) REVERT: N 23 MET cc_start: 0.8408 (mtt) cc_final: 0.8057 (mtp) REVERT: M 3 GLN cc_start: 0.8360 (tp-100) cc_final: 0.8042 (tp-100) REVERT: M 49 ARG cc_start: 0.8843 (mtm-85) cc_final: 0.8412 (mtm-85) REVERT: M 59 GLU cc_start: 0.8896 (tp30) cc_final: 0.7923 (tp30) REVERT: I 28 LEU cc_start: 0.8394 (tt) cc_final: 0.8135 (tt) REVERT: I 109 THR cc_start: 0.8877 (m) cc_final: 0.8601 (m) REVERT: I 149 ASP cc_start: 0.8121 (t70) cc_final: 0.7844 (t0) REVERT: J 48 ASP cc_start: 0.8827 (t70) cc_final: 0.8439 (t0) REVERT: J 104 ARG cc_start: 0.8738 (ttp80) cc_final: 0.8271 (ttp80) REVERT: J 139 ASP cc_start: 0.8552 (p0) cc_final: 0.8112 (p0) REVERT: J 158 MET cc_start: 0.7185 (mmt) cc_final: 0.6954 (mmt) REVERT: J 173 ASP cc_start: 0.8358 (m-30) cc_final: 0.8096 (m-30) outliers start: 41 outliers final: 27 residues processed: 501 average time/residue: 0.2034 time to fit residues: 159.5742 Evaluate side-chains 464 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 436 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 205 SER Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 85 TRP Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain K residue 35 ASP Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain P residue 46 ASP Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 185 VAL Chi-restraints excluded: chain M residue 78 MET Chi-restraints excluded: chain M residue 237 GLN Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 133 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 82 optimal weight: 0.9990 chunk 298 optimal weight: 1.9990 chunk 125 optimal weight: 7.9990 chunk 182 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 285 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 349 optimal weight: 5.9990 chunk 207 optimal weight: 0.5980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 32 HIS C 74 ASN C 95 GLN D 17 ASN D 89 GLN H 164 GLN ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 237 GLN N 164 GLN ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.107682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.076772 restraints weight = 58275.658| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.90 r_work: 0.2953 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 30080 Z= 0.152 Angle : 0.594 8.845 40664 Z= 0.293 Chirality : 0.046 0.196 4392 Planarity : 0.004 0.059 5104 Dihedral : 11.134 172.268 4200 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.61 % Favored : 95.31 % Rotamer: Outliers : 1.69 % Allowed : 13.75 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.14), residues: 3536 helix: -0.22 (0.13), residues: 1568 sheet: -0.82 (0.22), residues: 584 loop : -1.40 (0.17), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 161 TYR 0.018 0.001 TYR L 113 PHE 0.016 0.001 PHE A 172 TRP 0.017 0.001 TRP A 85 HIS 0.005 0.001 HIS J 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (30080) covalent geometry : angle 0.59448 / 0.29 (40664) hydrogen bonds : bond 0.03405 / 2.29 ( 1180) hydrogen bonds : angle 4.39220 / 3.00 ( 3465) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 465 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 ASN cc_start: 0.8128 (t0) cc_final: 0.7772 (t0) REVERT: C 74 ASN cc_start: 0.8171 (t0) cc_final: 0.7791 (t0) REVERT: C 86 ASP cc_start: 0.8583 (t0) cc_final: 0.8346 (t0) REVERT: C 143 ASP cc_start: 0.7782 (m-30) cc_final: 0.7454 (m-30) REVERT: D 1 MET cc_start: 0.7405 (tpt) cc_final: 0.7104 (tpt) REVERT: D 2 ASN cc_start: 0.9141 (m-40) cc_final: 0.8422 (m-40) REVERT: D 95 GLN cc_start: 0.8213 (pm20) cc_final: 0.7587 (mp10) REVERT: D 158 MET cc_start: 0.8489 (tmm) cc_final: 0.8195 (tmm) REVERT: H 212 LYS cc_start: 0.9383 (mmtp) cc_final: 0.8914 (ptpt) REVERT: G 3 GLN cc_start: 0.8259 (pm20) cc_final: 0.8009 (pm20) REVERT: G 78 MET cc_start: 0.8679 (mmm) cc_final: 0.8340 (mmm) REVERT: G 169 GLU cc_start: 0.8206 (tp30) cc_final: 0.7981 (tp30) REVERT: G 210 GLU cc_start: 0.9010 (tp30) cc_final: 0.8793 (tp30) REVERT: G 211 GLN cc_start: 0.8673 (mp10) cc_final: 0.8318 (mp10) REVERT: F 136 ASP cc_start: 0.8471 (t0) cc_final: 0.8100 (t0) REVERT: F 200 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8564 (tt) REVERT: F 237 GLN cc_start: 0.9014 (mm110) cc_final: 0.8703 (mt0) REVERT: E 83 ASP cc_start: 0.8662 (p0) cc_final: 0.8393 (p0) REVERT: E 151 ASP cc_start: 0.7836 (m-30) cc_final: 0.7237 (m-30) REVERT: E 173 ASP cc_start: 0.8938 (m-30) cc_final: 0.8682 (m-30) REVERT: E 214 GLU cc_start: 0.8395 (pm20) cc_final: 0.7899 (pm20) REVERT: E 215 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7917 (mm-30) REVERT: E 252 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8582 (mt-10) REVERT: A 94 SER cc_start: 0.8533 (p) cc_final: 0.8175 (t) REVERT: A 158 MET cc_start: 0.7931 (tpp) cc_final: 0.6728 (tpp) REVERT: A 161 ARG cc_start: 0.8394 (ttp-110) cc_final: 0.7889 (ttp-110) REVERT: B 9 ASN cc_start: 0.7276 (t0) cc_final: 0.6907 (t0) REVERT: B 82 GLN cc_start: 0.6566 (tt0) cc_final: 0.6345 (tt0) REVERT: B 138 ARG cc_start: 0.7902 (mtt90) cc_final: 0.7413 (mtt90) REVERT: B 143 ASP cc_start: 0.8196 (m-30) cc_final: 0.7210 (p0) REVERT: K 91 ASP cc_start: 0.8410 (m-30) cc_final: 0.8110 (m-30) REVERT: K 106 VAL cc_start: 0.8059 (t) cc_final: 0.7782 (p) REVERT: L 113 TYR cc_start: 0.8799 (t80) cc_final: 0.8558 (t80) REVERT: L 158 MET cc_start: 0.7618 (mtp) cc_final: 0.7298 (ttm) REVERT: P 226 ARG cc_start: 0.8215 (ttm170) cc_final: 0.7947 (mmt90) REVERT: P 256 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8377 (mm-30) REVERT: O 3 GLN cc_start: 0.7792 (tp-100) cc_final: 0.7418 (tp40) REVERT: O 173 ASP cc_start: 0.8691 (m-30) cc_final: 0.8296 (m-30) REVERT: O 248 ASP cc_start: 0.8679 (p0) cc_final: 0.8138 (t70) REVERT: O 256 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.8393 (mp0) REVERT: N 23 MET cc_start: 0.8543 (mtt) cc_final: 0.8182 (mtp) REVERT: M 3 GLN cc_start: 0.8537 (tp-100) cc_final: 0.8171 (tp-100) REVERT: I 28 LEU cc_start: 0.8382 (tt) cc_final: 0.8138 (tt) REVERT: I 82 GLN cc_start: 0.7761 (tm-30) cc_final: 0.7405 (tm-30) REVERT: I 95 GLN cc_start: 0.9147 (tp-100) cc_final: 0.8934 (tp-100) REVERT: I 109 THR cc_start: 0.8998 (m) cc_final: 0.8643 (m) REVERT: I 149 ASP cc_start: 0.8184 (t70) cc_final: 0.7949 (t0) REVERT: J 8 ARG cc_start: 0.7627 (ptp90) cc_final: 0.7062 (ptp90) REVERT: J 48 ASP cc_start: 0.8875 (t70) cc_final: 0.8494 (t0) REVERT: J 82 GLN cc_start: 0.7357 (tt0) cc_final: 0.6850 (tt0) REVERT: J 104 ARG cc_start: 0.8748 (ttp80) cc_final: 0.8255 (ttp80) REVERT: J 139 ASP cc_start: 0.8587 (p0) cc_final: 0.8202 (p0) REVERT: J 173 ASP cc_start: 0.8454 (m-30) cc_final: 0.8162 (m-30) outliers start: 54 outliers final: 36 residues processed: 492 average time/residue: 0.2136 time to fit residues: 163.6105 Evaluate side-chains 458 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 420 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 205 SER Chi-restraints excluded: chain F residue 242 MET Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain E residue 210 GLU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain K residue 35 ASP Chi-restraints excluded: chain K residue 84 PHE Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain O residue 185 VAL Chi-restraints excluded: chain O residue 256 GLU Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 180 VAL Chi-restraints excluded: chain N residue 262 VAL Chi-restraints excluded: chain N residue 264 VAL Chi-restraints excluded: chain M residue 78 MET Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 116 SER Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 133 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 158 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 326 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 129 optimal weight: 0.7980 chunk 264 optimal weight: 5.9990 chunk 223 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 266 optimal weight: 0.3980 chunk 339 optimal weight: 0.9980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 32 HIS D 17 ASN H 164 GLN G 164 GLN F 24 ASN ** E 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 32 GLN O 137 ASN O 237 GLN N 24 ASN ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.105137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.075096 restraints weight = 59270.080| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.75 r_work: 0.2924 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30080 Z= 0.172 Angle : 0.604 9.112 40664 Z= 0.297 Chirality : 0.046 0.201 4392 Planarity : 0.004 0.059 5104 Dihedral : 11.100 177.443 4200 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.75 % Favored : 95.16 % Rotamer: Outliers : 1.84 % Allowed : 15.41 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.14), residues: 3536 helix: -0.01 (0.13), residues: 1520 sheet: -0.64 (0.25), residues: 464 loop : -1.35 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 168 TYR 0.018 0.001 TYR L 113 PHE 0.023 0.002 PHE D 172 TRP 0.056 0.001 TRP A 85 HIS 0.004 0.001 HIS J 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (30080) covalent geometry : angle 0.60367 / 0.30 (40664) hydrogen bonds : bond 0.03422 / 2.30 ( 1180) hydrogen bonds : angle 4.31457 / 2.95 ( 3465) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 440 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 ASN cc_start: 0.8282 (t0) cc_final: 0.7895 (t0) REVERT: C 74 ASN cc_start: 0.8212 (t0) cc_final: 0.7798 (t0) REVERT: C 86 ASP cc_start: 0.8645 (t0) cc_final: 0.8372 (t0) REVERT: D 1 MET cc_start: 0.7493 (tpt) cc_final: 0.7192 (tpt) REVERT: D 2 ASN cc_start: 0.9170 (m-40) cc_final: 0.8494 (m-40) REVERT: D 95 GLN cc_start: 0.8188 (pm20) cc_final: 0.7519 (mp10) REVERT: D 158 MET cc_start: 0.8543 (tmm) cc_final: 0.8275 (tmm) REVERT: H 212 LYS cc_start: 0.9280 (mmtp) cc_final: 0.8980 (ptpt) REVERT: G 210 GLU cc_start: 0.8978 (tp30) cc_final: 0.8755 (tp30) REVERT: G 211 GLN cc_start: 0.8557 (mp10) cc_final: 0.8222 (mp10) REVERT: F 136 ASP cc_start: 0.8462 (t0) cc_final: 0.8161 (t0) REVERT: F 200 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8734 (tt) REVERT: E 59 GLU cc_start: 0.8776 (tp30) cc_final: 0.8459 (tp30) REVERT: E 83 ASP cc_start: 0.8642 (p0) cc_final: 0.8384 (p0) REVERT: E 151 ASP cc_start: 0.7876 (m-30) cc_final: 0.7323 (m-30) REVERT: A 15 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8075 (mp0) REVERT: A 94 SER cc_start: 0.8630 (p) cc_final: 0.8288 (t) REVERT: A 141 GLN cc_start: 0.8094 (mp10) cc_final: 0.6570 (mt0) REVERT: A 158 MET cc_start: 0.7812 (tpp) cc_final: 0.6693 (tpp) REVERT: A 161 ARG cc_start: 0.8389 (ttp-110) cc_final: 0.7898 (ttp-110) REVERT: B 9 ASN cc_start: 0.7657 (t0) cc_final: 0.7289 (t0) REVERT: B 138 ARG cc_start: 0.8106 (mtt90) cc_final: 0.7688 (mtt90) REVERT: K 91 ASP cc_start: 0.8352 (m-30) cc_final: 0.8088 (m-30) REVERT: K 106 VAL cc_start: 0.8172 (t) cc_final: 0.7953 (p) REVERT: P 226 ARG cc_start: 0.8302 (ttm170) cc_final: 0.8031 (mmt90) REVERT: P 256 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8479 (mm-30) REVERT: O 3 GLN cc_start: 0.7765 (tp-100) cc_final: 0.7413 (tp40) REVERT: O 23 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8383 (mtp) REVERT: O 32 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8247 (mp10) REVERT: O 173 ASP cc_start: 0.8630 (m-30) cc_final: 0.8286 (m-30) REVERT: O 248 ASP cc_start: 0.8555 (p0) cc_final: 0.8171 (t70) REVERT: N 23 MET cc_start: 0.8565 (mtt) cc_final: 0.8299 (mtp) REVERT: M 3 GLN cc_start: 0.8443 (tp-100) cc_final: 0.8110 (tp-100) REVERT: I 28 LEU cc_start: 0.8656 (tt) cc_final: 0.8397 (tt) REVERT: I 86 ASP cc_start: 0.8275 (m-30) cc_final: 0.7987 (m-30) REVERT: I 109 THR cc_start: 0.9086 (m) cc_final: 0.8786 (m) REVERT: I 158 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7634 (mtm) REVERT: J 8 ARG cc_start: 0.7935 (ptp90) cc_final: 0.7240 (ptp90) REVERT: J 48 ASP cc_start: 0.8923 (t70) cc_final: 0.8589 (t0) REVERT: J 82 GLN cc_start: 0.7706 (tt0) cc_final: 0.7167 (tt0) REVERT: J 139 ASP cc_start: 0.8494 (p0) cc_final: 0.8131 (p0) REVERT: J 173 ASP cc_start: 0.8384 (m-30) cc_final: 0.8075 (m-30) outliers start: 59 outliers