Starting phenix.real_space_refine on Tue Aug 26 22:24:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p4i_17409/08_2025/8p4i_17409.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p4i_17409/08_2025/8p4i_17409.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8p4i_17409/08_2025/8p4i_17409.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p4i_17409/08_2025/8p4i_17409.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8p4i_17409/08_2025/8p4i_17409.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p4i_17409/08_2025/8p4i_17409.map" } resolution = 3.83 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 289 5.16 5 C 27472 2.51 5 N 6970 2.21 5 O 8245 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 157 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42976 Number of models: 1 Model: "" Number of chains: 17 Chain: "B" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2528 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 299} Chain: "D" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2528 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 299} Chain: "F" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2528 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 299} Chain: "G" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2528 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 299} Chain: "H" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2528 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 299} Chain: "I" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2528 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 299} Chain: "J" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2528 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 299} Chain: "K" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2528 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 299} Chain: "L" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2528 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 299} Chain: "M" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2528 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 299} Chain: "N" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2528 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 299} Chain: "O" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2528 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 299} Chain: "P" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2528 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 299} Chain: "Q" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2528 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 299} Chain: "R" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2528 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 299} Chain: "S" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2528 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 299} Chain: "U" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2528 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 299} Time building chain proxies: 9.32, per 1000 atoms: 0.22 Number of scatterers: 42976 At special positions: 0 Unit cell: (137.55, 139.65, 217.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 289 16.00 O 8245 8.00 N 6970 7.00 C 27472 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: 2.88 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 476.8 nanoseconds 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10132 Finding SS restraints... Secondary structure from input PDB file: 205 helices and 47 sheets defined 34.1% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'B' and resid 21 through 39 removed outlier: 4.119A pdb=" N GLU B 27 " --> pdb=" O GLU B 23 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER B 38 " --> pdb=" O ASP B 34 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.826A pdb=" N ILE B 60 " --> pdb=" O TRP B 56 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY B 61 " --> pdb=" O PHE B 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 56 through 61' Processing helix chain 'B' and resid 62 through 74 removed outlier: 3.713A pdb=" N THR B 66 " --> pdb=" O HIS B 62 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG B 67 " --> pdb=" O PRO B 63 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LYS B 68 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE B 69 " --> pdb=" O TYR B 65 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU B 72 " --> pdb=" O LYS B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 95 removed outlier: 3.657A pdb=" N GLN B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 140 Processing helix chain 'B' and resid 165 through 168 Processing helix chain 'B' and resid 169 through 178 removed outlier: 3.716A pdb=" N LEU B 173 " --> pdb=" O VAL B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 206 removed outlier: 3.502A pdb=" N ALA B 202 " --> pdb=" O SER B 198 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE B 203 " --> pdb=" O ARG B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 224 Processing helix chain 'B' and resid 227 through 232 Processing helix chain 'B' and resid 233 through 237 removed outlier: 3.703A pdb=" N PHE B 237 " --> pdb=" O PHE B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 277 removed outlier: 4.104A pdb=" N TYR B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 39 removed outlier: 3.983A pdb=" N ASN D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 61 removed outlier: 3.801A pdb=" N ILE D 60 " --> pdb=" O TRP D 56 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY D 61 " --> pdb=" O PHE D 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 56 through 61' Processing helix chain 'D' and resid 62 through 76 removed outlier: 3.633A pdb=" N THR D 66 " --> pdb=" O HIS D 62 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG D 67 " --> pdb=" O PRO D 63 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LYS D 68 " --> pdb=" O GLU D 64 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N PHE D 69 " --> pdb=" O TYR D 65 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N HIS D 71 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLU D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS D 75 " --> pdb=" O HIS D 71 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN D 76 " --> pdb=" O GLU D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 94 removed outlier: 3.851A pdb=" N ILE D 88 " --> pdb=" O ALA D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 140 Processing helix chain 'D' and resid 165 through 168 Processing helix chain 'D' and resid 169 through 178 removed outlier: 3.664A pdb=" N LEU D 173 " --> pdb=" O VAL D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 206 removed outlier: 3.744A pdb=" N TYR D 201 " --> pdb=" O SER D 197 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA D 202 " --> pdb=" O SER D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 222 Processing helix chain 'D' and resid 227 through 232 Processing helix chain 'D' and resid 233 through 237 removed outlier: 3.640A pdb=" N PHE D 237 " --> pdb=" O PHE D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 277 removed outlier: 4.501A pdb=" N TYR D 276 " --> pdb=" O ARG D 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 37 Processing helix chain 'F' and resid 38 through 40 No H-bonds generated for 'chain 'F' and resid 38 through 40' Processing helix chain 'F' and resid 56 through 61 removed outlier: 3.695A pdb=" N ILE F 60 " --> pdb=" O TRP F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 75 removed outlier: 3.748A pdb=" N HIS F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLU F 72 " --> pdb=" O LYS F 68 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS F 75 " --> pdb=" O HIS F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.755A pdb=" N GLN F 86 " --> pdb=" O SER F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 140 Processing helix chain 'F' and resid 165 through 168 Processing helix chain 'F' and resid 169 through 178 removed outlier: 3.835A pdb=" N LEU F 173 " --> pdb=" O VAL F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 206 removed outlier: 3.709A pdb=" N SER F 198 " --> pdb=" O ASP F 194 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA F 202 " --> pdb=" O SER F 198 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE F 203 " --> pdb=" O ARG F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 225 removed outlier: 3.689A pdb=" N LYS F 221 " --> pdb=" O THR F 217 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N MET F 223 " --> pdb=" O GLU F 219 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N CYS F 225 " --> pdb=" O LYS F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 235 Processing helix chain 'F' and resid 273 through 278 removed outlier: 3.593A pdb=" N LYS F 277 " --> pdb=" O VAL F 273 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR F 278 " --> pdb=" O ILE F 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 273 through 278' Processing helix chain 'G' and resid 21 through 39 removed outlier: 3.646A pdb=" N GLU G 31 " --> pdb=" O GLU G 27 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 61 removed outlier: 3.796A pdb=" N ILE G 60 " --> pdb=" O TRP G 56 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLY G 61 " --> pdb=" O PHE G 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 56 through 61' Processing helix chain 'G' and resid 66 through 77 removed outlier: 4.019A pdb=" N HIS G 71 " --> pdb=" O ARG G 67 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLU G 72 " --> pdb=" O LYS G 68 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LYS G 75 " --> pdb=" O HIS G 71 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN G 76 " --> pdb=" O GLU G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 94 removed outlier: 3.603A pdb=" N ILE G 88 " --> pdb=" O ALA G 84 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA G 91 " --> pdb=" O LYS G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 168 Processing helix chain 'G' and resid 169 through 178 removed outlier: 3.859A pdb=" N LEU G 173 " --> pdb=" O VAL G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 206 Processing helix chain 'G' and resid 217 through 223 Processing helix chain 'G' and resid 227 through 234 Processing helix chain 'G' and resid 273 through 278 removed outlier: 3.720A pdb=" N TYR G 278 " --> pdb=" O ILE G 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 37 removed outlier: 4.270A pdb=" N GLU H 27 " --> pdb=" O GLU H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 61 removed outlier: 3.762A pdb=" N ILE H 60 " --> pdb=" O TRP H 56 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY H 61 " --> pdb=" O PHE H 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 56 through 61' Processing helix chain 'H' and resid 65 through 75 removed outlier: 4.080A pdb=" N PHE H 69 " --> pdb=" O TYR H 65 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N HIS H 71 " --> pdb=" O ARG H 67 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N GLU H 72 " --> pdb=" O LYS H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 96 removed outlier: 3.816A pdb=" N ASN H 95 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 140 Processing helix chain 'H' and resid 165 through 168 Processing helix chain 'H' and resid 169 through 178 removed outlier: 3.718A pdb=" N LEU H 173 " --> pdb=" O VAL H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 205 Processing helix chain 'H' and resid 217 through 222 Processing helix chain 'H' and resid 227 through 235 Processing helix chain 'H' and resid 272 through 278 removed outlier: 4.424A pdb=" N TYR H 276 " --> pdb=" O ARG H 272 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 39 removed outlier: 3.940A pdb=" N GLU I 27 " --> pdb=" O GLU I 23 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS I 30 " --> pdb=" O VAL I 26 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU I 31 " --> pdb=" O GLU I 27 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU I 32 " --> pdb=" O LYS I 28 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN I 39 " --> pdb=" O GLU I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 60 removed outlier: 3.734A pdb=" N ILE I 60 " --> pdb=" O PHE I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 75 removed outlier: 4.126A pdb=" N GLU I 72 " --> pdb=" O LYS I 68 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS I 75 " --> pdb=" O HIS I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 94 removed outlier: 3.884A pdb=" N ILE I 88 " --> pdb=" O ALA I 84 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ALA I 91 " --> pdb=" O LYS I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 136 through 140 removed outlier: 3.731A pdb=" N LEU I 139 " --> pdb=" O ALA I 136 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 149 removed outlier: 3.733A pdb=" N MET I 149 " --> pdb=" O GLY I 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 165 through 168 Processing helix chain 'I' and resid 169 through 178 removed outlier: 3.751A pdb=" N LEU I 173 " --> pdb=" O VAL I 169 " (cutoff:3.500A) Processing helix chain 'I' and resid 193 through 206 removed outlier: 4.149A pdb=" N SER I 197 " --> pdb=" O ASP I 193 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR I 200 " --> pdb=" O ILE I 196 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR I 201 " --> pdb=" O SER I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 217 through 219 No H-bonds generated for 'chain 'I' and resid 217 through 219' Processing helix chain 'I' and resid 220 through 225 removed outlier: 3.865A pdb=" N CYS I 225 " --> pdb=" O LYS I 221 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 234 Processing helix chain 'I' and resid 269 through 272 Processing helix chain 'I' and resid 273 through 278 Processing helix chain 'J' and resid 21 through 39 removed outlier: 3.583A pdb=" N SER J 25 " --> pdb=" O ASN J 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU J 27 " --> pdb=" O GLU J 23 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASN J 39 " --> pdb=" O GLU