Starting phenix.real_space_refine on Thu Jul 25 23:46:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcf_18329/07_2024/8qcf_18329.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcf_18329/07_2024/8qcf_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcf_18329/07_2024/8qcf_18329.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcf_18329/07_2024/8qcf_18329.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcf_18329/07_2024/8qcf_18329.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qcf_18329/07_2024/8qcf_18329.cif" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Residue "G PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 480": "OE1" <-> "OE2" Residue "M PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 956": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/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: {'GLN:plan1': 1, 'GLU:plan': 4, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 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: {'GLU:plan': 3, 'ASP:plan': 2} 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, 'ASP:plan': 3, 'HIS:plan': 1} 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: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} 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: {'GLN:plan1': 6, 'ASP:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 7} 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: 16.69, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 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: 10.81 Conformation dependent library (CDL) restraints added in 5.6 seconds 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: 4.02 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: 14.79 Time building geometry restraints manager: 11.71 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: 99.74 - 106.71: 969 106.71 - 113.69: 17788 113.69 - 120.66: 12527 120.66 - 127.64: 11072 127.64 - 134.61: 218 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 2.520 nonbonded pdb=" OE1 GLN K 275 " pdb=" NE2 GLN K 315 " model vdw 2.226 2.520 nonbonded pdb=" OD1 ASP D 51 " pdb=" NH2 ARG D 391 " model vdw 2.242 2.520 nonbonded pdb=" OE2 GLU K 120 " pdb=" ND2 ASN K 170 " model vdw 2.250 2.520 nonbonded pdb=" O ARG K 309 " pdb=" NH2 ARG K 398 " model vdw 2.262 2.520 ... (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 ========== 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: 2.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.240 Check model and map are aligned: 0.230 Set scattering table: 0.290 Process input model: 82.270 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.140 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: 0.020 Load rotamer database and sin/cos tables:11.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.040 ------------------------------------------------------------------------------- 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= 0.209 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.013 0.001 TRP F 217 HIS 0.005 0.001 HIS K 888 PHE 0.021 0.001 PHE F 122 TYR 0.013 0.001 TYR C 157 ARG 0.005 0.000 ARG D 138 *********************** 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 fitting. rotamer outliers: 0 poor density : 367 time to evaluate : 3.419 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: 1.7266 time to fit residues: 724.6098 Evaluate side-chains 263 residues out of total 3449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 3.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 326 optimal weight: 2.9990 chunk 293 optimal weight: 6.9990 chunk 162 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 197 optimal weight: 0.0670 chunk 156 optimal weight: 0.7980 chunk 303 optimal weight: 8.9990 chunk 117 optimal weight: 8.9990 chunk 184 optimal weight: 5.9990 chunk 225 optimal weight: 4.9990 chunk 351 optimal weight: 9.9990 overall best weight: 1.5522 ------------------------------------------------------------------------------- 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 H 114 GLN J 105 ASN ** K 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 184 ASN ** M 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.0794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31321 Z= 0.169 Angle : 0.511 7.012 42574 Z= 0.276 Chirality : 0.044 0.172 5027 Planarity : 0.004 0.057 5384 Dihedral : 8.860 169.033 4702 