final: 43 residues processed: 471 average time/residue: 0.2087 time to fit residues: 154.3319 Evaluate side-chains 460 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 412 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 102 ASN Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 205 SER Chi-restraints excluded: chain F residue 242 MET Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain E residue 210 GLU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain K residue 35 ASP Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 84 PHE Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 23 MET Chi-restraints excluded: chain O residue 32 GLN Chi-restraints excluded: chain O residue 185 VAL Chi-restraints excluded: chain O residue 256 GLU Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 180 VAL Chi-restraints excluded: chain N residue 262 VAL Chi-restraints excluded: chain N residue 264 VAL Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 158 MET Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 133 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 100 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 221 optimal weight: 4.9990 chunk 224 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 263 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 275 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 242 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 32 HIS H 164 GLN G 164 GLN ** E 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 137 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.107182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.076432 restraints weight = 57953.802| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.88 r_work: 0.2944 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 30080 Z= 0.126 Angle : 0.581 8.929 40664 Z= 0.285 Chirality : 0.045 0.212 4392 Planarity : 0.004 0.059 5104 Dihedral : 10.977 179.730 4200 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.69 % Favored : 95.22 % Rotamer: Outliers : 2.00 % Allowed : 16.28 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.14), residues: 3536 helix: 0.16 (0.14), residues: 1520 sheet: -0.75 (0.22), residues: 584 loop : -1.22 (0.17), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 239 TYR 0.016 0.001 TYR L 113 PHE 0.016 0.001 PHE J 155 TRP 0.032 0.001 TRP A 85 HIS 0.004 0.001 HIS B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (30080) covalent geometry : angle 0.58137 / 0.29 (40664) hydrogen bonds : bond 0.03204 / 2.14 ( 1180) hydrogen bonds : angle 4.17876 / 2.86 ( 3465) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 455 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 17 ASN cc_start: 0.9197 (m110) cc_final: 0.8843 (m110) REVERT: C 41 ASN cc_start: 0.8143 (t0) cc_final: 0.7750 (t0) REVERT: C 74 ASN cc_start: 0.8268 (t0) cc_final: 0.7852 (t0) REVERT: C 86 ASP cc_start: 0.8548 (t70) cc_final: 0.8294 (t0) REVERT: C 143 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7502 (m-30) REVERT: D 1 MET cc_start: 0.7382 (tpt) cc_final: 0.7057 (tpt) REVERT: D 2 ASN cc_start: 0.9210 (m-40) cc_final: 0.8467 (m-40) REVERT: D 48 ASP cc_start: 0.9016 (OUTLIER) cc_final: 0.8789 (t0) REVERT: D 59 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.6636 (mtm110) REVERT: D 95 GLN cc_start: 0.8234 (pm20) cc_final: 0.7584 (mp10) REVERT: D 158 MET cc_start: 0.8497 (tmm) cc_final: 0.8277 (tmm) REVERT: D 173 ASP cc_start: 0.9260 (m-30) cc_final: 0.8940 (m-30) REVERT: H 148 ASP cc_start: 0.8165 (t0) cc_final: 0.7826 (t0) REVERT: H 212 LYS cc_start: 0.9349 (mmtp) cc_final: 0.8943 (ptpt) REVERT: G 210 GLU cc_start: 0.8989 (tp30) cc_final: 0.8703 (tp30) REVERT: G 211 GLN cc_start: 0.8660 (mp10) cc_final: 0.8217 (mp10) REVERT: G 256 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8727 (mm-30) REVERT: F 136 ASP cc_start: 0.8497 (t0) cc_final: 0.8051 (t0) REVERT: F 200 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8549 (tt) REVERT: E 151 ASP cc_start: 0.7755 (m-30) cc_final: 0.7153 (m-30) REVERT: E 252 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8458 (mt-10) REVERT: A 15 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8013 (mp0) REVERT: A 94 SER cc_start: 0.8610 (p) cc_final: 0.8202 (t) REVERT: A 158 MET cc_start: 0.7989 (tpp) cc_final: 0.6740 (tpp) REVERT: A 161 ARG cc_start: 0.8374 (ttp-110) cc_final: 0.7885 (ttp-110) REVERT: A 178 TYR cc_start: 0.8872 (t80) cc_final: 0.8653 (t80) REVERT: B 9 ASN cc_start: 0.7434 (t0) cc_final: 0.6997 (t0) REVERT: B 94 SER cc_start: 0.7260 (m) cc_final: 0.6925 (p) REVERT: B 138 ARG cc_start: 0.8173 (mtt90) cc_final: 0.7617 (mtt90) REVERT: K 91 ASP cc_start: 0.8466 (m-30) cc_final: 0.8218 (m-30) REVERT: K 106 VAL cc_start: 0.7938 (t) cc_final: 0.7709 (p) REVERT: K 161 ARG cc_start: 0.8352 (mtp-110) cc_final: 0.7944 (ptm160) REVERT: P 32 GLN cc_start: 0.9160 (mp10) cc_final: 0.8700 (mp10) REVERT: P 226 ARG cc_start: 0.8192 (ttm170) cc_final: 0.7908 (mmt90) REVERT: P 256 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8392 (mm-30) REVERT: O 3 GLN cc_start: 0.7900 (tp-100) cc_final: 0.7468 (tp40) REVERT: O 23 MET cc_start: 0.8651 (ttp) cc_final: 0.8268 (mtp) REVERT: O 31 SER cc_start: 0.8105 (m) cc_final: 0.7905 (p) REVERT: O 173 ASP cc_start: 0.8615 (m-30) cc_final: 0.8207 (m-30) REVERT: O 248 ASP cc_start: 0.8677 (p0) cc_final: 0.8211 (t70) REVERT: N 23 MET cc_start: 0.8713 (mtt) cc_final: 0.8410 (mtp) REVERT: M 3 GLN cc_start: 0.8647 (tp-100) cc_final: 0.8229 (tp40) REVERT: M 59 GLU cc_start: 0.8932 (tp30) cc_final: 0.8678 (tp30) REVERT: I 28 LEU cc_start: 0.8417 (tt) cc_final: 0.8139 (tt) REVERT: I 109 THR cc_start: 0.8999 (m) cc_final: 0.8640 (m) REVERT: I 149 ASP cc_start: 0.8598 (t0) cc_final: 0.8342 (m-30) REVERT: I 161 ARG cc_start: 0.8370 (tmm-80) cc_final: 0.7918 (ptm160) REVERT: I 168 ARG cc_start: 0.7880 (ptp-110) cc_final: 0.7494 (ptm160) REVERT: J 8 ARG cc_start: 0.7882 (ptp90) cc_final: 0.7095 (ptp90) REVERT: J 48 ASP cc_start: 0.8862 (t70) cc_final: 0.8481 (t0) REVERT: J 82 GLN cc_start: 0.7697 (tt0) cc_final: 