Starting phenix.real_space_refine on Sun Aug 9 22:27:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/22vl_68717/08_2026/22vl_68717.cif Found real_map, /net/cci-nas-00/data/ceres_data/22vl_68717/08_2026/22vl_68717.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/22vl_68717/08_2026/22vl_68717.cif" } default_model = "/net/cci-nas-00/data/ceres_data/22vl_68717/08_2026/22vl_68717.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/22vl_68717/08_2026/22vl_68717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/22vl_68717/08_2026/22vl_68717.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.047 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: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 3 5.21 5 S 135 5.16 5 C 24461 2.51 5 N 6476 2.21 5 O 7296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 38386 Number of models: 1 Model: "" Number of chains: 31 Chain: "a" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1742 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 11, 'TRANS': 211} Chain: "p" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 989 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain: "D" Number of atoms: 2468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2468 Classifications: {'peptide': 322} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 311} Chain: "d" Number of atoms: 1341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1341 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 3, 'TRANS': 169} Chain: "b" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1238 Classifications: {'peptide': 152} Link IDs: {'TRANS': 151} Chain: "e" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1000 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain breaks: 1 Chain: "M" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 548 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "F" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 548 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "G" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 548 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "H" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 548 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "I" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 548 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "J" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 548 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "K" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 548 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "L" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 548 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "N" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 548 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "O" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 548 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "P" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 548 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "Q" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 548 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "R" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 548 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "S" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 548 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "A" Number of atoms: 3655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3655 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 20, 'TRANS': 463} Chain: "B" Number of atoms: 3641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3641 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 20, 'TRANS': 461} Chain: "E" Number of atoms: 3609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3609 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 22, 'TRANS': 452} Chain: "T" Number of atoms: 3609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3609 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 22, 'TRANS': 452} Chain: "U" Number of atoms: 3609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3609 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 22, 'TRANS': 452} Chain: "V" Number of atoms: 3655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3655 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 20, 'TRANS': 463} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.60, per 1000 atoms: 0.20 Number of scatterers: 38386 At special positions: 0 Unit cell: (130.9, 141.95, 239.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 135 16.00 P 15 15.00 Mg 3 11.99 O 7296 8.00 N 6476 7.00 C 24461 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: 3.25 Conformation dependent library (CDL) restraints added in 1.3 seconds 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9252 Finding SS restraints... Secondary structure from input PDB file: 206 helices and 26 sheets defined 60.2% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'a' and resid 37 through 57 removed outlier: 3.875A pdb=" N LEU a 56 " --> pdb=" O VAL a 52 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY a 57 " --> pdb=" O LEU a 53 " (cutoff:3.500A) Processing helix chain 'a' and resid 68 through 87 removed outlier: 3.643A pdb=" N LEU a 74 " --> pdb=" O ASN a 70 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N THR a 76 " --> pdb=" O THR a 72 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU a 77 " --> pdb=" O GLU a 73 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE a 79 " --> pdb=" O VAL a 75 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG a 80 " --> pdb=" O THR a 76 " (cutoff:3.500A) Processing helix chain 'a' and resid 90 through 94 removed outlier: 3.713A pdb=" N LEU a 93 " --> pdb=" O GLU a 90 " (cutoff:3.500A) Processing helix chain 'a' and resid 95 through 103 removed outlier: 3.910A pdb=" N LEU a 99 " --> pdb=" O TRP a 95 " (cutoff:3.500A) Processing helix chain 'a' and resid 103 through 116 removed outlier: 4.039A pdb=" N GLY a 113 " --> pdb=" O SER a 109 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA a 114 " --> pdb=" O ASN a 110 " (cutoff:3.500A) Processing helix chain 'a' and resid 130 through 133 Processing helix chain 'a' and resid 134 through 157 removed outlier: 3.858A pdb=" N THR a 138 " --> pdb=" O ASP a 134 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL a 139 " --> pdb=" O ILE a 135 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE a 150 " --> pdb=" O SER a 146 " (cutoff:3.500A) Processing helix chain 'a' and resid 171 through 188 removed outlier: 4.371A pdb=" N ILE a 175 " --> pdb=" O PHE a 171 " (cutoff:3.500A) Proline residue: a 184 - end of helix Processing helix chain 'a' and resid 189 through 206 removed outlier: 4.389A pdb=" N VAL a 202 " --> pdb=" O ASP a 198 " (cutoff:3.500A) Processing helix chain 'a' and resid 214 through 244 removed outlier: 3.941A pdb=" N MET a 218 " --> pdb=" O PRO a 214 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE a 223 " --> pdb=" O LEU a 219 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA a 243 " --> pdb=" O TYR a 239 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU a 244 " --> pdb=" O ILE a 240 " (cutoff:3.500A) Processing helix chain 'p' and resid 93 through 102 removed outlier: 3.909A pdb=" N PHE p 97 " --> pdb=" O MET p 93 " (cutoff:3.500A) Processing helix chain 'p' and resid 105 through 219 Proline residue: p 111 - end of helix removed outlier: 4.271A pdb=" N LEU p 122 " --> pdb=" O GLU p 118 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ILE p 123 " --> pdb=" O ARG p 119 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLY p 128 " --> pdb=" O ARG p 124 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASP p 138 " --> pdb=" O THR p 134 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS p 139 " --> pdb=" O GLY p 135 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA p 144 " --> pdb=" O LEU p 140 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU p 145 " --> pdb=" O VAL p 141 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA p 179 " --> pdb=" O ASN p 175 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLN p 194 " --> pdb=" O ALA p 190 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP p 204 " --> pdb=" O LEU p 200 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ALA p 205 " --> pdb=" O LYS p 201 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN p 206 " --> pdb=" O SER p 202 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL p 218 " --> pdb=" O VAL p 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 75 removed outlier: 3.673A pdb=" N LYS D 52 " --> pdb=" O LYS D 48 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP D 55 " --> pdb=" O GLN D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 93 removed outlier: 4.398A pdb=" N SER D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS D 84 " --> pdb=" O GLU D 80 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN D 91 " --> pdb=" O TYR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 144 removed outlier: 3.733A pdb=" N PHE D 129 " --> pdb=" O GLY D 125 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE D 130 " --> pdb=" O TYR D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 165 removed outlier: 4.192A pdb=" N ARG D 164 " --> pdb=" O TYR D 160 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS D 165 " --> pdb=" O PHE D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 196 removed outlier: 3.695A pdb=" N SER D 194 " --> pdb=" O GLU D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 283 Processing helix chain 'D' and resid 284 through 358 Proline residue: D 290 - end of helix removed outlier: 4.286A pdb=" N VAL D 332 " --> pdb=" O LYS D 328 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLN D 333 " --> pdb=" O GLY D 329 " (cutoff:3.500A) Processing helix chain 'd' and resid 75 through 89 removed outlier: 4.062A pdb=" N ALA d 85 " --> pdb=" O LEU d 81 " (cutoff:3.500A) Processing helix chain 'd' and resid 93 through 106 Processing helix chain 'd' and resid 108 through 117 removed outlier: 3.849A pdb=" N ALA d 113 " --> pdb=" O ALA d 109 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LEU d 114 " --> pdb=" O LYS d 110 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN d 117 " --> pdb=" O ALA d 113 " (cutoff:3.500A) Processing helix chain 'd' and resid 121 through 137 Processing helix chain 'd' and resid 139 through 152 Processing helix chain 'd' and resid 161 through 172 removed outlier: 3.664A pdb=" N ASP d 167 " --> pdb=" O GLU d 163 " (cutoff:3.500A) Processing helix chain 'd' and resid 190 through 203 removed outlier: 3.750A pdb=" N ILE d 194 " --> pdb=" O GLN d 190 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS d 197 " --> pdb=" O LEU d 193 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR d 202 " --> pdb=" O LEU d 198 " (cutoff:3.500A) Processing helix chain 'd' and resid 234 through 243 removed outlier: 3.508A pdb=" N ILE d 238 " --> pdb=" O VAL d 234 " (cutoff:3.500A) Processing helix chain 'b' and resid 31 through 106 removed outlier: 4.275A pdb=" N ALA b 36 " --> pdb=" O ILE b 32 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL b 37 " --> pdb=" O ASN b 33 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY b 39 " --> pdb=" O ALA b 35 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ILE b 40 " --> pdb=" O ALA b 36 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER b 43 " --> pdb=" O GLY b 39 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS b 90 " --> pdb=" O GLU b 86 " (cutoff:3.500A) Processing helix chain 'b' and resid 106 through 159 removed outlier: 3.898A pdb=" N LYS b 125 " --> pdb=" O LEU b 121 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLN b 126 " --> pdb=" O GLN b 122 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU b 127 " --> pdb=" O GLU b 123 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY b 159 " --> pdb=" O ARG b 155 " (cutoff:3.500A) Processing helix chain 'b' and resid 160 through 177 removed outlier: 3.514A pdb=" N TYR b 164 " --> pdb=" O LEU b 160 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL b 166 " --> pdb=" O SER b 162 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N VAL b 167 " --> pdb=" O THR b 163 " (cutoff:3.500A) Processing helix chain 'e' and resid 91 through 93 No H-bonds generated for 'chain 'e' and resid 91 through 93' Processing helix chain 'e' and resid 94 through 110 removed outlier: 4.229A pdb=" N ALA e 101 " --> pdb=" O GLU e 97 " (cutoff:3.500A) Processing helix chain 'e' and resid 114 through 130 removed outlier: 4.143A pdb=" N ARG e 127 " --> pdb=" O PHE e 123 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ALA e 128 " --> pdb=" O ALA e 124 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 135 removed outlier: 3.641A pdb=" N VAL e 134 " --> pdb=" O ARG e 131 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 22 removed outlier: 4.304A pdb=" N VAL M 11 " --> pdb=" O ALA M 7 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER M 12 " --> pdb=" O THR M 8 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N VAL M 17 " --> pdb=" O ALA M 13 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLY M 18 " --> pdb=" O GLY M 14 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE M 22 " --> pdb=" O GLY M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 42 removed outlier: 4.129A pdb=" N MET M 26 " --> pdb=" O ILE M 22 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY M 27 " --> pdb=" O GLY M 23 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLY M 29 " --> pdb=" O GLY M 25 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR M 34 " --> pdb=" O THR M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 61 removed outlier: 4.287A pdb=" N ALA M 52 " --> pdb=" O LYS M 48 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE M 59 " --> pdb=" O LEU M 55 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU M 61 " --> pdb=" O PHE M 57 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 76 removed outlier: 3.596A pdb=" N GLY M 67 " --> pdb=" O LEU M 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 20 removed outlier: 3.866A pdb=" N ALA F 20 " --> pdb=" O ALA F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 42 removed outlier: 3.742A pdb=" N GLY F 29 " --> pdb=" O GLY F 25 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N TYR F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA F 35 " --> pdb=" O ALA F 31 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA F 40 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN F 42 " --> pdb=" O GLY F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 