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.82 % Allowed : 6.35 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.14), residues: 3838 helix: 2.02 (0.15), residues: 1242 sheet: 1.12 (0.18), residues: 799 loop : -0.75 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 214 HIS 0.011 0.001 HIS K 888 PHE 0.015 0.001 PHE D 227 TYR 0.013 0.001 TYR C 157 ARG 0.005 0.000 ARG K 806 *********************** 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 302 residues out of total 3449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 275 time to evaluate : 3.770 Fit side-chains REVERT: B 147 PHE cc_start: 0.8687 (OUTLIER) cc_final: 0.8337 (m-10) REVERT: C 237 GLN cc_start: 0.7616 (tp40) cc_final: 0.7313 (tp40) REVERT: D 20 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: D 28 GLU cc_start: 0.8121 (mp0) cc_final: 0.7862 (mp0) REVERT: F 72 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7693 (mm-30) REVERT: G 164 GLN cc_start: 0.7163 (pm20) cc_final: 0.6732 (tp40) REVERT: I 317 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7457 (tm-30) REVERT: I 327 MET cc_start: 0.9292 (mmt) cc_final: 0.9054 (mmt) REVERT: J 192 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.8150 (mt0) REVERT: K 386 ILE cc_start: 0.6360 (mp) cc_final: 0.6143 (pt) REVERT: K 563 ASN cc_start: 0.4533 (OUTLIER) cc_final: 0.4006 (t0) REVERT: K 672 MET cc_start: 0.4265 (OUTLIER) cc_final: 0.4028 (mpm) REVERT: K 705 MET cc_start: 0.4080 (tpt) cc_final: 0.2627 (tmt) REVERT: K 808 MET cc_start: 0.7067 (tpt) cc_final: 0.6859 (tpt) REVERT: K 905 GLN cc_start: 0.6560 (tp40) cc_final: 0.6014 (tm-30) REVERT: M 306 VAL cc_start: 0.7377 (p) cc_final: 0.7109 (m) REVERT: M 621 LEU cc_start: 0.8255 (mp) cc_final: 0.8029 (mp) REVERT: M 790 LYS cc_start: 0.7018 (mtmm) cc_final: 0.6731 (mttp) REVERT: M 965 MET cc_start: 0.8032 (mtm) cc_final: 0.7679 (mtp) REVERT: M 1023 ARG cc_start: 0.7494 (mmm160) cc_final: 0.7138 (mtp-110) outliers start: 27 outliers final: 5 residues processed: 287 average time/residue: 1.7256 time to fit residues: 568.5149 Evaluate side-chains 271 residues out of total 3449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 260 time to evaluate : 3.379 ------------------------------------------------------------------------------- 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 273 GLU Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain I residue 317 GLN Chi-restraints excluded: chain J residue 192 GLN 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 195 optimal weight: 2.9990 chunk 109 optimal weight: 0.2980 chunk 292 optimal weight: 9.9990 chunk 239 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 352 optimal weight: 0.9990 chunk 380 optimal weight: 1.9990 chunk 313 optimal weight: 10.0000 chunk 349 optimal weight: 5.9990 chunk 120 optimal weight: 0.5980 chunk 282 optimal weight: 8.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 ** K 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 184 ASN ** M 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 31321 Z= 0.151 Angle : 0.478 6.912 42574 Z= 0.257 Chirality : 0.043 0.170 5027 Planarity : 0.004 0.055 5384 Dihedral : 8.662 169.406 4702 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.82 % Allowed : 8.48 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.14), residues: 3838 helix: 2.12 (0.15), residues: 1250 sheet: 1.10 (0.18), residues: 816 loop : -0.70 (0.14), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 214 HIS 0.010 0.001 HIS K 888 PHE 0.044 0.001 PHE K 842 TYR 0.012 0.001 TYR C 157 ARG 0.007 0.000 ARG K 806 *********************** 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 302 residues out of total 3449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 275 time to evaluate : 3.315 Fit side-chains REVERT: B 4 ASP cc_start: 0.7966 (m-30) cc_final: 0.7732 (m-30) REVERT: C 237 GLN cc_start: 0.7604 (tp40) cc_final: 0.7310 (tp40) REVERT: D 20 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7904 (mp0) REVERT: D 28 GLU cc_start: 0.8131 (mp0) cc_final: 0.7834 (mp0) REVERT: E 181 ASP cc_start: 0.8904 (t0) cc_final: 0.8702 (t70) REVERT: F 197 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8728 (mmm) REVERT: G 164 GLN cc_start: 0.7155 (pm20) cc_final: 0.6719 (tp40) REVERT: I 278 TRP cc_start: 0.7086 (OUTLIER) cc_final: 0.6875 (t60) REVERT: I 327 MET cc_start: 0.9292 (mmt) cc_final: 0.9041 (mmt) REVERT: K 705 MET cc_start: 0.4093 (tpt) cc_final: 0.2635 (tmt) REVERT: K 808 MET cc_start: 0.6955 (tpt) cc_final: 0.6720 (tpt) REVERT: K 905 GLN cc_start: 0.6532 (tp40) cc_final: 0.5968 (tm-30) REVERT: K 938 LEU cc_start: 0.3464 (tm) cc_final: 0.3061 (tp) REVERT: M 306 VAL cc_start: 0.7475 (p) cc_final: 0.7178 (m) REVERT: M 621 LEU cc_start: 0.8255 (mp) cc_final: 0.7985 (mp) REVERT: M 790 LYS cc_start: 0.7118 (mtmm) cc_final: 0.6785 (mttp) REVERT: M 824 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6594 (mp0) REVERT: M 1023 ARG cc_start: 0.7509 (mmm160) cc_final: 0.7158 (mtp-110) outliers start: 27 outliers final: 7 residues processed: 288 average time/residue: 1.7089 time to fit residues: 565.6043 Evaluate side-chains 274 residues out of total 3449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 263 time to evaluate : 3.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 F residue 197 MET Chi-restraints excluded: chain I residue 278 TRP Chi-restraints excluded: chain J residue 214 ASP Chi-restraints excluded: chain K residue 703 VAL Chi-restraints excluded: chain L residue 198 THR 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 347 optimal weight: 6.9990 chunk 264 optimal weight: 4.9990 chunk 182 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 236 optimal weight: 0.1980 chunk 353 optimal weight: 9.9990 chunk 374 optimal weight: 3.9990 chunk 184 optimal weight: 4.9990 chunk 334 optimal weight: 7.9990 chunk 100 optimal weight: 7.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- 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 73 ASN H 114 GLN I 158 GLN I 170 ASN J 105 ASN ** K 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 184 ASN ** M 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 400 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 31321 Z= 0.284 Angle : 0.592 8.353 42574 Z= 0.319 Chirality : 0.047 0.194 5027 Planarity : 0.005 0.056 5384 Dihedral : 8.866 166.553 4702 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.37 % Allowed : 9.15 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.13), residues: 3838 helix: 1.88 (0.15), residues: 1250 sheet: 0.97 (0.18), residues: 806 loop : -0.87 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 214 HIS 0.009 0.001 HIS K 888 PHE 0.044 0.002 PHE K 842 TYR 0.021 0.002 TYR K 181 ARG 0.006 0.000 ARG K 806 *********************** 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 308 residues out of total 3449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 263 time to evaluate : 3.867 Fit side-chains REVERT: B 109 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8602 (tt0) REVERT: C 65 MET cc_start: 0.8611 (tmm) cc_final: 0.8172 (tmm) REVERT: C 237 GLN cc_start: 0.7691 (tp40) cc_final: 0.7367 (tp40) REVERT: D 28 GLU cc_start: 0.8142 (mp0) cc_final: 0.7858 (mp0) REVERT: G 164 GLN cc_start: 0.7224 (pm20) cc_final: 0.6757 (tp40) REVERT: I 156 GLU cc_start: 0.7679 (tt0) cc_final: 0.7400 (tt0) REVERT: I 278 TRP cc_start: 0.7100 (OUTLIER) cc_final: 0.6864 (t60) REVERT: I 317 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7463 (tm-30) REVERT: J 160 ASP cc_start: 0.7855 (p0) cc_final: 0.7628 (p0) REVERT: K 413 ASP cc_start: 0.6115 (t0) cc_final: 0.5762 (t0) REVERT: K 563 ASN cc_start: 0.4576 (OUTLIER) cc_final: 0.3977 (t0) REVERT: K 705 MET cc_start: 0.3950 (tpt) cc_final: 0.2486 (tmt) REVERT: K 808 MET cc_start: 0.6991 (tpt) cc_final: 0.6752 (tpt) REVERT: M 790 LYS cc_start: 0.7093 (mtmm) cc_final: 0.6870 (mttp) REVERT: M 824 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6638 (mp0) REVERT: M 983 MET cc_start: 0.7266 (OUTLIER) cc_final: 0.6772 (ptt) outliers start: 45 outliers final: 17 residues processed: 286 average time/residue: 1.6492 time to fit residues: 543.6764 Evaluate side-chains 272 residues out of total 3449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 249 time to evaluate : 3.