Starting phenix.real_space_refine on Wed Apr 8 17:23:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ob1_70289/04_2026/9ob1_70289.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ob1_70289/04_2026/9ob1_70289.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ob1_70289/04_2026/9ob1_70289.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ob1_70289/04_2026/9ob1_70289.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ob1_70289/04_2026/9ob1_70289.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ob1_70289/04_2026/9ob1_70289.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.031 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 300 5.49 5 S 99 5.16 5 C 24553 2.51 5 N 7156 2.21 5 O 8390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40498 Number of models: 1 Model: "" Number of chains: 26 Chain: "I" Number of atoms: 2954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2954 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2985 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "Q" Number of atoms: 3372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3372 Classifications: {'peptide': 419} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 22, 'TRANS': 396} Chain breaks: 5 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "R" Number of atoms: 3512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3512 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 28, 'TRANS': 413} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "S" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1015 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 118} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "T" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3351 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 17, 'TRANS': 419} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 4 Chain: "U" Number of atoms: 3421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3421 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 434} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "V" Number of atoms: 3394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3394 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 423} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 3398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3398 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 431} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3404 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 18, 'TRANS': 424} Chain: "Y" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3351 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 425} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Z" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 245 Classifications: {'peptide': 28} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 25} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "B" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 621 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 794 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 620 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 827 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "T" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.26, per 1000 atoms: 0.23 Number of scatterers: 40498 At special positions: 0 Unit cell: (125.292, 177.701, 212.914, 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 99 16.00 P 300 15.00 O 8390 8.00 N 7156 7.00 C 24553 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.27 Conformation dependent library (CDL) restraints added in 1.5 seconds 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8240 Finding SS restraints... Secondary structure from input PDB file: 182 helices and 41 sheets defined 48.2% alpha, 10.0% beta 131 base pairs and 257 stacking pairs defined. Time for finding SS restraints: 5.46 Creating SS restraints... Processing helix chain 'Q' and resid 957 through 972 Processing helix chain 'Q' and resid 974 through 985 removed outlier: 3.699A pdb=" N ASP Q 985 " --> pdb=" O ALA Q 981 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1000 through 1013 removed outlier: 3.695A pdb=" N VAL Q1004 " --> pdb=" O LEU Q1000 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1014 through 1017 removed outlier: 3.544A pdb=" N PHE Q1017 " --> pdb=" O PRO Q1014 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 1014 through 1017' Processing helix chain 'Q' and resid 1086 through 1094 Processing helix chain 'Q' and resid 1101 through 1111 Processing helix chain 'Q' and resid 1121 through 1133 Processing helix chain 'Q' and resid 1138 through 1144 Processing helix chain 'Q' and resid 1147 through 1154 Processing helix chain 'Q' and resid 1169 through 1178 Processing helix chain 'Q' and resid 1185 through 1191 Processing helix chain 'Q' and resid 1193 through 1201 Processing helix chain 'Q' and resid 1202 through 1206 removed outlier: 4.037A pdb=" N ILE Q1206 " --> pdb=" O LEU Q1203 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1226 through 1238 removed outlier: 3.820A pdb=" N THR Q1230 " --> pdb=" O SER Q1226 