J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 removed outlier: 3.601A pdb=" N ILE J 60 " --> pdb=" O TRP J 56 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY J 61 " --> pdb=" O PHE J 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 56 through 61' Processing helix chain 'J' and resid 65 through 75 removed outlier: 4.349A pdb=" N PHE J 69 " --> pdb=" O TYR J 65 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU J 72 " --> pdb=" O LYS J 68 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS J 75 " --> pdb=" O HIS J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 94 removed outlier: 3.785A pdb=" N GLN J 86 " --> pdb=" O SER J 82 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS J 87 " --> pdb=" O LEU J 83 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE J 88 " --> pdb=" O ALA J 84 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA J 91 " --> pdb=" O LYS J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 163 through 168 removed outlier: 3.661A pdb=" N HIS J 167 " --> pdb=" O CYS J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 169 through 179 removed outlier: 3.588A pdb=" N LEU J 173 " --> pdb=" O VAL J 169 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN J 179 " --> pdb=" O ALA J 175 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 206 removed outlier: 3.596A pdb=" N ILE J 203 " --> pdb=" O ARG J 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 217 through 225 removed outlier: 3.894A pdb=" N LYS J 221 " --> pdb=" O THR J 217 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 235 removed outlier: 3.937A pdb=" N TYR J 233 " --> pdb=" O GLU J 229 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU J 235 " --> pdb=" O ARG J 231 " (cutoff:3.500A) Processing helix chain 'J' and resid 273 through 278 removed outlier: 3.579A pdb=" N LYS J 277 " --> pdb=" O VAL J 273 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR J 278 " --> pdb=" O ILE J 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 273 through 278' Processing helix chain 'K' and resid 21 through 39 removed outlier: 4.169A pdb=" N GLU K 27 " --> pdb=" O GLU K 23 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N CYS K 30 " --> pdb=" O VAL K 26 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU K 31 " --> pdb=" O GLU K 27 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN K 39 " --> pdb=" O GLU K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 59 Processing helix chain 'K' and resid 62 through 74 removed outlier: 4.251A pdb=" N LYS K 68 " --> pdb=" O GLU K 64 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N PHE K 69 " --> pdb=" O TYR K 65 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLU K 72 " --> pdb=" O LYS K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 77 No H-bonds generated for 'chain 'K' and resid 75 through 77' Processing helix chain 'K' and resid 82 through 95 removed outlier: 3.886A pdb=" N GLN K 86 " --> pdb=" O SER K 82 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE K 88 " --> pdb=" O ALA K 84 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA K 91 " --> pdb=" O LYS K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 140 removed outlier: 3.913A pdb=" N ARG K 138 " --> pdb=" O VAL K 135 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU K 139 " --> pdb=" O ALA K 136 " (cutoff:3.500A) Processing helix chain 'K' and resid 165 through 168 Processing helix chain 'K' and resid 169 through 178 removed outlier: 3.654A pdb=" N LEU K 173 " --> pdb=" O VAL K 169 " (cutoff:3.500A) Processing helix chain 'K' and resid 193 through 206 removed outlier: 4.016A pdb=" N SER K 197 " --> pdb=" O ASP K 193 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR K 201 " --> pdb=" O SER K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 217 through 225 removed outlier: 3.726A pdb=" N LYS K 221 " --> pdb=" O THR K 217 " (cutoff:3.500A) Processing helix chain 'K' and resid 227 through 234 Processing helix chain 'K' and resid 269 through 272 Processing helix chain 'K' and resid 273 through 278 removed outlier: 3.761A pdb=" N TYR K 278 " --> pdb=" O ILE K 274 " (cutoff:3.500A) Processing helix chain 'L' and resid 21 through 37 removed outlier: 4.121A pdb=" N GLU L 27 " --> pdb=" O GLU L 23 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU L 35 " --> pdb=" O GLU L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 40 No H-bonds generated for 'chain 'L' and resid 38 through 40' Processing helix chain 'L' and resid 55 through 60 removed outlier: 3.632A pdb=" N ILE L 60 " --> pdb=" O PHE L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 74 removed outlier: 4.247A pdb=" N LYS L 68 " --> pdb=" O GLU L 64 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE L 69 " --> pdb=" O TYR L 65 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU L 72 " --> pdb=" O LYS L 68 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 77 No H-bonds generated for 'chain 'L' and resid 75 through 77' Processing helix chain 'L' and resid 82 through 94 removed outlier: 4.017A pdb=" N ILE L 88 " --> pdb=" O ALA L 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 136 through 140 removed outlier: 3.712A pdb=" N LEU L 139 " --> pdb=" O ALA L 136 " (cutoff:3.500A) Processing helix chain 'L' and resid 165 through 168 Processing helix chain 'L' and resid 169 through 178 Processing helix chain 'L' and resid 194 through 206 removed outlier: 3.719A pdb=" N SER L 198 " --> pdb=" O ASP L 194 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE L 203 " --> pdb=" O ARG L 199 " (cutoff:3.500A) Processing helix chain 'L' and resid 217 through 225 removed outlier: 3.905A pdb=" N LYS L 221 " --> pdb=" O THR L 217 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N MET L 223 " --> pdb=" O GLU L 219 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N CYS L 225 " --> pdb=" O LYS L 221 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 234 Processing helix chain 'L' and resid 235 through 237 No H-bonds generated for 'chain 'L' and resid 235 through 237' Processing helix chain 'L' and resid 271 through 277 removed outlier: 4.053A pdb=" N ASP L 275 " --> pdb=" O ARG L 272 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR L 276 " --> pdb=" O VAL L 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 21 through 39 removed outlier: 3.517A pdb=" N CYS M 30 " --> pdb=" O VAL M 26 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP M 34 " --> pdb=" O CYS M 30 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN M 39 " --> pdb=" O GLU M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 60 removed outlier: 3.808A pdb=" N ILE M 60 " --> pdb=" O PHE M 57 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 77 removed outlier: 4.276A pdb=" N LYS M 68 " --> pdb=" O GLU M 64 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N PHE M 69 " --> pdb=" O TYR M 65 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS M 71 " --> pdb=" O ARG M 67 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLU M 72 " --> pdb=" O LYS M 68 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS M 75 " --> pdb=" O HIS M 71 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN M 76 " --> pdb=" O GLU M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 95 removed outlier: 4.375A pdb=" N ALA M 91 " --> pdb=" O LYS M 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 136 through 140 removed outlier: 3.972A pdb=" N LEU M 139 " --> pdb=" O ALA M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 165 through 168 Processing helix chain 'M' and resid 169 through 178 removed outlier: 3.866A pdb=" N LEU M 173 " --> pdb=" O VAL M 169 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 206 removed outlier: 3.796A pdb=" N TYR M 201 " --> pdb=" O SER M 197 " (cutoff:3.500A) Processing helix chain 'M' and resid 217 through 219 No H-bonds generated for 'chain 'M' and resid 217 through 219' Processing helix chain 'M' and resid 220 through 225 Processing helix chain 'M' and resid 227 through 235 Processing helix chain 'M' and resid 273 through 278 removed outlier: 3.802A pdb=" N TYR M 278 " --> pdb=" O ILE M 274 " (cutoff:3.500A) Processing helix chain 'N' and resid 21 through 37 removed outlier: 4.112A pdb=" N GLU N 27 " --> pdb=" O GLU N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 40 No H-bonds generated for 'chain 'N' and resid 38 through 40' Processing helix chain 'N' and resid 55 through 60 Processing helix chain 'N' and resid 66 through 74 removed outlier: 4.470A pdb=" N GLU N 72 " --> pdb=" O LYS N 68 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 95 removed outlier: 4.136A pdb=" N ILE N 88 " --> pdb=" O ALA N 84 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA N 91 " --> pdb=" O LYS N 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 136 through 140 removed outlier: 4.289A pdb=" N LEU N 139 " --> pdb=" O ALA N 136 " (cutoff:3.500A) Processing helix chain 'N' and resid 165 through 168 Processing helix chain 'N' and resid 169 through 178 removed outlier: 3.827A pdb=" N LEU N 173 " --> pdb=" O VAL N 169 " (cutoff:3.500A) Processing helix chain 'N' and resid 194 through 206 removed outlier: 3.767A pdb=" N TYR N 201 " --> pdb=" O SER N 197 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA N 202 " --> pdb=" O SER N 198 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE N 203 " --> pdb=" O ARG N 199 " (cutoff:3.500A) Processing helix chain 'N' and resid 218 through 223 removed outlier: 4.029A pdb=" N MET N 223 " --> pdb=" O GLU N 219 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 235 removed outlier: 3.917A pdb=" N TYR N 233 " --> pdb=" O GLU N 229 " (cutoff:3.500A) Processing helix chain 'N' and resid 273 through 278 Processing helix chain 'O' and resid 21 through 39 removed outlier: 3.643A pdb=" N GLU O 27 " --> pdb=" O GLU O 23 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU O 31 " --> pdb=" O GLU O 27 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN O 39 " --> pdb=" O GLU O 35 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 60 removed outlier: 3.501A pdb=" N PHE O 59 " --> pdb=" O TRP O 56 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE O 60 " --> pdb=" O PHE O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 74 removed outlier: 3.642A pdb=" N THR O 66 " --> pdb=" O HIS O 62 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG O 67 " --> pdb=" O PRO O 63 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LYS O 68 " --> pdb=" O GLU O 64 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE O 69 " --> pdb=" O TYR O 65 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU O 72 " --> pdb=" O LYS O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 77 No H-bonds generated for 'chain 'O' and resid 75 through 77' Processing helix chain 'O' and resid 82 through 94 removed outlier: 3.736A pdb=" N GLN O 86 " --> pdb=" O SER O 82 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA O 91 " --> pdb=" O LYS O 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 136 through 140 removed outlier: 3.816A pdb=" N LEU O 139 " --> pdb=" O ALA O 136 " (cutoff:3.500A) Processing helix chain 'O' and resid 163 through 168 removed outlier: 3.556A pdb=" N HIS O 167 " --> pdb=" O CYS O 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 169 through 178 removed outlier: 3.640A pdb=" N LEU O 173 " --> pdb=" O VAL O 169 " (cutoff:3.500A) Processing helix chain 'O' and resid 195 through 206 removed outlier: 4.558A pdb=" N TYR O 201 " --> pdb=" O SER O 197 " (cutoff:3.500A) Processing helix chain 'O' and resid 217 through 225 removed outlier: 4.023A pdb=" N LYS O 221 " --> pdb=" O THR O 217 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N MET O 223 " --> pdb=" O GLU O 219 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N CYS O 225 " --> pdb=" O LYS O 221 " (cutoff:3.500A) Processing helix chain 'O' and resid 227 through 234 Processing helix chain 'O' and resid 273 through 278 removed outlier: 3.663A pdb=" N LYS O 277 " --> pdb=" O VAL O 273 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR O 278 " --> pdb=" O ILE O 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 273 through 278' Processing helix chain 'P' and resid 21 through 37 removed outlier: 3.518A pdb=" N SER P 25 " --> pdb=" O ASN P 21 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU P 27 " --> pdb=" O GLU P 23 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 40 No H-bonds generated for 'chain 'P' and resid 38 through 40' Processing helix chain 'P' and resid 55 through 59 Processing helix chain 'P' and resid 62 through 74 removed outlier: 3.670A pdb=" N ARG P 67 " --> pdb=" O PRO P 63 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYS P 68 " --> pdb=" O GLU P 64 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N PHE P 69 " --> pdb=" O TYR P 65 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS P 71 " --> pdb=" O ARG P 67 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLU P 72 " --> pdb=" O LYS P 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 75 through 77 No H-bonds generated for 'chain 'P' and resid 75 through 77' Processing helix chain 'P' and resid 82 through 95 removed outlier: 4.167A pdb=" N ILE P 88 " --> pdb=" O ALA P 84 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA P 91 " --> pdb=" O LYS P 87 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN P 95 " --> pdb=" O ALA P 91 " (cutoff:3.500A) Processing helix chain 'P' and resid 136 through 140 removed outlier: 3.799A pdb=" N LEU P 139 " --> pdb=" O ALA P 136 " (cutoff:3.500A) Processing helix chain 'P' and resid 165 through 168 Processing helix chain 'P' and resid 169 through 178 removed outlier: 3.972A pdb=" N LEU P 173 " --> pdb=" O VAL P 169 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N MET P 174 " --> pdb=" O PRO P 170 " (cutoff:3.500A) Processing helix chain 'P' and resid 194 through 206 Processing helix chain 'P' and resid 218 through 225 Processing helix chain 'P' and resid 227 through 235 removed outlier: 3.912A pdb=" N ARG P 231 " --> pdb=" O THR P 227 " (cutoff:3.500A) Processing helix chain 'P' and resid 273 through 