Starting phenix.real_space_refine on Mon Aug 25 20:49:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qcf_18329/08_2025/8qcf_18329.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qcf_18329/08_2025/8qcf_18329.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qcf_18329/08_2025/8qcf_18329.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qcf_18329/08_2025/8qcf_18329.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qcf_18329/08_2025/8qcf_18329.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qcf_18329/08_2025/8qcf_18329.map" } resolution = 2.55 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= 0.008 sd= 0.156 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 37 5.49 5 S 150 5.16 5 C 19380 2.51 5 N 5220 2.21 5 O 5964 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30751 Number of models: 1 Model: "" Number of chains: 14 Chain: "B" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2261 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 10, 'TRANS': 286} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1881 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 233} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2358 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 13, 'TRANS': 291} Chain breaks: 5 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1691 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 211} Chain: "F" Number of atoms: 1998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1998 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 248} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1581 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 203} Chain breaks: 2 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'HIS:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 27 Chain: "H" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1765 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 2084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2084 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 8, 'TRANS': 259} Chain breaks: 2 Chain: "J" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1689 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 214} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 7231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 915, 7231 Classifications: {'peptide': 915} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 867} Chain breaks: 6 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 49 Chain: "L" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 618 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 5050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 5050 Classifications: {'peptide': 657} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 27, 'TRANS': 629} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 283 Unresolved non-hydrogen angles: 341 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 6, 'ASN:plan1': 4, 'GLN:plan1': 6, 'ARG:plan': 7, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 141 Chain: "N" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 513 Classifications: {'RNA': 34} Modifications used: {'rna2p_pyr': 2, 'rna3p_pyr': 32} Link IDs: {'rna2p': 2, 'rna3p': 31} Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 292 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {' U%rna3p_pyr:plan': 21} Unresolved non-hydrogen planarities: 167 Chain: "M" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.31, per 1000 atoms: 0.21 Number of scatterers: 30751 At special positions: 0 Unit cell: (145.555, 131.936, 196.627, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 150 16.00 P 37 15.00 O 5964 8.00 N 5220 7.00 C 19380 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 476.8 nanoseconds 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7390 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 43 sheets defined 36.3% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'B' and resid 8 through 21 Processing helix chain 'B' and resid 84 through 88 Processing helix chain 'B' and resid 98 through 113 Processing helix chain 'B' and resid 119 through 122 removed outlier: 3.524A pdb=" N GLY B 122 " --> pdb=" O ASP B 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 119 through 122' Processing helix chain 'B' and resid 146 through 162 Processing helix chain 'B' and resid 178 through 183 removed outlier: 3.530A pdb=" N ARG B 182 " --> pdb=" O PRO B 178 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU B 183 " --> pdb=" O VAL B 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 178 through 183' Processing helix chain 'B' and resid 205 through 212 Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 258 through 297 removed outlier: 3.960A pdb=" N TYR B 269 " --> pdb=" O CYS B 265 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N SER B 270 " --> pdb=" O HIS B 266 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE B 271 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS B 274 " --> pdb=" O SER B 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 110 removed outlier: 4.301A pdb=" N LYS C 110 " --> pdb=" O ARG C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'C' and resid 134 through 150 removed outlier: 3.676A pdb=" N SER C 138 " --> pdb=" O GLY C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 180 Processing helix chain 'C' and resid 209 through 243 removed outlier: 4.142A pdb=" N VAL C 213 " --> pdb=" O ARG C 209 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN C 242 " --> pdb=" O LYS C 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 26 Processing helix chain 'D' and resid 26 through 37 removed outlier: 3.888A pdb=" N LEU D 37 " --> pdb=" O ARG D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 127 removed outlier: 3.626A pdb=" N TYR D 127 " --> pdb=" O ILE D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 162 Processing helix chain 'D' and resid 166 through 171 removed outlier: 3.794A pdb=" N LYS D 171 " --> pdb=" O LYS D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 239 removed outlier: 3.714A pdb=" N GLN D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 291 removed outlier: 3.931A pdb=" N ILE D 291 " --> pdb=" O ALA D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 307 removed outlier: 3.613A pdb=" N GLN D 307 " --> pdb=" O PRO D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 343 removed outlier: 4.230A pdb=" N GLU D 339 " --> pdb=" O ASP D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 390 removed outlier: 3.543A pdb=" N THR D 390 " --> pdb=" O ASP D 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 75 removed outlier: 3.606A pdb=" N LYS E 64 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL E 65 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU E 66 " --> pdb=" O ARG E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'E' and resid 105 through 124 Processing helix chain 'E' and resid 150 through 155 removed outlier: 3.675A pdb=" N LYS E 155 " --> pdb=" O ALA E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 218 removed outlier: 3.594A pdb=" N GLU E 196 " --> pdb=" O PHE E 192 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN E 200 " --> pdb=" O GLU E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 221 No H-bonds generated for 'chain 'E' and resid 219 through 221' Processing helix chain 'F' and resid 4 through 16 Processing helix chain 'F' and resid 89 through 103 Processing helix chain 'F' and resid 110 through 113 removed outlier: 3.718A pdb=" N LYS F 113 " --> pdb=" O ASP F 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 110 through 113' Processing helix chain 'F' and resid 137 through 150 removed outlier: 3.519A pdb=" N ILE F 141 " --> pdb=" O PRO F 137 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN F 150 " --> pdb=" O TYR F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 207 removed outlier: 3.537A pdb=" N GLU F 207 " --> pdb=" O ALA F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 262 removed outlier: 3.876A pdb=" N LYS F 245 " --> pdb=" O PRO F 241 " (cutoff:3.500A) Proline residue: F 256 - end of helix Processing helix chain 'G' and resid 106 through 122 Processing helix chain 'G' and resid 126 through 130 Processing helix chain 'G' and resid 165 through 167 No H-bonds generated for 'chain 'G' and resid 165 through 167' Processing helix chain 'G' and resid 168 through 184 Processing helix chain 'G' and resid 223 through 248 removed outlier: 3.724A pdb=" N ARG G 236 " --> pdb=" O GLU G 232 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 169 Processing helix chain 'H' and resid 173 through 180 Processing helix chain 'H' and resid 200 through 217 Processing helix chain 'H' and resid 219 through 221 No H-bonds generated for 'chain 'H' and resid 219 through 221' Processing helix chain 'H' and resid 222 through 234 removed outlier: 3.566A pdb=" N ILE H 234 " --> pdb=" O GLN H 230 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 141 No H-bonds generated for 'chain 'I' and resid 139 through 141' Processing helix chain 'I' and resid 158 through 162 Processing helix chain 'I' and resid 203 through 207 Processing helix chain 'I' and resid 237 through 244 removed outlier: 3.702A pdb=" N ASP I 244 " --> pdb=" O ASP I 240 " (cutoff:3.500A) Processing helix chain 'I' and resid 277 through 282 removed outlier: 4.007A pdb=" N ILE I 280 " --> pdb=" O SER I 277 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR I 281 " --> pdb=" O TRP I 278 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 310 Processing helix chain 'I' and resid 315 through 326 Processing helix chain 'I' and