62 removed outlier: 4.098A pdb=" N LEU F 55 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N PHE F 59 " --> pdb=" O LEU F 55 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N MET F 60 " --> pdb=" O SER F 56 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 77 removed outlier: 3.515A pdb=" N TYR F 66 " --> pdb=" O SER F 62 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY F 67 " --> pdb=" O LEU F 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 21 removed outlier: 3.536A pdb=" N ALA G 13 " --> pdb=" O SER G 9 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY G 14 " --> pdb=" O VAL G 10 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU G 19 " --> pdb=" O LEU G 15 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA G 21 " --> pdb=" O VAL G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 42 removed outlier: 4.084A pdb=" N GLY G 25 " --> pdb=" O ALA G 21 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET G 26 " --> pdb=" O ILE G 22 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN G 42 " --> pdb=" O GLY G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 74 removed outlier: 3.827A pdb=" N ARG G 50 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N GLY G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA G 52 " --> pdb=" O LYS G 48 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU G 55 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR G 64 " --> pdb=" O MET G 60 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLY G 67 " --> pdb=" O LEU G 63 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU G 68 " --> pdb=" O THR G 64 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU G 74 " --> pdb=" O VAL G 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 19 removed outlier: 3.995A pdb=" N VAL H 11 " --> pdb=" O ALA H 7 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER H 12 " --> pdb=" O THR H 8 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL H 17 " --> pdb=" O ALA H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 42 removed outlier: 4.107A pdb=" N TYR H 34 " --> pdb=" O THR H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 61 Processing helix chain 'H' and resid 62 through 76 removed outlier: 4.078A pdb=" N GLY H 67 " --> pdb=" O LEU H 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 20 removed outlier: 3.653A pdb=" N VAL I 11 " --> pdb=" O ALA I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 42 removed outlier: 3.715A pdb=" N GLY I 25 " --> pdb=" O ALA I 21 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR I 34 " --> pdb=" O THR I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 76 removed outlier: 3.744A pdb=" N GLY I 51 " --> pdb=" O GLY I 47 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU I 55 " --> pdb=" O GLY I 51 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY I 67 " --> pdb=" O LEU I 63 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N VAL I 70 " --> pdb=" O TYR I 66 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA I 71 " --> pdb=" O GLY I 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 20 removed outlier: 3.920A pdb=" N SER J 12 " --> pdb=" O THR J 8 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY J 14 " --> pdb=" O VAL J 10 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU J 15 " --> pdb=" O VAL J 11 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA J 20 " --> pdb=" O ALA J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 42 removed outlier: 3.936A pdb=" N TYR J 34 " --> pdb=" O THR J 30 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLU J 37 " --> pdb=" O GLY J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 72 removed outlier: 4.346A pdb=" N GLY J 51 " --> pdb=" O GLY J 47 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU J 55 " --> pdb=" O GLY J 51 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR J 64 " --> pdb=" O MET J 60 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL J 70 " --> pdb=" O TYR J 66 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 21 removed outlier: 4.043A pdb=" N VAL K 11 " --> pdb=" O ALA K 7 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER K 12 " --> pdb=" O THR K 8 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ALA K 21 " --> pdb=" O VAL K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 42 removed outlier: 3.609A pdb=" N MET K 26 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR K 34 " --> pdb=" O THR K 30 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA K 35 " --> pdb=" O ALA K 31 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU K 37 " --> pdb=" O GLY K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 76 removed outlier: 4.575A pdb=" N GLY K 51 " --> pdb=" O GLY K 47 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALA K 52 " --> pdb=" O LYS K 48 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU K 55 " --> pdb=" O GLY K 51 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE K 59 " --> pdb=" O LEU K 55 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N MET K 60 " --> pdb=" O SER K 56 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLY K 67 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU K 68 " --> pdb=" O THR K 64 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA K 71 " --> pdb=" O GLY K 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 21 removed outlier: 3.647A pdb=" N VAL L 10 " --> pdb=" O ALA L 6 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL L 11 " --> pdb=" O ALA L 7 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY L 14 " --> pdb=" O VAL L 10 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU L 15 " --> pdb=" O VAL L 11 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA L 20 " --> pdb=" O ALA L 16 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA L 21 " --> pdb=" O VAL L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 21 through 42 removed outlier: 4.191A pdb=" N TYR L 34 " --> pdb=" O THR L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 50 Processing helix chain 'L' and resid 53 through 77 removed outlier: 4.209A pdb=" N PHE L 57 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TYR L 66 " --> pdb=" O SER L 62 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLY L 67 " --> pdb=" O LEU L 63 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU L 68 " --> pdb=" O THR L 64 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 21 removed outlier: 3.932A pdb=" N VAL N 11 " --> pdb=" O ALA N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 42 removed outlier: 3.764A pdb=" N GLY N 29 " --> pdb=" O GLY N 25 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY N 33 " --> pdb=" O GLY N 29 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N TYR N 34 " --> pdb=" O THR N 30 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA N 35 " --> pdb=" O ALA N 31 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 77 removed outlier: 3.734A pdb=" N ALA N 52 " --> pdb=" O LYS N 48 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU N 55 " --> pdb=" O GLY N 51 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET N 60 " --> pdb=" O SER N 56 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR N 64 " --> pdb=" O MET N 60 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N TYR N 66 " --> pdb=" O SER N 62 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N GLY N 67 " --> pdb=" O LEU N 63 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU N 68 " --> pdb=" O THR N 64 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU N 75 " --> pdb=" O ALA N 71 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 12 removed outlier: 3.882A pdb=" N SER O 12 " --> pdb=" O THR O 8 " (cutoff:3.500A) Processing helix chain 'O' and resid 12 through 19 removed outlier: 3.556A pdb=" N LEU O 19 " --> pdb=" O LEU O 15 " (cutoff:3.500A) Processing helix chain 'O' and resid 21 through 40 removed outlier: 3.878A pdb=" N GLY O 33 " --> pdb=" O GLY O 29 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TYR O 34 " --> pdb=" O THR O 30 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA O 35 " --> pdb=" O ALA O 31 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA O 40 " --> pdb=" O VAL O 36 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 51 Processing helix chain 'O' and resid 52 through 73 removed outlier: 3.810A pdb=" N PHE O 59 " --> pdb=" O LEU O 55 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR O 64 " --> pdb=" O MET O 60 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR O 66 " --> pdb=" O SER O 62 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLY O 67 " --> pdb=" O LEU O 63 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU O 68 " --> pdb=" O THR O 64 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ALA O 73 " --> pdb=" O VAL O 69 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 10 removed outlier: 3.651A pdb=" N VAL P 10 " --> pdb=" O ALA P 6 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 19 removed outlier: 3.998A pdb=" N GLY P 14 " --> pdb=" O VAL P 10 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU P 15 " --> pdb=" O VAL P 11 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 42 removed outlier: 4.010A pdb=" N GLY P 25 " --> pdb=" O ALA P 21 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N MET P 26 " --> pdb=" O ILE P 22 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR P 34 " --> pdb=" O THR P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 77 removed outlier: 3.693A pdb=" N ALA P 52 " --> pdb=" O LYS P 48 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU P 54 " --> pdb=" O ARG P 50 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU P 55 " --> pdb=" O GLY P 51 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N MET P 60 " --> pdb=" O SER P 56 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLY P 67 " --> pdb=" O LEU P 63 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU P 75 " --> pdb=" O ALA P 71 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 19 removed outlier: 3.858A pdb=" N SER Q 12 " --> pdb=" O THR Q 8 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY Q 14 " --> pdb=" O VAL Q 10 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU Q 15 " --> pdb=" O VAL Q 11 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL Q 17 " --> pdb=" O ALA Q 13 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU Q 19 " --> pdb=" O LEU Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 21 through 42 removed outlier: 3.969A pdb=" N GLY Q 25 " --> pdb=" O ALA Q 21 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR Q 34 " --> pdb=" O THR Q 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 77 removed outlier: 4.109A pdb=" N GLY Q 51 " --> pdb=" O GLY Q 47 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA Q 52 " --> pdb=" O LYS Q 48 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU Q 55 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU Q 61 " --> pdb=" O PHE Q 57 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N THR Q 64 " --> pdb=" O MET Q 60 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE Q 65 " --> pdb=" O GLU Q 61 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TYR Q 66 " --> pdb=" O SER Q 62 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N GLY Q 67 " --> pdb=" O LEU Q 63 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU Q 68 " --> pdb=" O THR Q 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 20 removed outlier: 3.918A pdb=" N THR R 8 " --> pdb=" O ILE R 4 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL R 11 " --> pdb=" O ALA R 7 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 42 removed outlier: 3.581A pdb=" N TYR R 34 " --> pdb=" O THR R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 76 removed outlier: 4.027A pdb=" N LEU R 63 " --> pdb=" O PHE R 59 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 21 removed outlier: 3.930A pdb=" N THR S 8 " --> pdb=" O ILE S 4 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL S 11 " --> pdb=" O ALA S 7 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY S 14 " --> pdb=" O VAL S 10 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL S 17 " --> pdb=" O ALA S 13 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA S 20 " --> pdb=" O ALA S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 22 through 42 removed outlier: 4.335A pdb=" N MET S 26 " --> pdb=" O ILE S 22 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY S 27 " --> pdb=" O GLY S 23 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR S 34 " --> pdb=" O THR S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 61 removed outlier: 4.088A pdb=" N ALA S 52 " --> pdb=" O LYS S 48 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 77 removed outlier: 3.925A pdb=" N GLY S 67 " --> pdb=" O LEU S 63 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N VAL S 70 " --> pdb=" O TYR S 66 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU S 75 " --> pdb=" O ALA S 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 105 removed outlier: 4.001A pdb=" N TYR A 104 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 105 " --> pdb=" O GLU A 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 101 through 105' Processing helix chain 'A' and resid 151 through 158 removed outlier: 3.829A pdb=" N MET A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 186 removed outlier: 3.668A pdb=" N ALA A 180 " --> pdb=" O LYS A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 217 removed outlier: 4.021A pdb=" N GLN A 208 " --> pdb=" O SER A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 232 through 252 removed outlier: 3.564A pdb=" N GLN A 236 " --> pdb=" O PRO A 232 " (cutoff:3.500A) Proline residue: A 240 - end of helix removed outlier: 3.744A pdb=" N TYR A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N PHE A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 278 removed outlier: 3.777A pdb=" N GLN A 267 " --> pdb=" O ASP A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 300 removed outlier: 3.527A pdb=" N ARG A 297 " --> pdb=" O TYR A 293 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 339 removed outlier: 3.575A pdb=" N SER A 337 " --> pdb=" O THR A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 353 removed outlier: 3.511A pdb=" N GLY A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 380 Processing helix chain 'A' and resid 382 through 397 removed outlier: 3.536A pdb=" N GLU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 418 removed outlier: 3.794A pdb=" N GLN A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 