278 removed outlier: 3.581A pdb=" N TYR P 278 " --> pdb=" O ILE P 274 " (cutoff:3.500A) Processing helix chain 'Q' and resid 21 through 39 removed outlier: 4.456A pdb=" N GLU Q 27 " --> pdb=" O GLU Q 23 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS Q 28 " --> pdb=" O ALA Q 24 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER Q 29 " --> pdb=" O SER Q 25 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N CYS Q 30 " --> pdb=" O VAL Q 26 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU Q 31 " --> pdb=" O GLU Q 27 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN Q 39 " --> pdb=" O GLU Q 35 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 60 removed outlier: 3.627A pdb=" N ILE Q 60 " --> pdb=" O PHE Q 57 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 76 removed outlier: 3.830A pdb=" N LYS Q 68 " --> pdb=" O GLU Q 64 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE Q 69 " --> pdb=" O TYR Q 65 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS Q 71 " --> pdb=" O ARG Q 67 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLU Q 72 " --> pdb=" O LYS Q 68 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS Q 75 " --> pdb=" O HIS Q 71 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN Q 76 " --> pdb=" O GLU Q 72 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 94 removed outlier: 3.866A pdb=" N GLN Q 86 " --> pdb=" O SER Q 82 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA Q 91 " --> pdb=" O LYS Q 87 " (cutoff:3.500A) Processing helix chain 'Q' and resid 136 through 140 removed outlier: 4.038A pdb=" N LEU Q 139 " --> pdb=" O ALA Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 165 through 168 Processing helix chain 'Q' and resid 169 through 178 removed outlier: 3.811A pdb=" N LEU Q 173 " --> pdb=" O VAL Q 169 " (cutoff:3.500A) Processing helix chain 'Q' and resid 196 through 206 removed outlier: 3.534A pdb=" N TYR Q 201 " --> pdb=" O SER Q 197 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA Q 202 " --> pdb=" O SER Q 198 " (cutoff:3.500A) Processing helix chain 'Q' and resid 220 through 225 removed outlier: 4.259A pdb=" N CYS Q 225 " --> pdb=" O LYS Q 221 " (cutoff:3.500A) Processing helix chain 'Q' and resid 227 through 234 Processing helix chain 'Q' and resid 235 through 237 No H-bonds generated for 'chain 'Q' and resid 235 through 237' Processing helix chain 'Q' and resid 271 through 276 removed outlier: 4.012A pdb=" N ILE Q 274 " --> pdb=" O GLU Q 271 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 39 removed outlier: 3.935A pdb=" N GLU R 27 " --> pdb=" O GLU R 23 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN R 39 " --> pdb=" O GLU R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 59 Processing helix chain 'R' and resid 62 through 74 removed outlier: 3.940A pdb=" N THR R 66 " --> pdb=" O HIS R 62 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARG R 67 " --> pdb=" O PRO R 63 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LYS R 68 " --> pdb=" O GLU R 64 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N PHE R 69 " --> pdb=" O TYR R 65 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLU R 72 " --> pdb=" O LYS R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 77 No H-bonds generated for 'chain 'R' and resid 75 through 77' Processing helix chain 'R' and resid 82 through 95 removed outlier: 3.822A pdb=" N GLN R 86 " --> pdb=" O SER R 82 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE R 88 " --> pdb=" O ALA R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 140 Processing helix chain 'R' and resid 163 through 168 removed outlier: 3.568A pdb=" N HIS R 167 " --> pdb=" O CYS R 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 169 through 178 removed outlier: 3.583A pdb=" N LEU R 173 " --> pdb=" O VAL R 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 206 removed outlier: 4.701A pdb=" N SER R 197 " --> pdb=" O ASP R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 225 removed outlier: 3.639A pdb=" N LYS R 221 " --> pdb=" O THR R 217 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET R 223 " --> pdb=" O GLU R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 227 through 234 Processing helix chain 'R' and resid 269 through 271 No H-bonds generated for 'chain 'R' and resid 269 through 271' Processing helix chain 'R' and resid 272 through 278 removed outlier: 4.218A pdb=" N TYR R 276 " --> pdb=" O ARG R 272 " (cutoff:3.500A) Processing helix chain 'S' and resid 21 through 39 removed outlier: 3.919A pdb=" N GLU S 27 " --> pdb=" O GLU S 23 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS S 28 " --> pdb=" O ALA S 24 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN S 39 " --> pdb=" O GLU S 35 " (cutoff:3.500A) Processing helix chain 'S' and resid 55 through 60 removed outlier: 3.591A pdb=" N PHE S 59 " --> pdb=" O TRP S 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 76 removed outlier: 3.898A pdb=" N THR S 66 " --> pdb=" O HIS S 62 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG S 67 " --> pdb=" O PRO S 63 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N LYS S 68 " --> pdb=" O GLU S 64 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N PHE S 69 " --> pdb=" O TYR S 65 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU S 72 " --> pdb=" O LYS S 68 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS S 75 " --> pdb=" O HIS S 71 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN S 76 " --> pdb=" O GLU S 72 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 94 removed outlier: 3.907A pdb=" N GLN S 86 " --> pdb=" O SER S 82 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA S 91 " --> pdb=" O LYS S 87 " (cutoff:3.500A) Processing helix chain 'S' and resid 136 through 140 removed outlier: 3.994A pdb=" N LEU S 139 " --> pdb=" O ALA S 136 " (cutoff:3.500A) Processing helix chain 'S' and resid 163 through 168 removed outlier: 3.598A pdb=" N HIS S 167 " --> pdb=" O CYS S 164 " (cutoff:3.500A) Processing helix chain 'S' and resid 169 through 178 removed outlier: 4.120A pdb=" N LEU S 173 " --> pdb=" O VAL S 169 " (cutoff:3.500A) Processing helix chain 'S' and resid 194 through 206 removed outlier: 3.830A pdb=" N TYR S 201 " --> pdb=" O SER S 197 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE S 203 " --> pdb=" O ARG S 199 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 225 removed outlier: 3.897A pdb=" N CYS S 225 " --> pdb=" O LYS S 221 " (cutoff:3.500A) Processing helix chain 'S' and resid 227 through 235 removed outlier: 3.957A pdb=" N GLU S 235 " --> pdb=" O ARG S 231 " (cutoff:3.500A) Processing helix chain 'S' and resid 273 through 278 removed outlier: 3.951A pdb=" N TYR S 278 " --> pdb=" O ILE S 274 " (cutoff:3.500A) Processing helix chain 'U' and resid 21 through 39 removed outlier: 3.791A pdb=" N GLU U 27 " --> pdb=" O GLU U 23 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN U 39 " --> pdb=" O GLU U 35 " (cutoff:3.500A) Processing helix chain 'U' and resid 55 through 60 removed outlier: 3.732A pdb=" N PHE U 59 " --> pdb=" O TRP U 56 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE U 60 " --> pdb=" O PHE U 57 " (cutoff:3.500A) Processing helix chain 'U' and resid 62 through 76 removed outlier: 4.303A pdb=" N ARG U 67 " --> pdb=" O PRO U 63 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LYS U 68 " --> pdb=" O GLU U 64 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE U 69 " --> pdb=" O TYR U 65 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU U 72 " --> pdb=" O LYS U 68 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS U 75 " --> pdb=" O HIS U 71 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN U 76 " --> pdb=" O GLU U 72 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 96 removed outlier: 3.858A pdb=" N GLN U 86 " --> pdb=" O SER U 82 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA U 91 " --> pdb=" O LYS U 87 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN U 95 " --> pdb=" O ALA U 91 " (cutoff:3.500A) Processing helix chain 'U' and resid 136 through 140 Processing helix chain 'U' and resid 165 through 168 Processing helix chain 'U' and resid 169 through 178 removed outlier: 3.950A pdb=" N LEU U 173 " --> pdb=" O VAL U 169 " (cutoff:3.500A) Processing helix chain 'U' and resid 193 through 206 removed outlier: 4.466A pdb=" N SER U 197 " --> pdb=" O ASP U 193 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER U 198 " --> pdb=" O ASP U 194 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR U 201 " --> pdb=" O SER U 197 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE U 203 " --> pdb=" O ARG U 199 " (cutoff:3.500A) Processing helix chain 'U' and resid 217 through 219 No H-bonds generated for 'chain 'U' and resid 217 through 219' Processing helix chain 'U' and resid 220 through 225 Processing helix chain 'U' and resid 227 through 235 removed outlier: 3.904A pdb=" N TYR U 233 " --> pdb=" O GLU U 229 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU U 235 " --> pdb=" O ARG U 231 " (cutoff:3.500A) Processing helix chain 'U' and resid 271 through 274 removed outlier: 3.644A pdb=" N ILE U 274 " --> pdb=" O GLU U 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 271 through 274' Processing sheet with id=AA1, first strand: chain 'B' and resid 123 through 129 removed outlier: 7.296A pdb=" N TRP B 117 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LYS B 127 " --> pdb=" O GLN B 115 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLN B 115 " --> pdb=" O LYS B 127 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ARG B 129 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N LEU B 113 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL B 44 " --> pdb=" O CYS B 100 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N SER B 102 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU B 43 " --> pdb=" O ARG B 9 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA B 45 " --> pdb=" O ALA B 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 159 through 163 removed outlier: 7.015A pdb=" N GLY B 160 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N SER B 187 " --> pdb=" O GLY B 160 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LEU B 162 " --> pdb=" O SER B 187 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 303 through 306 removed outlier: 3.661A pdb=" N PHE D 295 " --> pdb=" O LYS B 304 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 124 through 129 removed outlier: 4.192A pdb=" N GLY D 126 " --> pdb=" O TRP D 117 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP D 117 " --> pdb=" O GLY D 126 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER D 110 " --> pdb=" O ASP D 107 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP D 107 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL D 44 " --> pdb=" O CYS D 100 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N SER D 102 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU D 43 " --> pdb=" O ARG D 9 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA D 266 " --> pdb=" O ALA D 10 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 152 through 154 removed outlier: 3.693A pdb=" N GLY D 160 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL D 185 " --> pdb=" O GLY D 160 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER D 187 " --> pdb=" O LEU D 162 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 303 through 308 removed outlier: 3.526A pdb=" N PHE F 295 " --> pdb=" O LYS D 304 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N GLN F 297 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N HIS D 308 " --> pdb=" O GLN F 297 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 124 through 129 removed outlier: 7.289A pdb=" N TRP F 117 " --> pdb=" O ILE F 125 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LYS F 127 " --> pdb=" O GLN F 115 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLN F 115 " --> pdb=" O LYS F 127 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ARG F 129 " --> pdb=" O LEU F 113 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N LEU F 113 " --> pdb=" O ARG F 129 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL F 44 " --> pdb=" O CYS F 100 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N SER F 102 " --> pdb=" O VAL F 44 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU F 43 " --> pdb=" O ARG F 9 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA F 266 " --> pdb=" O ALA F 10 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 159 through 163 Processing sheet with id=AA9, first strand: chain 'F' and resid 303 through 306 removed outlier: 6.337A pdb=" N LYS F 304 " --> pdb=" O PHE H 295 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS I 304 " --> pdb=" O MET G 293 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE G 295 " --> pdb=" O LYS I 304 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 124 through 129 removed outlier: 7.017A pdb=" N TRP G 117 " --> pdb=" O ILE G 125 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LYS G 127 " --> pdb=" O GLN G 115 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLN G 115 " --> pdb=" O LYS G 127 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ARG G 129 " --> pdb=" O LEU G 113 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N LEU G 113 " --> pdb=" O ARG G 129 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL G 99 " --> pdb=" O PHE G 118 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU G 43 " --> pdb=" O ARG G 9 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 152 through 154 removed outlier: 3.677A pdb=" N THR G 154 " --> pdb=" O GLY G 157 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASN G 158 " --> pdb=" O VAL G 183 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N VAL G 185 " --> pdb=" O ASN G 158 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLY G 160 " --> pdb=" O VAL G 185 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N SER G 187 " --> pdb=" O GLY G 160 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU G 162 " --> pdb=" O