0.7087 (tt0) REVERT: J 104 ARG cc_start: 0.8759 (ttp80) cc_final: 0.8379 (ttp80) REVERT: J 108 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7741 (mtmm) REVERT: J 139 ASP cc_start: 0.8602 (p0) cc_final: 0.8275 (p0) REVERT: J 173 ASP cc_start: 0.8464 (m-30) cc_final: 0.8156 (m-30) outliers start: 64 outliers final: 43 residues processed: 492 average time/residue: 0.2108 time to fit residues: 162.2773 Evaluate side-chains 474 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 425 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 102 ASN Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 205 SER Chi-restraints excluded: chain F residue 242 MET Chi-restraints excluded: chain E residue 210 GLU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain K residue 35 ASP Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 84 PHE Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain O residue 185 VAL Chi-restraints excluded: chain O residue 211 GLN Chi-restraints excluded: chain O residue 256 GLU Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 180 VAL Chi-restraints excluded: chain N residue 262 VAL Chi-restraints excluded: chain N residue 264 VAL Chi-restraints excluded: chain M residue 78 MET Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 116 SER Chi-restraints excluded: chain I residue 123 GLU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 158 MET Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 108 LYS Chi-restraints excluded: chain J residue 133 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 293 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 200 optimal weight: 7.9990 chunk 190 optimal weight: 0.7980 chunk 299 optimal weight: 0.9990 chunk 155 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 180 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 312 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 32 HIS D 32 HIS H 164 GLN ** F 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 ASN B 95 GLN ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 137 ASN O 164 GLN O 237 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.107706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.076922 restraints weight = 58105.888| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.90 r_work: 0.2953 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30080 Z= 0.118 Angle : 0.583 11.316 40664 Z= 0.285 Chirality : 0.045 0.245 4392 Planarity : 0.004 0.058 5104 Dihedral : 10.898 179.415 4200 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.36 % Favored : 95.56 % Rotamer: Outliers : 1.78 % Allowed : 17.72 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.14), residues: 3536 helix: 0.36 (0.14), residues: 1488 sheet: -1.19 (0.23), residues: 536 loop : -1.01 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 10 TYR 0.016 0.001 TYR C 178 PHE 0.026 0.001 PHE I 93 TRP 0.052 0.001 TRP A 85 HIS 0.004 0.001 HIS B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (30080) covalent geometry : angle 0.58348 / 0.28 (40664) hydrogen bonds : bond 0.03116 / 2.09 ( 1180) hydrogen bonds : angle 4.12481 / 2.81 ( 3465) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 434 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 17 ASN cc_start: 0.9191 (m110) cc_final: 0.8831 (m110) REVERT: C 41 ASN cc_start: 0.8139 (t0) cc_final: 0.7741 (t0) REVERT: C 74 ASN cc_start: 0.8273 (t0) cc_final: 0.7848 (t0) REVERT: C 86 ASP cc_start: 0.8608 (t70) cc_final: 0.8341 (t0) REVERT: C 143 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.7479 (m-30) REVERT: D 1 MET cc_start: 0.7444 (tpt) cc_final: 0.7153 (tpt) REVERT: D 2 ASN cc_start: 0.9199 (m-40) cc_final: 0.8444 (m-40) REVERT: D 48 ASP cc_start: 0.9016 (OUTLIER) cc_final: 0.8791 (t0) REVERT: D 59 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.6501 (mtm110) REVERT: D 95 GLN cc_start: 0.8244 (pm20) cc_final: 0.7597 (mp10) REVERT: D 158 MET cc_start: 0.8497 (tmm) cc_final: 0.8252 (tmm) REVERT: H 148 ASP cc_start: 0.8215 (t0) cc_final: 0.7853 (t0) REVERT: H 212 LYS cc_start: 0.9351 (mmtp) cc_final: 0.8944 (ptpt) REVERT: G 78 MET cc_start: 0.8605 (mmm) cc_final: 0.8378 (mmm) REVERT: G 167 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7812 (mm-30) REVERT: G 210 GLU cc_start: 0.8980 (tp30) cc_final: 0.8684 (tp30) REVERT: G 211 GLN cc_start: 0.8654 (mp10) cc_final: 0.8180 (mp10) REVERT: G 249 ASN cc_start: 0.8244 (t0) cc_final: 0.7748 (m-40) REVERT: G 256 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8731 (mm-30) REVERT: F 108 TYR cc_start: 0.9051 (OUTLIER) cc_final: 0.8154 (m-80) REVERT: F 136 ASP cc_start: 0.8555 (t0) cc_final: 0.8120 (t0) REVERT: F 239 ARG cc_start: 0.8860 (mtp85) cc_final: 0.8400 (mtp85) REVERT: E 59 GLU cc_start: 0.8707 (tp30) cc_final: 0.8301 (tp30) REVERT: E 83 ASP cc_start: 0.8719 (p0) cc_final: 0.8372 (p0) REVERT: E 151 ASP cc_start: 0.7825 (m-30) cc_final: 0.7217 (m-30) REVERT: E 237 GLN cc_start: 0.9168 (mm-40) cc_final: 0.8817 (mt0) REVERT: E 252 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8447 (mt-10) REVERT: A 15 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.7985 (mp0) REVERT: A 94 SER cc_start: 0.8608 (p) cc_final: 0.8192 (t) REVERT: A 143 ASP cc_start: 0.7933 (m-30) cc_final: 0.7511 (m-30) REVERT: A 158 MET cc_start: 0.7964 (tpp) cc_final: 0.6704 (tpp) REVERT: A 161 ARG cc_start: 0.8377 (ttp-110) cc_final: 0.7870 (ttp-110) REVERT: A 177 GLU cc_start: 0.9135 (tp30) cc_final: 0.8856 (tm-30) REVERT: A 178 TYR cc_start: 0.8867 (t80) cc_final: 0.8478 (t80) REVERT: B 9 ASN cc_start: 0.7578 (t0) cc_final: 0.7208 (t0) REVERT: B 94 SER cc_start: 0.7040 (m) cc_final: 0.6647 (p) REVERT: B 138 ARG cc_start: 0.8173 (mtt90) cc_final: 0.7617 (mtt90) REVERT: B 168 ARG cc_start: 0.7913 (ttm-80) cc_final: 0.7468 (ttm-80) REVERT: K 91 ASP cc_start: 0.8510 (m-30) cc_final: 0.8276 (m-30) REVERT: K 106 VAL cc_start: 0.7904 (t) cc_final: 0.7684 (p) REVERT: P 32 GLN cc_start: 0.9187 (mp10) cc_final: 0.8747 (mp10) REVERT: P 226 ARG cc_start: 0.8194 (ttm170) cc_final: 0.7907 (mmt90) REVERT: P 246 