Starting phenix.real_space_refine on Sat Aug 8 20:03:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xvc_67286/08_2026/9xvc_67286.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xvc_67286/08_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_67286/08_2026/9xvc_67286.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xvc_67286/08_2026/9xvc_67286.map" model { file = "/net/cci-nas-00/data/ceres_data/9xvc_67286/08_2026/9xvc_67286.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xvc_67286/08_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-2.2rc3-6140/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: 6.38, 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: 2.35 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 0.71 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: 4.93 Time building geometry restraints manager: 3.22 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: 40022 4.26 - 8.52: 590 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: 17564 34.15 - 68.30: 554 68.30 - 102.45: 44 102.45 - 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: 4050 0.107 - 0.215: 315 0.215 - 0.322: 19 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: 0.00 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: 4.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 26.140 Find NCS groups from input model: 0.810 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.200 ------------------------------------------------------------------------------- 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= 0.458 Angle : 1.247 21.305 40664 Z= 0.697 Chirality : 0.062 0.536 4392 Planarity : 0.009 0.106 5104 Dihedral : 16.630 170.756 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 0.00890 / 0.46 (30080) covalent geometry : angle 1.24670 / 0.70 (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 : 1.203 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: 0.1983 time to fit residues: 189.7607 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 : 1.162 ------------------------------------------------------------------------------- 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... D 17 ASN H 164 GLN G 24 ASN G 231 GLN ** F 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 HIS L 38 GLN L 102 ASN O 107 ASN M 92 HIS I 74 ASN J 32 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.111311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.081507 restraints weight = 59366.000| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.79 r_work: 0.3046 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30080 Z= 0.122 Angle : 0.618 8.562 40664 Z= 0.311 Chirality : 0.045 0.223 4392 Planarity : 0.005 0.066 5104 Dihedral : 12.338 174.296 4202 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.33 % Favored : 95.59 % Rotamer: Outliers : 0.97 % Allowed : 9.31 % Favored : 89.72 % 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: -1.89 (0.13), residues: 3536 helix: -0.81 (0.13), residues: 1496 sheet: -1.18 (0.27), residues: 408 loop : -1.63 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 59 TYR 0.021 0.001 TYR J 69 PHE 0.026 0.001 PHE I 93 TRP 0.017 0.001 TRP L 85 HIS 0.009 0.001 HIS K 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (30080) covalent geometry : angle 0.61819 / 0.31 (40664) hydrogen bonds : bond 0.04027 / 2.68 ( 1180) hydrogen bonds : angle 5.07664 / 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 559 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 528 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 ASN cc_start: 0.8292 (t0) cc_final: 0.8029 (t0) REVERT: C 74 ASN cc_start: 0.8406 (t0) cc_final: 0.7817 (t0) REVERT: C 158 MET cc_start: 0.6068 (mtt) cc_final: 0.5861 (mtt) REVERT: D 1 MET cc_start: 0.7433 (tpt) cc_final: 0.7205 (tpt) REVERT: D 2 ASN cc_start: 0.8806 (m-40) cc_final: 0.8363 (m-40) REVERT: D 158 MET cc_start: 0.8442 (tmm) cc_final: 0.8161 (tmm) REVERT: H 23 MET cc_start: 0.8152 (mtp) cc_final: 0.7941 (mtp) REVERT: E 56 GLU cc_start: 0.8463 (mp0) cc_final: 0.8229 (mp0) REVERT: E 151 ASP cc_start: 0.7815 (m-30) cc_final: 0.7292 (m-30) REVERT: A 94 SER cc_start: 0.8465 (p) cc_final: 0.8218 (t) REVERT: A 158 MET cc_start: 0.7713 (tpp) cc_final: 0.6493 (tpp) REVERT: A 161 ARG cc_start: 0.8358 (ttp-110) cc_final: 0.7850 (ttp-110) REVERT: B 19 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8781 (mp) REVERT: B 85 TRP cc_start: 0.7967 (t-100) cc_final: 0.7751 (t-100) REVERT: B 138 ARG cc_start: 0.7820 (mtt90) cc_final: 0.7386 (mtt90) REVERT: B 143 ASP cc_start: 0.7778 (m-30) cc_final: 0.6853 (p0) REVERT: K 173 ASP cc_start: 0.8739 (m-30) cc_final: 0.8476 (m-30) REVERT: L 104 ARG cc_start: 0.8718 (ptm160) cc_final: 0.8464 (ptm160) REVERT: P 226 ARG cc_start: 0.8264 (ttm170) cc_final: 0.8005 (mmt90) REVERT: P 256 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8434 (mm-30) REVERT: O 3 GLN cc_start: 0.7377 (tp-100) cc_final: 0.7169 (tp40) REVERT: O 209 LYS cc_start: 0.8718 (mttp) cc_final: 0.8419 (mptt) REVERT: N 164 GLN cc_start: 0.8869 (mt0) cc_final: 0.8649 (mt0) REVERT: I 109 THR cc_start: 0.8970 (m) cc_final: 0.8754 (m) REVERT: I 127 GLN cc_start: 0.8502 (mm110) cc_final: 0.8284 (mm110) REVERT: I 149 ASP cc_start: 0.7945 (t70) cc_final: 0.7556 (t0) REVERT: J 38 GLN cc_start: 0.8750 (mt0) cc_final: 0.8490 (mt0) REVERT: J 48 ASP cc_start: 0.8815 (t70) cc_final: 0.8505 (t0) REVERT: J 139 ASP cc_start: 0.8445 (p0) cc_final: 0.7964 (p0) REVERT: J 173 ASP cc_start: 0.8273 (m-30) cc_final: 0.7998 (m-30) outliers start: 31 outliers final: 17 residues processed: 539 average time/residue: 0.2002 time to fit residues: 170.4527 Evaluate side-chains 464 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 446 time to evaluate : 1.180 ------------------------------------------------------------------------------- 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 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 P residue 46 ASP Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain M residue 7 ASP 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: 7.9990 chunk 283 optimal weight: 1.9990 chunk 143 optimal weight: 0.2980 chunk 334 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 345 optimal weight: 0.0970 chunk 113 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 32 HIS D 17 ASN H 24 ASN H 164 GLN E 237 GLN O 211 GLN J 127 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.110451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.079919 restraints weight = 58299.387| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.91 r_work: 0.3003 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 30080 Z= 0.118 Angle : 0.576 8.162 40664 Z= 0.287 Chirality : 0.045 0.202 4392 Planarity : 0.005 0.060 5104 Dihedral : 11.625 174.947 4200 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.44 % Favored : 95.48 % Rotamer: Outliers : 1.34 % Allowed : 12.84 % Favored : 85.81 % 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: -1.45 (0.14), residues: 3536 helix: -0.44 (0.13), residues: 1560 sheet: -0.64 (0.25), residues: 464 loop : -1.54 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 168 TYR 0.015 0.001 TYR J 69 PHE 0.017 0.001 PHE A 172 TRP 0.014 0.001 TRP H 74 HIS 0.016 0.001 