443 removed outlier: 3.505A pdb=" N ASN A 443 " --> pdb=" O TYR A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 452 No H-bonds generated for 'chain 'A' and resid 450 through 452' Processing helix chain 'A' and resid 453 through 469 removed outlier: 3.923A pdb=" N GLY A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N SER A 463 " --> pdb=" O SER A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 480 removed outlier: 4.132A pdb=" N GLY A 473 " --> pdb=" O TYR A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 508 removed outlier: 3.892A pdb=" N GLU A 499 " --> pdb=" O ASN A 495 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU A 500 " --> pdb=" O GLU A 496 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA A 508 " --> pdb=" O GLN A 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 105 removed outlier: 4.006A pdb=" N TYR B 104 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 105 " --> pdb=" O GLU B 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 101 through 105' Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 175 through 186 removed outlier: 3.637A pdb=" N ILE B 179 " --> pdb=" O GLY B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 216 removed outlier: 3.607A pdb=" N VAL B 206 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN B 208 " --> pdb=" O SER B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 220 removed outlier: 4.005A pdb=" N ASP B 220 " --> pdb=" O GLY B 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 217 through 220' Processing helix chain 'B' and resid 232 through 252 Proline residue: B 240 - end of helix removed outlier: 3.691A pdb=" N TYR B 249 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N PHE B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 277 removed outlier: 3.744A pdb=" N GLN B 267 " --> pdb=" O ASP B 263 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 300 removed outlier: 3.566A pdb=" N HIS B 295 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG B 297 " --> pdb=" O TYR B 293 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 339 Processing helix chain 'B' and resid 346 through 352 Processing helix chain 'B' and resid 368 through 372 Processing helix chain 'B' and resid 379 through 393 removed outlier: 4.252A pdb=" N LEU B 383 " --> pdb=" O VAL B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 400 Processing helix chain 'B' and resid 404 through 418 removed outlier: 3.538A pdb=" N ARG B 416 " --> pdb=" O ALA B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 443 Processing helix chain 'B' and resid 453 through 468 removed outlier: 3.688A pdb=" N GLY B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER B 463 " --> pdb=" O SER B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 480 removed outlier: 4.369A pdb=" N GLY B 473 " --> pdb=" O TYR B 469 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU B 474 " --> pdb=" O PRO B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 506 removed outlier: 3.759A pdb=" N GLU B 499 " --> pdb=" O ASN B 495 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 97 removed outlier: 3.532A pdb=" N THR E 96 " --> pdb=" O GLY E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 149 Processing helix chain 'E' and resid 167 through 183 removed outlier: 3.755A pdb=" N HIS E 183 " --> pdb=" O ILE E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 209 Processing helix chain 'E' and resid 216 through 220 Processing helix chain 'E' and resid 232 through 237 removed outlier: 3.557A pdb=" N ARG E 236 " --> pdb=" O PRO E 232 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET E 237 " --> pdb=" O PRO E 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 232 through 237' Processing helix chain 'E' and resid 238 through 253 removed outlier: 3.817A pdb=" N PHE E 250 " --> pdb=" O MET E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 280 removed outlier: 3.568A pdb=" N GLY E 272 " --> pdb=" O PHE E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 301 removed outlier: 3.519A pdb=" N LEU E 299 " --> pdb=" O GLU E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 333 Processing helix chain 'E' and resid 343 through 350 Processing helix chain 'E' and resid 366 through 371 Processing helix chain 'E' and resid 371 through 391 Processing helix chain 'E' and resid 391 through 399 removed outlier: 3.822A pdb=" N ALA E 396 " --> pdb=" O GLN E 392 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE E 397 " --> pdb=" O ASP E 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 403 removed outlier: 3.623A pdb=" N LEU E 403 " --> pdb=" O LEU E 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 400 through 403' Processing helix chain 'E' and resid 404 through 421 removed outlier: 3.655A pdb=" N LEU E 409 " --> pdb=" O GLU E 405 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG E 419 " --> pdb=" O ARG E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 433 Processing helix chain 'E' and resid 441 through 454 removed outlier: 3.629A pdb=" N GLY E 454 " --> pdb=" O LYS E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 459 removed outlier: 4.378A pdb=" N ASP E 458 " --> pdb=" O GLU E 455 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU E 459 " --> pdb=" O LEU E 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 455 through 459' Processing helix chain 'E' and resid 460 through 465 removed outlier: 3.596A pdb=" N PHE E 464 " --> pdb=" O GLU E 461 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR E 465 " --> pdb=" O GLN E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 481 Processing helix chain 'T' and resid 93 through 97 Processing helix chain 'T' and resid 128 through 132 removed outlier: 3.705A pdb=" N LEU T 132 " --> pdb=" O PHE T 129 " (cutoff:3.500A) Processing helix chain 'T' and resid 145 through 150 Processing helix chain 'T' and resid 167 through 180 Processing helix chain 'T' and resid 195 through 209 Processing helix chain 'T' and resid 216 through 220 Processing helix chain 'T' and resid 232 through 237 removed outlier: 3.556A pdb=" N MET T 237 " --> pdb=" O PRO T 233 " (cutoff:3.500A) Processing helix chain 'T' and resid 238 through 253 Processing helix chain 'T' and resid 265 through 280 removed outlier: 3.820A pdb=" N VAL T 269 " --> pdb=" O ILE T 265 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU T 278 " --> pdb=" O GLU T 274 " (cutoff:3.500A) Processing helix chain 'T' and resid 291 through 301 removed outlier: 3.511A pdb=" N LEU T 299 " --> pdb=" O GLU T 295 " (cutoff:3.500A) Processing helix chain 'T' and resid 319 through 323 Processing helix chain 'T' and resid 326 through 333 removed outlier: 3.695A pdb=" N THR T 332 " --> pdb=" O ALA T 328 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE T 333 " --> pdb=" O PRO T 329 " (cutoff:3.500A) Processing helix chain 'T' and resid 334 through 336 No H-bonds generated for 'chain 'T' and resid 334 through 336' Processing helix chain 'T' and resid 343 through 349 Processing helix chain 'T' and resid 366 through 371 Processing helix chain 'T' and resid 371 through 391 removed outlier: 3.501A pdb=" N TYR T 375 " --> pdb=" O GLY T 371 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR T 384 " --> pdb=" O SER T 380 " (cutoff:3.500A) Processing helix chain 'T' and resid 391 through 399 removed outlier: 4.403A pdb=" N ILE T 397 " --> pdb=" O ASP T 393 " (cutoff:3.500A) Processing helix chain 'T' and resid 404 through 421 removed outlier: 3.698A pdb=" N LYS T 416 " --> pdb=" O ALA T 412 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG T 419 " --> pdb=" O ARG T 415 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU T 421 " --> pdb=" O ILE T 417 " (cutoff:3.500A) Processing helix chain 'T' and resid 426 through 431 removed outlier: 3.569A pdb=" N GLU T 429 " --> pdb=" O PHE T 426 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL T 430 " --> pdb=" O VAL T 427 " (cutoff:3.500A) Processing helix chain 'T' and resid 440 through 453 Processing helix chain 'T' and resid 460 through 465 Processing helix chain 'T' and resid 469 through 479 removed outlier: 3.600A pdb=" N ALA T 473 " --> pdb=" O ASN T 469 " (cutoff:3.500A) Processing helix chain 'U' and resid 93 through 97 removed outlier: 3.626A pdb=" N LEU U 97 " --> pdb=" O LYS U 94 " (cutoff:3.500A) Processing helix chain 'U' and resid 143 through 150 Processing helix chain 'U' and resid 167 through 180 Processing helix chain 'U' and resid 181 through 183 No H-bonds generated for 'chain 'U' and resid 181 through 183' Processing helix chain 'U' and resid 195 through 209 Processing helix chain 'U' and resid 216 through 220 Processing helix chain 'U' and resid 232 through 237 removed outlier: 3.763A pdb=" N MET U 237 " --> pdb=" O PRO U 233 " (cutoff:3.500A) Processing helix chain 'U' and resid 238 through 253 removed outlier: 3.800A pdb=" N PHE U 250 " --> pdb=" O MET U 246 " (cutoff:3.500A) Processing helix chain 'U' and resid 264 through 277 removed outlier: 3.713A pdb=" N PHE U 268 " --> pdb=" O ASN U 264 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY U 272 " --> pdb=" O PHE U 268 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL U 275 " --> pdb=" O ALA U 271 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA U 277 " --> pdb=" O ALA U 273 " (cutoff:3.500A) Processing helix chain 'U' and resid 284 through 288 Processing helix chain 'U' and resid 291 through 301 Processing helix chain 'U' and resid 320 through 323 removed outlier: 3.610A pdb=" N ASP U 323 " --> pdb=" O PRO U 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 320 through 323' Processing helix chain 'U' and resid 326 through 333 removed outlier: 3.753A pdb=" N THR U 331 " --> pdb=" O PRO U 327 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR U 332 " --> pdb=" O ALA U 328 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE U 333 " --> pdb=" O PRO U 329 " (cutoff:3.500A) Processing helix chain 'U' and resid 343 through 350 Processing helix chain 'U' and resid 366 through 371 Processing helix chain 'U' and resid 371 through 391 removed outlier: 3.614A pdb=" N SER U 377 " --> pdb=" O LYS U 373 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU U 391 " --> pdb=" O ARG U 387 " (cutoff:3.500A) Processing helix chain 'U' and resid 391 through 399 Processing helix chain 'U' and resid 400 through 403 Processing helix chain 'U' and resid 404 through 421 removed outlier: 3.594A pdb=" N LYS U 416 " --> pdb=" O ALA U 412 " (cutoff:3.500A) Processing helix chain 'U' and resid 428 through 433 Processing helix chain 'U' and resid 440 through 453 removed outlier: 3.501A pdb=" N THR U 444 " --> pdb=" O SER U 440 " (cutoff:3.500A) Processing helix chain 'U' and resid 461 through 465 Processing helix chain 'U' and resid 469 through 481 removed outlier: 3.508A pdb=" N ALA U 473 " --> pdb=" O ASN U 469 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA U 478 " --> pdb=" O ILE U 474 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER U 479 " --> pdb=" O SER U 475 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU U 480 " --> pdb=" O LYS U 476 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS U 481 " --> pdb=" O ALA U 477 " (cutoff:3.500A) Processing helix chain 'V' and resid 101 through 105 removed outlier: 3.954A pdb=" N TYR V 104 " --> pdb=" O GLY V 101 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU V 105 " --> pdb=" O GLU V 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 101 through 105' Processing helix chain 'V' and resid 151 through 156 Processing helix chain 'V' and resid 175 through 187 removed outlier: 3.756A pdb=" N GLN V 187 " --> pdb=" O THR V 183 " (cutoff:3.500A) Processing helix chain 'V' and resid 202 through 216 removed outlier: 3.827A pdb=" N VAL V 206 " --> pdb=" O LYS V 202 " (cutoff:3.500A) Processing helix chain 'V' and resid 217 through 220 removed outlier: 4.155A pdb=" N ASP V 220 " --> pdb=" O GLY V 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 217 through 220' Processing helix chain 'V' and resid 232 through 252 Proline residue: V 240 - end of helix removed outlier: 3.751A pdb=" N TYR V 249 " --> pdb=" O THR V 245 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N PHE V 250 " --> pdb=" O LEU V 246 " (cutoff:3.500A) Processing helix chain 'V' and resid 263 through 277 removed outlier: 3.612A pdb=" N GLN V 267 " --> pdb=" O ASP V 263 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU V 277 " --> pdb=" O GLU V 273 " (cutoff:3.500A) Processing helix chain 'V' and resid 290 through 300 removed outlier: 3.548A pdb=" N LEU V 294 " --> pdb=" O ASP V 290 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS V 295 " --> pdb=" O VAL V 291 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU V 298 " --> pdb=" O LEU V 294 " (cutoff:3.500A) Processing helix chain 'V' and resid 329 through 337 Processing helix chain 'V' and resid 346 through 351 Processing helix chain 'V' and resid 367 through 372 removed outlier: 3.820A pdb=" N ALA V 370 " --> pdb=" O VAL V 367 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA V 371 " --> pdb=" O GLY V 368 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN V 372 " --> pdb=" O SER V 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 367 through 372' Processing helix chain 'V' and resid 373 through 393 removed outlier: 3.544A pdb=" N VAL V 379 " --> pdb=" O ALA V 375 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLY V 381 " --> pdb=" O LYS V 377 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LYS V 382 " --> pdb=" O GLN V 378 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU V 383 " --> pdb=" O VAL V 379 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU V 392 " --> pdb=" O ALA V 388 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU V 393 " --> pdb=" O GLN V 389 " (cutoff:3.500A) Processing helix chain 'V' and resid 394 through 398 removed outlier: 3.986A pdb=" N SER V 397 " --> pdb=" O GLU V 394 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN V 398 " --> pdb=" O ALA V 395 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 394 through 398' Processing helix chain 'V' and resid 404 through 419 removed outlier: 3.657A pdb=" N GLU V 419 " --> pdb=" O ALA V 415 " (cutoff:3.500A) Processing helix chain 'V' and resid 430 through 443 Processing helix chain 'V' and resid 444 through 449 removed outlier: 4.146A pdb=" N LYS V 448 " --> pdb=" O TYR V 445 " (cutoff:3.500A) Processing helix chain 'V' and resid 450 through 452 No H-bonds generated for 'chain 'V' and resid 450 through 452' Processing helix chain 'V' and resid 453 through 469 removed outlier: 3.546A