GLU cc_start: 0.7467 (mp0) cc_final: 0.7253 (mt-10) REVERT: P 256 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8402 (mm-30) REVERT: O 3 GLN cc_start: 0.7904 (tp-100) cc_final: 0.7447 (tp40) REVERT: O 23 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8196 (mtp) REVERT: O 162 TYR cc_start: 0.8487 (t80) cc_final: 0.8241 (t80) REVERT: O 173 ASP cc_start: 0.8648 (m-30) cc_final: 0.8258 (m-30) REVERT: O 248 ASP cc_start: 0.8646 (p0) cc_final: 0.8193 (t70) REVERT: N 23 MET cc_start: 0.8782 (mtt) cc_final: 0.8492 (mtp) REVERT: M 3 GLN cc_start: 0.8665 (tp-100) cc_final: 0.8450 (tp-100) REVERT: I 28 LEU cc_start: 0.8370 (tt) cc_final: 0.8094 (tt) REVERT: I 109 THR cc_start: 0.8968 (m) cc_final: 0.8603 (m) REVERT: I 149 ASP cc_start: 0.8640 (t0) cc_final: 0.8419 (m-30) REVERT: I 161 ARG cc_start: 0.8466 (tmm-80) cc_final: 0.7927 (ptm160) REVERT: J 8 ARG cc_start: 0.7803 (ptp90) cc_final: 0.6817 (ptp90) REVERT: J 48 ASP cc_start: 0.8861 (t70) cc_final: 0.8481 (t0) REVERT: J 82 GLN cc_start: 0.7728 (tt0) cc_final: 0.7198 (tt0) REVERT: J 104 ARG cc_start: 0.8703 (ttp80) cc_final: 0.8316 (ttp80) REVERT: J 139 ASP cc_start: 0.8588 (p0) cc_final: 0.8283 (p0) REVERT: J 143 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.8072 (m-30) REVERT: J 173 ASP cc_start: 0.8463 (m-30) cc_final: 0.8161 (m-30) outliers start: 57 outliers final: 39 residues processed: 467 average time/residue: 0.2016 time to fit residues: 147.0651 Evaluate side-chains 460 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 414 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 108 TYR Chi-restraints excluded: chain F residue 205 SER Chi-restraints excluded: chain F residue 242 MET Chi-restraints excluded: chain E residue 210 GLU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 84 PHE Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 23 MET Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain O residue 185 VAL Chi-restraints excluded: chain O residue 256 GLU Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 262 VAL Chi-restraints excluded: chain N residue 264 VAL Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 158 MET Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 143 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 248 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 303 optimal weight: 0.1980 chunk 57 optimal weight: 0.9990 chunk 323 optimal weight: 8.9990 chunk 231 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 237 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 282 optimal weight: 0.6980 chunk 218 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 32 HIS C 95 GLN D 32 HIS H 164 GLN E 137 ASN ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 137 ASN O 164 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.108269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.077441 restraints weight = 58250.314| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.91 r_work: 0.2962 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30080 Z= 0.114 Angle : 0.582 9.735 40664 Z= 0.284 Chirality : 0.045 0.204 4392 Planarity : 0.004 0.058 5104 Dihedral : 10.819 179.513 4200 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.52 % Favored : 95.39 % Rotamer: Outliers : 1.94 % Allowed : 17.75 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.14), residues: 3536 helix: 0.48 (0.14), residues: 1488 sheet: -1.14 (0.23), residues: 536 loop : -0.96 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 10 TYR 0.016 0.001 TYR C 178 PHE 0.023 0.001 PHE I 93 TRP 0.038 0.001 TRP A 85 HIS 0.003 0.001 HIS K 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (30080) covalent geometry : angle 0.58222 / 0.28 (40664) hydrogen bonds : bond 0.03037 / 2.04 ( 1180) hydrogen bonds : angle 4.05396 / 2.77 ( 3465) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 441 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 17 ASN cc_start: 0.9193 (m110) cc_final: 0.8854 (m110) REVERT: C 41 ASN cc_start: 0.8144 (t0) cc_final: 0.7746 (t0) REVERT: C 74 ASN cc_start: 0.8348 (t0) cc_final: 0.7934 (t0) REVERT: C 86 ASP cc_start: 0.8600 (t70) cc_final: 0.8328 (t0) REVERT: C 143 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7485 (m-30) REVERT: D 1 MET cc_start: 0.7540 (tpt) cc_final: 0.7261 (tpt) REVERT: D 2 ASN cc_start: 0.9208 (m-40) cc_final: 0.8464 (m-40) REVERT: D 48 ASP cc_start: 0.9019 (t70) cc_final: 0.8793 (t0) REVERT: D 59 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.6462 (mtm110) REVERT: D 95 GLN cc_start: 0.8239 (pm20) cc_final: 0.7558 (mp10) REVERT: D 158 MET cc_start: 0.8570 (tmm) cc_final: 0.8314 (tmm) REVERT: D 173 ASP cc_start: 0.9331 (m-30) cc_final: 0.9043 (m-30) REVERT: H 148 ASP cc_start: 0.8161 (t0) cc_final: 0.7780 (t0) REVERT: H 212 LYS cc_start: 0.9337 (mmtp) cc_final: 0.8941 (ptpt) REVERT: G 167 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7768 (mm-30) REVERT: G 210 GLU cc_start: 0.8984 (tp30) cc_final: 0.8688 (tp30) REVERT: G 211 GLN cc_start: 0.8658 (mp10) cc_final: 0.8167 (mp10) REVERT: G 249 ASN cc_start: 0.8241 (t0) cc_final: 0.7745 (m-40) REVERT: G 256 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8720 (mm-30) REVERT: F 108 TYR cc_start: 0.9052 (OUTLIER) cc_final: 0.8168 (m-80) REVERT: F 136 ASP cc_start: 0.8572 (t0) cc_final: 0.8121 (t0) REVERT: F 237 GLN cc_start: 0.8688 (mt0) cc_final: 0.8478 (mt0) REVERT: F 239 ARG cc_start: 0.8853 (mtp85) cc_final: 0.8414 (mtp85) REVERT: E 59 GLU cc_start: 0.8743 (tp30) cc_final: 0.8382 (tp30) REVERT: E 83 ASP cc_start: 0.8739 (p0) cc_final: 0.8394 (p0) REVERT: E 151 ASP cc_start: 0.7805 (m-30) cc_final: 0.7186 (m-30) REVERT: E 237 GLN cc_start: 0.9142 (mm-40) cc_final: 0.8882 (mt0) REVERT: E 252 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8445 (mt-10) REVERT: A 15 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8039 (mp0) REVERT: A 94 SER cc_start: 0.8615 (p) cc_final: 0.8203 (t) REVERT: A 141 GLN cc_start: 0.7767 (mm-40) cc_final: 0.7535 (mm-40) REVERT: A 143 ASP cc_start: 0.7842 (m-30) cc_final: 0.7420 (m-30) REVERT: A 158 MET cc_start: 0.7956 (tpp) cc_final: 0.6813 (tpp) REVERT: A 161 ARG cc_start: 0.8409 (ttp-110) cc_final: 0.7952 (ttp-110) REVERT: A 177 GLU cc_start: 0.9117 (tp30) cc_final: 0.8856 (tm-30) REVERT: B 9 ASN cc_start: 0.7549 (t0) cc_final: 0.7230 (t0) REVERT: B 94 SER cc_start: 0.7209 (m) cc_final: 0.6979 (p) REVERT: B 138 ARG cc_start: 0.8166 (mtt90) cc_final: 0.7615 (mtt90) REVERT: B 173 ASP cc_start: 0.8618 (m-30) cc_final: 0.8266 (m-30) REVERT: K 91 ASP cc_start: 0.8494 (m-30) cc_final: 0.8272 (m-30) REVERT: K 106 VAL cc_start: 0.7913 (t) cc_final: 0.7688 (p) REVERT: L 14 LYS cc_start: 0.8862 (mttp) cc_final: 0.8631 (mmtm) REVERT: P 32 GLN cc_start: 0.9196 (mp10) cc_final: 0.8750 (mp10) REVERT: P 226 ARG cc_start: 0.8185 (ttm170) cc_final: 0.7969 (mmt90) REVERT: P 246 GLU cc_start: 0.7479 (mp0) cc_final: 0.7222 (tt0) REVERT: P 256 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8362 (mm-30) REVERT: O 3 GLN cc_start: 0.7936 (tp-100) cc_final: 0.7469 (tp40) REVERT: O 162 TYR cc_start: 0.8473 (t80) cc_final: 0.8225 (t80) REVERT: O 173 ASP cc_start: 0.8650 (m-30) cc_final: 0.8265 (m-30) REVERT: O 248 ASP cc_start: 0.8638 (p0) cc_final: 0.8201 (t70) REVERT: N 23 MET cc_start: 0.8715 (mtt) cc_final: 0.8477 (mtp) REVERT: N 78 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8010 (mpp) REVERT: M 3 GLN cc_start: 0.8714 (tp-100) cc_final: 0.8485 (tp-100) REVERT: I 28 LEU cc_start: 0.8365 (tt) cc_final: 0.8078 (tt) REVERT: I 109 THR cc_start: 0.8965 (m) cc_final: 0.8636 (m) REVERT: I 161 ARG cc_start: 0.8578 (tmm-80) cc_final: 0.7924 (ptm160) REVERT: J 8 ARG cc_start: 0.7815 (ptp90) cc_final: 0.6966 (ptp90) REVERT: J 48 ASP cc_start: 0.8855 (t70) cc_final: 0.8477 (t0) REVERT: J 82 GLN cc_start: 0.7766 (tt0) cc_final: 0.7233 (tt0) REVERT: J 104 ARG cc_start: 0.8725 (ttp80) cc_final: 0.8343 (ttp80) REVERT: J 125 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8009 (mp0) REVERT: J 139 ASP cc_start: 0.8547 (p0) cc_final: 0.8235 (p0) REVERT: J 173 ASP cc_start: 0.8431 (m-30) cc_final: 0.8141 (m-30) outliers start: 62 outliers final: 46 residues processed: 478 average time/residue: 0.2144 time to fit residues: 159.6885 Evaluate side-chains 472 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 421 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 108 TYR Chi-restraints excluded: chain F residue 205 SER Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 210 GLU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 84 PHE Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 23 MET Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain O residue 185 VAL Chi-restraints excluded: chain O residue 211 GLN Chi-restraints excluded: chain O residue 256 GLU Chi-restraints excluded: chain N residue 78 MET Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 180 VAL Chi-restraints excluded: chain N residue 242 MET Chi-restraints excluded: chain N residue 262 VAL Chi-restraints excluded: chain N residue 264 VAL Chi-restraints excluded: chain M residue 17 VAL Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 123 GLU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 81 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 130 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 230 optimal weight: 0.6980 chunk 60 optimal weight: 10.0000 chunk 301 optimal weight: 4.9990 chunk 294 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 256 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 196 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 32 HIS C 95 GLN D 32 HIS H 164 GLN A 11 HIS B 32 HIS ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 137 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.104766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.074713 restraints weight = 59326.623| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.74 r_work: 0.2917 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 30080 Z= 0.177 Angle : 0.622 12.282 40664 Z= 0.304 Chirality : 0.047 0.214 4392 Planarity : 0.004 0.058 5104 Dihedral : 10.851 177.739 4200 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.98 % Favored : 94.94 % Rotamer: Outliers : 1.88 % Allowed : 18.09 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.14), residues: 3536 helix: 0.46 (0.14), residues: 1488 sheet: -1.17 (0.23), residues: 536 loop : -0.95 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 49 TYR 0.025 0.001 TYR B 113 PHE 0.023 0.001 PHE I 93 TRP 0.040 0.001 TRP A 85 HIS 0.005 0.001 HIS I 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (30080) covalent geometry : angle 0.62209 / 0.30 (40664) hydrogen bonds : bond 0.03357 / 2.26 ( 1180) hydrogen bonds : angle 4.16579 / 2.84 ( 3465) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 433 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 17 ASN cc_start: 0.9225 (m110) cc_final: 0.8845 (m110) REVERT: C 41 ASN cc_start: 0.8226 (t0) cc_final: 0.7826 (t0) REVERT: C 86 ASP cc_start: 0.8645 (t70) cc_final: 0.8346 (t0) REVERT: C 120 TYR cc_start: 0.8372 (m-80) cc_final: 0.8000 (m-80) REVERT: C 157 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7680 (tm-30) REVERT: D 1 MET cc_start: 0.7517 (tpt) cc_final: 0.7270 (tpt) REVERT: D 2 ASN cc_start: 0.9226 (m-40) cc_final: 0.8547 (m-40) REVERT: D 48 ASP cc_start: 0.8977 (t70) cc_final: 0.8747 (t0) REVERT: D 59 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.6683 (mtm110) REVERT: D 95 GLN cc_start: 0.8179 (pm20) cc_final: 0.7482 (mp10) REVERT: D 158 MET cc_start: 0.8594 (tmm) cc_final: 0.8211 (tmm) REVERT: H 212 LYS cc_start: 0.9285 (mmtp) cc_final: 0.8897 (ptpt) REVERT: G 210 GLU cc_start: 0.8971 (tp30) cc_final: 0.8718 (tp30) REVERT: G 211 GLN cc_start: 0.8581 (mp10) cc_final: 0.8374 (mp10) REVERT: G 249 ASN cc_start: 0.8210 (t0) cc_final: 0.7812 (m-40) REVERT: G 256 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8726 (mm-30) REVERT: F 108 TYR cc_start: 0.9168 (OUTLIER) cc_final: 0.8323 (m-80) REVERT: F 136 ASP cc_start: 0.8541 (t0) cc_final: 0.8198 (t0) REVERT: F 239 ARG cc_start: 0.9023 (mtp85) cc_final: 0.8627 (mtp85) REVERT: E 59 GLU cc_start: 0.8782 (tp30) cc_final: 0.8576 (tt0) REVERT: E 151 ASP cc_start: 0.7846 (m-30) cc_final: 0.7273 (m-30) REVERT: E 252 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8470 (mt-10) REVERT: A 15 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8106 (mp0) REVERT: A 158 MET cc_start: 0.7875 (tpp) cc_final: 0.6687 (tpp) REVERT: A 161 ARG cc_start: 0.8411 (ttp-110) cc_final: 0.7944 (ttp-110) REVERT: A 178 TYR cc_start: 0.8707 (t80) cc_final: 0.8344 (t80) REVERT: B 9 ASN cc_start: 0.7795 (t0) cc_final: 0.7495 (t0) REVERT: B 138 ARG cc_start: 0.8282 (mtt90) cc_final: 0.7768 (mtt90) REVERT: B 173 ASP cc_start: 0.8616 (m-30) cc_final: 0.8273 (m-30) REVERT: K 91 ASP cc_start: 0.8368 (m-30) cc_final: 0.8166 (m-30) REVERT: K 106 VAL cc_start: 0.8182 (t) cc_final: 0.7968 (p) REVERT: L 42 VAL cc_start: 0.8499 (t) cc_final: 0.8285 (p) REVERT: P 32 GLN cc_start: 0.9132 (mp10) cc_final: 0.8758 (mp10) REVERT: P 226 ARG cc_start: 0.8301 (ttm170) cc_final: 0.8047 (mmt90) REVERT: P 256 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8508 (mm-30) REVERT: O 3 GLN cc_start: 0.7862 (tp-100) cc_final: 0.7483 (tp40) REVERT: O 31 SER cc_start: 0.8477 (m) cc_final: 0.8250 (p) REVERT: O 248 ASP cc_start: 0.8507 (p0) cc_final: 0.8178 (t70) REVERT: N 78 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8038 (mpp) REVERT: N 156 VAL cc_start: 0.9468 (p) cc_final: 0.9233 (m) REVERT: N 159 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8087 (mm-30) REVERT: N 226 ARG cc_start: 0.8960 (mtp180) cc_final: 0.8747 (mtp85) REVERT: M 3 GLN cc_start: 0.8583 (tp-100) cc_final: 0.8252 (tp40) REVERT: I 28 LEU cc_start: 0.8661 (tt) cc_final: 0.8391 (tt) REVERT: I 109 THR cc_start: 0.9130 (m) cc_final: 0.8860 (m) REVERT: I 161 ARG cc_start: 0.8522 (tmm-80) cc_final: 0.7931 (ptm160) REVERT: J 8 ARG cc_start: 0.8093 (ptp90) cc_final: 0.7227 (ptp90) REVERT: J 48 ASP cc_start: 0.8930 (t70) cc_final: 0.8590 (t0) REVERT: J 82 GLN cc_start: 0.7928 (tt0) cc_final: 0.7456 (tt0) REVERT: J 125 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7940 (mp0) REVERT: J 139 ASP cc_start: 0.8489 (p0) cc_final: 0.8191 (p0) REVERT: J 143 ASP cc_start: 0.8435 (t0) cc_final: 0.7975 (m-30) REVERT: J 173 ASP cc_start: 0.8362 (m-30) cc_final: 0.8067 (m-30) outliers start: 60 outliers final: 52 residues processed: 474 average time/residue: 0.2112 time to fit residues: 156.2363 Evaluate side-chains 474 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 418 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 108 TYR Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 205 SER Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain E residue 210 GLU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 84 PHE Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain O residue 185 VAL Chi-restraints excluded: chain O residue 211 GLN Chi-restraints excluded: chain O residue 256 GLU Chi-restraints excluded: chain N residue 78 MET Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 180 VAL Chi-restraints excluded: chain N residue 242 MET Chi-restraints excluded: chain N residue 262 VAL Chi-restraints excluded: chain N residue 264 VAL Chi-restraints excluded: chain M residue 200 LEU Chi-restraints excluded: chain M residue 262 VAL Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 116 SER Chi-restraints excluded: chain I residue 123 GLU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 168 ARG Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 160 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 134 optimal weight: 0.8980 chunk 287 optimal weight: 0.9990 chunk 347 optimal weight: 0.0770 chunk 295 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 344 optimal weight: 20.0000 chunk 19 optimal weight: 3.9990 chunk 234 optimal weight: 2.9990 chunk 314 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 overall best weight: 0.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 32 HIS C 74 ASN C 95 GLN D 32 HIS H 164 GLN E 137 ASN ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 137 ASN M 237 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.106859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.077025 restraints weight = 58596.222| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.74 r_work: 0.2963 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30080 Z= 0.118 Angle : 0.599 11.381 40664 Z= 0.293 Chirality : 0.045 0.210 4392 Planarity : 0.004 0.058 5104 Dihedral : 10.808 177.621 4200 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.67 % Favored : 95.25 % Rotamer: Outliers : 1.84 % Allowed : 18.44 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.14), residues: 3536 helix: 0.50 (0.14), residues: 1504 sheet: -1.07 (0.23), residues: 536 loop : -0.90 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 168 TYR 0.024 0.001 TYR B 113 PHE 0.021 0.001 PHE I 93 TRP 0.069 0.001 TRP A 85 HIS 0.005 0.001 HIS I 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (30080) covalent geometry : angle 0.59905 / 0.29 (40664) hydrogen bonds : bond 0.03107 / 2.08 ( 1180) hydrogen bonds : angle 4.06203 / 2.77 ( 3465) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 435 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 ASN cc_start: 0.8274 (t0) cc_final: 0.7903 (t0) REVERT: C 86 ASP cc_start: 0.8649 (t70) cc_final: 0.8374 (t0) REVERT: C 143 ASP cc_start: 0.7527 (OUTLIER) cc_final: 0.7271 (m-30) REVERT: C 157 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7527 (tm-30) REVERT: D 1 MET cc_start: 0.7570 (tpt) cc_final: 0.7314 (tpt) REVERT: D 2 ASN cc_start: 0.9172 (m-40) cc_final: 0.8530 (t0) REVERT: D 48 ASP cc_start: 0.8945 (t70) cc_final: 0.8716 (t0) REVERT: D 59 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.6723 (mtm110) REVERT: D 95 GLN cc_start: 0.8132 (pm20) cc_final: 0.7430 (mp10) REVERT: D 104 ARG cc_start: 0.7734 (mtm-85) cc_final: 0.7351 (mtm-85) REVERT: D 158 MET cc_start: 0.8586 (tmm) cc_final: 0.8236 (tmm) REVERT: D 173 ASP cc_start: 0.9223 (m-30) cc_final: 0.8923 (m-30) REVERT: H 212 LYS cc_start: 0.9249 (mmtp) cc_final: 0.8956 (ptpt) REVERT: H 237 GLN cc_start: 0.8726 (mt0) cc_final: 0.8515 (mt0) REVERT: G 210 GLU cc_start: 0.8950 (tp30) cc_final: 0.8706 (tp30) REVERT: G 211 GLN cc_start: 0.8552 (mp10) cc_final: 0.8148 (mp10) REVERT: G 249 ASN cc_start: 0.8190 (t0) cc_final: 0.7833 (m-40) REVERT: G 256 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8712 (mm-30) REVERT: F 108 TYR cc_start: 0.9134 (OUTLIER) cc_final: 0.8378 (m-80) REVERT: F 136 ASP cc_start: 0.8494 (t0) cc_final: 0.8168 (t0) REVERT: E 59 GLU cc_start: 0.8650 (tp30) cc_final: 0.8360 (tp30) REVERT: E 83 ASP cc_start: 0.8552 (p0) cc_final: 0.8248 (p0) REVERT: E 151 ASP cc_start: 0.7684 (m-30) cc_final: 0.7101 (m-30) REVERT: E 252 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8446 (mt-10) REVERT: A 15 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8129 (mp0) REVERT: A 85 TRP cc_start: 0.7879 (t60) cc_final: 0.7312 (t60) REVERT: A 94 SER cc_start: 0.8428 (p) cc_final: 0.8077 (t) REVERT: A 143 ASP cc_start: 0.7772 (m-30) cc_final: 0.7475 (m-30) REVERT: A 158 MET cc_start: 0.7725 (tpp) cc_final: 0.6572 (tpp) REVERT: A 161 ARG cc_start: 0.8401 (ttp-110) cc_final: 0.7925 (ttp-110) REVERT: B 9 ASN cc_start: 0.7826 (t0) cc_final: 0.7552 (t0) REVERT: B 138 ARG cc_start: 0.8231 (mtt90) cc_final: 0.7760 (mtt90) REVERT: B 143 ASP cc_start: 0.8000 (OUTLIER) cc_final: 0.7159 (p0) REVERT: K 91 ASP cc_start: 0.8357 (m-30) cc_final: 0.8149 (m-30) REVERT: K 106 VAL cc_start: 0.8174 (t) cc_final: 0.7963 (p) REVERT: K 177 GLU cc_start: 0.8848 (tp30) cc_final: 0.8586 (tm-30) REVERT: L 42 VAL cc_start: 0.8509 (t) cc_final: 0.8296 (p) REVERT: L 161 ARG cc_start: 0.8699 (ptt90) cc_final: 0.8020 (tmm-80) REVERT: P 32 GLN cc_start: 0.9105 (mp10) cc_final: 0.8787 (mp10) REVERT: P 226 ARG cc_start: 0.8255 (ttm170) cc_final: 0.7985 (mmt90) REVERT: P 256 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8460 (mm-30) REVERT: O 3 GLN cc_start: 0.7778 (tp-100) cc_final: 0.7435 (tp40) REVERT: O 162 TYR cc_start: 0.8590 (t80) cc_final: 0.8361 (t80) REVERT: O 173 ASP cc_start: 0.8580 (m-30) cc_final: 0.8232 (m-30) REVERT: O 248 ASP cc_start: 0.8533 (p0) cc_final: 0.8185 (t70) REVERT: N 78 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8052 (mpp) REVERT: N 156 VAL cc_start: 0.9437 (p) cc_final: 0.9210 (m) REVERT: N 159 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8032 (mm-30) REVERT: I 28 LEU cc_start: 0.8641 (tt) cc_final: 0.8379 (tt) REVERT: I 109 THR cc_start: 0.9068 (m) cc_final: 0.8796 (m) REVERT: J 8 ARG cc_start: 0.8140 (ptp90) cc_final: 0.7203 (ptp90) REVERT: J 48 ASP cc_start: 0.8895 (t70) cc_final: 0.8572 (t0) REVERT: J 82 GLN cc_start: 0.7963 (tt0) cc_final: 0.7521 (tt0) REVERT: J 104 ARG cc_start: 0.8778 (ttp80) cc_final: 0.8382 (ttp80) REVERT: J 125 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7912 (mp0) REVERT: J 139 ASP cc_start: 0.8500 (p0) cc_final: 0.8198 (p0) REVERT: J 143 ASP cc_start: 0.8386 (t0) cc_final: 0.7942 (m-30) REVERT: J 173 ASP cc_start: 0.8327 (m-30) cc_final: 0.8033 (m-30) outliers start: 59 outliers final: 44 residues processed: 471 average time/residue: 0.2128 time to fit residues: 156.7494 Evaluate side-chains 472 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 422 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 108 TYR Chi-restraints excluded: chain F residue 205 SER Chi-restraints excluded: chain E residue 210 GLU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 84 PHE Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain P residue 170 THR Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 23 MET Chi-restraints excluded: chain O residue 140 THR Chi-restraints excluded: chain O residue 185 VAL Chi-restraints excluded: chain O residue 256 GLU Chi-restraints excluded: chain N residue 78 MET Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 180 VAL Chi-restraints excluded: chain N residue 242 MET Chi-restraints excluded: chain N residue 262 VAL Chi-restraints excluded: chain N residue 264 VAL Chi-restraints excluded: chain M residue 262 VAL Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain I residue 116 SER Chi-restraints excluded: chain I residue 123 GLU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 81 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 228 optimal weight: 0.2980 chunk 186 optimal weight: 7.9990 chunk 92 optimal weight: 0.5980 chunk 209 optimal weight: 8.9990 chunk 227 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 302 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 137 optimal weight: 0.7980 chunk 200 optimal weight: 7.9990 chunk 162 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 32 HIS D 32 HIS H 164 GLN ** F 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 HIS ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 137 ASN O 237 GLN M 237 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.107646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.077697 restraints weight = 59273.747| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.76 r_work: 0.2975 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30080 Z= 0.115 Angle : 0.593 11.251 40664 Z= 0.288 Chirality : 0.045 0.207 4392 Planarity : 0.004 0.057 5104 Dihedral : 10.696 177.305 4200 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.47 % Favored : 95.45 % Rotamer: Outliers : 1.81 % Allowed : 18.53 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.14), residues: 3536 helix: 0.57 (0.14), residues: 1504 sheet: -1.01 (0.23), residues: 536 loop : -0.86 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 10 TYR 0.021 0.001 TYR B 113 PHE 0.022 0.001 PHE I 93 TRP 0.053 0.001 TRP A 85 HIS 0.005 0.001 HIS I 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 (30080) covalent geometry : angle 0.59251 / 0.29 (40664) hydrogen bonds : bond 0.03039 / 2.03 ( 1180) hydrogen bonds : angle 4.01197 / 2.74 ( 3465) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7228.19 seconds wall clock time: 125 minutes 8.40 seconds (7508.40 seconds total)