HIS B 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (30080) covalent geometry : angle 0.57625 / 0.29 (40664) hydrogen bonds : bond 0.03389 / 2.28 ( 1180) hydrogen bonds : angle 4.53552 / 3.11 ( 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 539 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 496 time to evaluate : 1.016 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: 0.8175 (t0) cc_final: 0.7871 (t0) REVERT: C 74 ASN cc_start: 0.8354 (t0) cc_final: 0.8147 (t0) REVERT: D 1 MET cc_start: 0.7363 (tpt) cc_final: 0.7129 (tpt) REVERT: D 2 ASN cc_start: 0.8929 (m-40) cc_final: 0.8334 (m-40) REVERT: D 95 GLN cc_start: 0.8175 (pm20) cc_final: 0.7920 (mp10) REVERT: H 169 GLU cc_start: 0.8300 (tp30) cc_final: 0.7879 (tp30) REVERT: G 78 MET cc_start: 0.8603 (mmm) cc_final: 0.8310 (mmm) REVERT: G 167 GLU cc_start: 0.8255 (mm-30) cc_final: 0.8011 (mm-30) REVERT: G 210 GLU cc_start: 0.8935 (tp30) cc_final: 0.8724 (tp30) REVERT: F 136 ASP cc_start: 0.8374 (t0) cc_final: 0.8135 (t0) REVERT: F 200 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8485 (tt) REVERT: F 237 GLN cc_start: 0.8986 (mm110) cc_final: 0.8617 (mt0) REVERT: E 56 GLU cc_start: 0.8511 (mp0) cc_final: 0.8136 (mp0) REVERT: E 151 ASP cc_start: 0.7819 (m-30) cc_final: 0.7232 (m-30) REVERT: E 173 ASP cc_start: 0.8916 (m-30) cc_final: 0.8607 (m-30) REVERT: A 94 SER cc_start: 0.8540 (p) cc_final: 0.8183 (t) REVERT: A 158 MET cc_start: 0.7864 (tpp) cc_final: 0.6632 (tpp) REVERT: A 161 ARG cc_start: 0.8372 (ttp-110) cc_final: 0.7897 (ttp-110) REVERT: A 177 GLU cc_start: 0.9030 (tp30) cc_final: 0.8758 (tm-30) REVERT: B 1 MET cc_start: 0.6701 (tpt) cc_final: 0.6449 (tpt) REVERT: B 138 ARG cc_start: 0.7801 (mtt90) cc_final: 0.7425 (mtt90) REVERT: B 143 ASP cc_start: 0.8108 (m-30) cc_final: 0.7177 (p0) REVERT: L 11 HIS cc_start: 0.8025 (m-70) cc_final: 0.7596 (m170) REVERT: L 42 VAL cc_start: 0.8131 (t) cc_final: 0.7916 (p) REVERT: L 163 ASN cc_start: 0.8117 (p0) cc_final: 0.7880 (p0) REVERT: P 226 ARG cc_start: 0.8185 (ttm170) cc_final: 0.7925 (mmt90) REVERT: P 256 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8306 (mm-30) REVERT: O 3 GLN cc_start: 0.7741 (tp-100) cc_final: 0.7202 (tp-100) REVERT: O 173 ASP cc_start: 0.8656 (m-30) cc_final: 0.8304 (m-30) REVERT: O 209 LYS cc_start: 0.8598 (mttp) cc_final: 0.8259 (mttm) REVERT: N 23 MET cc_start: 0.8382 (mtt) cc_final: 0.8026 (mtp) REVERT: M 3 GLN cc_start: 0.8368 (tp-100) cc_final: 0.8012 (tp-100) REVERT: M 49 ARG cc_start: 0.8825 (mtm-85) cc_final: 0.8340 (mtm-85) REVERT: I 28 LEU cc_start: 0.8391 (tt) cc_final: 0.8147 (tt) REVERT: I 109 THR cc_start: 0.8853 (m) cc_final: 0.8573 (m) REVERT: I 149 ASP cc_start: 0.8099 (t70) cc_final: 0.7845 (t0) REVERT: I 158 MET cc_start: 0.7996 (tpp) cc_final: 0.7766 (mtp) REVERT: J 8 ARG cc_start: 0.7688 (ptp90) cc_final: 0.7082 (ptp90) REVERT: J 48 ASP cc_start: 0.8804 (t70) cc_final: 0.8421 (t0) REVERT: J 82 GLN cc_start: 0.7277 (tt0) cc_final: 0.6828 (tt0) REVERT: J 104 ARG cc_start: 0.8778 (ttp80) cc_final: 0.8524 (ttp80) REVERT: J 139 ASP cc_start: 0.8545 (p0) cc_final: 0.8108 (p0) REVERT: J 173 ASP cc_start: 0.8356 (m-30) cc_final: 0.8087 (m-30) outliers start: 43 outliers final: 26 residues processed: 519 average time/residue: 0.1812 time to fit residues: 149.2734 Evaluate side-chains 466 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 439 time to evaluate : 1.222 ------------------------------------------------------------------------------- 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 86 ILE Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 205 SER Chi-restraints excluded: chain E residue 237 GLN 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 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 M residue 78 MET 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: 0.8980 chunk 298 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 182 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 285 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 349 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 32 HIS C 95 GLN D 17 ASN D 89 GLN H 164 GLN G 24 ASN ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 17 ASN ** O 32 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.103646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.073520 restraints weight = 59568.352| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.74 r_work: 0.2894 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 30080 Z= 0.242 Angle : 0.654 9.860 40664 Z= 0.328 Chirality : 0.048 0.219 4392 Planarity : 0.005 0.062 5104 Dihedral : 11.509 170.617 4200 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.26 % Favored : 94.65 % Rotamer: Outliers : 2.12 % Allowed : 14.09 % Favored : 83.78 % 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: -1.34 (0.14), residues: 3536 helix: -0.28 (0.13), residues: 1552 sheet: -0.69 (0.25), residues: 464 loop : -1.51 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 161 TYR 0.019 0.002 TYR L 113 PHE 0.022 0.002 PHE D 172 TRP 0.018 0.002 TRP A 85 HIS 0.007 0.001 HIS J 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.24 (30080) covalent geometry : angle 0.65402 / 0.33 (40664) hydrogen bonds : bond 0.03849 / 2.59 ( 1180) hydrogen bonds : angle 4.56323 / 3.12 ( 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 528 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 460 time to evaluate : 1.330 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: 0.8237 (t0) cc_final: 0.7866 (t0) REVERT: C 74 ASN cc_start: 0.8319 (t0) cc_final: 0.7845 (t0) REVERT: C 86 ASP cc_start: 0.8657 (t0) cc_final: 0.8409 (t0) REVERT: C 167 MET cc_start: 0.8138 (pmm) cc_final: 0.7821 (pmm) REVERT: D 1 MET cc_start: 0.7485 (tpt) cc_final: 0.7173 (tpt) REVERT: D 2 ASN cc_start: 0.9183 (m-40) cc_final: 0.8474 (m-40) REVERT: D 95 GLN cc_start: 0.8196 (pm20) cc_final: 0.7534 (mp10) REVERT: D 158 MET cc_start: 0.8537 (tmm) cc_final: 0.8207 (tmm) REVERT: H 23 MET cc_start: 0.8376 (mtp) cc_final: 0.8074 (mtp) REVERT: G 210 GLU cc_start: 0.8929 (tp30) cc_final: 0.8455 (tp30) REVERT: F 136 ASP cc_start: 0.8424 (t0) cc_final: 0.8128 (t0) REVERT: F 200 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8762 (tt) REVERT: E 83 ASP cc_start: 0.8631 (p0) cc_final: 0.8371 (p0) REVERT: E 151 ASP cc_start: 0.7890 (m-30) cc_final: 0.7347 (m-30) REVERT: E 170 THR cc_start: 0.8514 (m) cc_final: 0.8219 (m) REVERT: E 252 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8521 (mt-10) REVERT: A 85 TRP cc_start: 0.8189 (OUTLIER) cc_final: 0.7803 (t-100) REVERT: A 94 SER cc_start: 0.8573 (p) cc_final: 0.8241 (t) REVERT: A 113 TYR cc_start: 0.8488 (t80) cc_final: 0.8274 (t80) REVERT: A 158 MET cc_start: 0.7799 (tpp) cc_final: 0.6561 (tpp) REVERT: A 161 ARG cc_start: 0.8392 (ttp-110) cc_final: 0.7867 (ttp-110) REVERT: B 9 ASN cc_start: 0.7633 (t0) cc_final: 0.7262 (t0) REVERT: B 138 ARG cc_start: 0.7958 (mtt90) cc_final: 0.7586 (mtt90) REVERT: K 161 ARG cc_start: 0.8146 (mtp-110) cc_final: 0.7944 (ptp-170) REVERT: P 226 ARG cc_start: 0.8296 (ttm170) cc_final: 0.8037 (mmt90) REVERT: P 256 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8496 (mm-30) REVERT: O 3 GLN cc_start: 0.7776 (tp-100) cc_final: 