SER G 187 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 124 through 129 removed outlier: 7.240A pdb=" N TRP H 117 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LYS H 127 " --> pdb=" O GLN H 115 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLN H 115 " --> pdb=" O LYS H 127 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ARG H 129 " --> pdb=" O LEU H 113 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEU H 113 " --> pdb=" O ARG H 129 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL H 44 " --> pdb=" O CYS H 100 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N SER H 102 " --> pdb=" O VAL H 44 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU H 43 " --> pdb=" O ARG H 9 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 152 through 154 removed outlier: 3.637A pdb=" N GLY H 160 " --> pdb=" O VAL H 183 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA H 186 " --> pdb=" O LEU H 210 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 304 through 306 removed outlier: 3.506A pdb=" N PHE J 295 " --> pdb=" O LYS H 304 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 124 through 129 removed outlier: 7.082A pdb=" N TRP I 117 " --> pdb=" O ILE I 125 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LYS I 127 " --> pdb=" O GLN I 115 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLN I 115 " --> pdb=" O LYS I 127 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ARG I 129 " --> pdb=" O LEU I 113 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N LEU I 113 " --> pdb=" O ARG I 129 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL I 44 " --> pdb=" O CYS I 100 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N SER I 102 " --> pdb=" O VAL I 44 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU I 43 " --> pdb=" O ARG I 9 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA I 266 " --> pdb=" O ALA I 10 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 152 through 154 removed outlier: 6.437A pdb=" N ASN I 158 " --> pdb=" O VAL I 183 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N VAL I 185 " --> pdb=" O ASN I 158 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLY I 160 " --> pdb=" O VAL I 185 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N SER I 187 " --> pdb=" O GLY I 160 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU I 162 " --> pdb=" O SER I 187 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N HIS I 184 " --> pdb=" O LEU I 210 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N THR I 212 " --> pdb=" O HIS I 184 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA I 186 " --> pdb=" O THR I 212 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 293 through 296 removed outlier: 7.188A pdb=" N MET I 293 " --> pdb=" O LYS K 304 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N LEU K 306 " --> pdb=" O MET I 293 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N PHE I 295 " --> pdb=" O LEU K 306 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'J' and resid 124 through 129 removed outlier: 4.155A pdb=" N GLY J 126 " --> pdb=" O TRP J 117 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL J 44 " --> pdb=" O CYS J 100 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N SER J 102 " --> pdb=" O VAL J 44 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU J 43 " --> pdb=" O ARG J 9 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA J 45 " --> pdb=" O ALA J 11 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 159 through 160 removed outlier: 6.907A pdb=" N GLY J 160 " --> pdb=" O VAL J 185 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N SER J 187 " --> pdb=" O GLY J 160 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU J 210 " --> pdb=" O HIS J 184 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA J 186 " --> pdb=" O LEU J 210 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 304 through 306 removed outlier: 3.579A pdb=" N SER L 292 " --> pdb=" O ASN K 294 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN K 294 " --> pdb=" O SER L 292 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS M 304 " --> pdb=" O MET K 293 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 124 through 129 removed outlier: 7.286A pdb=" N TRP K 117 " --> pdb=" O ILE K 125 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LYS K 127 " --> pdb=" O GLN K 115 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLN K 115 " --> pdb=" O LYS K 127 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ARG K 129 " --> pdb=" O LEU K 113 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU K 113 " --> pdb=" O ARG K 129 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU K 43 " --> pdb=" O ARG K 9 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA K 45 " --> pdb=" O ALA K 11 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL K 13 " --> pdb=" O ALA K 45 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 159 through 163 removed outlier: 7.012A pdb=" N GLY K 160 " --> pdb=" O VAL K 185 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N SER K 187 " --> pdb=" O GLY K 160 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LEU K 162 " --> pdb=" O SER K 187 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N HIS K 184 " --> pdb=" O LEU K 210 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N THR K 212 " --> pdb=" O HIS K 184 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA K 186 " --> pdb=" O THR K 212 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 124 through 129 removed outlier: 7.156A pdb=" N TRP L 117 " --> pdb=" O ILE L 125 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LYS L 127 " --> pdb=" O GLN L 115 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN L 115 " --> pdb=" O LYS L 127 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ARG L 129 " --> pdb=" O LEU L 113 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N LEU L 113 " --> pdb=" O ARG L 129 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL L 44 " --> pdb=" O CYS L 100 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N SER L 102 " --> pdb=" O VAL L 44 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU L 43 " --> pdb=" O ARG L 9 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA L 45 " --> pdb=" O ALA L 11 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 159 through 163 removed outlier: 6.930A pdb=" N GLY L 160 " --> pdb=" O VAL L 185 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N SER L 187 " --> pdb=" O GLY L 160 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU L 162 " --> pdb=" O SER L 187 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N HIS L 184 " --> pdb=" O LEU L 210 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N THR L 212 " --> pdb=" O HIS L 184 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA L 186 " --> pdb=" O THR L 212 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 303 through 306 removed outlier: 3.501A pdb=" N PHE N 295 " --> pdb=" O LYS L 304 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER M 292 " --> pdb=" O ASN N 294 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N LYS O 304 " --> pdb=" O LEU M 291 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N MET M 293 " --> pdb=" O LYS O 304 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 124 through 129 removed outlier: 3.838A pdb=" N GLY M 126 " --> pdb=" O TRP M 117 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL M 44 " --> pdb=" O CYS M 100 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N SER M 102 " --> pdb=" O VAL M 44 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU M 43 " --> pdb=" O ARG M 9 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 106 through 107 Processing sheet with id=AD1, first strand: chain 'M' and resid 152 through 153 removed outlier: 3.595A pdb=" N GLY M 160 " --> pdb=" O VAL M 183 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER M 187 " --> pdb=" O LEU M 162 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N HIS M 184 " --> pdb=" O LEU M 210 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N THR M 212 " --> pdb=" O HIS M 184 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA M 186 " --> pdb=" O THR M 212 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 124 through 129 removed outlier: 7.281A pdb=" N TRP N 117 " --> pdb=" O ILE N 125 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LYS N 127 " --> pdb=" O GLN N 115 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLN N 115 " --> pdb=" O LYS N 127 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ARG N 129 " --> pdb=" O LEU N 113 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LEU N 113 " --> pdb=" O ARG N 129 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL N 44 " --> pdb=" O CYS N 100 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N SER N 102 " --> pdb=" O VAL N 44 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU N 43 " --> pdb=" O ARG N 9 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 152 through 154 removed outlier: 6.418A pdb=" N ASN N 158 " --> pdb=" O VAL N 183 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N VAL N 185 " --> pdb=" O ASN N 158 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLY N 160 " --> pdb=" O VAL N 185 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N SER N 187 " --> pdb=" O GLY N 160 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU N 162 " --> pdb=" O SER N 187 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA N 186 " --> pdb=" O LEU N 210 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 303 through 306 removed outlier: 3.538A pdb=" N PHE P 295 " --> pdb=" O LYS N 304 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER O 292 " --> pdb=" O ASN P 294 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS Q 304 " --> pdb=" O MET O 293 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE O 295 " --> pdb=" O LYS Q 304 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 124 through 129 removed outlier: 7.184A pdb=" N TRP O 117 " --> pdb=" O ILE O 125 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N LYS O 127 " --> pdb=" O GLN O 115 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLN O 115 " --> pdb=" O LYS O 127 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ARG O 129 " --> pdb=" O LEU O 113 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LEU O 113 " --> pdb=" O ARG O 129 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL O 44 " --> pdb=" O CYS O 100 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N SER O 102 " --> pdb=" O VAL O 44 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU O 43 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA O 45 " --> pdb=" O ALA O 11 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 159 through 160 removed outlier: 6.928A pdb=" N GLY O 160 " --> pdb=" O VAL O 185 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N SER O 187 " --> pdb=" O GLY O 160 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 124 through 129 removed outlier: 3.977A pdb=" N GLY P 126 " --> pdb=" O TRP P 117 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL P 44 " --> pdb=" O CYS P 100 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N SER P 102 " --> pdb=" O VAL P 44 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU P 43 " --> pdb=" O ARG P 9 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'P' and resid 152 through 154 removed outlier: 6.412A pdb=" N ASN P 158 " --> pdb=" O VAL P 183 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N VAL P 185 " --> pdb=" O ASN P 158 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLY P 160 " --> pdb=" O VAL P 185 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N SER P 187 " --> pdb=" O GLY P 160 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LEU P 162 " --> pdb=" O SER P 187 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N HIS P 184 " --> pdb=" O LEU P 210 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N THR P 212 " --> pdb=" O HIS P 184 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA P 186 " --> pdb=" O THR P 212 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'P' and resid 303 through 306 removed outlier: 6.005A pdb=" N LYS P 304 " --> pdb=" O PHE R 295 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N LYS S 304 " --> pdb=" O LEU Q 291 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N MET Q 293 " --> pdb=" O LYS S 304 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N LEU S 306 " --> pdb=" O MET Q 293 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N PHE Q 295 " --> pdb=" O LEU S 306 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Q' and resid 124 through 129 removed outlier: 7.051A pdb=" N TRP Q 117 " --> pdb=" O ILE Q 125 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LYS Q 127 " --> pdb=" O GLN Q 115 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLN Q 115 " --> pdb=" O LYS Q 127 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL Q 44 " --> pdb=" O CYS Q 100 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N SER Q 102 " --> pdb=" O VAL Q 44 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU Q 43 " --> pdb=" O ARG Q 9 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Q' and resid 162 through 163 removed outlier: 6.971A pdb=" N LEU Q 162 " --> pdb=" O SER Q 187 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N HIS Q 184 " --> pdb=" O LEU Q 210 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N THR Q 212 " --> pdb=" O HIS Q 184 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA Q 186 " --> pdb=" O THR Q 212 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'R' and resid 124 through 129 removed outlier: 7.284A pdb=" N TRP R 117 " --> pdb=" O ILE R 125 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LYS R 127 " --> pdb=" O GLN R 115 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLN R 115 " --> pdb=" O LYS R 127 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG R 129 " --> pdb=" O LEU R 113 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N LEU R 113 " --> pdb=" O