pdb=" N SER V 459 " --> pdb=" O ARG V 455 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY V 460 " --> pdb=" O ALA V 456 " (cutoff:3.500A) Processing helix chain 'V' and resid 469 through 477 removed outlier: 3.877A pdb=" N GLY V 473 " --> pdb=" O TYR V 469 " (cutoff:3.500A) Processing helix chain 'V' and resid 483 through 508 removed outlier: 3.790A pdb=" N GLU V 499 " --> pdb=" O ASN V 495 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'D' and resid 168 through 172 removed outlier: 4.445A pdb=" N ASN D 168 " --> pdb=" O VAL D 148 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N CYS D 152 " --> pdb=" O VAL D 170 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER D 172 " --> pdb=" O CYS D 152 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL D 111 " --> pdb=" O ASN D 149 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N VAL D 151 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU D 113 " --> pdb=" O VAL D 151 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N SER D 110 " --> pdb=" O LYS D 202 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N GLU D 204 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU D 112 " --> pdb=" O GLU D 204 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL D 206 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL D 114 " --> pdb=" O VAL D 206 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL D 203 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N CYS D 233 " --> pdb=" O THR D 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 247 through 252 Processing sheet with id=AA4, first strand: chain 'd' and resid 206 through 213 removed outlier: 7.157A pdb=" N GLN d 176 " --> pdb=" O LYS d 208 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N LYS d 210 " --> pdb=" O GLN d 176 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA d 178 " --> pdb=" O LYS d 210 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL d 212 " --> pdb=" O ALA d 178 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N LEU d 180 " --> pdb=" O VAL d 212 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'e' and resid 12 through 19 removed outlier: 6.152A pdb=" N THR e 9 " --> pdb=" O PRO e 13 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLN e 4 " --> pdb=" O VAL e 80 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ILE e 82 " --> pdb=" O GLN e 4 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N SER e 6 " --> pdb=" O ILE e 82 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ALA e 84 " --> pdb=" O SER e 6 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N LEU e 8 " --> pdb=" O ALA e 84 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'e' and resid 29 through 33 removed outlier: 8.006A pdb=" N ALA e 48 " --> pdb=" O PRO e 25 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY e 53 " --> pdb=" O GLU e 62 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU e 62 " --> pdb=" O GLY e 53 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 29 through 36 removed outlier: 6.662A pdb=" N ARG A 41 " --> pdb=" O PHE A 33 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL A 35 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE A 39 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASN A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LEU A 67 " --> pdb=" O ASN A 71 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLY A 73 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA A 64 " --> pdb=" O GLU A 52 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLU A 52 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LEU A 53 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 97 through 99 Processing sheet with id=AA9, first strand: chain 'A' and resid 108 through 109 removed outlier: 6.398A pdb=" N VAL A 109 " --> pdb=" O MET A 226 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 319 through 321 removed outlier: 6.028A pdb=" N ILE A 168 " --> pdb=" O VAL A 320 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 29 through 36 removed outlier: 5.658A pdb=" N VAL B 32 " --> pdb=" O TYR B 43 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N TYR B 43 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN B 34 " --> pdb=" O ARG B 41 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL B 75 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ALA B 64 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLU B 52 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU B 53 " --> pdb=" O THR B 92 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 97 through 100 removed outlier: 3.754A pdb=" N ASP B 126 " --> pdb=" O VAL B 100 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 108 through 109 removed outlier: 6.297A pdb=" N VAL B 109 " --> pdb=" O MET B 226 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR B 261 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE B 168 " --> pdb=" O VAL B 320 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 9 through 17 removed outlier: 6.857A pdb=" N ASP E 22 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ILE E 16 " --> pdb=" O VAL E 20 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL E 20 " --> pdb=" O ILE E 16 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N CYS E 63 " --> pdb=" O LEU E 58 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LEU E 58 " --> pdb=" O CYS E 63 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ARG E 65 " --> pdb=" O GLN E 56 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA E 36 " --> pdb=" O THR E 84 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ARG E 40 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU E 80 " --> pdb=" O ARG E 40 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ASN E 9 " --> pdb=" O ASP E 83 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 89 through 91 Processing sheet with id=AB7, first strand: chain 'E' and resid 100 through 101 removed outlier: 6.311A pdb=" N PHE E 101 " --> pdb=" O TYR E 226 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N GLN E 228 " --> pdb=" O PHE E 101 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL E 188 " --> pdb=" O PHE E 261 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL E 258 " --> pdb=" O THR E 312 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ILE E 314 " --> pdb=" O VAL E 258 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE E 260 " --> pdb=" O ILE E 314 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ALA E 316 " --> pdb=" O PHE E 260 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE E 262 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA E 338 " --> pdb=" O LYS E 157 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 138 through 139 removed outlier: 4.471A pdb=" N TYR E 152 " --> pdb=" O PHE E 139 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'T' and resid 10 through 17 removed outlier: 6.637A pdb=" N ASP T 22 " --> pdb=" O VAL T 14 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ILE T 16 " --> pdb=" O VAL T 20 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL T 20 " --> pdb=" O ILE T 16 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N CYS T 63 " --> pdb=" O LEU T 59 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N VAL T 67 " --> pdb=" O VAL T 55 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N VAL T 55 " --> pdb=" O VAL T 67 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR T 47 " --> pdb=" O ASN T 43 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA T 36 " --> pdb=" O THR T 84 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ARG T 40 " --> pdb=" O GLU T 80 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLU T 80 " --> pdb=" O ARG T 40 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ALA V 64 " --> pdb=" O VAL V 75 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL V 75 " --> pdb=" O ALA V 64 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN V 34 " --> pdb=" O ARG V 41 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR V 92 " --> pdb=" O LEU V 53 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N LEU V 53 " --> pdb=" O THR V 92 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLU V 52 " --> pdb=" O ALA V 64 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'T' and resid 89 through 90 Processing sheet with id=AC2, first strand: chain 'T' and resid 100 through 101 removed outlier: 6.763A pdb=" N PHE T 101 " --> pdb=" O TYR T 226 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL T 188 " --> pdb=" O PHE T 261 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE T 158 " --> pdb=" O GLN T 315 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'T' and resid 138 through 139 removed outlier: 3.528A pdb=" N PHE T 139 " --> pdb=" O TYR T 152 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N TYR T 152 " --> pdb=" O PHE T 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'U' and resid 9 through 17 removed outlier: 6.537A pdb=" N ASP U 22 " --> pdb=" O VAL U 14 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE U 16 " --> pdb=" O VAL U 20 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL U 20 " --> pdb=" O ILE U 16 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N CYS U 63 " --> pdb=" O LEU U 58 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LEU U 58 " --> pdb=" O CYS U 63 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ARG U 65 " --> pdb=" O GLN U 56 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA U 36 " --> pdb=" O THR U 84 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASN U 9 " --> pdb=" O ASP U 83 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'U' and resid 89 through 91 Processing sheet with id=AC6, first strand: chain 'U' and resid 100 through 101 removed outlier: 6.638A pdb=" N PHE U 101 " --> pdb=" O TYR U 226 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL U 258 " --> pdb=" O THR U 312 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N ILE U 314 " --> pdb=" O VAL U 258 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N PHE U 260 " --> pdb=" O ILE U 314 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ALA U 316 " --> pdb=" O PHE U 260 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE U 262 " --> pdb=" O ALA U 316 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N TYR U 318 " --> pdb=" O ILE U 262 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE U 158 " --> pdb=" O GLN U 315 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL U 317 " --> pdb=" O ILE U 158 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU U 160 " --> pdb=" O VAL U 317 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'V' and resid 97 through 100 removed outlier: 3.790A pdb=" N ASP V 126 " --> pdb=" O VAL V 100 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'V' and resid 108 through 109 removed outlier: 6.270A pdb=" N ILE V 193 " --> pdb=" O LEU V 258 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ILE V 260 " --> pdb=" O ILE V 193 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL V 195 " --> pdb=" O ILE V 260 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR V 261 " --> pdb=" O LEU V 317 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE V 168 " --> pdb=" O VAL V 320 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LEU V 167 " --> pdb=" O ILE V 343 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU V 345 " --> pdb=" O LEU V 167 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE V 169 " --> pdb=" O LEU V 345 " (cutoff:3.500A) 2183 hydrogen bonds defined for protein. 6387 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: 8.48 Time building geometry restraints manager: 4.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11853 1.34 - 1.46: 5533 1.46 - 1.58: 21320 1.58 - 1.70: 18 1.70 - 1.82: 249 Bond restraints: 38973 Sorted by residual: bond pdb=" CA MET H 26 " pdb=" CB MET H 26 " ideal model delta sigma weight residual 1.528 1.552 -0.024 1.66e-02 3.63e+03 2.02e+00 bond pdb=" CA ASN U 216 " pdb=" CB ASN U 216 " ideal model delta sigma weight residual 1.527 1.549 -0.022 1.61e-02 3.86e+03 1.80e+00 bond pdb=" CB ASP d 86 " pdb=" CG ASP d 86 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.76e+00 bond pdb=" C ALA V 113 " pdb=" N ARG V 114 " ideal model delta sigma weight residual 1.333 1.312 0.021 1.61e-02 3.86e+03 1.72e+00 bond pdb=" CB GLU T 372 " pdb=" CG GLU T 372 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.54e+00 ... (remaining 38968 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 52159 2.33 - 4.66: 595 4.66 - 7.00: 62 7.00 - 9.33: 15 9.33 - 11.66: 6 Bond angle restraints: 52837 Sorted by residual: angle pdb=" N GLY A 368 " pdb=" CA GLY A 368 " pdb=" C GLY A 368 " ideal model delta sigma weight residual 114.40 120.55 -6.15 1.11e+00 8.12e-01 3.07e+01 angle pdb=" N VAL A 27 " pdb=" CA VAL A 27 " pdb=" C VAL A 27 " ideal model delta sigma weight residual 112.12 109.02 3.10 8.40e-01 1.42e+00 1.36e+01 angle pdb=" N VAL E 286 " pdb=" CA VAL E 286 " pdb=" C VAL E 286 " ideal model delta sigma weight residual 111.91 108.81 3.10 8.90e-01 1.26e+00 1.21e+01 angle pdb=" C VAL a 96 " pdb=" CA VAL a 96 " pdb=" CB VAL a 96 " ideal model delta sigma weight residual 114.35 110.70 3.65 1.06e+00 8.90e-01 1.19e+01 angle pdb=" CB MET P 26 " pdb=" CG MET P 26 " pdb=" SD MET P 26 " ideal model delta sigma weight residual 112.70 123.01 -10.31 3.00e+00 1.11e-01 1.18e+01 ... (remaining 52832 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 21396 17.97 - 35.93: 1682 35.93 - 53.90: 420 53.90 - 71.87: 77 71.87 - 89.83: 42 Dihedral angle restraints: 23617 sinusoidal: 9125 harmonic: 14492 Sorted by residual: dihedral pdb=" CA GLN A 164 " pdb=" C GLN A 164 " pdb=" N ARG A 165 " pdb=" CA ARG A 165 " ideal model delta harmonic sigma weight residual 180.00 -153.18 -26.82 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA ILE U 351 " pdb=" C ILE U 351 " pdb=" N TYR U 352 " pdb=" CA TYR U 352 " ideal model delta harmonic sigma weight residual -180.00 -157.44 -22.56 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA LEU M 15 " pdb=" C LEU M 15 " pdb=" N ALA M 16 " pdb=" CA ALA M 16 " ideal model delta harmonic sigma weight residual -180.00 -158.00 -22.00 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 23614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 4863 0.049 - 0.097: 1127 0.097 - 0.146: 247 0.146 - 0.194: 9 0.194 - 0.243: 2 Chirality restraints: 6248 Sorted by residual: chirality pdb=" CA TYR U 352 " pdb=" N TYR U 352 " pdb=" C TYR U 352 " pdb=" CB TYR U 352 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA TYR T 352 " pdb=" N TYR T 352 " pdb=" C TYR T 352 " pdb=" CB TYR T 352 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ASP U 61 " pdb=" N ASP U 61 " pdb=" C ASP U 61 " pdb=" CB ASP U 61 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.48e-01 ... (remaining 6245 not shown) Planarity restraints: 6787 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 326 " -0.046 5.00e-02 4.00e+02 6.98e-02 7.80e+00 pdb=" N PRO E 327 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO E 327 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 327 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP U 61 " -0.012 2.00e-02 2.50e+03 2.51e-02 6.31e+00 pdb=" CG ASP U 61 " 0.043 2.00e-02 2.50e+03 pdb=" OD1 ASP U 61 " -0.016 2.00e-02 2.50e+03 pdb=" OD2 ASP U 61 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN F 42 " 0.037 5.00e-02 4.00e+02 5.64e-02 5.09e+00 pdb=" N PRO F 43 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO F 43 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 43 " 0.031 5.00e-02 4.00e+02 ... (remaining 6784 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 12 2.52 - 3.11: 29199 3.11 - 3.71: 57845 3.71 - 4.30: 81133 4.30 - 4.90: 137604 Nonbonded interactions: 305793 Sorted by model distance: nonbonded pdb="MG MG A 601 " pdb=" O1B ATP A 602 " model vdw 1.919 2.170 nonbonded pdb="MG MG A 601 " pdb=" O2G ATP A 602 " model vdw 1.951 2.170 nonbonded pdb=" O2B ATP B 600 " pdb="MG MG B 601 " model vdw 1.971 2.170 nonbonded pdb="MG MG V 601 " pdb=" O2B ATP V 602 " model vdw 2.021 2.170 nonbonded pdb=" OG1 THR B 177 " pdb="MG MG B 601 " model vdw 2.119 2.170 ... (remaining 305788 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 26 through 507) selection = (chain 'B' and resid 26 through 507) selection = (chain 'V' and resid 26 through 507) } ncs_group { reference = chain 'E' selection = (chain 'T' and resid 7 through 481) selection = (chain 'U' and resid 7 through 481) } ncs_group { reference = 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.840 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 32.690 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.160 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6356 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 : 0.003 0.041 38973 Z= 0.161 Angle : 0.662 11.660 52837 Z= 0.374 Chirality : 0.042 0.243 6248 Planarity : 0.005 0.070 6787 Dihedral : 14.693 89.834 14365 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.26 % Allowed : 11.69 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.12), residues: 5056 helix: 0.34 (0.10), residues: 2671 sheet: -0.25 (0.22), residues: 582 loop : -1.03 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG b 96 TYR 0.027 0.001 TYR a 149 PHE 0.035 0.002 PHE d 165 TRP 0.012 0.001 TRP a 95 HIS 0.002 0.001 HIS T 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (38973) covalent geometry : angle 0.66210 / 0.37 (52837) hydrogen bonds : bond 0.16183 / 10.61 ( 2183) hydrogen bonds : angle 6.63215 / 4.78 ( 6387) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 250 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 149 MET cc_start: 0.3601 (ttt) cc_final: 0.3099 (ttt) REVERT: e 1 MET cc_start: 0.4009 (OUTLIER) cc_final: 0.2817 (ptt) REVERT: F 26 MET cc_start: 0.4351 (mmp) cc_final: 0.3828 (tpt) REVERT: H 26 MET cc_start: 0.1611 (ppp) cc_final: 0.1407 (ppp) REVERT: K 15 LEU cc_start: 0.5320 (OUTLIER) cc_final: 0.4901 (pp) REVERT: O 60 MET cc_start: 0.4801 (mtm) cc_final: 0.4268 (mtt) REVERT: R 26 MET cc_start: 0.6738 (ppp) cc_final: 0.6139 (mmt) REVERT: R 59 PHE cc_start: 0.6488 (t80) cc_final: 0.6096 (t80) REVERT: R 60 MET cc_start: 0.3176 (mmt) cc_final: 0.2228 (mmt) REVERT: R 66 TYR cc_start: 0.1578 (OUTLIER) cc_final: 0.0567 (m-10) REVERT: A 237 TYR cc_start: 0.8965 (OUTLIER) cc_final: 0.8139 (t80) REVERT: E 61 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8188 (p0) REVERT: T 49 MET cc_start: 0.7814 (mmm) cc_final: 0.7607 (mmt) REVERT: T 228 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7649 (mt0) REVERT: U 17 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8398 (mt) REVERT: V 300 GLU cc_start: 0.9055 (OUTLIER) cc_final: 0.8848 (tp30) REVERT: V 450 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7543 (pp20) outliers start: 50 outliers final: 39 residues processed: 289 average time/residue: 0.2300 time to fit residues: 114.4508 Evaluate side-chains 279 residues out of total 3970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 231 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 123 CYS Chi-restraints excluded: chain D residue 167 TYR Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain d residue 161 ILE Chi-restraints excluded: chain d residue 172 MET Chi-restraints excluded: chain d residue 221 PHE Chi-restraints excluded: chain d residue 223 VAL Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 42 THR Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 82 ILE Chi-restraints excluded: chain e residue 135 VAL Chi-restraints excluded: chain M residue 12 SER Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 66 TYR Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 352 TYR Chi-restraints excluded: chain T residue 10 MET Chi-restraints excluded: chain T residue 116 VAL Chi-restraints excluded: chain T residue 228 GLN Chi-restraints excluded: chain T residue 242 THR Chi-restraints excluded: chain T residue 295 GLU Chi-restraints excluded: chain U residue 10 MET Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain U residue 215 LYS Chi-restraints excluded: chain U residue 258 VAL Chi-restraints excluded: chain U residue 352 TYR Chi-restraints excluded: chain V residue 98 ILE Chi-restraints excluded: chain V residue 100 VAL Chi-restraints excluded: chain V residue 234 THR Chi-restraints excluded: chain V residue 300 GLU Chi-restraints excluded: chain V residue 450 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 3.9990 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 470 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 28 GLN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.149324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.091293 restraints weight = 76440.112| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.87 r_work: 0.3167 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.0862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 38973 Z= 0.238 Angle : 0.646 13.702 52837 Z= 0.338 Chirality : 0.045 0.285 6248 Planarity : 0.005 0.071 6787 Dihedral : 7.906 89.381 5722 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.77 % Allowed : 12.37 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.12), residues: 5056 helix: 0.55 (0.10), residues: 2699 sheet: -0.34 (0.21), residues: 595 loop : -1.14 (0.15), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 41 TYR 0.027 0.002 TYR N 66 PHE 0.025 0.002 PHE T 268 TRP 0.007 0.001 TRP d 145 HIS 0.004 0.001 HIS U 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.24 (38973) covalent geometry : angle 0.64561 / 0.34 (52837) hydrogen bonds : bond 0.05778 / 3.82 ( 2183) hydrogen bonds : angle 4.99410 / 3.61 ( 6387) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 235 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: e 1 MET cc_start: 0.3686 (OUTLIER) cc_final: 0.3449 (ptt) REVERT: e 12 ARG cc_start: 0.8281 (ptt90) cc_final: 0.7990 (ptm-80) REVERT: M 26 MET cc_start: 0.5485 (ppp) cc_final: 0.5283 (tmm) REVERT: F 26 MET cc_start: 0.5943 (mmp) cc_final: 0.5501 (tpt) REVERT: F 48 LYS cc_start: 0.0922 (OUTLIER) cc_final: 0.0657 (ttmt) REVERT: J 57 PHE cc_start: 0.7117 (m-80) cc_final: 0.6507 (m-80) REVERT: J 60 MET cc_start: 0.4264 (tpp) cc_final: 0.3779 (mtp) REVERT: N 26 MET cc_start: 0.8014 (mpp) cc_final: 0.7637 (tmm) REVERT: O 60 MET cc_start: 0.4982 (mtm) cc_final: 0.4453 (mtt) REVERT: P 60 MET cc_start: 0.1931 (pmm) cc_final: 0.1448 (ptp) REVERT: R 60 MET cc_start: 0.4562 (mmt) cc_final: 0.3387 (mmt) REVERT: R 66 TYR cc_start: 0.2018 (OUTLIER) cc_final: 0.0760 (m-10) REVERT: A 237 TYR cc_start: 0.9088 (OUTLIER) cc_final: 0.8348 (t80) REVERT: A 263 ASP cc_start: 0.8294 (m-30) cc_final: 0.8092 (m-30) REVERT: E 61 ASP cc_start: 0.8733 (OUTLIER) cc_final: 0.8321 (p0) REVERT: E 62 ASN cc_start: 0.9229 (OUTLIER) cc_final: 0.8863 (p0) REVERT: E 118 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8238 (pm20) REVERT: T 228 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8015 (mt0) REVERT: T 352 TYR cc_start: 0.7966 (OUTLIER) cc_final: 0.7505 (t80) REVERT: U 61 ASP cc_start: 0.8118 (p0) cc_final: 0.7914 (p0) REVERT: U 237 MET cc_start: 0.9513 (ptp) cc_final: 0.9272 (ptp) REVERT: U 352 TYR cc_start: 0.8132 (OUTLIER) cc_final: 0.7849 (t80) REVERT: V 450 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7598 (pp20) outliers start: 110 outliers final: 61 residues processed: 325 average time/residue: 0.2198 time to fit residues: 123.3141 Evaluate side-chains 300 residues out of total 3970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 228 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 211 LEU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 167 TYR Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain d residue 223 VAL Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 42 THR Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 69 MET Chi-restraints excluded: chain e residue 81 THR Chi-restraints excluded: chain e residue 82 ILE Chi-restraints excluded: chain e residue 115 VAL Chi-restraints excluded: chain e residue 135 VAL Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 48 LYS Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain L residue 44 GLU Chi-restraints excluded: chain N residue 39 ILE Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain P residue 15 LEU Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 66 TYR Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 86 LYS Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 352 TYR Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 116 VAL Chi-restraints excluded: chain T residue 145 VAL Chi-restraints excluded: chain T residue 228 GLN Chi-restraints excluded: chain T residue 239 VAL Chi-restraints excluded: chain T residue 242 THR Chi-restraints excluded: chain T residue 258 VAL Chi-restraints excluded: chain T residue 352 TYR Chi-restraints excluded: chain U residue 10 MET Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain U residue 258 VAL Chi-restraints excluded: chain U residue 270 GLN Chi-restraints excluded: chain U residue 352 TYR Chi-restraints excluded: chain U residue 359 GLU Chi-restraints excluded: chain V residue 98 ILE Chi-restraints excluded: chain V residue 100 VAL Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain V residue 234 THR Chi-restraints excluded: chain V residue 274 MET Chi-restraints excluded: chain V residue 333 THR Chi-restraints excluded: chain V residue 450 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 184 optimal weight: 30.0000 chunk 475 optimal weight: 3.9990 chunk 228 optimal weight: 0.8980 chunk 221 optimal weight: 0.7980 chunk 161 optimal weight: 50.0000 chunk 454 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 217 optimal weight: 0.8980 chunk 239 optimal weight: 0.7980 chunk 196 optimal weight: 9.9990 chunk 446 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 170 ASN ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 GLN T 230 ASN ** T 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.152929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.097360 restraints weight = 75882.593| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 3.46 r_work: 0.3171 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 38973 Z= 0.120 Angle : 0.534 7.552 52837 Z= 0.279 Chirality : 0.041 0.202 6248 Planarity : 0.004 0.066 6787 Dihedral : 7.191 88.251 5692 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.54 % Allowed : 13.10 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.12), residues: 5056 helix: 0.88 (0.10), residues: 2695 sheet: -0.10 (0.22), residues: 594 loop : -0.97 (0.15), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG e 127 TYR 0.037 0.001 TYR e 125 PHE 0.021 0.001 PHE R 59 TRP 0.008 0.001 TRP T 368 HIS 0.002 0.000 HIS T 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (38973) covalent geometry : angle 0.53372 / 0.28 (52837) hydrogen bonds : bond 0.04597 / 3.03 ( 2183) hydrogen bonds : angle 4.52349 / 3.26 ( 6387) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 247 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: e 1 MET cc_start: 0.3759 (OUTLIER) cc_final: 0.3539 (ptt) REVERT: e 12 ARG cc_start: 0.8107 (ptt90) cc_final: 0.7823 (ptm-80) REVERT: e 42 THR cc_start: 0.8146 (OUTLIER) cc_final: 0.7834 (p) REVERT: e 79 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7018 (pm20) REVERT: F 26 MET cc_start: 0.5928 (mmp) cc_final: 0.5326 (tpt) REVERT: F 48 LYS cc_start: 0.0641 (OUTLIER) cc_final: 0.0358 (ttmt) REVERT: J 57 PHE cc_start: 0.6828 (m-80) cc_final: 0.6089 (m-80) REVERT: J 60 MET cc_start: 0.4154 (tpp) cc_final: 0.3866 (mtp) REVERT: K 15 LEU cc_start: 0.5028 (OUTLIER) cc_final: 0.4769 (pp) REVERT: O 34 TYR cc_start: 0.6863 (m-80) cc_final: 0.6566 (m-80) REVERT: O 60 MET cc_start: 0.4948 (mtm) cc_final: 0.4731 (mtt) REVERT: P 60 MET cc_start: 0.1848 (pmm) cc_final: 0.1433 (ptp) REVERT: R 46 GLU cc_start: 0.6414 (mt-10) cc_final: 0.6165 (mt-10) REVERT: R 59 PHE cc_start: 0.6784 (t80) cc_final: 0.6567 (t80) REVERT: R 60 MET cc_start: 0.4421 (mmt) cc_final: 0.3219 (mmt) REVERT: R 66 TYR cc_start: 0.2044 (OUTLIER) cc_final: 0.0716 (m-10) REVERT: A 263 ASP cc_start: 0.7888 (m-30) cc_final: 0.7670 (m-30) REVERT: E 23 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8819 (mm) REVERT: E 61 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.8312 (p0) REVERT: T 10 MET cc_start: 0.8570 (mtm) cc_final: 0.8286 (mtt) REVERT: T 228 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7614 (mt0) REVERT: U 61 ASP cc_start: 0.7866 (p0) cc_final: 0.7647 (p0) REVERT: U 69 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8668 (mmt) REVERT: U 228 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8303 (mp10) REVERT: V 366 ARG cc_start: 0.8401 (tpt-90) cc_final: 0.8185 (mmm160) outliers start: 101 outliers final: 47 residues processed: 327 average time/residue: 0.2164 time to fit residues: 120.8840 Evaluate side-chains 290 residues out of total 3970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 232 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain d residue 199 GLN Chi-restraints excluded: chain d residue 223 VAL Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 