0.7289 (tp-100) REVERT: O 248 ASP cc_start: 0.8554 (p0) cc_final: 0.8200 (t70) REVERT: N 23 MET cc_start: 0.8547 (mtt) cc_final: 0.8242 (mtp) REVERT: M 3 GLN cc_start: 0.8421 (tp-100) cc_final: 0.8151 (tp-100) REVERT: I 28 LEU cc_start: 0.8630 (tt) cc_final: 0.8385 (tt) REVERT: I 82 GLN cc_start: 0.8044 (tm-30) cc_final: 0.7833 (tm-30) REVERT: I 86 ASP cc_start: 0.8293 (m-30) cc_final: 0.8040 (m-30) REVERT: I 95 GLN cc_start: 0.9049 (tp-100) cc_final: 0.8833 (tp-100) REVERT: I 109 THR cc_start: 0.9115 (m) cc_final: 0.8841 (m) REVERT: I 143 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.8119 (t0) REVERT: I 149 ASP cc_start: 0.8138 (t70) cc_final: 0.7846 (t0) REVERT: I 178 TYR cc_start: 0.8622 (t80) cc_final: 0.8399 (t80) REVERT: J 8 ARG cc_start: 0.7935 (ptp90) cc_final: 0.7233 (ptp90) REVERT: J 48 ASP cc_start: 0.8945 (t70) cc_final: 0.8621 (t0) REVERT: J 82 GLN cc_start: 0.7785 (tt0) cc_final: 0.7302 (tt0) REVERT: J 139 ASP cc_start: 0.8520 (p0) cc_final: 0.8147 (p0) REVERT: J 173 ASP cc_start: 0.8346 (m-30) cc_final: 0.8059 (m-30) outliers start: 68 outliers final: 45 residues processed: 500 average time/residue: 0.1940 time to fit residues: 152.2480 Evaluate side-chains 469 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 421 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain D residue 48 ASP 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 F residue 56 GLU Chi-restraints excluded: chain F residue 91 VAL 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 25 VAL 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 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 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 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 M residue 200 LEU Chi-restraints excluded: chain I residue 61 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 133 VAL Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 160 ASP 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: 10.0000 chunk 120 optimal weight: 2.9990 chunk 326 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 264 optimal weight: 4.9990 chunk 223 optimal weight: 0.0570 chunk 7 optimal weight: 10.0000 chunk 98 optimal weight: 0.9980 chunk 266 optimal weight: 0.1980 chunk 339 optimal weight: 0.7980 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 32 HIS D 17 ASN H 164 GLN ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 127 GLN O 237 GLN ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.107571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.076839 restraints weight = 57917.345| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.89 r_work: 0.2952 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2769 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 : 0.568 8.921 40664 Z= 0.281 Chirality : 0.045 0.188 4392 Planarity : 0.004 0.060 5104 Dihedral : 11.354 170.935 4200 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.38 % Favored : 95.53 % Rotamer: Outliers : 1.69 % Allowed : 15.91 % Favored : 82.41 % 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: -1.08 (0.14), residues: 3536 helix: -0.06 (0.13), residues: 1568 sheet: -0.63 (0.25), residues: 464 loop : -1.37 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 239 TYR 0.017 0.001 TYR L 113 PHE 0.020 0.001 PHE D 172 TRP 0.018 0.001 TRP A 85 HIS 0.005 0.001 HIS J 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (30080) covalent geometry : angle 0.56758 / 0.28 (40664) hydrogen bonds : bond 0.03208 / 2.16 ( 1180) hydrogen bonds : angle 4.24917 / 2.90 ( 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 511 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 457 time to evaluate : 1.028 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: 0.9208 (m110) cc_final: 0.8864 (m110) REVERT: C 41 ASN cc_start: 0.8202 (t0) cc_final: 0.7840 (t0) REVERT: C 74 ASN cc_start: 0.8322 (t0) cc_final: 0.7817 (t0) REVERT: C 86 ASP cc_start: 0.8579 (t0) cc_final: 0.8315 (t0) REVERT: C 167 MET cc_start: 0.8295 (pmm) cc_final: 0.8007 (pmm) REVERT: D 1 MET cc_start: 0.7374 (tpt) cc_final: 0.7078 (tpt) REVERT: D 2 ASN cc_start: 0.9163 (m-40) cc_final: 0.8612 (m-40) REVERT: D 48 ASP cc_start: 0.8983 (t70) cc_final: 0.8725 (t0) REVERT: D 95 GLN cc_start: 0.8246 (pm20) cc_final: 0.7607 (mp10) REVERT: D 158 MET cc_start: 0.8550 (tmm) cc_final: 0.8335 (tmm) REVERT: H 212 LYS cc_start: 0.9366 (mmtp) cc_final: 0.8909 (ptpt) REVERT: G 1 MET cc_start: 0.7070 (OUTLIER) cc_final: 0.6385 (mpp) REVERT: G 210 GLU cc_start: 0.8950 (tp30) cc_final: 0.8446 (tp30) REVERT: G 214 GLU cc_start: 0.8471 (pm20) cc_final: 0.8161 (pm20) REVERT: F 136 ASP cc_start: 0.8499 (t0) cc_final: 0.8112 (t0) REVERT: F 200 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8554 (tt) REVERT: E 56 GLU cc_start: 0.8637 (mp0) cc_final: 0.8371 (mp0) REVERT: E 151 ASP cc_start: 0.7844 (m-30) cc_final: 0.7237 (m-30) REVERT: E 237 GLN cc_start: 0.9180 (tp40) cc_final: 0.8831 (mt0) REVERT: E 252 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8437 (mt-10) REVERT: A 15 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8022 (mp0) REVERT: A 85 TRP cc_start: 0.7992 (OUTLIER) cc_final: 0.7628 (t-100) REVERT: A 94 SER cc_start: 0.8605 (p) cc_final: 0.8250 (t) REVERT: A 141 GLN cc_start: 0.8149 (mp10) cc_final: 0.6742 (mt0) REVERT: A 158 MET cc_start: 0.7942 (tpp) cc_final: 0.6725 (tpp) REVERT: A 161 ARG cc_start: 0.8395 (ttp-110) cc_final: 0.7899 (ttp-110) REVERT: B 138 ARG cc_start: 0.8113 (mtt90) cc_final: 0.7608 (mtt90) REVERT: B 143 ASP cc_start: 0.8228 (m-30) cc_final: 0.7215 (p0) REVERT: K 106 VAL cc_start: 0.7934 (t) cc_final: 0.7710 (p) REVERT: L 161 ARG cc_start: 0.8605 (ptm-80) cc_final: 0.8278 (ptm160) REVERT: P 226 ARG cc_start: 0.8190 (ttm170) cc_final: 0.7896 (mmt90) REVERT: P 256 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8366 (mm-30) REVERT: O 3 GLN cc_start: 0.7816 (tp-100) cc_final: 0.7397 (tp40) REVERT: O 23 MET cc_start: 0.8668 (ttp) cc_final: 0.8305 (mtp) REVERT: O 173 ASP cc_start: 0.8649 (m-30) cc_final: 0.8226 (m-30) REVERT: O 248 ASP cc_start: 0.8696 (p0) cc_final: 0.8189 (t70) REVERT: N 23 MET cc_start: 0.8739 (mtt) cc_final: 0.8407 (mtp) REVERT: N 124 ILE cc_start: 0.8802 (mm) cc_final: 0.8569 (mt) REVERT: I 28 LEU cc_start: 0.8377 (tt) cc_final: 0.8119 (tt) REVERT: I 86 ASP cc_start: 0.8287 (m-30) cc_final: 0.8022 (m-30) REVERT: I 109 THR cc_start: 0.9007 (m) cc_final: 0.8637 (m) REVERT: I 143 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.8135 (t0) REVERT: I 158 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7444 (mtm) REVERT: J 8 ARG cc_start: 0.7797 (ptp90) cc_final: 0.7004 (ptp90) REVERT: J 48 ASP cc_start: 0.8860 (t70) cc_final: 0.8477 (t0) REVERT: J 82 GLN cc_start: 0.7688 (tt0) cc_final: 0.7234 (tt0) REVERT: J 104 ARG cc_start: 0.8755 (ttp80) cc_final: 0.8399 (ttp80) REVERT: J 139 ASP cc_start: 0.8600 (p0) cc_final: 0.8264 (p0) REVERT: J 173 ASP cc_start: 0.8459 (m-30) cc_final: 0.8150 (m-30) outliers start: 54 outliers final: 36 residues processed: 487 average time/residue: 0.2025 time to fit residues: 154.5235 Evaluate side-chains 456 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 414 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 100 