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 GLU 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 216 LYS 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 H residue 20 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 214 ASP Chi-restraints excluded: chain K residue 300 LEU Chi-restraints excluded: chain K residue 323 GLN 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 451 ASP 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 311 optimal weight: 8.9990 chunk 212 optimal weight: 0.5980 chunk 5 optimal weight: 7.9990 chunk 278 optimal weight: 8.9990 chunk 154 optimal weight: 0.2980 chunk 319 optimal weight: 30.0000 chunk 258 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 191 optimal weight: 0.9980 chunk 335 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 ** K 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 184 ASN ** M 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 400 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 31321 Z= 0.137 Angle : 0.473 10.974 42574 Z= 0.253 Chirality : 0.043 0.167 5027 Planarity : 0.004 0.056 5384 Dihedral : 8.635 168.766 4702 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.91 % Allowed : 10.33 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.14), residues: 3838 helix: 2.09 (0.15), residues: 1256 sheet: 1.01 (0.18), residues: 834 loop : -0.77 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 214 HIS 0.008 0.001 HIS K 888 PHE 0.046 0.001 PHE K 842 TYR 0.011 0.001 TYR C 157 ARG 0.007 0.000 ARG K 806 *********************** 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 291 residues out of total 3449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 261 time to evaluate : 3.711 Fit side-chains REVERT: C 65 MET cc_start: 0.8539 (tmm) cc_final: 0.8143 (tmm) REVERT: C 237 GLN cc_start: 0.7632 (tp40) cc_final: 0.7335 (tp40) REVERT: D 20 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7888 (mp0) REVERT: D 28 GLU cc_start: 0.8152 (mp0) cc_final: 0.7844 (mp0) REVERT: G 164 GLN cc_start: 0.7202 (pm20) cc_final: 0.6733 (tp40) REVERT: I 278 TRP cc_start: 0.7053 (OUTLIER) cc_final: 0.6841 (t60) REVERT: I 317 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7425 (tm-30) REVERT: I 327 MET cc_start: 0.9260 (mmt) cc_final: 0.9053 (mmt) REVERT: J 160 ASP cc_start: 0.7813 (p0) cc_final: 0.7607 (p0) REVERT: J 192 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8108 (mt0) REVERT: K 563 ASN cc_start: 0.4490 (OUTLIER) cc_final: 0.3886 (t0) REVERT: K 705 MET cc_start: 0.4031 (tpt) cc_final: 0.2553 (tmt) REVERT: K 808 MET cc_start: 0.7115 (tpt) cc_final: 0.6854 (tpt) REVERT: K 905 GLN cc_start: 0.6492 (tp40) cc_final: 0.5925 (tm-30) REVERT: K 938 LEU cc_start: 0.3445 (tm) cc_final: 0.2873 (mt) REVERT: M 511 ASN cc_start: 0.7721 (OUTLIER) cc_final: 0.7176 (m110) REVERT: M 790 LYS cc_start: 0.7075 (mtmm) cc_final: 0.6840 (mttp) REVERT: M 824 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6566 (mp0) REVERT: M 1023 ARG cc_start: 0.7515 (mmm160) cc_final: 0.7106 (mtp-110) outliers start: 30 outliers final: 9 residues processed: 276 average time/residue: 1.7109 time to fit residues: 545.0246 Evaluate side-chains 267 residues out of total 3449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 251 time to evaluate : 3.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 216 LYS 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 K residue 296 SER Chi-restraints excluded: chain K residue 563 ASN 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 824 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 125 optimal weight: 9.9990 chunk 336 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 219 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 chunk 374 optimal weight: 3.9990 chunk 310 optimal weight: 10.0000 chunk 173 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 123 optimal weight: 0.5980 chunk 196 optimal weight: 1.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- 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 170 ASN J 45 GLN J 105 ASN ** K 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 400 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 31321 Z= 0.251 Angle : 0.562 8.456 42574 Z= 0.301 Chirality : 0.046 0.182 5027 Planarity : 0.004 0.056 5384 Dihedral : 8.765 166.726 4702 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.22 % Allowed : 10.79 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.13), residues: 3838 helix: 1.97 (0.15), residues: 1249 sheet: 0.97 (0.18), residues: 809 loop : -0.87 (0.14), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 214 HIS 0.008 0.001 HIS K 888 PHE 0.050 0.002 PHE K 842 TYR 0.016 0.002 TYR C 157 ARG 0.007 0.000 ARG K 806 *********************** 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 294 residues out of total 3449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 254 time to evaluate : 3.895 