ARG R 129 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL R 99 " --> pdb=" O PHE R 118 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU R 43 " --> pdb=" O ARG R 9 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA R 45 " --> pdb=" O ALA R 11 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL R 13 " --> pdb=" O ALA R 45 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'R' and resid 159 through 160 removed outlier: 7.039A pdb=" N GLY R 160 " --> pdb=" O VAL R 185 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N SER R 187 " --> pdb=" O GLY R 160 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N HIS R 184 " --> pdb=" O LEU R 210 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N THR R 212 " --> pdb=" O HIS R 184 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA R 186 " --> pdb=" O THR R 212 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'S' and resid 124 through 129 removed outlier: 6.998A pdb=" N TRP S 117 " --> pdb=" O ILE S 125 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LYS S 127 " --> pdb=" O GLN S 115 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLN S 115 " --> pdb=" O LYS S 127 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL S 44 " --> pdb=" O CYS S 100 " (cutoff:3.500A) removed outlier: 8.774A pdb=" N SER S 102 " --> pdb=" O VAL S 44 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU S 43 " --> pdb=" O ARG S 9 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL S 13 " --> pdb=" O ALA S 45 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'S' and resid 106 through 107 Processing sheet with id=AE7, first strand: chain 'S' and resid 159 through 160 removed outlier: 6.776A pdb=" N GLY S 160 " --> pdb=" O VAL S 185 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N SER S 187 " --> pdb=" O GLY S 160 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'S' and resid 293 through 295 removed outlier: 7.162A pdb=" N MET S 293 " --> pdb=" O LYS U 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'U' and resid 98 through 100 removed outlier: 3.924A pdb=" N LEU U 43 " --> pdb=" O ARG U 9 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL U 13 " --> pdb=" O ALA U 45 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'U' and resid 102 through 107 removed outlier: 7.459A pdb=" N LEU U 113 " --> pdb=" O ARG U 129 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ARG U 129 " --> pdb=" O LEU U 113 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLN U 115 " --> pdb=" O LYS U 127 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS U 127 " --> pdb=" O GLN U 115 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N TRP U 117 " --> pdb=" O ILE U 125 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP U 123 " --> pdb=" O ASN U 119 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'U' and resid 152 through 154 removed outlier: 3.551A pdb=" N PHE U 152 " --> pdb=" O LEU U 159 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU U 159 " --> pdb=" O PHE U 152 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ASN U 158 " --> pdb=" O VAL U 183 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL U 185 " --> pdb=" O ASN U 158 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLY U 160 " --> pdb=" O VAL U 185 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N SER U 187 " --> pdb=" O GLY U 160 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LEU U 162 " --> pdb=" O SER U 187 " (cutoff:3.500A) 1321 hydrogen bonds defined for protein. 3537 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: 8.61 Time building geometry restraints manager: 4.00 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: 11740 1.33 - 1.46: 8470 1.46 - 1.58: 23462 1.58 - 1.70: 1 1.70 - 1.82: 476 Bond restraints: 44149 Sorted by residual: bond pdb=" ND1 HIS P 305 " pdb=" CE1 HIS P 305 " ideal model delta sigma weight residual 1.321 1.374 -0.053 1.00e-02 1.00e+04 2.82e+01 bond pdb=" CG ASN L 294 " pdb=" OD1 ASN L 294 " ideal model delta sigma weight residual 1.231 1.327 -0.096 1.90e-02 2.77e+03 2.53e+01 bond pdb=" CG ASN R 294 " pdb=" OD1 ASN R 294 " ideal model delta sigma weight residual 1.231 1.326 -0.095 1.90e-02 2.77e+03 2.51e+01 bond pdb=" CD GLN S 297 " pdb=" OE1 GLN S 297 " ideal model delta sigma weight residual 1.231 1.326 -0.095 1.90e-02 2.77e+03 2.51e+01 bond pdb=" CG ASN K 294 " pdb=" OD1 ASN K 294 " ideal model delta sigma weight residual 1.231 1.326 -0.095 1.90e-02 2.77e+03 2.50e+01 ... (remaining 44144 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 51490 2.56 - 5.13: 8079 5.13 - 7.69: 377 7.69 - 10.25: 10 10.25 - 12.82: 3 Bond angle restraints: 59959 Sorted by residual: angle pdb=" N MET H 131 " pdb=" CA MET H 131 " pdb=" C MET H 131 " ideal model delta sigma weight residual 110.97 119.17 -8.20 1.09e+00 8.42e-01 5.66e+01 angle pdb=" N VAL M 135 " pdb=" CA VAL M 135 " pdb=" C VAL M 135 " ideal model delta sigma weight residual 110.36 117.30 -6.94 1.05e+00 9.07e-01 4.37e+01 angle pdb=" CB HIS P 305 " pdb=" CG HIS P 305 " pdb=" CD2 HIS P 305 " ideal model delta sigma weight residual 131.20 122.63 8.57 1.30e+00 5.92e-01 4.35e+01 angle pdb=" N VAL Q 99 " pdb=" CA VAL Q 99 " pdb=" C VAL Q 99 " ideal model delta sigma weight residual 107.78 117.18 -9.40 1.49e+00 4.50e-01 3.98e+01 angle pdb=" N TYR F 233 " pdb=" CA TYR F 233 " pdb=" C TYR F 233 " ideal model delta sigma weight residual 111.36 104.53 6.83 1.09e+00 8.42e-01 3.93e+01 ... (remaining 59954 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 23855 17.91 - 35.83: 1767 35.83 - 53.74: 435 53.74 - 71.65: 108 71.65 - 89.56: 49 Dihedral angle restraints: 26214 sinusoidal: 10370 harmonic: 15844 Sorted by residual: dihedral pdb=" CA VAL G 256 " pdb=" C VAL G 256 " pdb=" N PRO G 257 " pdb=" CA PRO G 257 " ideal model delta harmonic sigma weight residual 180.00 -150.30 -29.70 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA ILE L 18 " pdb=" C ILE L 18 " pdb=" N TYR L 19 " pdb=" CA TYR L 19 " ideal model delta harmonic sigma weight residual -180.00 -150.89 -29.11 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA TYR I 5 " pdb=" C TYR I 5 " pdb=" N PRO I 6 " pdb=" CA PRO I 6 " ideal model delta harmonic sigma weight residual -180.00 -150.95 -29.05 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 26211 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 4500 0.092 - 0.183: 1492 0.183 - 0.275: 236 0.275 - 0.367: 51 0.367 - 0.459: 11 Chirality restraints: 6290 Sorted by residual: chirality pdb=" CA GLU D 96 " pdb=" N GLU D 96 " pdb=" C GLU D 96 " pdb=" CB GLU D 96 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.26e+00 chirality pdb=" CA PHE M 192 " pdb=" N PHE M 192 " pdb=" C PHE M 192 " pdb=" CB PHE M 192 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.05e+00 chirality pdb=" CA GLU J 96 " pdb=" N GLU J 96 " pdb=" C GLU J 96 " pdb=" CB GLU J 96 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.55e+00 ... (remaining 6287 not shown) Planarity restraints: 7837 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 165 " 0.144 2.00e-02 2.50e+03 6.77e-02 1.15e+02 pdb=" CG TRP D 165 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP D 165 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP D 165 " -0.063 2.00e-02 2.50e+03 pdb=" NE1 TRP D 165 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TRP D 165 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP D 165 " -0.085 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 165 " 0.064 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 165 " -0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP D 165 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP P 165 " 0.129 2.00e-02 2.50e+03 6.00e-02 9.01e+01 pdb=" CG TRP P 165 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP P 165 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP P 165 " -0.061 2.00e-02 2.50e+03 pdb=" NE1 TRP P 165 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP P 165 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP P 165 " -0.067 2.00e-02 2.50e+03 pdb=" CZ2 TRP P 165 " 0.057 2.00e-02 2.50e+03 pdb=" CZ3 TRP P 165 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP P 165 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 165 " 0.121 2.00e-02 2.50e+03 5.63e-02 7.94e+01 pdb=" CG TRP H 165 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP H 165 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP H 165 " -0.053 2.00e-02 2.50e+03 pdb=" NE1 TRP H 165 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP H 165 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP H 165 " -0.062 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 165 " 0.053 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 165 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP H 165 " 0.054 2.00e-02 2.50e+03 ... (remaining 7834 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5102 2.79 - 3.32: 41613 3.32 - 3.85: 61498 3.85 - 4.37: 75035 4.37 - 4.90: 129603 Nonbonded interactions: 312851 Sorted by model distance: nonbonded pdb=" O THR P 300 " pdb=" OG1 THR P 300 " model vdw 2.265 3.040 nonbonded pdb=" O THR B 300 " pdb=" OG1 THR B 300 " model vdw 2.276 3.040 nonbonded pdb=" O THR N 300 " pdb=" OG1 THR N 300 " model vdw 2.294 3.040 nonbonded pdb=" O THR O 300 " pdb=" OG1 THR O 300 " model vdw 2.325 3.040 nonbonded pdb=" OD1 ASP R 318 " pdb=" N ILE R 319 " model vdw 2.352 3.120 ... (remaining 312846 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 34.050 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.100 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 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 : 0.012 0.098 44149 Z= 0.709 Angle : 1.734 12.815 59959 Z= 1.157 Chirality : 0.092 0.459 6290 Planarity : 0.012 0.129 7837 Dihedral : 14.633 89.564 16082 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 0.43 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.84 % Favored : 94.92 % Rotamer: Outliers : 1.50 % Allowed : 6.84 % Favored : 91.66 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.25 (0.10), residues: 5355 helix: -2.61 (0.10), residues: 1581 sheet: 0.30 (0.16), residues: 850 loop : -1.35 (0.11), residues: 2924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 132 TYR 0.108 0.017 TYR U 65 PHE 0.080 0.009 PHE J 59 TRP 0.144 0.018 TRP D 165 HIS 0.015 0.002 HIS J 71 Details of bonding type rmsd covalent geometry : bond 0.01214 (44149) covalent geometry : angle 1.73362 (59959) hydrogen bonds : bond 0.23231 ( 1321) hydrogen bonds : angle 7.93442 ( 3537) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 616 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 131 MET cc_start: 0.7598 (tpt) cc_final: 0.6876 (tpt) REVERT: B 132 ARG cc_start: 0.7218 (mmt90) cc_final: 0.6806 (ttp-170) REVERT: B 211 MET cc_start: 0.7787 (ttp) cc_final: 0.7542 (ttp) REVERT: B 255 MET cc_start: 0.6822 (tpp) cc_final: 0.6600 (tpp) REVERT: B 268 ILE cc_start: 0.9261 (mt) cc_final: 0.8878 (mm) REVERT: F 94 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7568 (ttm110) REVERT: F 132 ARG cc_start: 0.7453 (ttt-90) cc_final: 0.6763 (ptt180) REVERT: F 220 MET cc_start: 0.8954 (ptp) cc_final: 0.8726 (ptp) REVERT: G 131 MET cc_start: 0.8234 (mmt) cc_final: 0.7960 (mmm) REVERT: G 180 ASN cc_start: 0.8702 (t0) cc_final: 0.8426 (t0) REVERT: H 281 ASP cc_start: 0.8205 (t0) cc_final: 0.7626 (t0) REVERT: I 255 MET cc_start: 0.7764 (tpp) cc_final: 0.7409 (tpp) REVERT: J 255 MET cc_start: 0.7876 (tpp) cc_final: 0.7483 (tpp) REVERT: K 123 ASP cc_start: 0.8357 (p0) cc_final: 0.8127 (p0) REVERT: K 125 ILE cc_start: 0.9297 (mt) cc_final: 0.8927 (mm) REVERT: K 152 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.7525 (p90) REVERT: K 255 MET cc_start: 0.8100 (tpp) cc_final: 0.7162 (tpt) REVERT: L 94 ARG cc_start: 0.7838 (ttp80) cc_final: 0.7630 (ttp80) REVERT: L 123 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.7993 (p0) REVERT: L 201 TYR cc_start: 0.8875 (t80) cc_final: 0.8625 (t80) REVERT: M 143 ASP cc_start: 0.6961 (t0) cc_final: 0.6662 (m-30) REVERT: M 163 MET cc_start: 0.8236 (mtp) cc_final: 0.7479 (mtp) REVERT: M 255 MET cc_start: 0.7448 (tpp) cc_final: 0.7064 (tpp) REVERT: N 117 TRP cc_start: 0.9095 (m100) cc_final: 0.8479 (m100) REVERT: N 281 ASP cc_start: 0.8457 (t0) cc_final: 0.8252 (t70) REVERT: O 125 ILE cc_start: 0.9379 (mt) cc_final: 0.9118 (mm) REVERT: O 138 ARG cc_start: 0.8756 (ptp-170) cc_final: 0.8551 (ptp-170) REVERT: O 163 MET cc_start: 0.7889 (mtp) cc_final: 0.6961 (mtp) REVERT: O 180 ASN cc_start: 0.8725 (t0) cc_final: 0.8443 (t0) REVERT: O 220 MET cc_start: 0.7658 (ptm) cc_final: 0.7445 (ptm) REVERT: Q 255 MET cc_start: 0.7151 (tpp) cc_final: 0.6450 (tpp) REVERT: Q 305 HIS cc_start: 0.8580 (m90) cc_final: 0.8365 (m90) REVERT: R 86 GLN cc_start: 0.7310 (tt0) cc_final: 0.6870 (tt0) REVERT: R 125 ILE cc_start: 0.9204 (mt) cc_final: 0.8899 (mm) REVERT: R 129 ARG cc_start: 0.8057 (mtt180) cc_final: 0.7594 (mtt-85) REVERT: R 148 MET cc_start: 0.8891 (mtt) cc_final: 0.8554 (mtm) REVERT: R 174 MET cc_start: 0.9386 (tpp) cc_final: 0.9090 (tpp) REVERT: S 149 MET cc_start: 0.8776 (ttm) cc_final: 0.8564 (ttt) REVERT: S 220 MET cc_start: 0.7765 (ttm) cc_final: 0.7468 (ttm) REVERT: U 82 SER cc_start: 0.8609 (t) cc_final: 0.8280 (p) REVERT: U 132 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.6318 (ttp-170) REVERT: U 149 MET cc_start: 0.8811 (ttp) cc_final: 0.8584 (ttt) REVERT: U 176 MET cc_start: 0.9306 (tpp) cc_final: 0.8590 (tpp) REVERT: U 199 ARG cc_start: 0.8595 (ttm-80) cc_final: 0.8107 (ttm-80) REVERT: U 234 PHE cc_start: 0.8829 (t80) cc_final: 0.8593 (t80) REVERT: U 255 MET cc_start: 0.7720 (tpp) cc_final: 0.7457 (tpp) REVERT: U 281 ASP cc_start: 0.8318 (t0) cc_final: 0.7857 (t70) outliers start: 69 outliers final: 21 residues processed: 675 average time/residue: 0.2176 time to fit residues: 240.7274 Evaluate side-chains 412 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 387 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain I residue 62 HIS Chi-restraints excluded: chain J residue 244 ILE Chi-restraints excluded: chain J residue 270 VAL Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain L residue 123 ASP Chi-restraints excluded: chain M residue 134 SER Chi-restraints excluded: chain O residue 209 VAL Chi-restraints excluded: chain O residue 298 GLN Chi-restraints excluded: chain O residue 303 VAL Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 85 ILE Chi-restraints excluded: chain Q residue 303 VAL Chi-restraints excluded: chain R residue 65 TYR Chi-restraints excluded: chain R residue 152 PHE Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 315 THR Chi-restraints excluded: chain U residue 80 ILE Chi-restraints excluded: chain U residue 132 ARG Chi-restraints excluded: chain U residue 265 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 527 random chunks: chunk 394 optimal weight: 10.0000 chunk 430 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 265 optimal weight: 7.9990 chunk 523 optimal weight: 3.9990 chunk 497 optimal weight: 0.7980 chunk 414 optimal weight: 4.9990 chunk 310 optimal weight: 5.9990 chunk 488 optimal weight: 4.9990 chunk 366 optimal weight: 0.0980 chunk 223 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN D 39 ASN D 119 ASN ** F 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 297 GLN ** H 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 241 HIS J 167 HIS ** J 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 294 ASN L 294 ASN N 308 HIS O 119 ASN O 228 GLN O 309 GLN ** P 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 158 ASN Q 177 ASN Q 180 ASN U 228 GLN U 285 HIS U 307 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.091154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.075357 restraints weight = 98871.