SER Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 236 GLU Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 200 LEU 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 23 THR 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 133 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 35 ASP 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 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 M residue 17 VAL Chi-restraints excluded: chain M residue 78 MET Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 143 ASP 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: 5.9990 chunk 30 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 221 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 chunk 98 optimal weight: 0.0970 chunk 263 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 275 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 242 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 32 HIS D 17 ASN D 32 HIS H 164 GLN G 164 GLN F 237 GLN ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 32 GLN M 237 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.108738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.077971 restraints weight = 58086.126| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.90 r_work: 0.2978 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 30080 Z= 0.107 Angle : 0.557 10.149 40664 Z= 0.275 Chirality : 0.044 0.184 4392 Planarity : 0.004 0.058 5104 Dihedral : 11.215 167.524 4200 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.81 % Favored : 95.11 % Rotamer: Outliers : 1.88 % Allowed : 16.91 % Favored : 81.22 % 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: -0.87 (0.14), residues: 3536 helix: 0.21 (0.13), residues: 1520 sheet: -1.18 (0.26), residues: 416 loop : -1.10 (0.16), residues: 1600 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 0.017 0.001 PHE I 93 TRP 0.019 0.001 TRP A 85 HIS 0.004 0.001 HIS B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (30080) covalent geometry : angle 0.55716 / 0.28 (40664) hydrogen bonds : bond 0.03039 / 2.04 ( 1180) hydrogen bonds : angle 4.08737 / 2.79 ( 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 520 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 460 time to evaluate : 1.270 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: 0.9205 (m110) cc_final: 0.8857 (m110) REVERT: C 41 ASN cc_start: 0.8173 (t0) cc_final: 0.7789 (t0) REVERT: C 74 ASN cc_start: 0.8295 (t0) cc_final: 0.7786 (t0) REVERT: C 86 ASP cc_start: 0.8588 (t70) cc_final: 0.8319 (t0) REVERT: C 167 MET cc_start: 0.8316 (pmm) cc_final: 0.7988 (pmm) REVERT: D 1 MET cc_start: 0.7507 (tpt) cc_final: 0.7203 (tpt) REVERT: D 2 ASN cc_start: 0.9188 (m-40) cc_final: 0.8434 (m-40) REVERT: D 48 ASP cc_start: 0.8995 (t70) cc_final: 0.8744 (t0) REVERT: D 95 GLN cc_start: 0.8221 (pm20) cc_final: 0.7575 (mp10) REVERT: D 158 MET cc_start: 0.8579 (tmm) cc_final: 0.8368 (tmm) REVERT: H 148 ASP cc_start: 0.8211 (t0) cc_final: 0.7857 (t0) REVERT: H 212 LYS cc_start: 0.9346 (mmtp) cc_final: 0.8911 (ptpt) REVERT: G 1 MET cc_start: 0.7076 (OUTLIER) cc_final: 0.6427 (mpp) REVERT: G 78 MET cc_start: 0.8634 (mmm) cc_final: 0.8420 (mmm) REVERT: G 167 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7712 (mm-30) REVERT: G 214 GLU cc_start: 0.8423 (pm20) cc_final: 0.8085 (pm20) REVERT: F 136 ASP cc_start: 0.8488 (t0) cc_final: 0.8044 (t0) REVERT: F 200 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8557 (tt) REVERT: E 56 GLU cc_start: 0.8586 (mp0) cc_final: 0.8351 (mp0) REVERT: E 83 ASP cc_start: 0.8705 (p0) cc_final: 0.8380 (p0) REVERT: E 151 ASP cc_start: 0.7808 (m-30) cc_final: 0.7217 (m-30) REVERT: E 173 ASP cc_start: 0.8932 (m-30) cc_final: 0.8708 (m-30) REVERT: A 10 ARG cc_start: 0.8746 (mpp80) cc_final: 0.8500 (mpp80) REVERT: A 15 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8007 (mp0) REVERT: A 85 TRP cc_start: 0.7974 (OUTLIER) cc_final: 0.7619 (t-100) REVERT: A 94 SER cc_start: 0.8609 (p) cc_final: 0.8206 (t) REVERT: A 141 GLN cc_start: 0.8144 (mp10) cc_final: 0.6712 (mt0) REVERT: A 158 MET cc_start: 0.7949 (tpp) cc_final: 0.6832 (tpp) REVERT: A 161 ARG cc_start: 0.8370 (ttp-110) cc_final: 0.7911 (ttp-110) REVERT: B 94 SER cc_start: 0.7341 (m) cc_final: 0.6982 (p) REVERT: B 138 ARG cc_start: 0.8112 (mtt90) cc_final: 0.7606 (mtt90) REVERT: B 168 ARG cc_start: 0.8011 (ttm-80) cc_final: 0.7594 (ttm-80) REVERT: K 106 VAL cc_start: 0.7907 (t) cc_final: 0.7678 (p) REVERT: L 11 HIS cc_start: 0.7940 (m-70) cc_final: 0.7667 (m-70) REVERT: L 14 LYS cc_start: 0.8875 (mttp) cc_final: 0.8647 (mmtm) REVERT: L 158 MET cc_start: 0.6902 (mmm) cc_final: 0.6410 (ttm) REVERT: L 161 ARG cc_start: 0.8564 (ptm-80) cc_final: 0.8345 (ptm160) REVERT: P 32 GLN cc_start: 0.9198 (mp10) cc_final: 0.8780 (mp10) REVERT: P 226 ARG cc_start: 0.8150 (ttm170) cc_final: 0.7912 (mmt90) REVERT: P 256 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8384 (mm-30) REVERT: O 3 GLN cc_start: 0.7854 (tp-100) cc_final: 0.7412 (tp40) REVERT: O 23 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8317 (mtp) REVERT: O 162 TYR cc_start: 0.8476 (t80) cc_final: 0.8251 (t80) REVERT: O 173 ASP cc_start: 0.8638 (m-30) cc_final: 0.8247 (m-30) REVERT: O 248 ASP cc_start: 0.8670 (p0) cc_final: 0.8204 (t70) REVERT: N 23 MET cc_start: 0.8701 (mtt) cc_final: 0.8456 (mtp) REVERT: N 124 ILE cc_start: 0.8793 (mm) cc_final: 0.8570 (mt) REVERT: I 28 LEU cc_start: 0.8376 (tt) cc_final: 0.8118 (tt) REVERT: I 82 GLN cc_start: 0.7959 (tm-30) cc_final: 0.7604 (tm-30) REVERT: I 109 THR cc_start: 0.8908 (m) cc_final: 0.8508 (m) REVERT: I 143 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.8096 (t0) REVERT: I 149 ASP cc_start: 0.8677 (t0) cc_final: 0.8404 (m-30) REVERT: I 161 ARG cc_start: 0.8413 (tmm-80) cc_final: 0.7960 (ptm160) REVERT: J 8 ARG cc_start: 0.7794 (ptp90) cc_final: 0.6866 (ptp90) REVERT: J 48 ASP cc_start: 0.8857 (t70) cc_final: 0.8480 (t0) REVERT: J 82 GLN cc_start: 0.7831 (tt0) cc_final: 0.7380 (tt0) REVERT: J 104 ARG cc_start: 0.8740 (ttp80) cc_final: 0.8380 (ttp80) REVERT: J 108 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7739 (mtmm) REVERT: J 139 ASP cc_start: 0.8597 (p0) cc_final: 0.8280 (p0) REVERT: J 173 ASP cc_start: 0.8446 (m-30) cc_final: 0.8141 (m-30) outliers start: 60 outliers final: 36 residues processed: 491 average time/residue: 0.2019 time to fit residues: 155.4878 Evaluate side-chains 466 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 423 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 96 LEU 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 1 MET Chi-restraints excluded: chain G residue 236 GLU Chi-restraints excluded: chain F residue 13 VAL 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 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 32 HIS Chi-restraints excluded: chain A residue 85 TRP 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 35 ASP 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 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 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 M residue 17 VAL 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 I residue 143 ASP 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: 3.9990 chunk 190 optimal weight: 1.9990 