Fit side-chains REVERT: C 65 MET cc_start: 0.8566 (tmm) cc_final: 0.8122 (tmm) REVERT: C 113 MET cc_start: 0.9594 (mtt) cc_final: 0.9353 (mtt) REVERT: C 237 GLN cc_start: 0.7666 (tp40) cc_final: 0.7351 (tp40) REVERT: D 20 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7950 (mp0) REVERT: D 28 GLU cc_start: 0.8187 (mp0) cc_final: 0.7877 (mp0) REVERT: G 164 GLN cc_start: 0.7217 (pm20) cc_final: 0.6744 (tp40) REVERT: I 156 GLU cc_start: 0.7628 (tt0) cc_final: 0.7375 (tt0) REVERT: I 187 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8293 (tpt-90) REVERT: I 278 TRP cc_start: 0.7090 (OUTLIER) cc_final: 0.6861 (t60) REVERT: I 317 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7462 (tm-30) REVERT: J 160 ASP cc_start: 0.7873 (p0) cc_final: 0.7667 (p0) REVERT: J 192 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8181 (mt0) REVERT: K 116 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8163 (tp) REVERT: K 413 ASP cc_start: 0.6103 (t0) cc_final: 0.5750 (t0) REVERT: K 563 ASN cc_start: 0.4465 (OUTLIER) cc_final: 0.3864 (t0) REVERT: K 672 MET cc_start: 0.4378 (OUTLIER) cc_final: 0.4170 (mpm) REVERT: K 705 MET cc_start: 0.3978 (tpt) cc_final: 0.2501 (tmt) REVERT: M 511 ASN cc_start: 0.7743 (OUTLIER) cc_final: 0.7216 (m110) REVERT: M 790 LYS cc_start: 0.6962 (mtmm) cc_final: 0.6639 (mttp) REVERT: M 824 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6621 (mp0) REVERT: M 983 MET cc_start: 0.7076 (OUTLIER) cc_final: 0.6208 (ptt) REVERT: M 1023 ARG cc_start: 0.7540 (mmm160) cc_final: 0.7089 (mtp-110) outliers start: 40 outliers final: 14 residues processed: 278 average time/residue: 1.6615 time to fit residues: 536.3005 Evaluate side-chains 277 residues out of total 3449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 252 time to evaluate : 3.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 216 LYS 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 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 300 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 361 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 213 optimal weight: 6.9990 chunk 273 optimal weight: 6.9990 chunk 211 optimal weight: 10.0000 chunk 315 optimal weight: 1.9990 chunk 209 optimal weight: 3.9990 chunk 373 optimal weight: 6.9990 chunk 233 optimal weight: 5.9990 chunk 227 optimal weight: 6.9990 chunk 172 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 I 170 ASN J 105 ASN ** K 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 184 ASN ** M 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 400 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 31321 Z= 0.255 Angle : 0.568 11.186 42574 Z= 0.304 Chirality : 0.046 0.181 5027 Planarity : 0.004 0.057 5384 Dihedral : 8.832 165.595 4702 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.37 % Allowed : 11.31 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.13), residues: 3838 helix: 1.89 (0.15), residues: 1249 sheet: 0.92 (0.18), residues: 811 loop : -0.93 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 214 HIS 0.007 0.001 HIS K 888 PHE 0.055 0.002 PHE K 842 TYR 0.015 0.002 TYR C 157 ARG 0.008 0.000 ARG K 806 *********************** 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 304 residues out of total 3449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 259 time to evaluate : 3.452 Fit side-chains REVERT: B 109 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8610 (tt0) REVERT: C 113 MET cc_start: 0.9607 (mtt) cc_final: 0.9352 (mtt) REVERT: C 237 GLN cc_start: 0.7725 (tp40) cc_final: 0.7387 (tp40) REVERT: D 28 GLU cc_start: 0.8172 (mp0) cc_final: 0.7864 (mp0) REVERT: E 169 ASN cc_start: 0.8694 (OUTLIER) cc_final: 0.8417 (m-40) REVERT: G 164 GLN cc_start: 0.7221 (pm20) cc_final: 0.6736 (tp40) REVERT: I 156 GLU cc_start: 0.7626 (tt0) cc_final: 0.7376 (tt0) REVERT: I 187 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8251 (tpt-90) REVERT: I 278 TRP cc_start: 0.7072 (OUTLIER) cc_final: 0.6830 (t60) REVERT: I 317 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7458 (tm-30) REVERT: J 45 GLN cc_start: 0.7332 (mm-40) cc_final: 0.6892 (mm110) REVERT: J 192 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8187 (mt0) REVERT: K 116 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8167 (tp) REVERT: K 413 ASP cc_start: 0.6108 (t0) cc_final: 0.5741 (t0) REVERT: K 563 ASN cc_start: 0.4430 (OUTLIER) cc_final: 0.3825 (t0) REVERT: K 672 MET cc_start: 0.4416 (OUTLIER) cc_final: 0.4212 (mpm) REVERT: K 705 MET cc_start: 0.3905 (tpt) cc_final: 0.2463 (tmt) REVERT: M 511 ASN cc_start: 0.7684 (OUTLIER) cc_final: 0.7148 (m110) REVERT: M 790 LYS cc_start: 0.7090 (mtmm) cc_final: 0.6834 (mttp) REVERT: M 824 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6612 (mp0) REVERT: M 983 MET cc_start: 0.7120 (OUTLIER) cc_final: 0.6222 (ptt) outliers start: 45 outliers final: 20 residues processed: 286 average time/residue: 1.6911 time to fit residues: 557.7808 Evaluate side-chains 284 residues out of total 3449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 252 time to evaluate : 3.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 GLU 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 216 LYS Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 169 ASN 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 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 300 LEU Chi-restraints excluded: chain K residue 323 GLN 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 451 ASP Chi-restraints excluded: chain M residue 506 VAL Chi-restraints excluded: chain M residue 511 ASN Chi-restraints excluded: chain M residue 741 ILE 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 230 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 chunk 222 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 72 optimal weight: 0.0980 chunk 237 optimal weight: 8.9990 chunk 254 optimal weight: 0.1980 chunk 184 optimal weight: 5.9990 chunk 34 optimal weight: 0.3980 chunk 293 optimal weight: 20.0000 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 GLN C 180 ASN E 200 GLN H 114 GLN I 170 ASN J 105 ASN ** K 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 184 ASN ** M 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 400 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31321 Z= 0.212 Angle : 0.541 10.654 42574 Z= 0.289 Chirality : 0.045 0.175 5027 Planarity : 0.004 0.057 5384 Dihedral : 8.776 165.979 4702 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.31 % Allowed : 11.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.13), residues: 3838 helix: 1.96 (0.15), residues: 1249 sheet: 0.94 (0.18), residues: 822 loop : -0.92 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 214 HIS 0.007 0.001 HIS K 888 PHE 0.054 0.001 PHE K 842 TYR 0.014 0.001 TYR C 157 ARG 0.012 0.000 ARG K 493 *********************** 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 296 residues out of total 3449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 253 time to evaluate : 4.046 Fit side-chains REVERT: C 65 MET cc_start: 0.8508 (tmm) cc_final: 0.8077 (tmm) REVERT: C 113 MET cc_start: 0.9599 (mtt) cc_final: 0.9323 (mtt) REVERT: C 237 GLN cc_start: 0.7691 (tp40) cc_final: 0.7368 (tp40) REVERT: D 20 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7927 (mp0) REVERT: D 28 GLU cc_start: 0.8156 (mp0) cc_final: 0.7847 (mp0) REVERT: G 164 GLN cc_start: 0.7205 (pm20) cc_final: 0.6726 (tp40) REVERT: I 156 GLU cc_start: 0.7620 (tt0) cc_final: 0.7394 (tt0) REVERT: I 187 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8283 (tpt-90) REVERT: I 278 TRP cc_start: 0.7082 (OUTLIER) cc_final: 0.6634 (t60) REVERT: I 317 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7453 (tm-30) REVERT: J 45 GLN cc_start: 0.7314 (mm-40) cc_final: 0.6813 (mm110) REVERT: J 192 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8177 (mt0) REVERT: K 116 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8142 (tp) REVERT: K 413 ASP cc_start: 0.6099 (t0) cc_final: 0.5746 (t0) REVERT: K 563 ASN cc_start: 0.4457 (OUTLIER) cc_final: 0.3847 (t0) REVERT: K 672 MET cc_start: 0.4420 (OUTLIER) cc_final: 0.4217 (mpm) REVERT: K 705 MET cc_start: 0.3984 (tpt) cc_final: 0.2527 (tmt) REVERT: M 511 ASN cc_start: 0.7712 (OUTLIER) cc_final: 0.7154 (m110) REVERT: M 621 LEU cc_start: 0.8226 (mp) cc_final: 0.7939 (mp) REVERT: M 790 LYS cc_start: 0.7037 (mtmm) cc_final: 0.6696 (mttp) REVERT: M 824 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6629 (mp0) REVERT: M 983 MET cc_start: 0.7143 (OUTLIER) cc_final: 0.6255 (ptt) outliers start: 43 outliers final: 18 residues processed: 281 average time/residue: 1.7488 time to fit residues: 567.2191 Evaluate side-chains 277 residues out of total 3449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 248 time to evaluate : 3.