42 THR Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 69 MET Chi-restraints excluded: chain e residue 79 GLN Chi-restraints excluded: chain e residue 81 THR Chi-restraints excluded: chain e residue 82 ILE Chi-restraints excluded: chain e residue 135 VAL Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 48 LYS Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain N residue 39 ILE Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain P residue 15 LEU Chi-restraints excluded: chain R residue 66 TYR Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain B residue 26 MET Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 352 TYR Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 116 VAL Chi-restraints excluded: chain T residue 145 VAL Chi-restraints excluded: chain T residue 228 GLN Chi-restraints excluded: chain T residue 242 THR Chi-restraints excluded: chain T residue 258 VAL Chi-restraints excluded: chain U residue 10 MET Chi-restraints excluded: chain U residue 69 MET Chi-restraints excluded: chain U residue 228 GLN Chi-restraints excluded: chain U residue 258 VAL Chi-restraints excluded: chain U residue 352 TYR Chi-restraints excluded: chain V residue 43 TYR Chi-restraints excluded: chain V residue 100 VAL Chi-restraints excluded: chain V residue 149 THR Chi-restraints excluded: chain V residue 234 THR Chi-restraints excluded: chain V residue 263 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 264 optimal weight: 6.9990 chunk 75 optimal weight: 30.0000 chunk 152 optimal weight: 1.9990 chunk 461 optimal weight: 1.9990 chunk 83 optimal weight: 0.0050 chunk 378 optimal weight: 4.9990 chunk 296 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 chunk 401 optimal weight: 0.0470 chunk 37 optimal weight: 9.9990 overall best weight: 1.2098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 30 ASN G 28 GLN G 42 GLN ** N 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.153239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.097475 restraints weight = 75612.207| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 3.52 r_work: 0.3152 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 38973 Z= 0.118 Angle : 0.520 10.039 52837 Z= 0.270 Chirality : 0.041 0.218 6248 Planarity : 0.004 0.063 6787 Dihedral : 6.936 89.178 5675 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.34 % Allowed : 13.78 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.12), residues: 5056 helix: 1.02 (0.10), residues: 2704 sheet: 0.06 (0.22), residues: 607 loop : -0.93 (0.15), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 77 TYR 0.023 0.001 TYR a 149 PHE 0.021 0.001 PHE M 57 TRP 0.007 0.001 TRP U 368 HIS 0.001 0.000 HIS T 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (38973) covalent geometry : angle 0.51996 / 0.27 (52837) hydrogen bonds : bond 0.04285 / 2.84 ( 2183) hydrogen bonds : angle 4.35359 / 3.14 ( 6387) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 250 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: p 207 VAL cc_start: 0.4018 (t) cc_final: 0.3742 (m) REVERT: d 172 MET cc_start: 0.4341 (OUTLIER) cc_final: 0.3947 (pmm) REVERT: e 1 MET cc_start: 0.3830 (OUTLIER) cc_final: 0.3371 (ptt) REVERT: e 12 ARG cc_start: 0.8225 (ptt90) cc_final: 0.7993 (ptm-80) REVERT: e 31 MET cc_start: 0.3906 (mtm) cc_final: 0.3536 (mtm) REVERT: e 50 LEU cc_start: 0.7354 (mt) cc_final: 0.6747 (tt) REVERT: e 66 TYR cc_start: 0.6218 (p90) cc_final: 0.6009 (p90) REVERT: e 79 GLN cc_start: 0.8084 (tp-100) cc_final: 0.6790 (pm20) REVERT: F 26 MET cc_start: 0.5977 (mmp) cc_final: 0.5632 (tpt) REVERT: F 48 LYS cc_start: 0.0441 (OUTLIER) cc_final: 0.0172 (ttmt) REVERT: F 57 PHE cc_start: -0.1244 (OUTLIER) cc_final: -0.2762 (m-80) REVERT: J 57 PHE cc_start: 0.6776 (m-80) cc_final: 0.6090 (m-80) REVERT: J 60 MET cc_start: 0.4183 (tpp) cc_final: 0.3882 (mtp) REVERT: N 37 GLU cc_start: 0.8485 (pp20) cc_final: 0.8027 (mm-30) REVERT: O 34 TYR cc_start: 0.7083 (m-80) cc_final: 0.6727 (m-80) REVERT: O 60 MET cc_start: 0.4914 (mtm) cc_final: 0.4656 (mtt) REVERT: P 60 MET cc_start: 0.1564 (pmm) cc_final: 0.0955 (ptp) REVERT: R 46 GLU cc_start: 0.6311 (mt-10) cc_final: 0.6108 (mt-10) REVERT: R 60 MET cc_start: 0.4445 (mmt) cc_final: 0.3175 (mmt) REVERT: R 66 TYR cc_start: 0.2102 (OUTLIER) cc_final: 0.1504 (m-10) REVERT: E 61 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8336 (p0) REVERT: T 206 MET cc_start: 0.8989 (mmp) cc_final: 0.8704 (mmt) REVERT: T 228 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7695 (mt0) REVERT: U 69 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8703 (mmt) REVERT: U 228 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8315 (mp10) outliers start: 93 outliers final: 53 residues processed: 324 average time/residue: 0.2057 time to fit residues: 114.5434 Evaluate side-chains 297 residues out of total 3970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 235 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 211 LEU Chi-restraints excluded: chain p residue 208 ASP Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 167 TYR Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain d residue 172 MET Chi-restraints excluded: chain d residue 199 GLN Chi-restraints excluded: chain d residue 223 VAL Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 69 MET Chi-restraints excluded: chain e residue 81 THR Chi-restraints excluded: chain e residue 82 ILE Chi-restraints excluded: chain e residue 135 VAL Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 48 LYS Chi-restraints excluded: chain F residue 57 PHE Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 26 MET Chi-restraints excluded: chain I residue 42 GLN Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain N residue 39 ILE Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain P residue 15 LEU Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain R residue 66 TYR Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 352 TYR Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 116 VAL Chi-restraints excluded: chain T residue 145 VAL Chi-restraints excluded: chain T residue 228 GLN Chi-restraints excluded: chain T residue 242 THR Chi-restraints excluded: chain T residue 258 VAL Chi-restraints excluded: chain U residue 10 MET Chi-restraints excluded: chain U residue 69 MET Chi-restraints excluded: chain U residue 228 GLN Chi-restraints excluded: chain U residue 258 VAL Chi-restraints excluded: chain U residue 352 TYR Chi-restraints excluded: chain V residue 43 TYR Chi-restraints excluded: chain V residue 100 VAL Chi-restraints excluded: chain V residue 149 THR Chi-restraints excluded: chain V residue 234 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 14 optimal weight: 50.0000 chunk 378 optimal weight: 0.9990 chunk 325 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 376 optimal weight: 2.9990 chunk 294 optimal weight: 7.9990 chunk 292 optimal weight: 0.9980 chunk 320 optimal weight: 8.9990 chunk 318 optimal weight: 4.9990 chunk 291 optimal weight: 0.3980 chunk 348 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 28 GLN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 71 ASN ** V 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.159406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.103647 restraints weight = 75550.978| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 3.18 r_work: 0.3168 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 38973 Z= 0.116 Angle : 0.520 16.418 52837 Z= 0.267 Chirality : 0.041 0.196 6248 Planarity : 0.004 0.060 6787 Dihedral : 6.836 89.392 5674 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.52 % Allowed : 13.98 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.12), residues: 5056 helix: 1.14 (0.10), residues: 2694 sheet: 0.19 (0.22), residues: 600 loop : -0.89 (0.15), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 41 TYR 0.022 0.001 TYR a 149 PHE 0.026 0.001 PHE e 72 TRP 0.006 0.001 TRP U 368 HIS 0.002 0.000 HIS d 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (38973) covalent geometry : angle 0.52013 / 0.27 (52837) hydrogen bonds : bond 0.04100 / 2.70 ( 2183) hydrogen bonds : angle 4.24075 / 3.05 ( 6387) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 245 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 172 MET cc_start: 0.4314 (OUTLIER) cc_final: 0.3962 (pmm) REVERT: d 225 TYR cc_start: 0.5636 (t80) cc_final: 0.4654 (t80) REVERT: e 1 MET cc_start: 0.3787 (OUTLIER) cc_final: 0.3308 (ptt) REVERT: e 12 ARG cc_start: 0.8234 (ptt90) cc_final: 0.7981 (ptm-80) REVERT: e 50 LEU cc_start: 0.7426 (mt) cc_final: 0.6840 (tt) REVERT: F 26 MET cc_start: 0.6086 (mmp) cc_final: 0.5800 (tpt) REVERT: F 57 PHE cc_start: -0.1281 (OUTLIER) cc_final: -0.2760 (m-80) REVERT: J 57 PHE cc_start: 0.6840 (m-80) cc_final: 0.6572 (m-80) REVERT: J 60 MET cc_start: 0.4053 (tpp) cc_final: 0.3758 (mtp) REVERT: N 37 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8139 (mm-30) REVERT: O 34 TYR cc_start: 0.7231 (m-80) cc_final: 0.6931 (m-80) REVERT: O 60 MET cc_start: 0.4857 (mtm) cc_final: 0.4524 (mtt) REVERT: P 60 MET cc_start: 0.1525 (pmm) cc_final: 0.1122 (ptp) REVERT: R 59 PHE cc_start: 0.5837 (t80) cc_final: 0.5342 (t80) REVERT: R 60 MET cc_start: 0.4393 (mmt) cc_final: 0.3301 (mmt) REVERT: R 66 TYR cc_start: 0.2161 (OUTLIER) cc_final: 0.0839 (m-10) REVERT: A 324 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7529 (tt0) REVERT: E 61 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.8334 (p0) REVERT: E 69 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.7660 (mmt) REVERT: E 480 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6378 (tt) REVERT: T 228 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7668 (mt0) REVERT: U 69 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8682 (mmt) REVERT: U 228 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8305 (mp10) REVERT: V 464 TYR cc_start: 0.8283 (t80) cc_final: 0.7928 (t80) outliers start: 100 outliers final: 60 residues processed: 328 average time/residue: 0.2074 time to fit residues: 116.9584 Evaluate side-chains 302 residues out of total 3970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 230 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 107 THR Chi-restraints excluded: chain p residue 208 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain d residue 161 ILE Chi-restraints excluded: chain d residue 172 MET Chi-restraints excluded: chain d residue 199 GLN Chi-restraints excluded: chain b residue 121 LEU Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 40 ILE Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 69 MET Chi-restraints excluded: chain e residue 82 ILE Chi-restraints excluded: chain e residue 115 VAL Chi-restraints excluded: chain e residue 135 VAL Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 57 PHE Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 41 ARG Chi-restraints excluded: chain I residue 42 GLN Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain N residue 39 ILE Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain P residue 15 LEU Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 66 TYR Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 69 MET Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 263 ASP Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 352 TYR Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 116 VAL Chi-restraints excluded: chain T residue 145 VAL Chi-restraints excluded: chain T residue 228 GLN Chi-restraints excluded: chain T residue 258 VAL Chi-restraints excluded: chain U residue 69 MET Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 228 GLN Chi-restraints excluded: chain U residue 258 VAL Chi-restraints excluded: chain U residue 352 TYR Chi-restraints excluded: chain V residue 100 VAL Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain V residue 149 THR Chi-restraints excluded: chain V residue 234 THR Chi-restraints excluded: chain V residue 342 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 409 optimal weight: 5.9990 chunk 264 optimal weight: 4.9990 chunk 0 optimal weight: 50.0000 chunk 99 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 258 optimal weight: 5.9990 chunk 138 optimal weight: 20.0000 chunk 267 optimal weight: 5.9990 chunk 69 optimal weight: 20.0000 chunk 192 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** e 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 374 HIS V 334 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.158818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.101978 restraints weight = 75847.848| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.75 r_work: 0.3218 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 38973 Z= 0.188 Angle : 0.579 14.823 52837 Z= 0.297 Chirality : 0.043 0.255 6248 Planarity : 0.005 0.059 6787 Dihedral : 7.072 89.192 5667 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.92 % Allowed : 14.13 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.12), residues: 5056 helix: 1.07 (0.10), residues: 2703 sheet: -0.03 (0.21), residues: 619 loop : -1.00 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 77 TYR 0.022 0.001 TYR a 149 PHE 0.023 0.001 PHE e 72 TRP 0.005 0.001 TRP a 95 HIS 0.003 0.001 HIS d 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 (38973) covalent geometry : angle 0.57877 / 0.30 (52837) hydrogen bonds : bond 0.04632 / 3.06 ( 2183) hydrogen bonds : angle 4.40204 / 3.17 ( 6387) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 231 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: p 124 ARG cc_start: 0.5510 (OUTLIER) cc_final: 0.5161 (ttp80) REVERT: D 108 VAL cc_start: 0.7727 (OUTLIER) cc_final: 0.7462 (t) REVERT: d 172 MET cc_start: 0.4569 (OUTLIER) cc_final: 0.4017 (pmm) REVERT: d 225 TYR cc_start: 0.5641 (t80) cc_final: 0.4715 (t80) REVERT: e 1 MET cc_start: 0.3837 (OUTLIER) cc_final: 0.3527 (ptt) REVERT: e 12 ARG cc_start: 0.8317 (ptt90) cc_final: 0.7998 (ptm-80) REVERT: e 79 GLN cc_start: 0.8282 (tp-100) cc_final: 0.6993 (mp10) REVERT: F 26 MET cc_start: 0.6043 (mmp) cc_final: 0.5564 (tpt) REVERT: F 48 LYS cc_start: 0.0621 (OUTLIER) cc_final: 0.0308 (ttmt) REVERT: F 57 PHE cc_start: -0.1437 (OUTLIER) cc_final: -0.3048 (m-80) REVERT: J 57 PHE cc_start: 0.7048 (m-80) cc_final: 0.6724 (m-80) REVERT: N 37 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8141 (mm-30) REVERT: N 48 LYS cc_start: 0.5649 (mttp) cc_final: 0.5145 (pttt) REVERT: O 34 TYR cc_start: 0.7021 (m-80) cc_final: 0.6650 (m-80) REVERT: O 60 MET cc_start: 0.5151 (mtm) cc_final: 0.4686 (mtt) REVERT: P 60 MET cc_start: 0.1469 (pmm) cc_final: 