chunk 299 optimal weight: 0.8980 chunk 155 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 180 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 312 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 32 HIS D 17 ASN D 32 HIS H 164 GLN G 164 GLN B 102 ASN O 137 ASN O 164 GLN ** M 237 GLN ** 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 = 0.3589 r_free = 0.3589 target = 0.107564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.076783 restraints weight = 58027.426| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.88 r_work: 0.2958 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30080 Z= 0.130 Angle : 0.570 8.652 40664 Z= 0.282 Chirality : 0.045 0.218 4392 Planarity : 0.004 0.058 5104 Dihedral : 11.198 175.453 4200 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.61 % Favored : 95.31 % Rotamer: Outliers : 1.88 % Allowed : 17.84 % Favored : 80.28 % 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 (0.26), residues: 416 loop : -1.06 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 165 TYR 0.015 0.001 TYR L 113 PHE 0.016 0.001 PHE I 93 TRP 0.021 0.001 TRP A 142 HIS 0.004 0.001 HIS K 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (30080) covalent geometry : angle 0.57046 / 0.28 (40664) hydrogen bonds : bond 0.03078 / 2.06 ( 1180) hydrogen bonds : angle 4.11170 / 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 485 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 425 time to evaluate : 1.117 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: 0.9197 (m110) cc_final: 0.8838 (m110) REVERT: C 41 ASN cc_start: 0.8174 (t0) cc_final: 0.7778 (t0) REVERT: C 74 ASN cc_start: 0.8289 (t0) cc_final: 0.7788 (t0) REVERT: C 86 ASP cc_start: 0.8599 (t70) cc_final: 0.8326 (t0) REVERT: C 120 TYR cc_start: 0.8170 (m-80) cc_final: 0.7520 (m-80) REVERT: C 167 MET cc_start: 0.8348 (pmm) cc_final: 0.7963 (pmm) REVERT: D 1 MET cc_start: 0.7489 (tpt) cc_final: 0.7166 (tpt) REVERT: D 2 ASN cc_start: 0.9207 (m-40) cc_final: 0.8443 (m-40) REVERT: D 48 ASP cc_start: 0.9026 (t70) cc_final: 0.8790 (t0) REVERT: D 59 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.6503 (mtm110) REVERT: D 95 GLN cc_start: 0.8221 (pm20) cc_final: 0.7572 (mp10) REVERT: D 158 MET cc_start: 0.8482 (tmm) cc_final: 0.8266 (tmm) REVERT: H 148 ASP cc_start: 0.8202 (t0) cc_final: 0.7821 (t0) REVERT: H 212 LYS cc_start: 0.9319 (mmtp) cc_final: 0.8912 (ptpt) REVERT: G 1 MET cc_start: 0.7103 (OUTLIER) cc_final: 0.6410 (mpp) REVERT: G 78 MET cc_start: 0.8658 (mmm) cc_final: 0.8416 (mmm) REVERT: G 214 GLU cc_start: 0.8525 (pm20) cc_final: 0.8119 (pm20) REVERT: G 249 ASN cc_start: 0.8260 (t0) cc_final: 0.7774 (m-40) REVERT: F 108 TYR cc_start: 0.9070 (OUTLIER) cc_final: 0.8189 (m-80) REVERT: F 136 ASP cc_start: 0.8550 (t0) cc_final: 0.8120 (t0) REVERT: F 200 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8560 (tt) REVERT: F 237 GLN cc_start: 0.8953 (mm110) cc_final: 0.8579 (mt0) REVERT: E 56 GLU cc_start: 0.8599 (mp0) cc_final: 0.8341 (mp0) REVERT: E 59 GLU cc_start: 0.8813 (tp30) cc_final: 0.8382 (tp30) REVERT: E 151 ASP cc_start: 0.7833 (m-30) cc_final: 0.7219 (m-30) REVERT: E 173 ASP cc_start: 0.8978 (m-30) cc_final: 0.8754 (m-30) REVERT: A 10 ARG cc_start: 0.8689 (mpp80) cc_final: 0.8429 (mpp80) REVERT: A 15 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8006 (mp0) REVERT: A 85 TRP cc_start: 0.8016 (OUTLIER) cc_final: 0.7702 (t-100) REVERT: A 94 SER cc_start: 0.8501 (p) cc_final: 0.8166 (t) REVERT: A 120 TYR cc_start: 0.8633 (m-10) cc_final: 0.8363 (m-10) REVERT: A 141 GLN cc_start: 0.8134 (mp10) cc_final: 0.7115 (mp10) REVERT: A 158 MET cc_start: 0.7963 (tpp) cc_final: 0.6864 (tpp) REVERT: A 161 ARG cc_start: 0.8390 (ttp-110) cc_final: 0.7922 (ttp-110) REVERT: A 177 GLU cc_start: 0.9134 (tp30) cc_final: 0.8863 (tm-30) REVERT: A 178 TYR cc_start: 0.8845 (t80) cc_final: 0.8508 (t80) REVERT: B 9 ASN cc_start: 0.7530 (t0) cc_final: 0.7105 (t0) REVERT: B 138 ARG cc_start: 0.8163 (mtt90) cc_final: 0.7614 (mtt90) REVERT: K 106 VAL cc_start: 0.7907 (t) cc_final: 0.7689 (p) REVERT: L 11 HIS cc_start: 0.7917 (m-70) cc_final: 0.7654 (m-70) REVERT: L 14 LYS cc_start: 0.8878 (mttp) cc_final: 0.8652 (mmtm) REVERT: L 158 MET cc_start: 0.6941 (mmm) cc_final: 0.6503 (ttm) REVERT: L 161 ARG cc_start: 0.8621 (ptm-80) cc_final: 0.8388 (ptm160) REVERT: P 32 GLN cc_start: 0.9199 (mp10) cc_final: 0.8759 (mp10) REVERT: P 226 ARG cc_start: 0.8185 (ttm170) cc_final: 0.7952 (mmt90) REVERT: P 256 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8377 (mm-30) REVERT: O 3 GLN cc_start: 0.7880 (tp-100) cc_final: 0.7419 (tp40) REVERT: O 23 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8308 (mtp) REVERT: O 162 TYR cc_start: 0.8492 (t80) cc_final: 0.8250 (t80) REVERT: O 173 ASP cc_start: 0.8676 (m-30) cc_final: 0.8269 (m-30) REVERT: O 248 ASP cc_start: 0.8630 (p0) cc_final: 0.8203 (t70) REVERT: N 23 MET cc_start: 0.8743 (mtt) cc_final: 0.8468 (mtp) REVERT: N 78 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8159 (mpp) REVERT: N 124 ILE cc_start: 0.8799 (mm) cc_final: 0.8575 (mt) REVERT: I 28 LEU cc_start: 0.8374 (tt) cc_final: 0.8093 (tt) REVERT: I 82 GLN cc_start: 0.7953 (tm-30) cc_final: 0.7590 (tm-30) REVERT: I 109 THR cc_start: 0.8944 (m) cc_final: 0.8611 (m) REVERT: I 143 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.8112 (t0) REVERT: I 149 ASP cc_start: 0.8646 (t0) cc_final: 0.8328 (m-30) REVERT: I 161 ARG cc_start: 0.8514 (tmm-80) cc_final: 0.7911 (ptm160) REVERT: J 8 ARG cc_start: 0.7880 (ptp90) cc_final: 0.6822 (ptp90) REVERT: J 48 ASP cc_start: 0.8859 (t70) cc_final: 0.8476 (t0) REVERT: J 82 GLN cc_start: 0.7786 (tt0) cc_final: 0.7331 (tt0) REVERT: J 104 ARG cc_start: 0.8734 (ttp80) cc_final: 0.8367 (ttp80) REVERT: J 139 ASP cc_start: 0.8581 (p0) cc_final: 0.8263 (p0) REVERT: J 173 ASP cc_start: 0.8411 (m-30) cc_final: 0.8119 (m-30) outliers start: 60 outliers final: 42 residues processed: 463 average time/residue: 0.2101 time to fit residues: 151.5459 Evaluate side-chains 469 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 418 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 96 LEU 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 1 MET 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 200 LEU 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 16 ILE 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 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 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 167 GLU 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 M residue 17 VAL 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 I residue 143 ASP Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 133 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 248 optimal weight: 2.9990 chunk 146 optimal weight: 7.9990 chunk 303 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 323 optimal weight: 5.9990 chunk 231 optimal weight: 0.0770 chunk 131 optimal weight: 0.5980 chunk 237 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 282 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 overall best weight: 1.5344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 32 HIS D 32 HIS H 164 GLN E 137 ASN ** E 