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 216 LYS 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 300 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 339 optimal weight: 20.0000 chunk 357 optimal weight: 7.9990 chunk 326 optimal weight: 6.9990 chunk 347 optimal weight: 5.9990 chunk 209 optimal weight: 9.9990 chunk 151 optimal weight: 0.8980 chunk 272 optimal weight: 9.9990 chunk 106 optimal weight: 4.9990 chunk 314 optimal weight: 3.9990 chunk 328 optimal weight: 6.9990 chunk 346 optimal weight: 0.4980 overall best weight: 3.2786 ------------------------------------------------------------------------------- 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 170 ASN J 105 ASN ** K 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 184 ASN ** M 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 400 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 31321 Z= 0.276 Angle : 0.594 10.338 42574 Z= 0.316 Chirality : 0.047 0.180 5027 Planarity : 0.005 0.057 5384 Dihedral : 8.863 164.269 4702 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.28 % Allowed : 12.04 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.13), residues: 3838 helix: 1.87 (0.15), residues: 1244 sheet: 0.91 (0.18), residues: 812 loop : -0.97 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 214 HIS 0.007 0.001 HIS K 888 PHE 0.056 0.002 PHE K 842 TYR 0.016 0.002 TYR C 157 ARG 0.012 0.000 ARG K 493 *********************** 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 fitting. rotamer outliers: 42 poor density : 249 time to evaluate : 3.456 Fit side-chains REVERT: B 109 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8607 (tt0) REVERT: C 113 MET cc_start: 0.9616 (mtt) cc_final: 0.9347 (mtt) REVERT: C 237 GLN cc_start: 0.7733 (tp40) cc_final: 0.7387 (tp40) REVERT: D 28 GLU cc_start: 0.8171 (mp0) cc_final: 0.7864 (mp0) REVERT: G 164 GLN cc_start: 0.7229 (pm20) cc_final: 0.6741 (tp40) REVERT: I 156 GLU cc_start: 0.7653 (tt0) cc_final: 0.7404 (tt0) REVERT: I 187 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8273 (tpt-90) REVERT: I 278 TRP cc_start: 0.7124 (OUTLIER) cc_final: 0.6645 (t60) REVERT: I 317 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7455 (tm-30) REVERT: J 45 GLN cc_start: 0.7399 (mm-40) cc_final: 0.6870 (mm110) REVERT: J 192 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8213 (mt0) REVERT: K 116 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8231 (tp) REVERT: K 413 ASP cc_start: 0.6116 (t0) cc_final: 0.5751 (t0) REVERT: K 563 ASN cc_start: 0.4406 (OUTLIER) cc_final: 0.3804 (t0) REVERT: K 672 MET cc_start: 0.4391 (OUTLIER) cc_final: 0.4190 (mpm) REVERT: K 705 MET cc_start: 0.3996 (tpt) cc_final: 0.2557 (tmt) REVERT: K 808 MET cc_start: 0.7181 (tpt) cc_final: 0.6974 (tpt) REVERT: M 511 ASN cc_start: 0.7679 (OUTLIER) cc_final: 0.7152 (m110) REVERT: M 621 LEU cc_start: 0.8239 (mp) cc_final: 0.7908 (mp) REVERT: M 790 LYS cc_start: 0.7079 (mtmm) cc_final: 0.6804 (mttp) REVERT: M 824 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6639 (mp0) REVERT: M 983 MET cc_start: 0.7141 (OUTLIER) cc_final: 0.6307 (ptt) outliers start: 42 outliers final: 23 residues processed: 273 average time/residue: 1.6708 time to fit residues: 526.0637 Evaluate side-chains 279 residues out of total 3449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 245 time to evaluate : 3.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 GLU 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 216 LYS 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 109 VAL 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 189 LEU 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 300 LEU 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 506 VAL Chi-restraints excluded: chain M residue 511 ASN Chi-restraints excluded: chain M residue 741 ILE 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 228 optimal weight: 3.9990 chunk 367 optimal weight: 5.9990 chunk 224 optimal weight: 0.2980 chunk 174 optimal weight: 0.0070 chunk 255 optimal weight: 4.9990 chunk 385 optimal weight: 30.0000 chunk 354 optimal weight: 8.9990 chunk 307 optimal weight: 0.0060 chunk 31 optimal weight: 3.9990 chunk 237 optimal weight: 8.9990 chunk 188 optimal weight: 10.0000 overall best weight: 1.