resid 327 through 329 No H-bonds generated for 'chain 'I' and resid 327 through 329' Processing helix chain 'I' and resid 331 through 336 removed outlier: 3.806A pdb=" N ILE I 336 " --> pdb=" O GLY I 333 " (cutoff:3.500A) Processing helix chain 'I' and resid 337 through 354 Processing helix chain 'J' and resid 183 through 188 removed outlier: 3.532A pdb=" N ALA J 186 " --> pdb=" O SER J 183 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE J 188 " --> pdb=" O ALA J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 189 through 193 removed outlier: 3.590A pdb=" N GLN J 192 " --> pdb=" O SER J 189 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA J 193 " --> pdb=" O VAL J 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 189 through 193' Processing helix chain 'J' and resid 208 through 210 No H-bonds generated for 'chain 'J' and resid 208 through 210' Processing helix chain 'J' and resid 219 through 223 Processing helix chain 'K' and resid 54 through 58 removed outlier: 3.628A pdb=" N GLN K 57 " --> pdb=" O LYS K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 98 Processing helix chain 'K' and resid 115 through 125 Processing helix chain 'K' and resid 125 through 138 Processing helix chain 'K' and resid 165 through 185 Processing helix chain 'K' and resid 186 through 189 Processing helix chain 'K' and resid 217 through 224 removed outlier: 3.631A pdb=" N LEU K 224 " --> pdb=" O GLN K 220 " (cutoff:3.500A) Processing helix chain 'K' and resid 227 through 232 removed outlier: 3.737A pdb=" N ILE K 231 " --> pdb=" O ASN K 227 " (cutoff:3.500A) Processing helix chain 'K' and resid 233 through 235 No H-bonds generated for 'chain 'K' and resid 233 through 235' Processing helix chain 'K' and resid 260 through 270 Processing helix chain 'K' and resid 322 through 326 Processing helix chain 'K' and resid 366 through 382 removed outlier: 4.394A pdb=" N ARG K 382 " --> pdb=" O MET K 378 " (cutoff:3.500A) Processing helix chain 'K' and resid 483 through 488 Processing helix chain 'K' and resid 496 through 502 removed outlier: 3.752A pdb=" N CYS K 502 " --> pdb=" O LYS K 498 " (cutoff:3.500A) Processing helix chain 'K' and resid 506 through 510 removed outlier: 3.691A pdb=" N TRP K 510 " --> pdb=" O GLY K 507 " (cutoff:3.500A) Processing helix chain 'K' and resid 518 through 525 Processing helix chain 'K' and resid 573 through 576 Processing helix chain 'K' and resid 581 through 590 Processing helix chain 'K' and resid 605 through 610 Processing helix chain 'K' and resid 653 through 663 Processing helix chain 'K' and resid 668 through 692 removed outlier: 3.678A pdb=" N MET K 672 " --> pdb=" O ASP K 668 " (cutoff:3.500A) Processing helix chain 'K' and resid 723 through 746 removed outlier: 3.571A pdb=" N VAL K 727 " --> pdb=" O THR K 723 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU K 728 " --> pdb=" O ASN K 724 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU K 729 " --> pdb=" O SER K 725 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE K 730 " --> pdb=" O LEU K 726 " (cutoff:3.500A) Processing helix chain 'K' and resid 760 through 773 removed outlier: 3.716A pdb=" N LEU K 766 " --> pdb=" O ASN K 762 " (cutoff:3.500A) Processing helix chain 'K' and resid 782 through 793 removed outlier: 3.712A pdb=" N CYS K 793 " --> pdb=" O SER K 789 " (cutoff:3.500A) Processing helix chain 'K' and resid 799 through 810 removed outlier: 4.178A pdb=" N THR K 803 " --> pdb=" O PRO K 799 " (cutoff:3.500A) Processing helix chain 'K' and resid 825 through 830 removed outlier: 3.686A pdb=" N ARG K 830 " --> pdb=" O PRO K 827 " (cutoff:3.500A) Processing helix chain 'K' and resid 848 through 861 removed outlier: 3.587A pdb=" N VAL K 852 " --> pdb=" O ARG K 848 " (cutoff:3.500A) Processing helix chain 'K' and resid 869 through 872 Processing helix chain 'K' and resid 873 through 910 removed outlier: 3.958A pdb=" N ASN K 910 " --> pdb=" O VAL K 906 " (cutoff:3.500A) Processing helix chain 'K' and resid 941 through 945 Processing helix chain 'K' and resid 947 through 951 Processing helix chain 'L' and resid 120 through 132 Processing helix chain 'L' and resid 149 through 156 Processing helix chain 'L' and resid 178 through 182 Processing helix chain 'L' and resid 196 through 207 removed outlier: 3.756A pdb=" N PHE L 207 " --> pdb=" O ALA L 203 " (cutoff:3.500A) Processing helix chain 'L' and resid 211 through 220 removed outlier: 3.565A pdb=" N ILE L 216 " --> pdb=" O PRO L 212 " (cutoff:3.500A) Processing helix chain 'M' and resid 315 through 319 Processing helix chain 'M' and resid 331 through 342 Processing helix chain 'M' and resid 357 through 372 removed outlier: 4.062A pdb=" N ALA M 361 " --> pdb=" O LYS M 357 " (cutoff:3.500A) Processing helix chain 'M' and resid 381 through 396 removed outlier: 3.852A pdb=" N SER M 385 " --> pdb=" O ILE M 381 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASN M 386 " --> pdb=" O LYS M 382 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN M 387 " --> pdb=" O ALA M 383 " (cutoff:3.500A) Processing helix chain 'M' and resid 421 through 431 Processing helix chain 'M' and resid 432 through 436 removed outlier: 3.669A pdb=" N ILE M 435 " --> pdb=" O ALA M 432 " (cutoff:3.500A) Processing helix chain 'M' and resid 445 through 449 Processing helix chain 'M' and resid 452 through 465 removed outlier: 3.887A pdb=" N VAL M 456 " --> pdb=" O GLN M 452 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL M 457 " --> pdb=" O ASP M 453 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TRP M 458 " --> pdb=" O ARG M 454 " (cutoff:3.500A) Processing helix chain 'M' and resid 481 through 492 removed outlier: 3.569A pdb=" N ALA M 485 " --> pdb=" O THR M 481 " (cutoff:3.500A) Processing helix chain 'M' and resid 529 through 540 removed outlier: 3.559A pdb=" N PHE M 533 " --> pdb=" O LEU M 529 " (cutoff:3.500A) Processing helix chain 'M' and resid 614 through 619 removed outlier: 3.570A pdb=" N ASN M 619 " --> pdb=" O PRO M 615 " (cutoff:3.500A) Processing helix chain 'M' and resid 619 through 624 removed outlier: 3.671A pdb=" N ARG M 624 " --> pdb=" O TYR M 620 " (cutoff:3.500A) Processing helix chain 'M' and resid 635 through 646 removed outlier: 3.520A pdb=" N CYS M 639 " --> pdb=" O SER M 635 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU M 640 " --> pdb=" O LYS M 636 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU M 646 " --> pdb=" O TYR M 642 " (cutoff:3.500A) Processing helix chain 'M' and resid 655 through 668 Processing helix chain 'M' and resid 669 through 671 No H-bonds generated for 'chain 'M' and resid 669 through 671' Processing helix chain 'M' and resid 672 through 676 removed outlier: 3.524A pdb=" N ARG M 676 " --> pdb=" O LYS M 673 " (cutoff:3.500A) Processing helix chain 'M' and resid 678 through 689 Processing helix chain 'M' and resid 700 through 713 Processing helix chain 'M' and resid 723 through 726 Processing helix chain 'M' and resid 753 through 762 Processing helix chain 'M' and resid 785 through 794 removed outlier: 3.534A pdb=" N PHE M 789 " --> pdb=" O SER M 785 " (cutoff:3.500A) Processing helix chain 'M' and resid 807 through 816 removed outlier: 3.771A pdb=" N ARG M 816 " --> pdb=" O LEU M 812 " (cutoff:3.500A) Processing helix chain 'M' and resid 822 through 827 removed outlier: 3.664A pdb=" N LYS M 827 " --> pdb=" O GLU M 823 " (cutoff:3.500A) Processing helix chain 'M' and resid 842 through 855 removed outlier: 3.635A pdb=" N LYS M 847 " --> pdb=" O PRO M 843 " (cutoff:3.500A) Processing helix chain 'M' and resid 865 through 872 Processing helix chain 'M' and resid 878 through 888 removed outlier: 3.603A pdb=" N LEU M 882 " --> pdb=" O TYR M 878 " (cutoff:3.500A) Processing helix chain 'M' and resid 895 through 903 Processing helix chain 'M' and resid 904 through 907 Processing helix chain 'M' and resid 925 through 945 Processing helix chain 'M' and resid 950 through 955 Processing helix chain 'M' and resid 964 through 974 Processing helix chain 'M' and resid 976 through 982 removed outlier: 3.655A pdb=" N GLU M 982 " --> pdb=" O LYS M 978 " (cutoff:3.500A) Processing helix chain 'M' and resid 987 through 1013 removed outlier: 3.547A pdb=" N ASP M 999 " --> pdb=" O ILE M 995 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLU M1000 " --> pdb=" O THR M 996 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE M1001 " --> pdb=" O TRP M 997 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE M1010 " --> pdb=" O LYS M1006 " (cutoff:3.500A) Processing helix chain 'M' and resid 1014 through 1028 removed outlier: 3.631A pdb=" N GLU M1026 " --> pdb=" O SER M1022 " (cutoff:3.500A) Processing helix chain 'M' and resid 1031 through 1035 removed outlier: 3.570A pdb=" N ALA M1035 " --> pdb=" O ILE M1032 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 37 through 40 removed outlier: 6.386A pdb=" N LYS B 55 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU B 76 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N ALA B 136 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL B 78 " --> pdb=" O ALA B 136 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N VAL B 138 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N SER B 80 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N PHE B 140 " --> pdb=" O SER B 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 37 through 40 removed outlier: 6.386A pdb=" N LYS B 55 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N TRP B 132 " --> pdb=" O CYS B 124 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N CYS B 124 " --> pdb=" O TRP B 132 