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 137 ASN O 164 GLN ** M 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.105662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.075601 restraints weight = 59363.380| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.74 r_work: 0.2932 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.3183 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 : 0.584 8.841 40664 Z= 0.290 Chirality : 0.045 0.190 4392 Planarity : 0.004 0.058 5104 Dihedral : 11.206 177.308 4200 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.81 % Favored : 95.11 % Rotamer: Outliers : 2.16 % Allowed : 17.66 % Favored : 80.19 % 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: -0.69 (0.14), residues: 3536 helix: 0.42 (0.14), residues: 1480 sheet: -1.18 (0.26), residues: 416 loop : -1.01 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 165 TYR 0.022 0.001 TYR B 113 PHE 0.028 0.001 PHE J 172 TRP 0.020 0.001 TRP A 85 HIS 0.004 0.001 HIS K 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (30080) covalent geometry : angle 0.58385 / 0.29 (40664) hydrogen bonds : bond 0.03253 / 2.18 ( 1180) hydrogen bonds : angle 4.14763 / 2.83 ( 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 498 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 429 time to evaluate : 1.237 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: 0.8244 (t0) cc_final: 0.7848 (t0) REVERT: C 74 ASN cc_start: 0.8396 (t0) cc_final: 0.8159 (t0) REVERT: C 86 ASP cc_start: 0.8668 (t70) cc_final: 0.8381 (t0) REVERT: C 120 TYR cc_start: 0.8385 (m-80) cc_final: 0.8003 (m-80) REVERT: C 143 ASP cc_start: 0.7778 (m-30) cc_final: 0.7562 (m-30) REVERT: C 157 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7536 (tm-30) REVERT: C 167 MET cc_start: 0.8384 (pmm) cc_final: 0.7933 (pmm) REVERT: D 1 MET cc_start: 0.7575 (tpt) cc_final: 0.7275 (tpt) REVERT: D 2 ASN cc_start: 0.9210 (m-40) cc_final: 0.8519 (m-40) REVERT: D 48 ASP cc_start: 0.8988 (t70) cc_final: 0.8759 (t0) REVERT: D 59 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.6709 (mtm110) REVERT: D 95 GLN cc_start: 0.8169 (pm20) cc_final: 0.7458 (mp10) REVERT: D 158 MET cc_start: 0.8570 (tmm) cc_final: 0.8115 (tmm) REVERT: H 212 LYS cc_start: 0.9252 (mmtp) cc_final: 0.8955 (ptpt) REVERT: G 1 MET cc_start: 0.7085 (OUTLIER) cc_final: 0.6733 (mpp) REVERT: G 167 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7588 (mm-30) REVERT: G 214 GLU cc_start: 0.8525 (pm20) cc_final: 0.8276 (pm20) REVERT: G 249 ASN cc_start: 0.8224 (t0) cc_final: 0.7834 (m-40) REVERT: G 256 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8708 (mm-30) REVERT: F 108 TYR cc_start: 0.9177 (OUTLIER) cc_final: 0.8443 (m-80) REVERT: F 136 ASP cc_start: 0.8504 (t0) cc_final: 0.8159 (t0) REVERT: E 59 GLU cc_start: 0.8831 (tp30) cc_final: 0.8470 (tp30) REVERT: E 83 ASP cc_start: 0.8529 (p0) cc_final: 0.8158 (p0) REVERT: E 151 ASP cc_start: 0.7778 (m-30) cc_final: 0.7208 (m-30) REVERT: E 252 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8462 (mt-10) REVERT: A 10 ARG cc_start: 0.8732 (mpp80) cc_final: 0.8501 (mpp80) REVERT: A 15 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8096 (mp0) REVERT: A 85 TRP cc_start: 0.8192 (OUTLIER) cc_final: 0.7888 (t60) REVERT: A 158 MET cc_start: 0.7842 (tpp) cc_final: 0.6758 (tpp) REVERT: A 161 ARG cc_start: 0.8406 (ttp-110) cc_final: 0.7936 (ttp-110) REVERT: A 178 TYR cc_start: 0.8840 (t80) cc_final: 0.8603 (t80) REVERT: B 9 ASN cc_start: 0.7705 (t0) cc_final: 0.7341 (t0) REVERT: B 138 ARG cc_start: 0.8245 (mtt90) cc_final: 0.7723 (mtt90) REVERT: B 168 ARG cc_start: 0.8326 (ttm-80) cc_final: 0.7914 (ttm-80) REVERT: K 106 VAL cc_start: 0.8162 (t) cc_final: 0.7958 (p) REVERT: L 161 ARG cc_start: 0.8571 (ptm-80) cc_final: 0.8368 (ptm160) REVERT: P 32 GLN cc_start: 0.9143 (mp10) cc_final: 0.8797 (mp10) REVERT: P 226 ARG cc_start: 0.8262 (ttm170) cc_final: 0.7995 (mmt90) REVERT: P 256 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8496 (mm-30) REVERT: O 3 GLN cc_start: 0.7875 (tp-100) cc_final: 0.7507 (tp40) REVERT: O 173 ASP cc_start: 0.8665 (m-30) cc_final: 0.8314 (m-30) REVERT: O 248 ASP cc_start: 0.8508 (p0) cc_final: 0.8181 (t70) REVERT: N 78 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8147 (mpp) REVERT: N 124 ILE cc_start: 0.8931 (mm) cc_final: 0.8722 (mt) REVERT: N 159 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8111 (mm-30) REVERT: I 28 LEU cc_start: 0.8648 (tt) cc_final: 0.8397 (tt) REVERT: I 82 GLN cc_start: 0.8375 (tm-30) cc_final: 0.7886 (tm-30) REVERT: I 109 THR cc_start: 0.9053 (m) cc_final: 0.8758 (m) REVERT: I 143 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.8179 (t0) REVERT: I 149 ASP cc_start: 0.8487 (t0) cc_final: 0.8271 (m-30) REVERT: I 161 ARG cc_start: 0.8513 (tmm-80) cc_final: 0.7899 (ptm160) REVERT: J 8 ARG cc_start: 0.8102 (ptp90) cc_final: 0.7093 (ptp90) REVERT: J 48 ASP cc_start: 0.8906 (t70) cc_final: 0.8562 (t0) REVERT: J 82 GLN cc_start: 0.7971 (tt0) cc_final: 0.7532 (tt0) REVERT: J 125 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7979 (mp0) REVERT: J 139 ASP cc_start: 0.8514 (p0) cc_final: 0.8191 (p0) REVERT: J 143 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.7969 (m-30) REVERT: J 166 SER cc_start: 0.8497 (t) cc_final: 0.8157 (p) REVERT: J 173 ASP cc_start: 0.8382 (m-30) cc_final: 0.8072 (m-30) outliers start: 69 outliers final: 45 residues processed: 475 average time/residue: 0.2160 time to fit residues: 159.3298 Evaluate side-chains 463 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 410 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain D residue 16 ILE 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 1 MET 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 262 VAL 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 85 TRP 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 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 167 GLU 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 M residue 17 VAL 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 I residue 143 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 130 optimal weight: 0.0470 chunk 54 optimal weight: 0.7980 chunk 230 optimal weight: 0.2980 chunk 60 optimal weight: 10.0000 chunk 301 optimal weight: 0.9990 chunk 294 optimal weight: 4.9990 chunk 155 optimal weight: 8.9990 chunk 256 optimal weight: 0.8980 chunk 170 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 196 optimal weight: 7.