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.077523 restraints weight = 62739.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.079020 restraints weight = 45698.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.080106 restraints weight = 36420.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.080896 restraints weight = 30780.019| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 44149 Z= 0.141 Angle : 0.665 16.566 59959 Z= 0.352 Chirality : 0.045 0.223 6290 Planarity : 0.005 0.056 7837 Dihedral : 6.676 86.340 5928 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.94 % Favored : 96.04 % Rotamer: Outliers : 1.44 % Allowed : 10.20 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.11), residues: 5355 helix: -1.48 (0.12), residues: 1615 sheet: 0.35 (0.15), residues: 1122 loop : -1.28 (0.12), residues: 2618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 94 TYR 0.021 0.001 TYR J 201 PHE 0.014 0.001 PHE J 59 TRP 0.019 0.001 TRP P 165 HIS 0.007 0.001 HIS U 285 Details of bonding type rmsd covalent geometry : bond 0.00306 (44149) covalent geometry : angle 0.66494 (59959) hydrogen bonds : bond 0.04767 ( 1321) hydrogen bonds : angle 5.62935 ( 3537) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 424 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 131 MET cc_start: 0.7554 (tpt) cc_final: 0.7341 (mmt) REVERT: B 132 ARG cc_start: 0.7784 (mmt90) cc_final: 0.6236 (ptt180) REVERT: F 123 ASP cc_start: 0.8777 (p0) cc_final: 0.8556 (p0) REVERT: F 132 ARG cc_start: 0.7649 (ttt-90) cc_final: 0.6626 (ptt180) REVERT: I 123 ASP cc_start: 0.7878 (p0) cc_final: 0.7592 (p0) REVERT: I 255 MET cc_start: 0.7459 (tpp) cc_final: 0.7080 (tpp) REVERT: J 255 MET cc_start: 0.7696 (tpp) cc_final: 0.7349 (tpp) REVERT: K 125 ILE cc_start: 0.9184 (mt) cc_final: 0.8906 (mm) REVERT: K 152 PHE cc_start: 0.8652 (OUTLIER) cc_final: 0.7156 (p90) REVERT: L 123 ASP cc_start: 0.8642 (OUTLIER) cc_final: 0.8139 (p0) REVERT: L 176 MET cc_start: 0.8612 (mmt) cc_final: 0.8334 (tpp) REVERT: M 255 MET cc_start: 0.7404 (tpp) cc_final: 0.7127 (tpp) REVERT: N 90 GLU cc_start: 0.7402 (tm-30) cc_final: 0.7143 (tm-30) REVERT: N 117 TRP cc_start: 0.9008 (m100) cc_final: 0.8553 (m100) REVERT: N 226 LEU cc_start: 0.8812 (mm) cc_final: 0.8358 (tp) REVERT: N 281 ASP cc_start: 0.8636 (t0) cc_final: 0.8223 (t70) REVERT: O 125 ILE cc_start: 0.9384 (mt) cc_final: 0.9143 (mm) REVERT: O 149 MET cc_start: 0.9057 (tpp) cc_final: 0.8770 (tpp) REVERT: O 163 MET cc_start: 0.7415 (mtp) cc_final: 0.7144 (mtp) REVERT: O 166 GLU cc_start: 0.7956 (mp0) cc_final: 0.7694 (mp0) REVERT: O 180 ASN cc_start: 0.8814 (t0) cc_final: 0.8581 (t0) REVERT: Q 255 MET cc_start: 0.6993 (tpp) cc_final: 0.6405 (tpp) REVERT: R 96 GLU cc_start: 0.6887 (pp20) cc_final: 0.6657 (pp20) REVERT: R 129 ARG cc_start: 0.7974 (mtt180) cc_final: 0.7750 (mtt-85) REVERT: S 207 THR cc_start: 0.9518 (p) cc_final: 0.9280 (p) REVERT: S 255 MET cc_start: 0.7699 (tpp) cc_final: 0.6995 (tpp) REVERT: U 90 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.7086 (pt0) REVERT: U 132 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.6139 (ttp-170) REVERT: U 166 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7242 (mt-10) REVERT: U 199 ARG cc_start: 0.8545 (ttm-80) cc_final: 0.8106 (ttm-80) REVERT: U 234 PHE cc_start: 0.8704 (t80) cc_final: 0.8374 (t80) REVERT: U 281 ASP cc_start: 0.8178 (t0) cc_final: 0.7665 (t0) outliers start: 66 outliers final: 25 residues processed: 478 average time/residue: 0.2006 time to fit residues: 161.4387 Evaluate side-chains 387 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 358 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 293 MET Chi-restraints excluded: chain H residue 303 VAL Chi-restraints excluded: chain I residue 62 HIS Chi-restraints excluded: chain J residue 211 MET Chi-restraints excluded: chain J residue 244 ILE Chi-restraints excluded: chain K residue 4 ILE Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain K residue 274 ILE Chi-restraints excluded: chain L residue 123 ASP Chi-restraints excluded: chain N residue 308 HIS Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain P residue 243 CYS Chi-restraints excluded: chain Q residue 303 VAL Chi-restraints excluded: chain R residue 152 PHE Chi-restraints excluded: chain R residue 232 ASP Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain U residue 90 GLU Chi-restraints excluded: chain U residue 132 ARG Chi-restraints excluded: chain U residue 265 TYR Chi-restraints excluded: chain U residue 305 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 527 random chunks: chunk 213 optimal weight: 3.9990 chunk 333 optimal weight: 10.0000 chunk 363 optimal weight: 9.9990 chunk 85 optimal weight: 8.9990 chunk 496 optimal weight: 10.0000 chunk 175 optimal weight: 5.9990 chunk 452 optimal weight: 8.9990 chunk 140 optimal weight: 3.9990 chunk 397 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 411 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 228 GLN D 177 ASN ** F 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 GLN H 119 ASN H 285 HIS I 184 HIS J 167 HIS ** J 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 307 ASN M 307 ASN N 184 HIS ** P 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 308 HIS Q 307 ASN U 285 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.088069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.072347 restraints weight = 98140.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.074528 restraints weight = 61055.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.076065 restraints weight = 43937.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.077153 restraints weight = 34621.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.077930 restraints weight = 29135.155| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 44149 Z= 0.261 Angle : 0.686 17.477 59959 Z= 0.362 Chirality : 0.047 0.226 6290 Planarity : 0.005 0.075 7837 Dihedral : 6.452 89.231 5905 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.83 % Favored : 94.15 % Rotamer: Outliers : 2.42 % Allowed : 11.61 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.11), residues: 5355 helix: -1.29 (0.12), residues: 1632 sheet: 0.06 (0.15), residues: 1139 loop : -1.42 (0.12), residues: 2584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 94 TYR 0.017 0.002 TYR U 65 PHE 0.020 0.002 PHE M 234 TRP 0.016 0.002 TRP H 165 HIS 0.028 0.001 HIS N 308 Details of bonding type rmsd covalent geometry : bond 0.00616 (44149) covalent geometry : angle 0.68581 (59959) hydrogen bonds : bond 0.05619 ( 1321) hydrogen bonds : angle 5.59205 ( 3537) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 363 time to evaluate : 1.247 Fit side-chains revert: symmetry clash REVERT: B 131 MET cc_start: 0.7594 (tpt) cc_final: 0.7163 (tpt) REVERT: B 132 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.6332 (ptt180) REVERT: B 243 CYS cc_start: 0.7592 (OUTLIER) cc_final: 0.7256 (m) REVERT: D 94 ARG cc_start: 0.7824 (ttm170) cc_final: 0.7591 (ttm-80) REVERT: F 132 ARG cc_start: 0.7627 (ttt-90) cc_final: 0.6632 (ptt180) REVERT: G 181 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7959 (tp30) REVERT: I 123 ASP cc_start: 0.7791 (p0) cc_final: 0.7538 (p0) REVERT: I 216 TYR cc_start: 0.7660 (OUTLIER) cc_final: 0.7405 (p90) REVERT: I 255 MET cc_start: 0.7688 (tpp) cc_final: 0.7368 (tpp) REVERT: K 125 ILE cc_start: 0.9231 (mt) cc_final: 0.8911 (mm) REVERT: K 152 PHE cc_start: 0.8698 (OUTLIER) cc_final: 0.7278 (p90) REVERT: L 123 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.8148 (p0) REVERT: L 220 MET cc_start: 0.8915 (mmt) cc_final: 0.8135 (mpp) REVERT: N 90 GLU cc_start: 0.7340 (tm-30) cc_final: 0.6666 (tm-30) REVERT: N 94 ARG cc_start: 0.7760 (ttp80) cc_final: 0.7541 (ttp80) REVERT: N 117 TRP cc_start: 0.9103 (m100) cc_final: 0.8441 (m100) REVERT: N 223 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8569 (pmm) REVERT: O 149 MET cc_start: 0.8896 (tpp) cc_final: 0.8428 (tpp) REVERT: P 255 MET cc_start: 0.6193 (mmt) cc_final: 0.5730 (mmt) REVERT: Q 211 MET cc_start: 0.8088 (ptm) cc_final: 0.7736 (ptm) REVERT: Q 255 MET cc_start: 0.7188 (tpp) cc_final: 0.6615 (tpp) REVERT: R 86 GLN cc_start: 0.7564 (tt0) cc_final: 0.7195 (tt0) REVERT: R 96 GLU cc_start: 0.6846 (pp20) cc_final: 0.6489 (pp20) REVERT: S 166 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7430 (mt-10) REVERT: S 255 MET cc_start: 0.7907 (tpp) cc_final: 0.7303 (tpp) REVERT: U 100 CYS cc_start: 0.8649 (t) cc_final: 0.8445 (t) REVERT: U 132 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.5982 (ttp-170) REVERT: U 163 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7907 (mtp) REVERT: U 234 PHE cc_start: 0.8772 (t80) cc_final: 0.8484 (t80) outliers start: 111 outliers final: 77 residues processed: 452 average time/residue: 0.2024 time to fit residues: 157.4023 Evaluate side-chains 413 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 328 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain G residue 293 MET Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 271 GLU Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 303 VAL Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 62 HIS Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain I residue 306 LEU Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 163 MET Chi-restraints excluded: chain J residue 211 MET Chi-restraints excluded: chain J residue 244 ILE Chi-restraints excluded: chain J residue 293 MET Chi-restraints excluded: chain K residue 4 ILE Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain K residue 156 ILE Chi-restraints excluded: chain K residue 165 TRP Chi-restraints excluded: chain K residue 274 ILE Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 123 ASP Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 259 GLU Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 307 ASN Chi-restraints excluded: chain M residue 30 CYS Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain N residue 223 MET Chi-restraints excluded: chain N residue 293 MET Chi-restraints excluded: chain N residue 303 VAL Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain O residue 30 CYS Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 195 GLU Chi-restraints excluded: chain O residue 226 LEU Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 62 HIS Chi-restraints excluded: chain P residue 80 ILE Chi-restraints excluded: chain P residue 85 ILE Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain P residue 243 CYS Chi-restraints excluded: chain P residue 308 HIS Chi-restraints excluded: chain Q residue 43 LEU Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 158 ASN Chi-restraints excluded: chain Q residue 260 THR Chi-restraints excluded: chain Q residue 308 HIS Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 152 PHE Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 232 ASP Chi-restraints excluded: chain R residue 263 ILE Chi-restraints excluded: chain S residue 97 THR Chi-restraints excluded: chain S residue 139 LEU Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 220 MET Chi-restraints excluded: chain U residue 97 THR Chi-restraints excluded: chain U residue 132 ARG Chi-restraints excluded: chain U residue 163 MET Chi-restraints excluded: chain U residue 265 TYR Chi-restraints excluded: chain U residue 285 HIS Chi-restraints excluded: chain U residue 305 HIS Chi-restraints excluded: chain U residue 308 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 527 random chunks: chunk 259 optimal weight: 0.9990 chunk 245 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 108 optimal weight: 0.6980 chunk 356 optimal weight: 0.0020 chunk 21 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 460 optimal weight: 7.9990 chunk 206 optimal weight: 0.9990 chunk 211 optimal weight: 1.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 HIS G 180 ASN H 167 HIS I 177 ASN ** J 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 206 GLN L 307 ASN M 62 HIS M 180 ASN P 71 HIS ** P 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 307 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.091204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.075617 restraints weight = 98343.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.077782 restraints weight = 62654.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.079288 restraints weight = 45645.