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 163 through 164 Processing sheet with id=AA4, first strand: chain 'B' and resid 167 through 170 Processing sheet with id=AA5, first strand: chain 'B' and resid 218 through 221 removed outlier: 7.176A pdb=" N VAL B 234 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ALA B 251 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN B 247 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 11.052A pdb=" N GLY B 252 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 9.913A pdb=" N LEU C 200 " --> pdb=" O GLY B 252 " (cutoff:3.500A) removed outlier: 10.637A pdb=" N LEU B 254 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU C 198 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LYS C 195 " --> pdb=" O VAL C 190 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLY C 188 " --> pdb=" O SER C 197 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU C 199 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR C 186 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N VAL C 201 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N THR C 184 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER C 183 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 218 through 221 removed outlier: 7.176A pdb=" N VAL B 234 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ALA B 251 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN B 247 " --> pdb=" O THR B 238 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 25 through 29 removed outlier: 6.419A pdb=" N LYS C 48 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL C 121 " --> pdb=" O PRO C 56 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU C 71 " --> pdb=" O ILE C 122 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ILE C 124 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASN C 73 " --> pdb=" O ILE C 124 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ILE C 126 " --> pdb=" O ASN C 73 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N SER C 75 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL C 128 " --> pdb=" O SER C 75 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASN C 77 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N GLU C 130 " --> pdb=" O ASN C 77 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 52 through 56 removed outlier: 3.689A pdb=" N GLY D 76 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N TYR D 131 " --> pdb=" O ALA D 215 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ILE D 217 " --> pdb=" O TYR D 131 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL D 133 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N VAL D 219 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLU D 135 " --> pdb=" O VAL D 219 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 52 through 56 removed outlier: 3.689A pdb=" N GLY D 76 " --> pdb=" O ILE D 91 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 186 through 188 removed outlier: 3.518A pdb=" N VAL D 176 " --> pdb=" O LEU D 188 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N LEU D 243 " --> pdb=" O THR D 279 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N THR D 279 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ARG D 245 " --> pdb=" O ASP D 277 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 328 through 332 removed outlier: 4.637A pdb=" N SER D 345 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N THR D 346 " --> pdb=" O LEU D 362 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU D 362 " --> pdb=" O THR D 346 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N SER D 348 " --> pdb=" O LEU D 360 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU D 360 " --> pdb=" O SER D 348 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU D 350 " --> pdb=" O LYS D 358 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LYS D 358 " --> pdb=" O GLY E 184 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N LEU E 178 " --> pdb=" O GLY D 364 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLU E 166 " --> pdb=" O LYS E 175 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N VAL E 177 " --> pdb=" O ALA E 164 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ALA E 164 " --> pdb=" O VAL E 177 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU E 179 " --> pdb=" O THR E 162 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR E 162 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ASP E 181 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL E 160 " --> pdb=" O ASP E 181 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ASN E 183 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU E 158 " --> pdb=" O ASN E 183 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER E 159 " --> pdb=" O ILE E 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 3 through 7 removed outlier: 6.427A pdb=" N LYS E 25 " --> pdb=" O LEU E 95 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LEU E 87 " --> pdb=" O PRO E 33 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ALA E 47 " --> pdb=" O CYS E 88 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE E 90 " --> pdb=" O ALA E 47 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLU E 49 " --> pdb=" O ILE E 90 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N CYS E 92 " --> pdb=" O GLU E 49 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE E 51 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ILE E 94 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ARG E 53 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N GLU E 96 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 34 through 38 removed outlier: 3.567A pdb=" N GLY F 46 " --> pdb=" O ILE F 62 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLU F 57 " --> pdb=" O ILE F 131 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLN F 77 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N VAL F 128 " --> pdb=" O GLN F 77 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASP F 79 " --> pdb=" O VAL F 128 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N VAL F 130 " --> pdb=" O ASP F 79 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ASP F 81 " --> pdb=" O VAL F 130 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N SER F 132 " --> pdb=" O ASP F 81 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 34 through 38 removed outlier: 3.567A pdb=" N GLY F 46 " --> pdb=" O ILE F 62 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLU F 57 " --> pdb=" O ILE F 131 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU F 116 " --> pdb=" O TYR F 120 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 153 through 157 removed outlier: 3.907A pdb=" N LYS F 156 " --> pdb=" O ASP F 176 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ASP F 176 " --> pdb=" O LYS F 156 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 196 through 199 removed outlier: 3.619A pdb=" N SER F 216 " --> pdb=" O PRO F 225 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N SER F 218 " --> pdb=" O THR F 223 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N THR F 223 " --> pdb=" O SER F 218 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N PHE G 213 " --> pdb=" O SER F 228 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ILE G 210 " --> pdb=" O ILE G 204 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE G 204 " --> pdb=" O ILE G 210 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY G 212 " --> pdb=" O SER G 202 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 45 through 50 removed outlier: 3.533A pdb=" N GLY G 58 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLN G 70 " --> pdb=" O ASP G 144 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP G 144 " --> pdb=" O GLN G 70 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N SER G 72 " --> pdb=" O THR G 142 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLY G 134 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.849A pdb=" N THR H 3 " --> pdb=" O LEU H 42 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LYS H 20 " --> pdb=" O ALA H 55 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N ILE H 57 " --> pdb=" O LYS H 20 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 25 through 27 Processing sheet with id=AC2, first strand: chain 'H' and resid 148 through 150 removed outlier: 4.623A pdb=" N LEU H 118 " --> pdb=" O LEU H 150 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLU H 133 " --> pdb=" O CYS H 124 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N SER H 96 " --> pdb=" O ILE H 134 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N SER H 87 " --> pdb=" O ILE H 76 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ILE H 76 " --> pdb=" O SER H 87 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 154 through 157 removed outlier: 3.519A pdb=" N LYS H 193 " --> pdb=" O GLY H 189 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 54 through 55 removed outlier: 6.201A pdb=" N MET I 68 " --> pdb=" O LEU I 95 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N VAL I 97 " --> pdb=" O MET I 68 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 60 through 62 removed outlier: 6.961A pdb=" N THR I 80 " --> pdb=" O VAL I 61 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 192 through 193 removed outlier: 6.792A pdb=" N SER I 183 " --> pdb=" O GLN I 174 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL I 135 " --> pdb=" O LEU I 184 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ARG I 123 " --> pdb=" O VAL I 119 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N VAL I 119 " --> pdb=" O ARG I 123 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LYS I 125 " --> pdb=" O ALA I 117 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 197 through 201 removed outlier: 3.569A pdb=" N ILE I 221 " --> pdb=" O LEU I 217 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 10 through 11 Processing sheet with id=AC9, first strand: chain 'J' and resid 16 through 18 removed outlier: 6.603A pdb=" N ILE J 56 " --> pdb=" O ILE J 17 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA J 55 " --> pdb=" O ILE J 44 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 253 through 256 removed outlier: 6.932A pdb=" N ILE J 229 " --> pdb=" O VAL J 255 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TYR J 244 " --> pdb=" O LEU J 235 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ARG J 202 " --> pdb=" O TYR J 243 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N LEU J 245 " --> pdb=" O ARG J 202 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE J 204 " --> pdb=" O LEU J 245 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ARG J 150 " --> pdb=" O LEU J 146 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LEU J 146 " --> pdb=" O ARG J 150 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASN J 152 " --> pdb=" O THR J 144 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU J 140 " --> pdb=" O LEU J 156 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N VAL J 158 " --> pdb=" O ILE J 138 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ILE J 138 " --> pdb=" O VAL J 158 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 268 through 271 removed outlier: 6.588A pdb=" N MET J 274 " --> pdb=" O THR J 270 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.522A pdb=" N LYS K 11 " --> pdb=" O VAL K 19 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 144 through 148 removed outlier: 8.008A pdb=" N HIS K 86 " --> pdb=" O ASP K 110 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N ILE K 112 " --> pdb=" O HIS K 86 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL K 88 " --> pdb=" O ILE K 112 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL K 192 " --> pdb=" O ILE K 214 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N LYS K 216 " --> pdb=" O VAL K 192 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N LEU K 194 " --> pdb=" O LYS K 216 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 299 through 302 removed outlier: 6.568A pdb=" N GLN K 315 " --> pdb=" O GLN K 396 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR K 394 " --> pdb=" O ILE K 317 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLU K 319 " --> pdb=" O VAL K 392 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N VAL K 392 " --> pdb=" O GLU K 319 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 403 through 407 removed outlier: 3.627A pdb=" N VAL K 434 " --> pdb=" O VAL K 424 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARG K 435 " --> pdb=" O GLY K 465 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N PHE K 467 " --> pdb=" O ARG K 435 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N ARG K 437 " --> pdb=" O PHE K 467 " (cutoff:3.500A) removed outlier: 10.989A pdb=" N ARG K 469 " --> pdb=" O ARG K 437 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N HIS K 466 " --> pdb=" O ASP K 454 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ASP K 454 " --> pdb=" O HIS K 466 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL K 468 " --> pdb=" O SER K 452 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N SER K 452 " --> pdb=" O VAL K 468 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ASP K 470 " --> pdb=" O VAL K 450 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL K 450 " --> pdb=" O ASP K 470 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY K 472 " --> pdb=" O ARG K 448 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 532 through 533 removed outlier: 4.145A pdb=" N ASN K 638 " --> pdb=" O GLU K 629 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA K 623 " --> pdb=" O SER K 644 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE K 646 " --> pdb=" O ARG K 621 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS K 557 " --> pdb=" O GLU K 565 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY K 567 " --> pdb=" O HIS K 555 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N HIS K 555 " --> pdb=" O GLY K 567 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 540 through 542 removed outlier: 6.244A pdb=" N SER K 541 " --> pdb=" O PHE K 652 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'K' and resid 594 through 595 Processing sheet with id=AE1, first strand: chain 'K' and resid 751 through 754 Processing sheet with id=AE2, first strand: chain 'K' and resid 917 through 922 removed outlier: 7.116A pdb=" N VAL K 927 " --> pdb=" O ILE K 919 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N VAL K 921 " --> pdb=" O GLY K 925 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLY K 925 " --> pdb=" O VAL K 921 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 952 through 954 Processing sheet with id=AE4, first strand: chain 'K' and resid 981 through 983 removed outlier: 3.508A pdb=" N GLN K 982 " --> pdb=" O LEU K 999 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 303 through 306 removed outlier: 6.858A pdb=" N HIS M 304 " --> pdb=" O VAL M 498 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N SER M 500 " --> pdb=" O HIS M 304 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N VAL M 306 " --> pdb=" O SER M 500 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLU M 439 " --> pdb=" O LYS M 470 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ILE M 472 " --> pdb=" O GLU M 439 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL M 441 " --> pdb=" O ILE M 472 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LEU M 474 " --> pdb=" O VAL M 441 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N PHE M 443 " --> pdb=" O LEU M 474 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LYS M 374 " --> pdb=" O PHE M 440 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N ILE M 442 " --> pdb=" O LYS M 374 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE M 376 " --> pdb=" O ILE M 442 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER M 379 " --> pdb=" O MET M 419 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR M 420 " --> pdb=" O ILE M 404 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 518 through 522 removed outlier: 6.901A pdb=" N ILE M 510 " --> pdb=" O VAL M 521 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL M 630 " --> pdb=" O ILE M 737 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N MET M 629 " --> pdb=" O LEU M 719 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ALA M 721 " --> pdb=" O MET M 629 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL M 631 " --> pdb=" O ALA M 721 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 742 through 744 1386 hydrogen bonds defined for protein. 3849 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: 6.16 Time building geometry restraints manager: 3.40 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: 9654 1.34 - 1.45: 3928 1.45 - 1.57: 17432 1.57 - 1.69: 73 1.69 - 1.81: 234 Bond restraints: 31321 Sorted by residual: bond pdb=" C1' ATP M1101 " pdb=" C2' ATP M1101 " ideal model delta sigma weight residual 1.531 1.304 0.227 1.20e-02 6.94e+03 3.57e+02 bond pdb=" C1' ATP M1101 " pdb=" O4' ATP M1101 " ideal model delta sigma weight residual 1.416 1.620 -0.204 1.30e-02 5.92e+03 2.47e+02 bond pdb=" C4' ATP M1101 " pdb=" O4' ATP M1101 " ideal model delta sigma weight residual 1.444 1.272 0.172 1.10e-02 8.26e+03 2.44e+02 bond pdb=" C6 ATP M1101 " pdb=" N6 ATP M1101 " ideal model delta sigma weight residual 1.337 1.450 -0.113 1.10e-02 8.26e+03 1.06e+02 bond pdb=" C2' ATP M1101 " pdb=" O2' ATP M1101 " ideal model delta sigma weight residual 1.423 1.508 -0.085 1.30e-02 5.92e+03 4.23e+01 ... (remaining 31316 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 42450 3.09 - 6.18: 114 6.18 - 9.27: 8 9.27 - 12.36: 0 12.36 - 15.45: 2 Bond angle restraints: 42574 Sorted by residual: angle pdb=" PB ATP M1101 " pdb=" O3B ATP M1101 " pdb=" PG ATP M1101 " ideal model delta sigma weight residual 139.87 124.42 15.45 1.00e+00 1.00e+00 2.39e+02 angle pdb=" PA ATP M1101 " pdb=" O3A ATP M1101 " pdb=" PB ATP M1101 " ideal model delta sigma weight residual 136.83 124.03 12.80 1.00e+00 1.00e+00 1.64e+02 angle pdb=" C5 ATP M1101 " pdb=" C4 ATP M1101 " pdb=" N3 ATP M1101 " ideal model delta sigma weight residual 126.80 119.26 7.54 1.00e+00 1.00e+00 5.69e+01 angle pdb=" N1 ATP M1101 " pdb=" C2 ATP M1101 " pdb=" N3 ATP M1101 " ideal model delta sigma weight residual 128.69 121.26 7.43 1.00e+00 1.00e+00 5.53e+01 angle pdb=" N3 ATP M1101 " pdb=" C4 ATP M1101 " pdb=" N9 ATP M1101 " ideal model delta sigma weight residual 127.04 134.61 -7.57 1.15e+00 7.59e-01 4.35e+01 ... (remaining 42569 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.71: 18814 33.71 - 67.42: 361 67.42 - 101.14: 31 101.14 - 134.85: 0 134.85 - 168.56: 1 Dihedral angle restraints: 19207 sinusoidal: 7833 harmonic: 11374 Sorted by residual: dihedral pdb=" O4' U N 10 " pdb=" C1' U N 10 " pdb=" N1 U N 10 " pdb=" C2 U N 10 " ideal model delta sinusoidal sigma weight residual 232.00 63.44 168.56 1 1.70e+01 3.46e-03 6.58e+01 dihedral pdb=" CA ARG B 182 " pdb=" C ARG B 182 " pdb=" N GLU B 183 " pdb=" CA GLU B 183 " ideal model delta harmonic sigma weight residual 180.00 156.77 23.23 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA PHE K 842 " pdb=" C PHE K 842 " pdb=" N THR K 843 " pdb=" CA THR K 843 " ideal model delta harmonic sigma weight residual -180.00 -158.83 -21.17 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 19204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 4324 0.061 - 0.121: 673 0.121 - 0.182: 29 0.182 - 0.243: 0 0.243 - 0.304: 1 Chirality restraints: 5027 Sorted by residual: chirality pdb=" C2' ATP M1101 " pdb=" C1' ATP M1101 " pdb=" C3' ATP M1101 " pdb=" O2' ATP M1101 " both_signs ideal model delta sigma weight residual False -2.68 -2.38 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CA ASP K 189 " pdb=" N ASP K 189 " pdb=" C ASP K 189 " pdb=" CB ASP K 189 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" CA ARG E 85 " pdb=" N ARG E 85 " pdb=" C ARG E 85 " pdb=" CB ARG E 85 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.54e-01 ... (remaining 5024 not shown) Planarity restraints: 5384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU M 895 " 0.037 5.00e-02 4.00e+02 5.68e-02 5.16e+00 pdb=" N PRO M 896 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO M 896 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO M 896 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR K 826 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.74e+00 pdb=" N PRO K 827 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO K 827 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO K 827 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP M 614 " -0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO M 615 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO M 615 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO M 615 " -0.023 5.00e-02 4.00e+02 ... (remaining 5381 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3707 2.76 - 3.29: 27222 3.29 - 3.83: 47614 3.83 - 4.36: 56726 4.36 - 4.90: 99529 Nonbonded interactions: 234798 Sorted by model distance: nonbonded pdb=" NH2 ARG I 123 " pdb=" O2' U N 8 " model vdw 2.221 3.120 nonbonded pdb=" OE1 GLN K 275 " pdb=" NE2 GLN K 315 " model vdw 2.226 3.120 nonbonded pdb=" OD1 ASP D 51 " pdb=" NH2 ARG D 391 " model vdw 2.242 3.120 nonbonded pdb=" OE2 GLU K 120 " pdb=" ND2 ASN K 170 " model vdw 2.250 3.120 nonbonded pdb=" O ARG K 309 " pdb=" NH2 ARG K 398 " model vdw 2.262 3.120 ... (remaining 234793 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 26.620 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 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 0.227 31321 Z= 0.227 Angle : 0.497 15.447 42574 Z= 0.285 Chirality : 0.043 0.304 5027 Planarity : 0.004 0.057 5384 Dihedral : 13.523 168.559 11817 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.13), residues: 3838 helix: 1.89 (0.16), residues: 1210 sheet: 0.93 (0.18), residues: 795 loop : -0.72 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 138 TYR 0.013 0.001 TYR C 157 PHE 0.021 0.001 PHE F 122 TRP 0.013 0.001 TRP F 217 HIS 0.005 0.001 HIS K 888 Details of bonding type rmsd covalent geometry : bond 0.00345 (31321) covalent geometry : angle 0.49748 (42574) hydrogen bonds : bond 0.20964 ( 1319) hydrogen bonds : angle 5.79307 ( 3849) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 0.956 Fit side-chains REVERT: C 237 GLN cc_start: 0.7583 (tp40) cc_final: 0.7311 (tp40) REVERT: D 28 GLU cc_start: 0.8083 (mp0) cc_final: 0.7835 (mp0) REVERT: F 72 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7699 (mm-30) REVERT: G 164 GLN cc_start: 0.7266 (pm20) cc_final: 0.6835 (tp40) REVERT: K 386 ILE cc_start: 0.6414 (mp) cc_final: 0.6208 (pt) REVERT: K 413 ASP cc_start: 0.5987 (t0) cc_final: 0.5654 (t0) REVERT: K 705 MET cc_start: 0.4075 (tpt) cc_final: 0.2621 (tmt) REVERT: K 869 LEU cc_start: 0.7567 (tp) cc_final: 0.7057 (pt) REVERT: K 905 GLN cc_start: 0.6538 (tp40) cc_final: 0.5994 (tm-30) REVERT: M 306 VAL cc_start: 0.7311 (p) cc_final: 0.7048 (m) REVERT: M 790 LYS cc_start: 0.6962 (mtmm) cc_final: 0.6707 (mtmm) REVERT: M 965 MET cc_start: 0.8027 (mtm) cc_final: 0.7728 (mtp) REVERT: M 1023 ARG cc_start: 0.7678 (mmm160) cc_final: 0.7336 (mtp-110) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.7795 time to fit residues: 325.2967 Evaluate side-chains 263 residues out of total 3449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 GLN D 56 ASN E 200 GLN F 115 GLN G 96 GLN H 114 GLN J 105 ASN K 275 GLN K 315 GLN L 184 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.160423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.104133 restraints weight = 35836.749| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.92 r_work: 0.2951 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 31321 Z= 0.190 Angle : 0.612 8.284 42574 Z= 0.330 Chirality : 0.047 0.184 5027 Planarity : 0.005 0.058 5384 Dihedral : 9.040 166.815 4702 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.22 % Allowed : 6.72 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.13), residues: 3838 helix: 1.75 (0.15), residues: 1243 sheet: 0.95 (0.18), residues: 785 loop : -0.85 (0.13), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 806 TYR 0.016 0.002 TYR C 157 PHE 0.023 0.002 PHE M 977 TRP 0.021 0.002 TRP G 214 HIS 0.011 0.001 HIS K 888 Details of bonding type rmsd covalent geometry : bond 0.00445 (31321) covalent geometry : angle 0.61207 (42574) hydrogen bonds : bond 0.07218 ( 1319) hydrogen bonds : angle 4.54614 ( 3849) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 277 time to evaluate : 1.147 Fit side-chains REVERT: B 147 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.8439 (m-10) REVERT: C 237 GLN cc_start: 0.7795 (tp40) cc_final: 0.7451 (tp40) REVERT: D 28 GLU cc_start: 0.8174 (mp0) cc_final: 0.7856 (mp0) REVERT: G 164 GLN cc_start: 0.7203 (pm20) cc_final: 0.6554 (tp40) REVERT: I 317 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7582 (tm-30) REVERT: J 192 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8271 (mt0) REVERT: K 386 ILE cc_start: 0.6205 (mp) cc_final: 0.5997 (pt) REVERT: K 413 ASP cc_start: 0.6112 (t0) cc_final: 0.5734 (t0) REVERT: K 563 ASN cc_start: 0.3960 (OUTLIER) cc_final: 0.3556 (t0) REVERT: K 602 ASP cc_start: 0.4956 (m-30) cc_final: 0.4720 (p0) REVERT: K 672 MET cc_start: 0.4363 (OUTLIER) cc_final: 0.4099 (mpm) REVERT: K 705 MET cc_start: 0.3977 (tpt) cc_final: 0.2677 (tmt) REVERT: K 808 MET cc_start: 0.6793 (tpt) cc_final: 0.6584 (tpt) REVERT: K 905 GLN cc_start: 0.6314 (tp40) cc_final: 0.5748 (tm-30) REVERT: M 790 LYS cc_start: 0.6886 (mtmm) cc_final: 0.6579 (mtmm) REVERT: M 824 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6717 (mp0) REVERT: M 965 MET cc_start: 0.8279 (mtm) cc_final: 0.7970 (mtp) REVERT: M 1023 ARG cc_start: 0.7704 (mmm160) cc_final: 0.7301 (mtp-110) outliers start: 40 outliers final: 11 residues processed: 295 average time/residue: 0.7658 time to fit residues: 257.5057 Evaluate side-chains 274 residues out of total 3449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 257 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain H residue 232 LYS Chi-restraints excluded: chain I residue 317 GLN Chi-restraints excluded: chain J residue 192 GLN Chi-restraints excluded: chain J residue 214 ASP Chi-restraints excluded: chain K residue 300 LEU Chi-restraints excluded: chain K residue 563 ASN Chi-restraints excluded: chain K residue 672 MET Chi-restraints excluded: chain K residue 703 VAL Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain M residue 451 ASP Chi-restraints excluded: chain M residue 824 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 156 optimal weight: 0.8980 chunk 123 optimal weight: 6.9990 chunk 285 optimal weight: 0.5980 chunk 349 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 362 optimal weight: 3.9990 chunk 352 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 chunk 341 optimal weight: 7.9990 chunk 32 optimal weight: 0.0980 chunk 358 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 GLN D 56 ASN E 169 ASN E 200 GLN H 114 GLN J 105 ASN K 420 GLN L 184 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.163726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.108305 restraints weight = 36282.302| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.92 r_work: 0.3034 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 31321 Z= 0.102 Angle : 0.467 6.545 42574 Z= 0.251 Chirality : 0.043 0.169 5027 Planarity : 0.004 0.056 5384 Dihedral : 8.684 169.238 4702 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.76 % Allowed : 8.66 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.14), residues: 3838 helix: 2.05 (0.15), residues: 1250 sheet: 1.03 (0.18), residues: 835 loop : -0.73 (0.14), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 493 TYR 0.011 0.001 TYR G 143 PHE 0.011 0.001 PHE F 122 TRP 0.016 0.001 TRP G 214 HIS 0.010 0.001 HIS K 888 Details of bonding type rmsd covalent geometry : bond 0.00204 (31321) covalent geometry : angle 0.46670 (42574) hydrogen bonds : bond 0.04602 ( 1319) hydrogen bonds : angle 4.09691 ( 3849) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 271 time to evaluate : 0.943 Fit side-chains REVERT: B 160 MET cc_start: 0.9251 (mtp) cc_final: 0.9031 (mtp) REVERT: C 237 GLN cc_start: 0.7721 (tp40) cc_final: 0.7430 (tp40) REVERT: D 20 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7776 (mp0) REVERT: D 28 GLU cc_start: 0.8135 (mp0) cc_final: 0.7846 (mp0) REVERT: G 164 GLN cc_start: 0.7135 (pm20) cc_final: 0.6543 (tp40) REVERT: I 278 TRP cc_start: 0.7313 (OUTLIER) cc_final: 0.7017 (t60) REVERT: K 705 MET cc_start: 0.3949 (tpt) cc_final: 0.2582 (tmt) REVERT: K 808 MET cc_start: 0.6865 (tpt) cc_final: 0.6599 (tpt) REVERT: K 905 GLN cc_start: 0.6354 (tp40) cc_final: 0.5825 (tm-30) REVERT: K 938 LEU cc_start: 0.3359 (tm) cc_final: 0.2991 (mt) REVERT: M 306 VAL cc_start: 0.7581 (OUTLIER) cc_final: 0.7274 (m) REVERT: M 790 LYS cc_start: 0.6906 (mtmm) cc_final: 0.6586 (mttp) REVERT: M 824 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6559 (mp0) outliers start: 25 outliers final: 3 residues processed: 283 average time/residue: 0.7856 time to fit residues: 254.8317 Evaluate side-chains 256 residues out of total 3449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 249 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain I residue 278 TRP Chi-restraints excluded: chain K residue 703 VAL Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain M residue 824 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 359 optimal weight: 20.0000 chunk 273 optimal weight: 8.9990 chunk 370 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 chunk 78 optimal weight: 7.9990 chunk 315 optimal weight: 0.0980 chunk 135 optimal weight: 8.9990 chunk 39 optimal weight: 0.8980 chunk 96 optimal weight: 0.5980 chunk 304 optimal weight: 10.0000 overall best weight: 1.