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- 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 O 137 ASN O 237 GLN N 24 ASN ** M 237 GLN ** 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 = 0.3599 r_free = 0.3599 target = 0.107809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.077892 restraints weight = 59060.572| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.75 r_work: 0.2977 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 30080 Z= 0.108 Angle : 0.573 11.902 40664 Z= 0.283 Chirality : 0.044 0.182 4392 Planarity : 0.004 0.058 5104 Dihedral : 11.127 174.916 4200 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.72 % Favored : 95.22 % Rotamer: Outliers : 1.62 % Allowed : 18.53 % Favored : 79.84 % 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: -0.57 (0.14), residues: 3536 helix: 0.59 (0.14), residues: 1456 sheet: -1.09 (0.26), residues: 416 loop : -1.01 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 10 TYR 0.023 0.001 TYR B 113 PHE 0.020 0.001 PHE J 172 TRP 0.027 0.001 TRP A 142 HIS 0.006 0.001 HIS L 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (30080) covalent geometry : angle 0.57293 / 0.28 (40664) hydrogen bonds : bond 0.03016 / 2.02 ( 1180) hydrogen bonds : angle 4.04150 / 2.76 ( 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: 52 poor density : 441 time to evaluate : 1.214 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: 0.9203 (m110) cc_final: 0.8816 (m110) REVERT: C 41 ASN cc_start: 0.8286 (t0) cc_final: 0.7903 (t0) REVERT: C 74 ASN cc_start: 0.8364 (t0) cc_final: 0.8129 (t0) REVERT: C 86 ASP cc_start: 0.8614 (t70) cc_final: 0.8327 (t0) REVERT: C 120 TYR cc_start: 0.8362 (m-80) cc_final: 0.7965 (m-80) REVERT: C 143 ASP cc_start: 0.7766 (m-30) cc_final: 0.7546 (m-30) REVERT: C 157 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7500 (tm-30) REVERT: C 167 MET cc_start: 0.8342 (pmm) cc_final: 0.7790 (pmm) REVERT: D 1 MET cc_start: 0.7556 (tpt) cc_final: 0.7293 (tpt) REVERT: D 2 ASN cc_start: 0.9136 (m-40) cc_final: 0.8499 (m-40) REVERT: D 48 ASP cc_start: 0.8962 (t70) cc_final: 0.8735 (t0) REVERT: D 59 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.6694 (mtm110) REVERT: D 95 GLN cc_start: 0.8129 (pm20) cc_final: 0.7441 (mp10) REVERT: D 103 PRO cc_start: 0.8008 (Cg_exo) cc_final: 0.7713 (Cg_endo) REVERT: D 104 ARG cc_start: 0.7855 (mtm-85) cc_final: 0.7377 (mtm-85) REVERT: D 158 MET cc_start: 0.8615 (tmm) cc_final: 0.8224 (tmm) REVERT: H 212 LYS cc_start: 0.9210 (mmtp) cc_final: 0.8929 (ptpt) REVERT: G 1 MET cc_start: 0.7107 (OUTLIER) cc_final: 0.6673 (mpp) REVERT: G 210 GLU cc_start: 0.8937 (tp30) cc_final: 0.8574 (tp30) REVERT: G 249 ASN cc_start: 0.8190 (t0) cc_final: 0.7838 (m-40) REVERT: G 256 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8692 (mm-30) REVERT: F 108 TYR cc_start: 0.9130 (OUTLIER) cc_final: 0.8468 (m-80) REVERT: F 136 ASP cc_start: 0.8465 (t0) cc_final: 0.8140 (t0) REVERT: F 239 ARG cc_start: 0.8874 (mtp85) cc_final: 0.8485 (mtp85) REVERT: E 59 GLU cc_start: 0.8645 (tp30) cc_final: 0.8413 (tp30) REVERT: E 83 ASP cc_start: 0.8577 (p0) cc_final: 0.8279 (p0) REVERT: E 151 ASP cc_start: 0.7801 (m-30) cc_final: 0.7227 (m-30) REVERT: E 237 GLN cc_start: 0.9084 (mm-40) cc_final: 0.8847 (mt0) REVERT: A 10 ARG cc_start: 0.8672 (mpp80) cc_final: 0.8436 (mpp80) REVERT: A 15 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8147 (mp0) REVERT: A 69 TYR cc_start: 0.7864 (m-80) cc_final: 0.7497 (m-80) REVERT: A 85 TRP cc_start: 0.8175 (OUTLIER) cc_final: 0.7929 (t60) REVERT: A 94 SER cc_start: 0.8277 (p) cc_final: 0.8012 (t) REVERT: A 158 MET cc_start: 0.7785 (tpp) cc_final: 0.6649 (tpp) REVERT: A 161 ARG cc_start: 0.8392 (ttp-110) cc_final: 0.7915 (ttp-110) REVERT: B 9 ASN cc_start: 0.7715 (t0) cc_final: 0.7360 (t0) REVERT: B 85 TRP cc_start: 0.7761 (t-100) cc_final: 0.7519 (t-100) REVERT: B 138 ARG cc_start: 0.8203 (mtt90) cc_final: 0.7677 (mtt90) REVERT: B 143 ASP cc_start: 0.8003 (t0) cc_final: 0.7231 (p0) REVERT: K 106 VAL cc_start: 0.8191 (t) cc_final: 0.7969 (p) REVERT: L 11 HIS cc_start: 0.7985 (m-70) cc_final: 0.7648 (m-70) REVERT: L 14 LYS cc_start: 0.8980 (mttp) cc_final: 0.8761 (mmtm) REVERT: L 74 ASN cc_start: 0.7933 (m-40) cc_final: 0.7628 (t0) REVERT: P 32 GLN cc_start: 0.9117 (mp10) cc_final: 0.8785 (mp10) REVERT: P 226 ARG cc_start: 0.8244 (ttm170) cc_final: 0.8039 (mmt90) REVERT: P 242 MET cc_start: 0.8962 (ttm) cc_final: 0.8332 (tpp) REVERT: P 256 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8467 (mm-30) REVERT: O 3 GLN cc_start: 0.7830 (tp-100) cc_final: 0.7486 (tp40) REVERT: O 162 TYR cc_start: 0.8561 (t80) cc_final: 0.8345 (t80) REVERT: O 173 ASP cc_start: 0.8582 (m-30) cc_final: 0.8273 (m-30) REVERT: O 248 ASP cc_start: 0.8541 (p0) cc_final: 0.8190 (t70) REVERT: N 78 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8067 (mpp) REVERT: N 124 ILE cc_start: 0.8961 (mm) cc_final: 0.8759 (mt) REVERT: N 159 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8028 (mm-30) REVERT: I 28 LEU cc_start: 0.8653 (tt) cc_final: 0.8397 (tt) REVERT: I 82 GLN cc_start: 0.8375 (tm-30) cc_final: 0.7914 (tm-30) REVERT: I 109 THR cc_start: 0.9048 (m) cc_final: 0.8774 (m) REVERT: I 143 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.8115 (t0) REVERT: I 161 ARG cc_start: 0.8539 (tmm-80) cc_final: 0.7965 (ptm160) REVERT: J 48 ASP cc_start: 0.8893 (t70) cc_final: 0.8572 (t0) REVERT: J 82 GLN cc_start: 0.8019 (tt0) cc_final: 0.7662 (tt0) REVERT: J 104 ARG cc_start: 0.8776 (ttp80) cc_final: 0.8403 (ttp80) REVERT: J 125 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7957 (mp0) REVERT: J 139 ASP cc_start: 0.8474 (p0) cc_final: 0.8182 (p0) REVERT: J 143 ASP cc_start: 0.8467 (t0) cc_final: 0.8050 (m-30) REVERT: J 173 ASP cc_start: 0.8301 (m-30) cc_final: 0.7992 (m-30) outliers start: 52 outliers final: 41 residues processed: 473 average time/residue: 0.2097 time to fit residues: 154.7327 Evaluate side-chains 467 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 419 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain D residue 16 ILE 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 H residue 254 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 197 ILE 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 262 VAL Chi-restraints excluded: chain E residue 210 GLU 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 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 P residue 170 THR Chi-restraints excluded: chain O residue 17 VAL Chi-restraints excluded: chain O residue 167 GLU 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 M residue 17 VAL Chi-restraints excluded: chain M residue 262 VAL Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 123 GLU Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 143 ASP 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 134 optimal weight: 1.9990 chunk 287 optimal weight: 4.9990 chunk 347 optimal weight: 3.9990 chunk 295 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 344 optimal weight: 5.9990 chunk 19 optimal weight: 0.0060 chunk 234 optimal weight: 2.9990 chunk 314 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 overall best weight: 1.2800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 32 HIS C 95 GLN D 32 HIS H 164 GLN F 24 ASN ** F 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 HIS O 137 ASN ** O 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.106533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.076496 restraints weight = 58846.546| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.74 r_work: 0.2949 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30080 Z= 0.139 Angle : 0.594 13.123 40664 Z= 0.293 Chirality : 0.045 0.183 4392 Planarity : 0.004 0.058 5104 Dihedral : 11.087 173.698 4200 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.67 % Favored : 95.28 % Rotamer: Outliers : 1.75 % Allowed : 18.38 % Favored : 79.88 % 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: -0.52 (0.14), residues: 3536 helix: 0.55 (0.14), residues: 1496 sheet: -0.65 (0.25), residues: 480 loop : -1.06 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 168 TYR 0.023 0.001 TYR B 113 PHE 0.023 0.001 PHE B 172 TRP 0.028 0.001 TRP A 142 HIS 0.005 0.001 HIS J 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (30080) covalent geometry : angle 0.59422 / 0.29 (40664) hydrogen bonds : bond 0.03140 / 2.11 ( 1180) hydrogen bonds : angle 4.06977 / 2.78 ( 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 485 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 429 time to evaluate : 1.179 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: 0.8256 (t0) cc_final: 0.7885 (t0) REVERT: C 74 ASN cc_start: 0.8375 (t0) cc_final: 0.8140 (t0) REVERT: C 86 ASP cc_start: 0.8611 (t70) cc_final: 0.8323 (t0) REVERT: C 120 TYR cc_start: 0.8375 (m-80) cc_final: 0.7960 (m-80) REVERT: C 143 ASP cc_start: 0.7819 (m-30) cc_final: 0.7557 (m-30) REVERT: C 157 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7525 (tm-30) REVERT: C 167 MET cc_start: 0.8407 (pmm) cc_final: 0.7871 (pmm) REVERT: D 1 MET cc_start: 0.7624 (tpt) cc_final: 0.7384 (tpt) REVERT: D 2 ASN cc_start: 0.9176 (m-40) cc_final: 0.8522 (t0) REVERT: D 48 ASP cc_start: 0.8991 (t70) cc_final: 0.8759 (t0) REVERT: D 59 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.6684 (mtm110) REVERT: D 95 GLN cc_start: 0.8126 (pm20) cc_final: 0.7459 (mp10) REVERT: D 158 MET cc_start: 0.8540 (tmm) cc_final: 0.8022 (tmm) REVERT: H 212 LYS cc_start: 0.9220 (mmtp) cc_final: 0.8955 (ptpt) REVERT: H 252 GLU cc_start: 0.8428 (mp0) cc_final: 0.8084 (mp0) REVERT: G 1 MET cc_start: 0.7108 (OUTLIER) cc_final: 0.6668 (mpp) REVERT: G 210 GLU cc_start: 0.8923 (tp30) cc_final: 0.8536 (tp30) REVERT: G 249 ASN cc_start: 0.8222 (t0) cc_final: 0.7843 (m-40) REVERT: G 256 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8711 (mm-30) REVERT: F 108 TYR cc_start: 0.9143 (OUTLIER) cc_final: 0.8372 (m-80) REVERT: F 136 ASP cc_start: 0.8513 (t0) cc_final: 0.8168 (t0) REVERT: E 83 ASP cc_start: 0.8611 (p0) cc_final: 0.8297 (p0) REVERT: E 151 ASP cc_start: 0.7826 (m-30) cc_final: 0.7242 (m-30) REVERT: E 237 GLN cc_start: 0.9078 (mm-40) cc_final: 0.8866 (mt0) REVERT: A 10 ARG cc_start: 0.8663 (mpp80) cc_final: 0.8437 (mpp80) REVERT: A 15 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8144 (mp0) REVERT: A 85 TRP cc_start: 0.8208 (OUTLIER) cc_final: 0.7918 (t60) REVERT: A 94 SER cc_start: 0.8290 (p) cc_final: 0.8006 (t) REVERT: A 158 MET cc_start: 0.7827 (tpp) cc_final: 0.6716 (tpp) REVERT: A 161 ARG cc_start: 0.8410 (ttp-110) cc_final: 0.7939 (ttp-110) REVERT: A 178 TYR cc_start: 0.8806 (t80) cc_final: 0.8509 (t80) REVERT: B 9 ASN cc_start: 0.7709 (t0) cc_final: 0.7349 (t0) REVERT: B 138 ARG cc_start: 0.8200 (mtt90) cc_final: 0.7726 (mtt90) REVERT: B 143 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7201 (p0) REVERT: K 106 VAL cc_start: 0.8122 (t) cc_final: 0.7899 (p) REVERT: L 74 ASN cc_start: 0.7967 (m-40) cc_final: 0.7622 (t0) REVERT: P 32 GLN cc_start: 0.9141 (mp10) cc_final: 0.8790 (mp10) REVERT: P 226 ARG cc_start: 0.8244 (ttm170) cc_final: 0.7985 (mmt90) REVERT: P 242 MET cc_start: 0.8980 (ttm) cc_final: 0.8363 (tpp) REVERT: P 256 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8409 (mm-30) REVERT: O 3 GLN cc_start: 0.7854 (tp-100) cc_final: 0.7488 (tp40) REVERT: O 162 TYR cc_start: 0.8669 (t80) cc_final: 0.8447 (t80) REVERT: O 173 ASP cc_start: 0.8653 (m-30) cc_final: 0.8310 (m-30) REVERT: O 248 ASP cc_start: 0.8533 (p0) cc_final: 0.8195 (t70) REVERT: N 78 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8031 (mpp) REVERT: N 124 ILE cc_start: 0.8953 (mm) cc_final: 0.8748 (mt) REVERT: N 159 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8041 (mm-30) REVERT: I 28 LEU cc_start: 0.8631 (tt) cc_final: 0.8368 (tt) REVERT: I 82 GLN cc_start: 0.8365 (tm-30) cc_final: 0.7890 (tm-30) REVERT: I 109 THR cc_start: 0.9059 (m) cc_final: 0.8778 (m) REVERT: I 143 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.8173 (t0) REVERT: I 161 ARG cc_start: 0.8586 (tmm-80) cc_final: 0.7989 (ptm160) REVERT: J 48 ASP cc_start: 0.8917 (t70) cc_final: 0.8575 (t0) REVERT: J 82 GLN cc_start: 0.8101 (tt0) cc_final: 0.7652 (tt0) REVERT: J 104 ARG cc_start: 0.8772 (ttp80) cc_final: 0.8372 (ttp80) REVERT: J 125 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7961 (mp0) REVERT: J 139 ASP cc_start: 0.8506 (p0) cc_final: 0.8207 (p0) REVERT: J 143 ASP cc_start: 0.8400 (t0) cc_final: 0.7960 (m-30) REVERT: J 166 SER cc_start: 0.8455 (t) cc_final: 0.8117 (p) REVERT: J 173 ASP cc_start: 0.8332 (m-30) cc_final: 0.8022 (m-30) outliers start: 56 outliers final: 45 residues processed: 463 average time/residue: 0.2087 time to fit residues: 151.0086 Evaluate side-chains 466 residues out of total 3200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 413 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain H residue 254 LEU Chi-restraints excluded: chain G residue 1 MET 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 105 THR Chi-restraints excluded: chain F residue 108 TYR 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 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 129 THR Chi-restraints excluded: chain A residue 133 VAL 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 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 167 GLU 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 M residue 17 VAL Chi-restraints excluded: chain M residue 242 MET Chi-restraints excluded: chain M residue 262 VAL Chi-restraints excluded: chain I residue 123 GLU Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 143 ASP 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: 0.9980 chunk 186 optimal weight: 10.0000 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: 0.7980 chunk 137 optimal weight: 0.8980 chunk 200 optimal weight: 0.9990 chunk 162 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 32 HIS D 32 HIS H 24 ASN H 164 GLN E 137 ASN B 11 HIS O 137 ASN ** O 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.107541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.077542 restraints weight = 59412.040| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.76 r_work: 0.2971 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3343 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= 0.116 Angle : 0.582 11.436 40664 Z= 0.287 Chirality : 0.045 0.187 4392 Planarity : 0.004 0.058 5104 Dihedral : 11.016 171.265 4200 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.41 % Favored : 95.53 % Rotamer: Outliers : 1.75 % Allowed : 18.53 % 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: -0.47 (0.14), residues: 3536 helix: 0.56 (0.14), residues: 1504 sheet: -0.59 (0.25), residues: 480 loop : -1.02 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 168 TYR 0.022 0.001 TYR B 113 PHE 0.021 0.001 PHE B 172 TRP 0.027 0.001 TRP A 142 HIS 0.005 0.001 HIS B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (30080) covalent geometry : angle 0.58156 / 0.29 (40664) hydrogen bonds : bond 0.03031 / 2.03 ( 1180) hydrogen bonds : angle 4.02390 / 2.75 ( 3465) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6841.25 seconds wall clock time: 118 minutes 20.65 seconds (7100.65 seconds total)