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.080358 restraints weight = 36248.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.081135 restraints weight = 30672.042| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 44149 Z= 0.101 Angle : 0.562 17.886 59959 Z= 0.289 Chirality : 0.043 0.220 6290 Planarity : 0.005 0.060 7837 Dihedral : 5.816 86.772 5904 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.00 % Favored : 95.99 % Rotamer: Outliers : 1.90 % Allowed : 12.90 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.11), residues: 5355 helix: -0.94 (0.13), residues: 1632 sheet: 0.26 (0.15), residues: 1139 loop : -1.36 (0.12), residues: 2584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG U 199 TYR 0.014 0.001 TYR G 200 PHE 0.011 0.001 PHE G 59 TRP 0.015 0.001 TRP K 165 HIS 0.024 0.001 HIS P 308 Details of bonding type rmsd covalent geometry : bond 0.00220 (44149) covalent geometry : angle 0.56194 (59959) hydrogen bonds : bond 0.03443 ( 1321) hydrogen bonds : angle 5.04525 ( 3537) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 370 time to evaluate : 1.354 Fit side-chains revert: symmetry clash REVERT: B 132 ARG cc_start: 0.7983 (mmt90) cc_final: 0.6174 (ptp-170) REVERT: B 174 MET cc_start: 0.9031 (tpp) cc_final: 0.8760 (tpt) REVERT: D 123 ASP cc_start: 0.8622 (p0) cc_final: 0.8404 (p0) REVERT: F 132 ARG cc_start: 0.7530 (ttt-90) cc_final: 0.6512 (ptt180) REVERT: F 220 MET cc_start: 0.8570 (ptp) cc_final: 0.8349 (ptp) REVERT: I 123 ASP cc_start: 0.7779 (p0) cc_final: 0.7537 (p0) REVERT: I 255 MET cc_start: 0.7459 (tpp) cc_final: 0.7171 (tpp) REVERT: J 255 MET cc_start: 0.7418 (tpp) cc_final: 0.7203 (tpp) REVERT: K 152 PHE cc_start: 0.8512 (OUTLIER) cc_final: 0.7126 (p90) REVERT: L 123 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8142 (p0) REVERT: M 255 MET cc_start: 0.7984 (tpp) cc_final: 0.7551 (tpp) REVERT: N 117 TRP cc_start: 0.9000 (m100) cc_final: 0.8621 (m100) REVERT: N 223 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8485 (pmm) REVERT: N 255 MET cc_start: 0.6218 (mmt) cc_final: 0.5957 (tpp) REVERT: P 255 MET cc_start: 0.6369 (mmt) cc_final: 0.5329 (tpt) REVERT: P 265 TYR cc_start: 0.6820 (OUTLIER) cc_final: 0.6403 (p90) REVERT: Q 255 MET cc_start: 0.7002 (tpp) cc_final: 0.6313 (tpp) REVERT: R 21 ASN cc_start: 0.7937 (m-40) cc_final: 0.7529 (m-40) REVERT: R 86 GLN cc_start: 0.7483 (tt0) cc_final: 0.7182 (tt0) REVERT: R 96 GLU cc_start: 0.6845 (pp20) cc_final: 0.6496 (pp20) REVERT: S 255 MET cc_start: 0.7853 (tpp) cc_final: 0.7268 (tpp) REVERT: U 100 CYS cc_start: 0.8379 (t) cc_final: 0.7848 (t) REVERT: U 132 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.6107 (ttp-170) REVERT: U 166 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6948 (mt-10) REVERT: U 176 MET cc_start: 0.9099 (tpp) cc_final: 0.8156 (tpp) REVERT: U 234 PHE cc_start: 0.8720 (t80) cc_final: 0.8484 (t80) outliers start: 87 outliers final: 45 residues processed: 436 average time/residue: 0.1970 time to fit residues: 147.4791 Evaluate side-chains 396 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 346 time to evaluate : 1.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain H residue 223 MET Chi-restraints excluded: chain H residue 271 GLU Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 303 VAL Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 62 HIS Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 163 MET Chi-restraints excluded: chain J residue 211 MET Chi-restraints excluded: chain J residue 244 ILE Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 123 ASP Chi-restraints excluded: chain L residue 307 ASN Chi-restraints excluded: chain M residue 30 CYS Chi-restraints excluded: chain M residue 163 MET Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain N residue 223 MET Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 195 GLU Chi-restraints excluded: chain O residue 226 LEU Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 62 HIS Chi-restraints excluded: chain P residue 80 ILE Chi-restraints excluded: chain P residue 100 CYS Chi-restraints excluded: chain P residue 265 TYR Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 152 PHE Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 232 ASP Chi-restraints excluded: chain R residue 263 ILE Chi-restraints excluded: chain S residue 139 LEU Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain U residue 132 ARG Chi-restraints excluded: chain U residue 163 MET Chi-restraints excluded: chain U residue 265 TYR Chi-restraints excluded: chain U residue 305 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 527 random chunks: chunk 440 optimal weight: 9.9990 chunk 134 optimal weight: 9.9990 chunk 271 optimal weight: 10.0000 chunk 210 optimal weight: 7.9990 chunk 390 optimal weight: 0.0570 chunk 355 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 446 optimal weight: 10.0000 chunk 434 optimal weight: 8.9990 chunk 162 optimal weight: 7.9990 overall best weight: 6.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 241 HIS F 119 ASN G 180 ASN J 294 ASN J 298 GLN K 180 ASN L 307 ASN M 180 ASN P 119 ASN P 308 HIS Q 62 HIS U 228 GLN U 285 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.086894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.071276 restraints weight = 98810.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.073421 restraints weight = 61705.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.074930 restraints weight = 44498.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.075998 restraints weight = 35136.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.076768 restraints weight = 29613.113| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 44149 Z= 0.315 Angle : 0.699 18.271 59959 Z= 0.368 Chirality : 0.047 0.225 6290 Planarity : 0.005 0.066 7837 Dihedral : 6.351 89.052 5903 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.76 % Favored : 93.22 % Rotamer: Outliers : 3.20 % Allowed : 13.01 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.73 (0.11), residues: 5355 helix: -1.07 (0.13), residues: 1615 sheet: 0.02 (0.16), residues: 1054 loop : -1.67 (0.11), residues: 2686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 129 TYR 0.017 0.002 TYR S 74 PHE 0.023 0.002 PHE J 59 TRP 0.015 0.002 TRP H 165 HIS 0.007 0.001 HIS U 128 Details of bonding type rmsd covalent geometry : bond 0.00744 (44149) covalent geometry : angle 0.69948 (59959) hydrogen bonds : bond 0.05669 ( 1321) hydrogen bonds : angle 5.49182 ( 3537) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 341 time to evaluate : 1.870 Fit side-chains revert: symmetry clash REVERT: B 132 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.6159 (ptt180) REVERT: B 148 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.8833 (ptp) REVERT: F 132 ARG cc_start: 0.7660 (ttt-90) cc_final: 0.6501 (ptt180) REVERT: G 181 GLU cc_start: 0.8249 (mm-30) cc_final: 0.8037 (tp30) REVERT: I 123 ASP cc_start: 0.7783 (p0) cc_final: 0.7539 (p0) REVERT: I 216 TYR cc_start: 0.7873 (OUTLIER) cc_final: 0.7580 (p90) REVERT: J 255 MET cc_start: 0.7532 (tpp) cc_final: 0.7307 (tpp) REVERT: K 125 ILE cc_start: 0.9230 (mp) cc_final: 0.8598 (mt) REVERT: K 152 PHE cc_start: 0.8748 (OUTLIER) cc_final: 0.7451 (p90) REVERT: M 255 MET cc_start: 0.8179 (tpp) cc_final: 0.7846 (tpp) REVERT: N 223 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8564 (pmm) REVERT: N 255 MET cc_start: 0.6195 (OUTLIER) cc_final: 0.5869 (tpp) REVERT: O 125 ILE cc_start: 0.9269 (mp) cc_final: 0.8931 (mt) REVERT: P 129 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.8114 (mtp85) REVERT: P 255 MET cc_start: 0.6245 (mmt) cc_final: 0.5758 (mmt) REVERT: P 265 TYR cc_start: 0.7094 (OUTLIER) cc_final: 0.6514 (p90) REVERT: Q 211 MET cc_start: 0.8110 (ptm) cc_final: 0.7774 (ptm) REVERT: Q 255 MET cc_start: 0.7241 (tpp) cc_final: 0.6682 (tpp) REVERT: R 86 GLN cc_start: 0.7574 (tt0) cc_final: 0.7231 (tt0) REVERT: R 96 GLU cc_start: 0.6985 (pp20) cc_final: 0.6770 (pp20) REVERT: U 132 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.6146 (ttp-170) REVERT: U 163 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.8101 (mtp) REVERT: U 234 PHE cc_start: 0.8925 (t80) cc_final: 0.8622 (t80) outliers start: 147 outliers final: 96 residues processed: 453 average time/residue: 0.2476 time to fit residues: 195.5458 Evaluate side-chains 427 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 321 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain F residue 163 MET Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 293 MET Chi-restraints excluded: chain H residue 223 MET Chi-restraints excluded: chain H residue 271 GLU Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 303 VAL Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 62 HIS Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 163 MET Chi-restraints excluded: chain J residue 244 ILE Chi-restraints excluded: chain J residue 293 MET Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain K residue 156 ILE Chi-restraints excluded: chain K residue 165 TRP Chi-restraints excluded: chain K residue 209 VAL Chi-restraints excluded: chain K residue 274 ILE Chi-restraints excluded: chain K residue 319 ILE Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 259 GLU Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 307 ASN Chi-restraints excluded: chain M residue 30 CYS Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 223 MET Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 293 MET Chi-restraints excluded: chain N residue 303 VAL Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 113 LEU Chi-restraints excluded: chain O residue 195 GLU Chi-restraints excluded: chain O residue 226 LEU Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 62 HIS Chi-restraints excluded: chain P residue 80 ILE Chi-restraints excluded: chain P residue 85 ILE Chi-restraints excluded: chain P residue 129 ARG Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain P residue 242 THR Chi-restraints excluded: chain P residue 263 ILE Chi-restraints excluded: chain P residue 265 TYR Chi-restraints excluded: chain P residue 307 ASN Chi-restraints excluded: chain P residue 308 HIS Chi-restraints excluded: chain Q residue 43 LEU Chi-restraints excluded: chain Q residue 97 THR Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 158 ASN Chi-restraints excluded: chain Q residue 165 TRP Chi-restraints excluded: chain Q residue 303 VAL Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 85 ILE Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 152 PHE Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 232 ASP Chi-restraints excluded: chain R residue 263 ILE Chi-restraints excluded: chain S residue 97 THR Chi-restraints excluded: chain S residue 139 LEU Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 163 MET Chi-restraints excluded: chain S residue 165 TRP Chi-restraints excluded: chain S residue 220 MET Chi-restraints excluded: chain U residue 132 ARG Chi-restraints excluded: chain U residue 163 MET Chi-restraints excluded: chain U residue 228 GLN Chi-restraints excluded: chain U residue 265 TYR Chi-restraints excluded: chain U residue 280 ILE Chi-restraints excluded: chain U residue 285 HIS Chi-restraints excluded: chain U residue 305 HIS Chi-restraints excluded: chain U residue 308 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 527 random chunks: chunk 184 optimal weight: 4.9990 chunk 304 optimal weight: 3.9990 chunk 456 optimal weight: 2.9990 chunk 235 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 238 optimal weight: 2.9990 chunk 172 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 chunk 265 optimal weight: 0.9980 chunk 344 optimal weight: 4.9990 chunk 355 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 298 GLN I 177 ASN K 180 ASN L 307 ASN M 180 ASN P 184 HIS S 180 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.088655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.072173 restraints weight = 97741.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.074653 restraints weight = 57146.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.076368 restraints weight = 39589.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.077575 restraints weight = 30546.