0.0972 (ptp) REVERT: R 59 PHE cc_start: 0.6057 (t80) cc_final: 0.5614 (t80) REVERT: R 60 MET cc_start: 0.4279 (mmt) cc_final: 0.3350 (mmt) REVERT: R 66 TYR cc_start: 0.1902 (OUTLIER) cc_final: 0.0529 (m-10) REVERT: S 28 GLN cc_start: 0.6798 (mt0) cc_final: 0.6542 (mt0) REVERT: A 324 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7720 (tt0) REVERT: E 61 ASP cc_start: 0.8714 (OUTLIER) cc_final: 0.8365 (p0) REVERT: E 69 MET cc_start: 0.9190 (OUTLIER) cc_final: 0.7803 (mmt) REVERT: E 480 LEU cc_start: 0.6795 (OUTLIER) cc_final: 0.6503 (tt) REVERT: U 69 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8777 (mmt) REVERT: U 228 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8470 (mp10) outliers start: 116 outliers final: 75 residues processed: 323 average time/residue: 0.2134 time to fit residues: 118.9212 Evaluate side-chains 312 residues out of total 3970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 223 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 211 LEU Chi-restraints excluded: chain p residue 107 THR Chi-restraints excluded: chain p residue 124 ARG Chi-restraints excluded: chain p residue 208 ASP Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain d residue 172 MET Chi-restraints excluded: chain d residue 199 GLN Chi-restraints excluded: chain b residue 121 LEU Chi-restraints excluded: chain b residue 148 ILE Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 40 ILE Chi-restraints excluded: chain e residue 41 ILE Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 69 MET Chi-restraints excluded: chain e residue 82 ILE Chi-restraints excluded: chain e residue 115 VAL Chi-restraints excluded: chain e residue 135 VAL Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 48 LYS Chi-restraints excluded: chain F residue 57 PHE Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 41 ARG Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain L residue 44 GLU Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain N residue 39 ILE Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain P residue 15 LEU Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 66 TYR Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 69 MET Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 263 ASP Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 352 TYR Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain T residue 10 MET Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 116 VAL Chi-restraints excluded: chain T residue 145 VAL Chi-restraints excluded: chain T residue 172 ILE Chi-restraints excluded: chain T residue 228 GLN Chi-restraints excluded: chain T residue 258 VAL Chi-restraints excluded: chain U residue 69 MET Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 228 GLN Chi-restraints excluded: chain U residue 258 VAL Chi-restraints excluded: chain U residue 276 SER Chi-restraints excluded: chain U residue 352 TYR Chi-restraints excluded: chain V residue 43 TYR Chi-restraints excluded: chain V residue 100 VAL Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain V residue 149 THR Chi-restraints excluded: chain V residue 234 THR Chi-restraints excluded: chain V residue 274 MET Chi-restraints excluded: chain V residue 432 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 202 optimal weight: 50.0000 chunk 229 optimal weight: 1.9990 chunk 29 optimal weight: 20.0000 chunk 291 optimal weight: 5.9990 chunk 375 optimal weight: 1.9990 chunk 219 optimal weight: 6.9990 chunk 215 optimal weight: 0.6980 chunk 112 optimal weight: 40.0000 chunk 77 optimal weight: 0.9980 chunk 53 optimal weight: 0.3980 chunk 301 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 30 ASN e 108 ASN ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.159277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.103981 restraints weight = 75815.202| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 3.45 r_work: 0.3155 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 38973 Z= 0.116 Angle : 0.523 13.297 52837 Z= 0.269 Chirality : 0.041 0.198 6248 Planarity : 0.004 0.058 6787 Dihedral : 6.869 89.921 5667 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.57 % Allowed : 14.66 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.12), residues: 5056 helix: 1.22 (0.10), residues: 2690 sheet: 0.11 (0.22), residues: 604 loop : -0.91 (0.15), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 40 TYR 0.030 0.001 TYR e 125 PHE 0.027 0.001 PHE e 72 TRP 0.007 0.001 TRP T 368 HIS 0.002 0.000 HIS d 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (38973) covalent geometry : angle 0.52270 / 0.27 (52837) hydrogen bonds : bond 0.04037 / 2.67 ( 2183) hydrogen bonds : angle 4.23589 / 3.06 ( 6387) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 244 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: p 131 LYS cc_start: 0.1414 (mmtt) cc_final: 0.1025 (mmtt) REVERT: D 108 VAL cc_start: 0.7691 (OUTLIER) cc_final: 0.7460 (t) REVERT: d 172 MET cc_start: 0.4438 (OUTLIER) cc_final: 0.4048 (pmm) REVERT: d 225 TYR cc_start: 0.5517 (t80) cc_final: 0.4651 (t80) REVERT: e 1 MET cc_start: 0.3963 (OUTLIER) cc_final: 0.3616 (ptt) REVERT: e 12 ARG cc_start: 0.8267 (ptt90) cc_final: 0.7974 (ptm-80) REVERT: e 50 LEU cc_start: 0.7258 (mt) cc_final: 0.6700 (tt) REVERT: e 79 GLN cc_start: 0.8103 (tp-100) cc_final: 0.6915 (pm20) REVERT: F 26 MET cc_start: 0.6108 (mmp) cc_final: 0.5778 (tpt) REVERT: F 48 LYS cc_start: 0.0392 (OUTLIER) cc_final: 0.0143 (ttmt) REVERT: F 57 PHE cc_start: -0.1599 (OUTLIER) cc_final: -0.2976 (m-80) REVERT: I 60 MET cc_start: 0.3045 (tpp) cc_final: 0.2836 (tpp) REVERT: J 57 PHE cc_start: 0.6950 (m-80) cc_final: 0.6516 (m-80) REVERT: N 37 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8134 (mm-30) REVERT: O 34 TYR cc_start: 0.7188 (m-80) cc_final: 0.6852 (m-80) REVERT: P 60 MET cc_start: 0.1419 (pmm) cc_final: 0.0983 (ptp) REVERT: R 59 PHE cc_start: 0.6067 (t80) cc_final: 0.5563 (t80) REVERT: R 60 MET cc_start: 0.4644 (mmt) cc_final: 0.3400 (mmt) REVERT: R 66 TYR cc_start: 0.1997 (OUTLIER) cc_final: 0.0576 (m-10) REVERT: S 28 GLN cc_start: 0.6735 (mt0) cc_final: 0.6466 (mt0) REVERT: A 324 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7519 (tt0) REVERT: E 61 ASP cc_start: 0.8642 (OUTLIER) cc_final: 0.8402 (p0) REVERT: E 69 MET cc_start: 0.9125 (OUTLIER) cc_final: 0.7711 (mmt) REVERT: E 480 LEU cc_start: 0.6654 (OUTLIER) cc_final: 0.6424 (tt) REVERT: T 228 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.7772 (mt0) REVERT: U 69 MET cc_start: 0.9056 (OUTLIER) cc_final: 0.8698 (mmt) REVERT: U 228 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8279 (mp10) REVERT: V 366 ARG cc_start: 0.7891 (mmm160) cc_final: 0.7602 (tpt-90) REVERT: V 464 TYR cc_start: 0.8245 (t80) cc_final: 0.7958 (t80) outliers start: 102 outliers final: 70 residues processed: 323 average time/residue: 0.2114 time to fit residues: 116.1908 Evaluate side-chains 319 residues out of total 3970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 235 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 107 THR Chi-restraints excluded: chain p residue 208 ASP Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain d residue 161 ILE Chi-restraints excluded: chain d residue 172 MET Chi-restraints excluded: chain b residue 121 LEU Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 40 ILE Chi-restraints excluded: chain e residue 41 ILE Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 69 MET Chi-restraints excluded: chain e residue 82 ILE Chi-restraints excluded: chain e residue 115 VAL Chi-restraints excluded: chain e residue 123 PHE Chi-restraints excluded: chain e residue 135 VAL Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 34 TYR Chi-restraints excluded: chain F residue 48 LYS Chi-restraints excluded: chain F residue 57 PHE Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 41 ARG Chi-restraints excluded: chain I residue 42 GLN Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain L residue 44 GLU Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain N residue 39 ILE Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain P residue 15 LEU Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 66 TYR Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 69 MET Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 263 ASP Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 352 TYR Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain T residue 10 MET Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 116 VAL Chi-restraints excluded: chain T residue 145 VAL Chi-restraints excluded: chain T residue 228 GLN Chi-restraints excluded: chain T residue 258 VAL Chi-restraints excluded: chain U residue 69 MET Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 228 GLN Chi-restraints excluded: chain U residue 258 VAL Chi-restraints excluded: chain U residue 352 TYR Chi-restraints excluded: chain V residue 100 VAL Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain V residue 149 THR Chi-restraints excluded: chain V residue 234 THR Chi-restraints excluded: chain V residue 342 GLN Chi-restraints excluded: chain V residue 385 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 461 optimal weight: 0.9990 chunk 325 optimal weight: 0.3980 chunk 393 optimal weight: 0.6980 chunk 311 optimal weight: 8.9990 chunk 128 optimal weight: 8.9990 chunk 44 optimal weight: 9.9990 chunk 493 optimal weight: 0.9980 chunk 451 optimal weight: 1.9990 chunk 472 optimal weight: 4.9990 chunk 421 optimal weight: 1.9990 chunk 231 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 90 ASN b 30 ASN e 108 ASN ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.152881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.096902 restraints weight = 75722.847| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 3.34 r_work: 0.3193 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 38973 Z= 0.111 Angle : 0.519 12.150 52837 Z= 0.266 Chirality : 0.041 0.199 6248 Planarity : 0.004 0.061 6787 Dihedral : 6.776 89.337 5667 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.42 % Allowed : 14.69 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.12), residues: 5056 helix: 1.27 (0.10), residues: 2694 sheet: 0.13 (0.22), residues: 617 loop : -0.85 (0.15), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG p 124 TYR 0.022 0.001 TYR a 149 PHE 0.031 0.001 PHE e 72 TRP 0.007 0.001 TRP T 368 HIS 0.004 0.000 HIS e 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (38973) covalent geometry : angle 0.51896 / 0.27 (52837) hydrogen bonds : bond 0.03879 / 2.56 ( 2183) hydrogen bonds : angle 4.17308 / 3.01 ( 6387) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 240 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: p 131 LYS cc_start: 0.1629 (mmtt) cc_final: 0.1115 (mmtt) REVERT: D 108 VAL cc_start: 0.7716 (OUTLIER) cc_final: 0.7476 (t) REVERT: d 225 TYR cc_start: 0.5505 (t80) cc_final: 0.4623 (t80) REVERT: e 1 MET cc_start: 0.4073 (OUTLIER) cc_final: 0.3837 (ptt) REVERT: e 12 ARG cc_start: 0.8221 (ptt90) cc_final: 0.7931 (ptm-80) REVERT: e 50 LEU cc_start: 0.7421 (mt) cc_final: 0.6880 (tt) REVERT: e 79 GLN cc_start: 0.8245 (tp-100) cc_final: 0.6973 (pm20) REVERT: F 26 MET cc_start: 0.6015 (mmp) cc_final: 0.5534 (tpt) REVERT: F 48 LYS cc_start: 0.0353 (OUTLIER) cc_final: 0.0057 (ttmt) REVERT: F 57 PHE cc_start: -0.1683 (OUTLIER) cc_final: -0.3134 (m-80) REVERT: G 41 ARG cc_start: 0.4513 (OUTLIER) cc_final: 0.4005 (ptm-80) REVERT: I 60 MET cc_start: 0.3374 (tpp) cc_final: 0.3120 (tpt) REVERT: J 57 PHE cc_start: 0.7084 (m-80) cc_final: 0.6796 (m-80) REVERT: N 26 MET cc_start: 0.7016 (mmp) cc_final: 0.6464 (mtt) REVERT: N 37 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8176 (mm-30) REVERT: N 48 LYS cc_start: 0.5633 (mttp) cc_final: 0.5117 (pttt) REVERT: O 34 TYR cc_start: 0.7050 (m-80) cc_final: 0.6754 (m-80) REVERT: P 48 LYS cc_start: 0.5001 (OUTLIER) cc_final: 0.3829 (mmtt) REVERT: P 60 MET cc_start: 0.1487 (pmm) cc_final: 0.1065 (ptp) REVERT: R 59 PHE cc_start: 0.6312 (t80) cc_final: 0.5767 (t80) REVERT: R 60 MET cc_start: 0.4377 (mmt) cc_final: 0.3345 (mmt) REVERT: R 66 TYR cc_start: 0.1972 (OUTLIER) cc_final: 0.0564 (m-10) REVERT: A 237 TYR cc_start: 0.8960 (OUTLIER) cc_final: 0.8433 (t80) REVERT: A 324 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7557 (tt0) REVERT: E 61 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8346 (p0) REVERT: E 69 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.7651 (mmt) REVERT: E 480 LEU cc_start: 0.6650 (OUTLIER) cc_final: 0.6438 (tt) REVERT: T 228 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7751 (mt0) REVERT: U 69 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8690 (mmt) REVERT: U 228 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8253 (mp10) REVERT: V 366 ARG cc_start: 0.7833 (mmm160) cc_final: 0.7571 (tpt-90) REVERT: V 464 TYR cc_start: 0.8357 (t80) cc_final: 0.8107 (t80) outliers start: 96 outliers final: 71 residues processed: 316 average time/residue: 0.2122 time to fit residues: 114.9093 Evaluate side-chains 321 residues out of total 3970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 234 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 107 THR Chi-restraints excluded: chain p residue 208 ASP Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain d residue 161 ILE Chi-restraints excluded: chain b residue 121 LEU Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 40 ILE Chi-restraints excluded: chain e residue 41 ILE Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 74 LEU Chi-restraints excluded: chain e residue 82 ILE Chi-restraints excluded: chain e residue 115 VAL Chi-restraints excluded: chain e residue 135 VAL Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 34 TYR Chi-restraints excluded: chain F residue 48 LYS Chi-restraints excluded: chain F residue 57 PHE Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 41 ARG Chi-restraints excluded: chain I residue 42 GLN Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain L residue 44 GLU Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain N residue 39 ILE Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain P residue 15 LEU Chi-restraints excluded: chain P residue 48 LYS Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 66 TYR Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 69 MET Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 352 TYR Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 116 VAL Chi-restraints excluded: chain T residue 145 VAL Chi-restraints excluded: chain T residue 228 GLN Chi-restraints excluded: chain T residue 258 VAL Chi-restraints excluded: chain U residue 10 MET Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain U residue 69 MET Chi-restraints excluded: chain U residue 228 GLN Chi-restraints excluded: chain U residue 258 VAL Chi-restraints excluded: chain U residue 352 TYR Chi-restraints excluded: chain V residue 100 VAL Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain V residue 149 THR Chi-restraints excluded: chain V residue 234 THR Chi-restraints excluded: chain V residue 274 MET Chi-restraints excluded: chain V residue 342 GLN Chi-restraints excluded: chain V residue 385 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 254 optimal weight: 2.9990 chunk 85 optimal weight: 20.0000 chunk 14 optimal weight: 0.4980 chunk 57 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 439 optimal weight: 7.9990 chunk 361 optimal weight: 5.9990 chunk 474 optimal weight: 3.9990 chunk 356 optimal weight: 5.