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 64 GLN E 200 GLN H 114 GLN I 170 ASN J 105 ASN ** K 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 184 ASN ** M 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 400 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1291 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= 0.171 Angle : 0.517 10.736 42574 Z= 0.273 Chirality : 0.044 0.165 5027 Planarity : 0.004 0.058 5384 Dihedral : 8.707 166.209 4702 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.85 % Allowed : 12.55 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.14), residues: 3838 helix: 2.02 (0.15), residues: 1255 sheet: 1.01 (0.18), residues: 813 loop : -0.89 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 214 HIS 0.007 0.001 HIS K 888 PHE 0.056 0.001 PHE K 842 TYR 0.015 0.001 TYR K 832 ARG 0.011 0.000 ARG K 493 ********************** 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 280 residues out of total 3449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 252 time to evaluate : 3.868 Fit side-chains REVERT: C 65 MET cc_start: 0.8488 (tmm) cc_final: 0.8190 (tmm) REVERT: C 113 MET cc_start: 0.9601 (mtt) cc_final: 0.9384 (mtt) REVERT: C 237 GLN cc_start: 0.7695 (tp40) cc_final: 0.7376 (tp40) REVERT: D 20 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7915 (mp0) REVERT: D 28 GLU cc_start: 0.8177 (mp0) cc_final: 0.7848 (mp0) REVERT: G 164 GLN cc_start: 0.7195 (pm20) cc_final: 0.6714 (tp40) REVERT: I 156 GLU cc_start: 0.7608 (tt0) cc_final: 0.7386 (tt0) REVERT: I 278 TRP cc_start: 0.7111 (OUTLIER) cc_final: 0.6607 (t60) REVERT: I 317 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7437 (tm-30) REVERT: J 45 GLN cc_start: 0.7263 (mm-40) cc_final: 0.6742 (mm110) REVERT: J 192 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.8159 (mt0) REVERT: K 116 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8095 (tp) REVERT: K 413 ASP cc_start: 0.6089 (t0) cc_final: 0.5740 (t0) REVERT: K 563 ASN cc_start: 0.4433 (OUTLIER) cc_final: 0.3831 (t0) REVERT: K 672 MET cc_start: 0.4371 (OUTLIER) cc_final: 0.4169 (mpm) REVERT: K 705 MET cc_start: 0.3969 (tpt) cc_final: 0.2534 (tmt) REVERT: K 808 MET cc_start: 0.7141 (tpt) cc_final: 0.6921 (tpt) REVERT: M 511 ASN cc_start: 0.7697 (OUTLIER) cc_final: 0.7114 (m110) REVERT: M 790 LYS cc_start: 0.7012 (mtmm) cc_final: 0.6669 (mttp) REVERT: M 824 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6619 (mp0) REVERT: M 983 MET cc_start: 0.7045 (OUTLIER) cc_final: 0.6113 (ptt) outliers start: 28 outliers final: 13 residues processed: 269 average time/residue: 1.7318 time to fit residues: 538.1012 Evaluate side-chains 270 residues out of total 3449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 247 time to evaluate : 3.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 216 LYS 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 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 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 741 ILE 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 243 optimal weight: 0.9980 chunk 327 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 283 optimal weight: 8.9990 chunk 45 optimal weight: 0.0770 chunk 85 optimal weight: 1.9990 chunk 307 optimal weight: 10.0000 chunk 128 optimal weight: 1.9990 chunk 315 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- 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 ** K 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 184 ASN ** M 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 400 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.163869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.109877 restraints weight = 36356.915| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.89 r_work: 0.3060 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 31321 Z= 0.133 Angle : 0.477 11.085 42574 Z= 0.250 Chirality : 0.043 0.161 5027 Planarity : 0.004 0.058 5384 Dihedral : 8.480 169.227 4702 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.88 % Allowed : 12.67 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.14), residues: 3838 helix: 2.18 (0.15), residues: 1257 sheet: 1.14 (0.18), residues: 818 loop : -0.77 (0.14), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 214 HIS 0.009 0.001 HIS K 888 PHE 0.055 0.001 PHE K 842 TYR 0.014 0.001 TYR K 832 ARG 0.011 0.000 ARG K 493 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10299.32 seconds wall clock time: 181 minutes 10.60 seconds (10870.60 seconds total)