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.078447 restraints weight = 25274.893| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 44149 Z= 0.167 Angle : 0.603 18.458 59959 Z= 0.311 Chirality : 0.044 0.260 6290 Planarity : 0.005 0.059 7837 Dihedral : 6.086 89.157 5901 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.56 % Favored : 94.42 % Rotamer: Outliers : 2.68 % Allowed : 14.18 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.11), residues: 5355 helix: -0.86 (0.13), residues: 1598 sheet: -0.06 (0.16), residues: 1071 loop : -1.66 (0.11), residues: 2686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 94 TYR 0.012 0.001 TYR U 65 PHE 0.013 0.001 PHE J 59 TRP 0.013 0.001 TRP K 165 HIS 0.017 0.001 HIS P 308 Details of bonding type rmsd covalent geometry : bond 0.00392 (44149) covalent geometry : angle 0.60301 (59959) hydrogen bonds : bond 0.04313 ( 1321) hydrogen bonds : angle 5.19227 ( 3537) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 339 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 132 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.6362 (ttp-170) REVERT: B 148 MET cc_start: 0.9196 (OUTLIER) cc_final: 0.8896 (ptp) REVERT: F 132 ARG cc_start: 0.7641 (ttt-90) cc_final: 0.6393 (ptt180) REVERT: F 226 LEU cc_start: 0.8815 (mm) cc_final: 0.8581 (mp) REVERT: I 4 ILE cc_start: 0.8799 (mm) cc_final: 0.8593 (mt) REVERT: I 123 ASP cc_start: 0.7916 (p0) cc_final: 0.7698 (p0) REVERT: I 165 TRP cc_start: 0.8998 (OUTLIER) cc_final: 0.8577 (m-10) REVERT: I 207 THR cc_start: 0.9565 (p) cc_final: 0.9339 (p) REVERT: I 255 MET cc_start: 0.7885 (tpp) cc_final: 0.7471 (tpp) REVERT: J 255 MET cc_start: 0.7520 (tpp) cc_final: 0.7249 (tpp) REVERT: K 125 ILE cc_start: 0.9223 (mp) cc_final: 0.8659 (mt) REVERT: K 152 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.7417 (p90) REVERT: K 220 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7481 (mmt) REVERT: M 255 MET cc_start: 0.7999 (tpp) cc_final: 0.7677 (tpp) REVERT: N 117 TRP cc_start: 0.9132 (m100) cc_final: 0.8501 (m100) REVERT: N 223 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8535 (ptt) REVERT: N 255 MET cc_start: 0.6134 (OUTLIER) cc_final: 0.5752 (tpp) REVERT: O 125 ILE cc_start: 0.9254 (mp) cc_final: 0.9020 (mt) REVERT: O 180 ASN cc_start: 0.8878 (t0) cc_final: 0.8662 (t0) REVERT: P 129 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.8040 (mtp85) REVERT: P 255 MET cc_start: 0.6149 (mmt) cc_final: 0.5194 (tpt) REVERT: P 265 TYR cc_start: 0.7129 (OUTLIER) cc_final: 0.6522 (p90) REVERT: Q 211 MET cc_start: 0.8160 (ptm) cc_final: 0.7833 (ptm) REVERT: Q 255 MET cc_start: 0.7198 (tpp) cc_final: 0.6624 (tpp) REVERT: R 86 GLN cc_start: 0.7653 (tt0) cc_final: 0.7273 (tt0) REVERT: R 96 GLU cc_start: 0.7044 (pp20) cc_final: 0.6830 (pp20) REVERT: U 100 CYS cc_start: 0.8706 (t) cc_final: 0.8316 (t) REVERT: U 132 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.6127 (ttp-170) REVERT: U 234 PHE cc_start: 0.8925 (t80) cc_final: 0.8600 (t80) outliers start: 123 outliers final: 88 residues processed: 433 average time/residue: 0.2286 time to fit residues: 171.8310 Evaluate side-chains 424 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 326 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain H residue 132 ARG Chi-restraints excluded: chain H residue 223 MET Chi-restraints excluded: chain H residue 271 GLU Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 303 VAL Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 62 HIS Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 165 TRP Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 105 GLU Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 163 MET Chi-restraints excluded: chain J residue 244 ILE Chi-restraints excluded: chain J residue 293 MET Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain K residue 220 MET Chi-restraints excluded: chain K residue 274 ILE Chi-restraints excluded: chain K residue 319 ILE Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 100 CYS Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 303 VAL Chi-restraints excluded: chain L residue 307 ASN Chi-restraints excluded: chain M residue 30 CYS Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 85 ILE Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain N residue 80 ILE Chi-restraints excluded: chain N residue 223 MET Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 293 MET Chi-restraints excluded: chain N residue 303 VAL Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 113 LEU Chi-restraints excluded: chain O residue 195 GLU Chi-restraints excluded: chain O residue 226 LEU Chi-restraints excluded: chain O residue 293 MET Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 62 HIS Chi-restraints excluded: chain P residue 80 ILE Chi-restraints excluded: chain P residue 85 ILE Chi-restraints excluded: chain P residue 100 CYS Chi-restraints excluded: chain P residue 129 ARG Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain P residue 242 THR Chi-restraints excluded: chain P residue 243 CYS Chi-restraints excluded: chain P residue 265 TYR Chi-restraints excluded: chain Q residue 43 LEU Chi-restraints excluded: chain Q residue 62 HIS Chi-restraints excluded: chain Q residue 100 CYS Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 158 ASN Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 152 PHE Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 232 ASP Chi-restraints excluded: chain R residue 263 ILE Chi-restraints excluded: chain S residue 97 THR Chi-restraints excluded: chain S residue 139 LEU Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 165 TRP Chi-restraints excluded: chain S residue 220 MET Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain U residue 132 ARG Chi-restraints excluded: chain U residue 163 MET Chi-restraints excluded: chain U residue 228 GLN Chi-restraints excluded: chain U residue 265 TYR Chi-restraints excluded: chain U residue 300 THR Chi-restraints excluded: chain U residue 305 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 527 random chunks: chunk 287 optimal weight: 7.9990 chunk 454 optimal weight: 7.9990 chunk 153 optimal weight: 6.9990 chunk 206 optimal weight: 4.9990 chunk 358 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 409 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 294 optimal weight: 8.9990 chunk 494 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 177 ASN K 180 ASN L 307 ASN M 180 ASN P 308 HIS U 228 GLN U 285 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.087747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.072045 restraints weight = 98161.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.074213 restraints weight = 61549.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.075737 restraints weight = 44418.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.076829 restraints weight = 35077.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.077595 restraints weight = 29495.051| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 44149 Z= 0.214 Angle : 0.626 18.607 59959 Z= 0.324 Chirality : 0.045 0.260 6290 Planarity : 0.005 0.057 7837 Dihedral : 6.084 87.089 5901 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.76 % Favored : 93.22 % Rotamer: Outliers : 3.05 % Allowed : 14.03 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.11), residues: 5355 helix: -0.86 (0.13), residues: 1598 sheet: -0.10 (0.16), residues: 1071 loop : -1.81 (0.11), residues: 2686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 94 TYR 0.013 0.001 TYR G 65 PHE 0.016 0.001 PHE J 59 TRP 0.013 0.001 TRP P 165 HIS 0.007 0.001 HIS U 285 Details of bonding type rmsd covalent geometry : bond 0.00505 (44149) covalent geometry : angle 0.62583 (59959) hydrogen bonds : bond 0.04647 ( 1321) hydrogen bonds : angle 5.21738 ( 3537) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 337 time to evaluate : 1.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 132 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.5862 (ptp-170) REVERT: B 148 MET cc_start: 0.9125 (OUTLIER) cc_final: 0.8862 (ptp) REVERT: F 132 ARG cc_start: 0.7559 (ttt-90) cc_final: 0.6477 (ptt180) REVERT: G 152 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.7354 (p90) REVERT: I 4 ILE cc_start: 0.8662 (mm) cc_final: 0.8456 (mt) REVERT: I 48 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7175 (mm-30) REVERT: I 123 ASP cc_start: 0.7779 (p0) cc_final: 0.7560 (p0) REVERT: I 165 TRP cc_start: 0.8927 (OUTLIER) cc_final: 0.8593 (m-10) REVERT: I 207 THR cc_start: 0.9558 (p) cc_final: 0.9347 (p) REVERT: J 255 MET cc_start: 0.7503 (tpp) cc_final: 0.7236 (tpp) REVERT: K 125 ILE cc_start: 0.9197 (mp) cc_final: 0.8602 (mt) REVERT: K 152 PHE cc_start: 0.8670 (OUTLIER) cc_final: 0.7426 (p90) REVERT: M 255 MET cc_start: 0.8033 (tpp) cc_final: 0.7733 (tpp) REVERT: N 223 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8409 (ptt) REVERT: N 255 MET cc_start: 0.6264 (OUTLIER) cc_final: 0.5883 (tpp) REVERT: O 125 ILE cc_start: 0.9268 (mp) cc_final: 0.8979 (mt) REVERT: P 129 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.8125 (mtp180) REVERT: P 255 MET cc_start: 0.6201 (mmt) cc_final: 0.5698 (tpt) REVERT: P 265 TYR cc_start: 0.7041 (OUTLIER) cc_final: 0.6450 (p90) REVERT: Q 211 MET cc_start: 0.8066 (ptm) cc_final: 0.7797 (ptm) REVERT: Q 255 MET cc_start: 0.7144 (tpp) cc_final: 0.6622 (tpp) REVERT: R 86 GLN cc_start: 0.7584 (tt0) cc_final: 0.7235 (tt0) REVERT: R 96 GLU cc_start: 0.6873 (pp20) cc_final: 0.6646 (pp20) REVERT: R 223 MET cc_start: 0.8177 (ptm) cc_final: 0.7968 (ptp) REVERT: S 166 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7342 (mt-10) REVERT: U 100 CYS cc_start: 0.8645 (t) cc_final: 0.8262 (t) REVERT: U 132 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.6168 (ttp-170) REVERT: U 234 PHE cc_start: 0.8874 (t80) cc_final: 0.8594 (t80) outliers start: 140 outliers final: 111 residues processed: 446 average time/residue: 0.2061 time to fit residues: 160.0242 Evaluate side-chains 448 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 327 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 100 CYS Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 100 CYS Chi-restraints excluded: chain G residue 152 PHE Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 132 ARG Chi-restraints excluded: chain H residue 149 MET Chi-restraints excluded: chain H residue 223 MET Chi-restraints excluded: chain H residue 271 GLU Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 303 VAL Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 62 HIS Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain I residue 165 TRP Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 163 MET Chi-restraints excluded: chain J residue 244 ILE Chi-restraints excluded: chain J residue 293 MET Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain K residue 209 VAL Chi-restraints excluded: chain K residue 274 ILE Chi-restraints excluded: chain K residue 319 ILE Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 100 CYS Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 303 VAL Chi-restraints excluded: chain L residue 307 ASN Chi-restraints excluded: chain L residue 319 ILE Chi-restraints excluded: chain M residue 30 CYS Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 85 ILE Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 100 CYS Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 235 GLU Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain N residue 80 ILE Chi-restraints excluded: chain N residue 163 MET Chi-restraints excluded: chain N residue 223 MET Chi-restraints excluded: chain N residue 255 MET Chi-restraints excluded: chain N residue 293 MET Chi-restraints excluded: chain N residue 303 VAL Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain O residue 30 CYS Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 113 LEU Chi-restraints excluded: chain O residue 195 GLU Chi-restraints excluded: chain O residue 226 LEU Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 62 HIS Chi-restraints excluded: chain P residue 80 ILE Chi-restraints excluded: chain P residue 85 ILE Chi-restraints excluded: chain P residue 129 ARG Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain P residue 242 THR Chi-restraints excluded: chain P residue 243 CYS Chi-restraints excluded: chain P residue 265 TYR Chi-restraints excluded: chain P residue 308 HIS Chi-restraints excluded: chain Q residue 43 LEU Chi-restraints excluded: chain Q residue 62 HIS Chi-restraints excluded: chain Q residue 100 CYS Chi-restraints excluded: chain Q residue 139 LEU Chi-restraints excluded: chain Q residue 158 ASN Chi-restraints excluded: chain Q residue 163 MET Chi-restraints excluded: chain Q residue 165 TRP Chi-restraints excluded: chain Q residue 260 THR Chi-restraints excluded: chain Q residue 303 VAL Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain R residue 100 CYS Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 152 PHE Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 163 MET Chi-restraints excluded: chain R residue 232 ASP Chi-restraints excluded: chain R residue 263 ILE Chi-restraints excluded: chain R residue 271 GLU Chi-restraints excluded: chain S residue 97 THR Chi-restraints excluded: chain S residue 139 LEU Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain S residue 163 MET Chi-restraints excluded: chain S residue 165 TRP Chi-restraints excluded: chain S residue 220 MET Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain U residue 97 THR Chi-restraints excluded: chain U residue 132 ARG Chi-restraints excluded: chain U residue 163 MET Chi-restraints excluded: chain U residue 228 GLN Chi-restraints excluded: chain U residue 265 TYR Chi-restraints excluded: chain U residue 285 HIS Chi-restraints excluded: chain U residue 300 THR Chi-restraints excluded: chain U residue 305 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.2255 > 50: distance: 46 - 111: 17.265 distance: 49 - 108: 11.819 distance: 82 - 87: 8.598 distance: 87 - 88: 8.136 distance: 88 - 89: 5.388 distance: 88 - 91: 7.771 distance: 89 - 90: 3.380 distance: 89 - 94: 11.528 distance: 91 - 92: 4.653 distance: 91 - 93: 6.754 distance: 94 - 95: 5.528 distance: 95 - 96: 4.399 distance: 95 - 98: 14.273 distance: 96 - 97: 22.695 distance: 96 - 100: 6.148 distance: 98 - 99: 9.473 distance: 100 - 101: 6.453 distance: 101 - 102: 11.164 distance: 101 - 104: 5.415 distance: 102 - 103: 32.335 distance: 102 - 108: 7.828 distance: 104 - 105: 5.632 distance: 104 - 106: 4.052 distance: 105 - 107: 3.749 distance: 108 - 109: 8.374 distance: 109 - 110: 11.329 distance: 109 - 112: 14.208 distance: 110 - 111: 19.492 distance: 110 - 120: 15.367 distance: 112 - 113: 8.059 distance: 113 - 114: 8.391 distance: 113 - 115: 5.413 distance: 114 - 116: 7.181 distance: 120 - 121: 14.298 distance: 121 - 122: 17.949 distance: 122 - 123: 30.077 distance: 122 - 124: 20.188 distance: 124 - 125: 14.557 distance: 124 - 130: 24.613 distance: 125 - 126: 10.924 distance: 125 - 128: 26.531 distance: 126 - 127: 18.006 distance: 126 - 131: 8.816 distance: 128 - 129: 11.835 distance: 129 - 130: 31.806 distance: 131 - 132: 4.435 distance: 132 - 133: 4.312 distance: 132 - 135: 5.267 distance: 133 - 139: 4.274 distance: 135 - 136: 3.933 distance: 136 - 137: 3.865 distance: 136 - 138: 3.429 distance: 139 - 140: 20.399 distance: 140 - 141: 31.977 distance: 141 - 142: 50.882 distance: 141 - 143: 64.226 distance: 143 - 144: 58.448 distance: 144 - 145: 33.440 distance: 144 - 147: 16.127 distance: 145 - 146: 21.737 distance: 145 - 152: 16.355 distance: 147 - 148: 7.618 distance: 148 - 149: 15.399 distance: 149 - 150: 3.024 distance: 152 - 153: 9.090 distance: 152 - 158: 16.745 distance: 153 - 154: 12.287 distance: 153 - 156: 15.539 distance: 154 - 155: 15.183 distance: 154 - 159: 10.797 distance: 156 - 157: 16.816 distance: 157 - 158: 25.633