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 30 ASN ** b 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 4 GLN e 79 GLN e 108 ASN ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.158454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.101969 restraints weight = 75813.762| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 3.36 r_work: 0.3097 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 38973 Z= 0.213 Angle : 0.608 11.401 52837 Z= 0.312 Chirality : 0.044 0.272 6248 Planarity : 0.005 0.060 6787 Dihedral : 7.173 88.263 5667 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.82 % Allowed : 14.43 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.12), residues: 5056 helix: 1.13 (0.10), residues: 2699 sheet: -0.04 (0.22), residues: 611 loop : -1.01 (0.15), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 77 TYR 0.047 0.001 TYR e 125 PHE 0.030 0.002 PHE e 72 TRP 0.006 0.001 TRP a 95 HIS 0.004 0.001 HIS e 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.21 (38973) covalent geometry : angle 0.60761 / 0.31 (52837) hydrogen bonds : bond 0.04739 / 3.13 ( 2183) hydrogen bonds : angle 4.41683 / 3.19 ( 6387) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 230 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: p 131 LYS cc_start: 0.1493 (mmtt) cc_final: 0.1020 (mmtt) REVERT: p 158 MET cc_start: -0.0763 (ttm) cc_final: -0.0977 (ttm) REVERT: D 108 VAL cc_start: 0.7720 (OUTLIER) cc_final: 0.7485 (t) REVERT: d 225 TYR cc_start: 0.5528 (t80) cc_final: 0.4603 (t80) REVERT: e 1 MET cc_start: 0.4221 (OUTLIER) cc_final: 0.3880 (ptt) REVERT: e 12 ARG cc_start: 0.8224 (ptt90) cc_final: 0.7908 (ptm-80) REVERT: e 50 LEU cc_start: 0.7462 (mt) cc_final: 0.6888 (tt) REVERT: e 79 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7001 (pm20) REVERT: F 26 MET cc_start: 0.5983 (mmp) cc_final: 0.5537 (mmt) REVERT: F 48 LYS cc_start: 0.0424 (OUTLIER) cc_final: 0.0167 (ttmt) REVERT: F 57 PHE cc_start: -0.2144 (OUTLIER) cc_final: -0.3384 (m-80) REVERT: J 57 PHE cc_start: 0.6947 (m-80) cc_final: 0.6500 (m-80) REVERT: L 60 MET cc_start: 0.3625 (mmt) cc_final: 0.2231 (mmt) REVERT: N 26 MET cc_start: 0.7286 (mmp) cc_final: 0.6814 (mtt) REVERT: N 37 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8127 (mm-30) REVERT: O 34 TYR cc_start: 0.7153 (m-80) cc_final: 0.6901 (m-80) REVERT: P 60 MET cc_start: 0.1490 (pmm) cc_final: 0.1056 (ptp) REVERT: R 46 GLU cc_start: 0.6494 (mt-10) cc_final: 0.6106 (mt-10) REVERT: R 59 PHE cc_start: 0.6421 (t80) cc_final: 0.5787 (t80) REVERT: R 60 MET cc_start: 0.4500 (mmt) cc_final: 0.3534 (mmt) REVERT: R 66 TYR cc_start: 0.1809 (OUTLIER) cc_final: 0.0560 (m-10) REVERT: A 237 TYR cc_start: 0.9041 (OUTLIER) cc_final: 0.8304 (t80) REVERT: A 324 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7702 (tt0) REVERT: E 8 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.7063 (mmtm) REVERT: E 61 ASP cc_start: 0.8741 (OUTLIER) cc_final: 0.8335 (p0) REVERT: E 69 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.7667 (mmt) REVERT: U 69 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.8714 (mmt) REVERT: U 228 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8382 (mp10) REVERT: V 366 ARG cc_start: 0.7922 (mmm160) cc_final: 0.7621 (tpt-90) outliers start: 112 outliers final: 84 residues processed: 318 average time/residue: 0.2012 time to fit residues: 108.7408 Evaluate side-chains 321 residues out of total 3970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 223 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 211 LEU Chi-restraints excluded: chain p residue 107 THR Chi-restraints excluded: chain p residue 208 ASP Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain b residue 121 LEU Chi-restraints excluded: chain b residue 148 ILE Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 4 GLN Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 40 ILE Chi-restraints excluded: chain e residue 41 ILE Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 74 LEU Chi-restraints excluded: chain e residue 79 GLN Chi-restraints excluded: chain e residue 81 THR Chi-restraints excluded: chain e residue 82 ILE Chi-restraints excluded: chain e residue 115 VAL Chi-restraints excluded: chain e residue 123 PHE Chi-restraints excluded: chain e residue 135 VAL Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 48 LYS Chi-restraints excluded: chain F residue 57 PHE Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain H residue 57 PHE Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain L residue 44 GLU Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain N residue 39 ILE Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain P residue 15 LEU Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 48 LYS Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 66 TYR Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 69 MET Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 263 ASP Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 352 TYR Chi-restraints excluded: chain T residue 10 MET Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 108 VAL Chi-restraints excluded: chain T residue 116 VAL Chi-restraints excluded: chain T residue 145 VAL Chi-restraints excluded: chain T residue 172 ILE Chi-restraints excluded: chain T residue 228 GLN Chi-restraints excluded: chain T residue 258 VAL Chi-restraints excluded: chain U residue 10 MET Chi-restraints excluded: chain U residue 69 MET Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 228 GLN Chi-restraints excluded: chain U residue 258 VAL Chi-restraints excluded: chain U residue 276 SER Chi-restraints excluded: chain U residue 352 TYR Chi-restraints excluded: chain V residue 43 TYR Chi-restraints excluded: chain V residue 100 VAL Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain V residue 149 THR Chi-restraints excluded: chain V residue 234 THR Chi-restraints excluded: chain V residue 274 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 157 optimal weight: 0.8980 chunk 454 optimal weight: 3.9990 chunk 214 optimal weight: 0.9990 chunk 394 optimal weight: 1.9990 chunk 289 optimal weight: 0.9990 chunk 322 optimal weight: 0.9980 chunk 354 optimal weight: 4.9990 chunk 185 optimal weight: 20.0000 chunk 392 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 355 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 30 ASN ** b 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 28 GLN ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.158629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.102651 restraints weight = 75678.267| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 3.24 r_work: 0.3119 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.152 38973 Z= 0.192 Angle : 0.767 59.187 52837 Z= 0.425 Chirality : 0.042 0.340 6248 Planarity : 0.005 0.061 6787 Dihedral : 7.175 88.479 5667 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.62 % Allowed : 14.71 % Favored : 82.67 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.12), residues: 5056 helix: 1.13 (0.10), residues: 2699 sheet: -0.07 (0.22), residues: 611 loop : -1.01 (0.15), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.039 0.000 ARG S 41 TYR 0.058 0.001 TYR e 125 PHE 0.027 0.001 PHE e 72 TRP 0.005 0.001 TRP a 95 HIS 0.005 0.001 HIS e 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (38973) covalent geometry : angle 0.76710 / 0.42 (52837) hydrogen bonds : bond 0.04618 / 3.05 ( 2183) hydrogen bonds : angle 4.41483 / 3.19 ( 6387) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 223 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: p 131 LYS cc_start: 0.1410 (mmtt) cc_final: 0.0989 (mmtt) REVERT: p 158 MET cc_start: -0.0758 (ttm) cc_final: -0.0971 (ttm) REVERT: D 108 VAL cc_start: 0.7696 (OUTLIER) cc_final: 0.7446 (t) REVERT: d 225 TYR cc_start: 0.5480 (t80) cc_final: 0.4599 (t80) REVERT: e 1 MET cc_start: 0.4242 (OUTLIER) cc_final: 0.3739 (ptt) REVERT: e 12 ARG cc_start: 0.8234 (ptt90) cc_final: 0.7917 (ptm-80) REVERT: e 50 LEU cc_start: 0.7407 (mt) cc_final: 0.6807 (tt) REVERT: F 26 MET cc_start: 0.5981 (mmp) cc_final: 0.5636 (mmt) REVERT: F 48 LYS cc_start: 0.0433 (OUTLIER) cc_final: 0.0183 (ttmt) REVERT: F 57 PHE cc_start: -0.2116 (OUTLIER) cc_final: -0.3360 (m-80) REVERT: J 57 PHE cc_start: 0.7057 (m-80) cc_final: 0.6519 (m-80) REVERT: L 60 MET cc_start: 0.3622 (mmt) cc_final: 0.2215 (mmt) REVERT: N 26 MET cc_start: 0.7361 (mmp) cc_final: 0.6881 (mtt) REVERT: N 37 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8146 (mm-30) REVERT: O 34 TYR cc_start: 0.7163 (m-80) cc_final: 0.6907 (m-80) REVERT: P 60 MET cc_start: 0.1450 (pmm) cc_final: 0.1011 (ptp) REVERT: R 46 GLU cc_start: 0.6514 (mt-10) cc_final: 0.6102 (mt-10) REVERT: R 59 PHE cc_start: 0.6380 (t80) cc_final: 0.5758 (t80) REVERT: R 60 MET cc_start: 0.4495 (mmt) cc_final: 0.3580 (mmt) REVERT: R 66 TYR cc_start: 0.1836 (OUTLIER) cc_final: 0.0613 (m-10) REVERT: E 8 LYS cc_start: 0.7360 (OUTLIER) cc_final: 0.6993 (mmtm) REVERT: E 61 ASP cc_start: 0.8717 (OUTLIER) cc_final: 0.8341 (p0) REVERT: E 69 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.7665 (mmt) REVERT: U 69 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.8650 (mmt) REVERT: U 228 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8352 (mp10) REVERT: V 366 ARG cc_start: 0.7923 (mmm160) cc_final: 0.7615 (tpt-90) outliers start: 104 outliers final: 85 residues processed: 305 average time/residue: 0.2100 time to fit residues: 110.0369 Evaluate side-chains 317 residues out of total 3970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 221 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 211 LEU Chi-restraints excluded: chain p residue 107 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain d residue 161 ILE Chi-restraints excluded: chain b residue 121 LEU Chi-restraints excluded: chain b residue 148 ILE Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 40 ILE Chi-restraints excluded: chain e residue 41 ILE Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 74 LEU Chi-restraints excluded: chain e residue 81 THR Chi-restraints excluded: chain e residue 82 ILE Chi-restraints excluded: chain e residue 115 VAL Chi-restraints excluded: chain e residue 123 PHE Chi-restraints excluded: chain e residue 135 VAL Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 48 LYS Chi-restraints excluded: chain F residue 57 PHE Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain H residue 57 PHE Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain L residue 44 GLU Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain N residue 39 ILE Chi-restraints excluded: chain O residue 36 VAL Chi-restraints excluded: chain P residue 15 LEU Chi-restraints excluded: chain P residue 68 LEU Chi-restraints excluded: chain Q residue 64 THR Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain R residue 66 TYR Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 69 MET Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 263 ASP Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 352 TYR Chi-restraints excluded: chain E residue 440 SER Chi-restraints excluded: chain T residue 10 MET Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 108 VAL Chi-restraints excluded: chain T residue 116 VAL Chi-restraints excluded: chain T residue 145 VAL Chi-restraints excluded: chain T residue 172 ILE Chi-restraints excluded: chain T residue 228 GLN Chi-restraints excluded: chain T residue 258 VAL Chi-restraints excluded: chain U residue 10 MET Chi-restraints excluded: chain U residue 64 VAL Chi-restraints excluded: chain U residue 69 MET Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 228 GLN Chi-restraints excluded: chain U residue 258 VAL Chi-restraints excluded: chain U residue 276 SER Chi-restraints excluded: chain U residue 352 TYR Chi-restraints excluded: chain V residue 43 TYR Chi-restraints excluded: chain V residue 100 VAL Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain V residue 149 THR Chi-restraints excluded: chain V residue 234 THR Chi-restraints excluded: chain V residue 274 MET Chi-restraints excluded: chain V residue 432 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 308 optimal weight: 1.9990 chunk 291 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 354 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 275 optimal weight: 0.7980 chunk 13 optimal weight: 7.9990 chunk 327 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 30 ASN ** b 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.158608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.102616 restraints weight = 75719.807| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 3.45 r_work: 0.3106 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.152 38973 Z= 0.192 Angle : 0.767 59.187 52837 Z= 0.425 Chirality : 0.042 0.340 6248 Planarity : 0.005 0.061 6787 Dihedral : 7.175 88.479 5667 Min Nonbonded Distance : 1.254 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.44 % Allowed : 14.91 % Favored : 82.64 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.12), residues: 5056 helix: 1.13 (0.10), residues: 2699 sheet: -0.07 (0.22), residues: 611 loop : -1.01 (0.15), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.039 0.000 ARG S 41 TYR 0.058 0.001 TYR e 125 PHE 0.027 0.001 PHE e 72 TRP 0.005 0.001 TRP a 95 HIS 0.005 0.001 HIS e 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (38973) covalent geometry : angle 0.76709 / 0.42 (52837) hydrogen bonds : bond 0.04618 / 3.05 ( 2183) hydrogen bonds : angle 4.41483 / 3.19 ( 6387) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11503.55 seconds wall clock time: 196 minutes 53.30 seconds (11813.30 seconds total)