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 GLN E 200 GLN H 114 GLN I 158 GLN J 105 ASN M 400 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.162569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.108123 restraints weight = 36121.550| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.86 r_work: 0.3029 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31321 Z= 0.126 Angle : 0.512 8.913 42574 Z= 0.274 Chirality : 0.044 0.179 5027 Planarity : 0.004 0.055 5384 Dihedral : 8.678 168.469 4702 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.19 % Allowed : 9.45 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.14), residues: 3838 helix: 2.01 (0.15), residues: 1256 sheet: 1.02 (0.18), residues: 813 loop : -0.76 (0.14), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 493 TYR 0.014 0.001 TYR C 157 PHE 0.017 0.001 PHE D 227 TRP 0.017 0.001 TRP G 214 HIS 0.009 0.001 HIS K 888 Details of bonding type rmsd covalent geometry : bond 0.00280 (31321) covalent geometry : angle 0.51209 (42574) hydrogen bonds : bond 0.05414 ( 1319) hydrogen bonds : angle 4.11156 ( 3849) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 265 time to evaluate : 0.836 Fit side-chains REVERT: B 160 MET cc_start: 0.9278 (mtp) cc_final: 0.9056 (mtp) REVERT: C 65 MET cc_start: 0.8587 (tmm) cc_final: 0.8191 (tmm) REVERT: C 237 GLN cc_start: 0.7795 (tp40) cc_final: 0.7492 (tp40) REVERT: D 20 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7797 (mp0) REVERT: D 28 GLU cc_start: 0.8113 (mp0) cc_final: 0.7808 (mp0) REVERT: G 164 GLN cc_start: 0.7152 (pm20) cc_final: 0.6512 (tp40) REVERT: I 156 GLU cc_start: 0.7681 (tt0) cc_final: 0.7423 (tt0) REVERT: I 278 TRP cc_start: 0.7282 (OUTLIER) cc_final: 0.7000 (t60) REVERT: I 317 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7577 (tm-30) REVERT: J 160 ASP cc_start: 0.7957 (p0) cc_final: 0.7738 (p0) REVERT: J 192 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8217 (mt0) REVERT: K 563 ASN cc_start: 0.4114 (OUTLIER) cc_final: 0.3610 (t0) REVERT: K 602 ASP cc_start: 0.5109 (m-30) cc_final: 0.4613 (p0) REVERT: K 705 MET cc_start: 0.4016 (tpt) cc_final: 0.2737 (tmt) REVERT: K 808 MET cc_start: 0.6896 (tpt) cc_final: 0.6639 (tpt) REVERT: K 905 GLN cc_start: 0.6312 (tp40) cc_final: 0.5760 (tm-30) REVERT: K 938 LEU cc_start: 0.3357 (tm) cc_final: 0.2971 (mt) REVERT: M 731 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7318 (mp) REVERT: M 790 LYS cc_start: 0.6904 (mtmm) cc_final: 0.6698 (mttp) REVERT: M 824 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6716 (mp0) REVERT: M 983 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.6487 (ptt) outliers start: 39 outliers final: 12 residues processed: 285 average time/residue: 0.7709 time to fit residues: 251.6295 Evaluate side-chains 275 residues out of total 3449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 255 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain I residue 278 TRP Chi-restraints excluded: chain I residue 317 GLN Chi-restraints excluded: chain J residue 192 GLN Chi-restraints excluded: chain J residue 214 ASP Chi-restraints excluded: chain K residue 296 SER Chi-restraints excluded: chain K residue 563 ASN Chi-restraints excluded: chain K residue 703 VAL Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain M residue 451 ASP Chi-restraints excluded: chain M residue 731 LEU Chi-restraints excluded: chain M residue 824 GLU Chi-restraints excluded: chain M residue 983 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 383 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 chunk 308 optimal weight: 0.8980 chunk 216 optimal weight: 0.0670 chunk 121 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 156 optimal weight: 0.7980 chunk 313 optimal weight: 10.0000 chunk 282 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.3522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 GLN E 200 GLN H 114 GLN I 158 GLN J 105 ASN K 275 GLN K 315 GLN L 184 ASN M 400 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.163464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.109999 restraints weight = 36203.768| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.76 r_work: 0.3063 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 31321 Z= 0.108 Angle : 0.480 8.695 42574 Z= 0.257 Chirality : 0.043 0.165 5027 Planarity : 0.004 0.055 5384 Dihedral : 8.565 168.852 4702 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.19 % Allowed : 9.97 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.14), residues: 3838 helix: 2.10 (0.15), residues: 1258 sheet: 1.08 (0.18), residues: 803 loop : -0.72 (0.14), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 493 TYR 0.012 0.001 TYR C 157 PHE 0.014 0.001 PHE D 227 TRP 0.016 0.001 TRP G 214 HIS 0.008 0.001 HIS K 888 Details of bonding type rmsd covalent geometry : bond 0.00230 (31321) covalent geometry : angle 0.48028 (42574) hydrogen bonds : bond 0.04753 ( 1319) hydrogen bonds : angle 3.98073 ( 3849) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 267 time to evaluate : 0.945 Fit side-chains REVERT: B 160 MET cc_start: 0.9243 (mtp) cc_final: 0.9020 (mtp) REVERT: C 65 MET cc_start: 0.8557 (tmm) cc_final: 0.8197 (tmm) REVERT: C 237 GLN cc_start: 0.7725 (tp40) cc_final: 0.7439 (tp40) REVERT: D 20 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7739 (mp0) REVERT: D 28 GLU cc_start: 0.8090 (mp0) cc_final: 0.7784 (mp0) REVERT: G 164 GLN cc_start: 0.7149 (pm20) cc_final: 0.6532 (tp40) REVERT: I 156 GLU cc_start: 0.7623 (tt0) cc_final: 0.7375 (tt0) REVERT: I 278 TRP cc_start: 0.7262 (OUTLIER) cc_final: 0.6999 (t60) REVERT: I 317 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7568 (tm-30) REVERT: J 192 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8172 (mt0) REVERT: K 563 ASN cc_start: 0.4163 (OUTLIER) cc_final: 0.3634 (t0) REVERT: K 602 ASP cc_start: 0.5152 (m-30) cc_final: 0.4619 (p0) REVERT: K 705 MET cc_start: 0.4019 (tpt) cc_final: 0.2719 (tmt) REVERT: K 808 MET cc_start: 0.6928 (tpt) cc_final: 0.6649 (tpt) REVERT: K 905 GLN cc_start: 0.6381 (tp40) cc_final: 0.5831 (tm-30) REVERT: K 938 LEU cc_start: 0.3375 (tm) cc_final: 0.2969 (mt) REVERT: M 511 ASN cc_start: 0.7600 (OUTLIER) cc_final: 0.7122 (m110) REVERT: M 731 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7435 (mt) REVERT: M 790 LYS cc_start: 0.6938 (mtmm) cc_final: 0.6717 (mttp) REVERT: M 824 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6718 (mp0) REVERT: M 983 MET cc_start: 0.7372 (OUTLIER) cc_final: 0.6540 (ptt) REVERT: M 1023 ARG cc_start: 0.7835 (mmm160) cc_final: 0.7423 (mtp-110) outliers start: 39 outliers final: 12 residues processed: 288 average time/residue: 0.7621 time to fit residues: 251.3285 Evaluate side-chains 271 residues out of total 3449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 250 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain I residue 278 TRP Chi-restraints excluded: chain I residue 317 GLN Chi-restraints excluded: chain J residue 192 GLN Chi-restraints excluded: chain J residue 214 ASP Chi-restraints excluded: chain K residue 296 SER Chi-restraints excluded: chain K residue 563 ASN Chi-restraints excluded: chain K residue 903 VAL Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain M residue 511 ASN Chi-restraints excluded: chain M residue 731 LEU Chi-restraints excluded: chain M residue 824 GLU Chi-restraints excluded: chain M residue 983 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 359 optimal weight: 0.0870 chunk 114 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 259 optimal weight: 3.9990 chunk 235 optimal weight: 7.9990 chunk 309 optimal weight: 6.9990 chunk 198 optimal weight: 1.9990 chunk 330 optimal weight: 9.9990 chunk 213 optimal weight: 1.9990 chunk 307 optimal weight: 0.1980 chunk 365 optimal weight: 8.9990 overall best weight: 1.4564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 GLN D 56 ASN E 200 GLN H 114 GLN I 158 GLN J 105 ASN M 400 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.163286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.108929 restraints weight = 36137.150| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.88 r_work: 0.3036 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 31321 Z= 0.111 Angle : 0.487 8.098 42574 Z= 0.260 Chirality : 0.043 0.175 5027 Planarity : 0.004 0.055 5384 Dihedral : 8.528 168.884 4702 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.34 % Allowed : 10.43 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.14), residues: 3838 helix: 2.11 (0.15), residues: 1258 sheet: 1.06 (0.18), residues: 824 loop : -0.70 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 806 TYR 0.013 0.001 TYR K 832 PHE 0.015 0.001 PHE D 227 TRP 0.015 0.001 TRP G 214 HIS 0.007 0.001 HIS K 888 Details of bonding type rmsd covalent geometry : bond 0.00239 (31321) covalent geometry : angle 0.48672 (42574) hydrogen bonds : bond 0.04865 ( 1319) hydrogen bonds : angle 3.96298 ( 3849) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 255 time to evaluate : 0.887 Fit side-chains REVERT: B 4 ASP cc_start: 0.8042 (m-30) cc_final: 0.7718 (m-30) REVERT: B 160 MET cc_start: 0.9267 (mtp) cc_final: 0.9048 (mtp) REVERT: C 65 MET cc_start: 0.8566 (tmm) cc_final: 0.8184 (tmm) REVERT: C 237 GLN cc_start: 0.7738 (tp40) cc_final: 0.7454 (tp40) REVERT: D 20 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7748 (mp0) REVERT: D 28 GLU cc_start: 0.8129 (mp0) cc_final: 0.7807 (mp0) REVERT: G 164 GLN cc_start: 0.7191 (pm20) cc_final: 0.6554 (tp40) REVERT: I 156 GLU cc_start: 0.7655 (tt0) cc_final: 0.7429 (tt0) REVERT: I 278 TRP cc_start: 0.7234 (OUTLIER) cc_final: 0.6935 (t60) REVERT: I 317 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7597 (tm-30) REVERT: J 192 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8185 (mt0) REVERT: K 563 ASN cc_start: 0.4119 (OUTLIER) cc_final: 0.3606 (t0) REVERT: K 672 MET cc_start: 0.4398 (OUTLIER) cc_final: 0.4109 (mpm) REVERT: K 705 MET cc_start: 0.3852 (tpt) cc_final: 0.2562 (tmt) REVERT: K 905 GLN cc_start: 0.6352 (tp40) cc_final: 0.5811 (tm-30) REVERT: K 938 LEU cc_start: 0.3525 (tm) cc_final: 0.3098 (mt) REVERT: M 511 ASN cc_start: 0.7596 (OUTLIER) cc_final: 0.7144 (m110) REVERT: M 731 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7433 (mt) REVERT: M 790 LYS cc_start: 0.6874 (mtmm) cc_final: 0.6636 (mttp) REVERT: M 824 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6682 (mp0) REVERT: M 983 MET cc_start: 0.7342 (OUTLIER) cc_final: 0.6481 (ptt) outliers start: 44 outliers final: 13 residues processed: 282 average time/residue: 0.7637 time to fit residues: 247.7701 Evaluate side-chains 271 residues out of total 3449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 248 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain I residue 278 TRP Chi-restraints excluded: chain I residue 317 GLN Chi-restraints excluded: chain J residue 192 GLN Chi-restraints excluded: chain J residue 214 ASP Chi-restraints excluded: chain K residue 296 SER Chi-restraints excluded: chain K residue 563 ASN Chi-restraints excluded: chain K residue 672 MET Chi-restraints excluded: chain K residue 903 VAL Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain M residue 506 VAL Chi-restraints excluded: chain M residue 511 ASN Chi-restraints excluded: chain M residue 731 LEU Chi-restraints excluded: chain M residue 824 GLU Chi-restraints excluded: chain M residue 983 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 197 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 160 optimal weight: 6.9990 chunk 222 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 297 optimal weight: 8.9990 chunk 120 optimal weight: 0.2980 chunk 35 optimal weight: 0.0570 chunk 115 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 overall best weight: 2.2704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 GLN E 200 GLN H 114 GLN I 158 GLN J 45 GLN J 105 ASN L 184 ASN M 400 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.161930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.107481 restraints weight = 36150.245| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.80 r_work: 0.3007 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31321 Z= 0.140 Angle : 0.534 8.743 42574 Z= 0.286 Chirality : 0.045 0.180 5027 Planarity : 0.004 0.055 5384 Dihedral : 8.622 167.171 4702 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.19 % Allowed : 11.09 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.14), residues: 3838 helix: 2.02 (0.15), residues: 1256 sheet: 1.00 (0.18), residues: 817 loop : -0.78 (0.14), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 806 TYR 0.014 0.001 TYR C 157 PHE 0.019 0.001 PHE D 227 TRP 0.017 0.001 TRP G 214 HIS 0.007 0.001 HIS K 888 Details of bonding type rmsd covalent geometry : bond 0.00318 (31321) covalent geometry : angle 0.53378 (42574) hydrogen bonds : bond 0.05722 ( 1319) hydrogen bonds : angle 4.08031 ( 3849) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 252 time to evaluate : 1.183 Fit side-chains REVERT: C 65 MET cc_start: 0.8593 (tmm) cc_final: 0.8196 (tmm) REVERT: C 237 GLN cc_start: 0.7833 (tp40) cc_final: 0.7540 (tp40) REVERT: D 20 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7832 (mp0) REVERT: D 28 GLU cc_start: 0.8173 (mp0) cc_final: 0.7850 (mp0) REVERT: G 164 GLN cc_start: 0.7166 (pm20) cc_final: 0.6582 (tp40) REVERT: I 156 GLU cc_start: 0.7673 (tt0) cc_final: 0.7428 (tt0) REVERT: I 278 TRP cc_start: 0.7181 (OUTLIER) cc_final: 0.6847 (t60) REVERT: I 317 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7581 (tm-30) REVERT: J 192 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8215 (mt0) REVERT: K 563 ASN cc_start: 0.4134 (OUTLIER) cc_final: 0.3616 (t0) REVERT: K 672 MET cc_start: 0.4320 (OUTLIER) cc_final: 0.4078 (mpm) REVERT: K 705 MET cc_start: 0.3790 (tpt) cc_final: 0.2484 (tmt) REVERT: K 808 MET cc_start: 0.7007 (tpt) cc_final: 0.6653 (tpp) REVERT: L 205 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7738 (tm-30) REVERT: M 511 ASN cc_start: 0.7632 (OUTLIER) cc_final: 0.7165 (m110) REVERT: M 790 LYS cc_start: 0.6856 (mtmm) cc_final: 0.6605 (mttp) REVERT: M 824 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6646 (mp0) REVERT: M 983 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.6531 (ptt) REVERT: M 1023 ARG cc_start: 0.7850 (mmm160) cc_final: 0.7395 (mtp-110) outliers start: 39 outliers final: 17 residues processed: 276 average time/residue: 0.7622 time to fit residues: 241.1568 Evaluate side-chains 271 residues out of total 3449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 245 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain I residue 187 ARG Chi-restraints excluded: chain I residue 278 TRP Chi-restraints excluded: chain I residue 317 GLN Chi-restraints excluded: chain J residue 192 GLN Chi-restraints excluded: chain J residue 214 ASP Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain K residue 296 SER Chi-restraints excluded: chain K residue 563 ASN Chi-restraints excluded: chain K residue 672 MET Chi-restraints excluded: chain K residue 903 VAL Chi-restraints excluded: chain K residue 944 LEU Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain M residue 506 VAL Chi-restraints excluded: chain M residue 511 ASN Chi-restraints excluded: chain M residue 824 GLU Chi-restraints excluded: chain M residue 983 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 153 optimal weight: 2.9990 chunk 264 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 344 optimal weight: 20.0000 chunk 331 optimal weight: 8.9990 chunk 342 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 293 optimal weight: 5.9990 chunk 261 optimal weight: 20.0000 chunk 308 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 GLN E 200 GLN H 114 GLN J 105 ASN L 184 ASN M 400 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.160073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.105423 restraints weight = 36161.827| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.84 r_work: 0.2991 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 31321 Z= 0.208 Angle : 0.625 8.981 42574 Z= 0.335 Chirality : 0.048 0.210 5027 Planarity : 0.005 0.056 5384 Dihedral : 8.883 164.054 4702 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.22 % Allowed : 11.31 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.13), residues: 3838 helix: 1.83 (0.15), residues: 1244 sheet: 0.89 (0.18), residues: 818 loop : -0.92 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 209 TYR 0.017 0.002 TYR C 157 PHE 0.025 0.002 PHE D 227 TRP 0.018 0.002 TRP G 214 HIS 0.007 0.001 HIS K 888 Details of bonding type rmsd covalent geometry : bond 0.00498 (31321) covalent geometry : angle 0.62539 (42574) hydrogen bonds : bond 0.07143 ( 1319) hydrogen bonds : angle 4.29432 ( 3849) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 253 time to evaluate : 1.202 Fit side-chains REVERT: C 237 GLN cc_start: 0.7878 (tp40) cc_final: 0.7530 (tp40) REVERT: D 28 GLU cc_start: 0.8160 (mp0) cc_final: 0.7855 (mp0) REVERT: F 223 THR cc_start: 0.8234 (m) cc_final: 0.8031 (m) REVERT: G 164 GLN cc_start: 0.7141 (pm20) cc_final: 0.6587 (tp40) REVERT: H 232 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7995 (mtpp) REVERT: I 156 GLU cc_start: 0.7746 (tt0) cc_final: 0.7478 (tt0) REVERT: I 278 TRP cc_start: 0.7261 (OUTLIER) cc_final: 0.6894 (t60) REVERT: I 317 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7596 (tm-30) REVERT: J 192 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8287 (mt0) REVERT: K 413 ASP cc_start: 0.6164 (t0) cc_final: 0.5779 (t0) REVERT: K 563 ASN cc_start: 0.4127 (OUTLIER) cc_final: 0.3603 (t0) REVERT: K 672 MET cc_start: 0.4358 (OUTLIER) cc_final: 0.4118 (mpm) REVERT: K 705 MET cc_start: 0.3780 (tpt) cc_final: 0.2499 (tmt) REVERT: M 511 ASN cc_start: 0.7709 (OUTLIER) cc_final: 0.7225 (m110) REVERT: M 790 LYS cc_start: 0.6878 (mtmm) cc_final: 0.6617 (mttp) REVERT: M 824 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6713 (mp0) REVERT: M 983 MET cc_start: 0.7429 (OUTLIER) cc_final: 0.6616 (ptt) REVERT: M 1023 ARG cc_start: 0.7875 (mmm160) cc_final: 0.7355 (mtp-110) outliers start: 40 outliers final: 20 residues processed: 277 average time/residue: 0.7372 time to fit residues: 235.1782 Evaluate side-chains 279 residues out of total 3449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 250 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain H residue 232 LYS Chi-restraints excluded: chain I residue 187 ARG Chi-restraints excluded: chain I residue 278 TRP Chi-restraints excluded: chain I residue 317 GLN Chi-restraints excluded: chain J residue 192 GLN Chi-restraints excluded: chain J residue 214 ASP Chi-restraints excluded: chain K residue 296 SER Chi-restraints excluded: chain K residue 323 GLN Chi-restraints excluded: chain K residue 563 ASN Chi-restraints excluded: chain K residue 592 THR Chi-restraints excluded: chain K residue 672 MET Chi-restraints excluded: chain K residue 903 VAL Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain M residue 451 ASP Chi-restraints excluded: chain M residue 506 VAL Chi-restraints excluded: chain M residue 511 ASN Chi-restraints excluded: chain M residue 824 GLU Chi-restraints excluded: chain M residue 983 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 146 optimal weight: 10.0000 chunk 98 optimal weight: 0.9980 chunk 339 optimal weight: 20.0000 chunk 266 optimal weight: 30.0000 chunk 370 optimal weight: 3.9990 chunk 298 optimal weight: 2.9990 chunk 383 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 290 optimal weight: 4.9990 chunk 367 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 GLN E 200 GLN H 114 GLN J 105 ASN L 184 ASN M 400 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.161957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.107563 restraints weight = 36165.723| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.92 r_work: 0.3026 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31321 Z= 0.125 Angle : 0.525 9.387 42574 Z= 0.280 Chirality : 0.044 0.183 5027 Planarity : 0.004 0.057 5384 Dihedral : 8.728 166.455 4702 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.12 % Allowed : 11.64 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.14), residues: 3838 helix: 1.98 (0.15), residues: 1249 sheet: 0.96 (0.18), residues: 814 loop : -0.86 (0.14), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 209 TYR 0.013 0.001 TYR C 157 PHE 0.015 0.001 PHE D 227 TRP 0.017 0.001 TRP G 214 HIS 0.007 0.001 HIS K 888 Details of bonding type rmsd covalent geometry : bond 0.00273 (31321) covalent geometry : angle 0.52538 (42574) hydrogen bonds : bond 0.05433 ( 1319) hydrogen bonds : angle 4.08315 ( 3849) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 254 time to evaluate : 1.270 Fit side-chains REVERT: C 237 GLN cc_start: 0.7823 (tp40) cc_final: 0.7497 (tp40) REVERT: D 28 GLU cc_start: 0.8109 (mp0) cc_final: 0.7792 (mp0) REVERT: G 164 GLN cc_start: 0.7117 (pm20) cc_final: 0.6544 (tp40) REVERT: I 156 GLU cc_start: 0.7663 (tt0) cc_final: 0.7442 (tt0) REVERT: I 278 TRP cc_start: 0.7263 (OUTLIER) cc_final: 0.6880 (t60) REVERT: I 317 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7575 (tm-30) REVERT: J 192 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8258 (mt0) REVERT: K 672 MET cc_start: 0.4309 (OUTLIER) cc_final: 0.4071 (mpm) REVERT: K 705 MET cc_start: 0.3895 (tpt) cc_final: 0.2618 (tmt) REVERT: M 511 ASN cc_start: 0.7625 (OUTLIER) cc_final: 0.7159 (m110) REVERT: M 790 LYS cc_start: 0.6841 (mtmm) cc_final: 0.6593 (mttp) REVERT: M 824 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6652 (mp0) REVERT: M 983 MET cc_start: 0.7335 (OUTLIER) cc_final: 0.6531 (ptt) outliers start: 37 outliers final: 16 residues processed: 278 average time/residue: 0.7933 time to fit residues: 253.9601 Evaluate side-chains 267 residues out of total 3449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 244 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain I residue 278 TRP Chi-restraints excluded: chain I residue 317 GLN Chi-restraints excluded: chain J residue 192 GLN Chi-restraints excluded: chain J residue 214 ASP Chi-restraints excluded: chain K residue 296 SER Chi-restraints excluded: chain K residue 592 THR Chi-restraints excluded: chain K residue 672 MET Chi-restraints excluded: chain K residue 903 VAL Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain M residue 506 VAL Chi-restraints excluded: chain M residue 511 ASN Chi-restraints excluded: chain M residue 824 GLU Chi-restraints excluded: chain M residue 983 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 13 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 181 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 chunk 278 optimal weight: 30.0000 chunk 349 optimal weight: 0.2980 chunk 89 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 GLN E 200 GLN J 105 ASN L 184 ASN M 400 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.162859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.108611 restraints weight = 36063.665| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.88 r_work: 0.3036 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 31321 Z= 0.113 Angle : 0.510 11.185 42574 Z= 0.268 Chirality : 0.043 0.164 5027 Planarity : 0.004 0.057 5384 Dihedral : 8.584 168.373 4702 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.82 % Allowed : 12.16 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.14), residues: 3838 helix: 2.09 (0.15), residues: 1251 sheet: 1.05 (0.18), residues: 818 loop : -0.76 (0.14), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 209 TYR 0.015 0.001 TYR K 832 PHE 0.014 0.001 PHE D 227 TRP 0.016 0.001 TRP G 214 HIS 0.009 0.001 HIS K 888 Details of bonding type rmsd covalent geometry : bond 0.00243 (31321) covalent geometry : angle 0.50954 (42574) hydrogen bonds : bond 0.04849 ( 1319) hydrogen bonds : angle 3.95123 ( 3849) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7676 Ramachandran restraints generated. 3838 Oldfield, 0 Emsley, 3838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 249 time to evaluate : 1.309 Fit side-chains REVERT: B 4 ASP cc_start: 0.8020 (m-30) cc_final: 0.7671 (m-30) REVERT: C 237 GLN cc_start: 0.7830 (tp40) cc_final: 0.7526 (tp40) REVERT: D 20 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7793 (mp0) REVERT: D 28 GLU cc_start: 0.8134 (mp0) cc_final: 0.7819 (mp0) REVERT: G 164 GLN cc_start: 0.7158 (pm20) cc_final: 0.6532 (tp40) REVERT: I 156 GLU cc_start: 0.7617 (tt0) cc_final: 0.7382 (tt0) REVERT: I 278 TRP cc_start: 0.7303 (OUTLIER) cc_final: 0.6804 (t60) REVERT: I 317 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7571 (tm-30) REVERT: J 192 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8244 (mt0) REVERT: K 705 MET cc_start: 0.3746 (tpt) cc_final: 0.2382 (tmt) REVERT: K 879 MET cc_start: 0.4717 (mmt) cc_final: 0.4466 (mtm) REVERT: M 511 ASN cc_start: 0.7596 (OUTLIER) cc_final: 0.7122 (m110) REVERT: M 790 LYS cc_start: 0.6813 (mtmm) cc_final: 0.6575 (mttp) REVERT: M 983 MET cc_start: 0.7229 (OUTLIER) cc_final: 0.6419 (ptt) outliers start: 27 outliers final: 17 residues processed: 266 average time/residue: 0.8746 time to fit residues: 265.6321 Evaluate side-chains 268 residues out of total 3449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 245 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain G residue 197 ASN Chi-restraints excluded: chain I residue 278 TRP Chi-restraints excluded: chain I residue 317 GLN Chi-restraints excluded: chain J residue 192 GLN Chi-restraints excluded: chain J residue 214 ASP Chi-restraints excluded: chain K residue 296 SER Chi-restraints excluded: chain K residue 592 THR Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain M residue 506 VAL Chi-restraints excluded: chain M residue 511 ASN Chi-restraints excluded: chain M residue 784 LEU Chi-restraints excluded: chain M residue 824 GLU Chi-restraints excluded: chain M residue 983 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 167 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 239 optimal weight: 9.9990 chunk 136 optimal weight: 0.0040 chunk 240 optimal weight: 4.9990 chunk 200 optimal weight: 5.9990 chunk 373 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 198 optimal weight: 4.9990 chunk 263 optimal weight: 6.9990 chunk 283 optimal weight: 10.0000 overall best weight: 3.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 200 GLN H 114 GLN J 105 ASN L 184 ASN M 400 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.160394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.105528 restraints weight = 36050.849| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.82 r_work: 0.2978 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 31321 Z= 0.192 Angle : 0.611 11.498 42574 Z= 0.324 Chirality : 0.047 0.192 5027 Planarity : 0.005 0.056 5384 Dihedral : 8.788 164.231 4702 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.82 % Allowed : 12.28 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.13), residues: 3838 helix: 1.89 (0.15), residues: 1244 sheet: 0.99 (0.18), residues: 795 loop : -0.90 (0.14), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 209 TYR 0.015 0.002 TYR C 157 PHE 0.025 0.002 PHE D 227 TRP 0.018 0.002 TRP G 214 HIS 0.010 0.001 HIS K 888 Details of bonding type rmsd covalent geometry : bond 0.00456 (31321) covalent geometry : angle 0.61087 (42574) hydrogen bonds : bond 0.06687 ( 1319) hydrogen bonds : angle 4.19641 ( 3849) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13036.42 seconds wall clock time: 221 minutes 30.26 seconds (13290.26 seconds total)