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1239 through 1246 Processing helix chain 'Q' and resid 1250 through 1259 Processing helix chain 'Q' and resid 1264 through 1268 Processing helix chain 'Q' and resid 1290 through 1298 removed outlier: 4.432A pdb=" N SER Q1298 " --> pdb=" O PHE Q1294 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1298 through 1311 Processing helix chain 'Q' and resid 1326 through 1334 removed outlier: 3.544A pdb=" N LEU Q1330 " --> pdb=" O LYS Q1326 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1357 through 1364 Processing helix chain 'Q' and resid 1397 through 1406 removed outlier: 3.845A pdb=" N ASP Q1401 " --> pdb=" O ASN Q1397 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1427 through 1434 removed outlier: 3.623A pdb=" N ARG Q1431 " --> pdb=" O THR Q1427 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 87 removed outlier: 3.592A pdb=" N THR R 86 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 94 Processing helix chain 'R' and resid 108 through 121 Processing helix chain 'R' and resid 143 through 159 removed outlier: 4.329A pdb=" N THR R 157 " --> pdb=" O ILE R 153 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 177 Processing helix chain 'R' and resid 216 through 231 Processing helix chain 'R' and resid 239 through 250 Processing helix chain 'R' and resid 259 through 264 removed outlier: 3.758A pdb=" N LYS R 263 " --> pdb=" O GLU R 259 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 274 removed outlier: 3.510A pdb=" N ASP R 274 " --> pdb=" O LEU R 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 589 through 596 Processing helix chain 'R' and resid 605 through 610 removed outlier: 3.647A pdb=" N GLN R 609 " --> pdb=" O ASN R 605 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N HIS R 610 " --> pdb=" O ILE R 606 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 605 through 610' Processing helix chain 'R' and resid 619 through 624 removed outlier: 3.748A pdb=" N VAL R 624 " --> pdb=" O ARG R 620 " (cutoff:3.500A) Processing helix chain 'R' and resid 625 through 626 No H-bonds generated for 'chain 'R' and resid 625 through 626' Processing helix chain 'R' and resid 627 through 632 removed outlier: 3.550A pdb=" N GLY R 632 " --> pdb=" O THR R 629 " (cutoff:3.500A) Processing helix chain 'R' and resid 637 through 649 removed outlier: 4.032A pdb=" N LYS R 649 " --> pdb=" O ILE R 645 " (cutoff:3.500A) Processing helix chain 'R' and resid 658 through 667 Processing helix chain 'R' and resid 672 through 677 removed outlier: 4.029A pdb=" N LYS R 676 " --> pdb=" O GLY R 673 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL R 677 " --> pdb=" O ASN R 674 " (cutoff:3.500A) Processing helix chain 'R' and resid 679 through 692 removed outlier: 3.690A pdb=" N PHE R 691 " --> pdb=" O GLU R 687 " (cutoff:3.500A) Processing helix chain 'R' and resid 708 through 720 removed outlier: 3.660A pdb=" N LYS R 712 " --> pdb=" O LEU R 708 " (cutoff:3.500A) Processing helix chain 'R' and resid 720 through 725 Processing helix chain 'R' and resid 731 through 738 Processing helix chain 'S' and resid 29 through 38 Processing helix chain 'S' and resid 64 through 83 removed outlier: 3.814A pdb=" N SER S 68 " --> pdb=" O ARG S 64 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS S 83 " --> pdb=" O THR S 79 " (cutoff:3.500A) Processing helix chain 'S' and resid 136 through 143 Processing helix chain 'S' and resid 151 through 160 removed outlier: 3.664A pdb=" N TYR S 155 " --> pdb=" O VAL S 151 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG S 159 " --> pdb=" O TYR S 155 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 68 removed outlier: 3.738A pdb=" N LYS T 68 " --> pdb=" O LEU T 64 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 97 Processing helix chain 'T' and resid 116 through 127 Processing helix chain 'T' and resid 182 through 192 Processing helix chain 'T' and resid 217 through 219 No H-bonds generated for 'chain 'T' and resid 217 through 219' Processing helix chain 'T' and resid 249 through 255 Processing helix chain 'T' and resid 281 through 297 Processing helix chain 'T' and resid 313 through 316 Processing helix chain 'T' and resid 317 through 328 Processing helix chain 'T' and resid 360 through 365 Processing helix chain 'T' and resid 376 through 391 Processing helix chain 'T' and resid 396 through 410 Processing helix chain 'T' and resid 411 through 418 removed outlier: 3.785A pdb=" N ALA T 415 " --> pdb=" O SER T 411 " (cutoff:3.500A) Processing helix chain 'T' and resid 418 through 428 Processing helix chain 'T' and resid 435 through 446 Processing helix chain 'T' and resid 448 through 459 Processing helix chain 'U' and resid 47 through 64 removed outlier: 3.578A pdb=" N GLY U 64 " --> pdb=" O MET U 60 " (cutoff:3.500A) Processing helix chain 'U' and resid 80 through 93 removed outlier: 3.679A pdb=" N GLY U 93 " --> pdb=" O SER U 89 " (cutoff:3.500A) Processing helix chain 'U' and resid 112 through 123 Processing helix chain 'U' and resid 172 through 182 removed outlier: 3.530A pdb=" N GLU U 182 " --> pdb=" O GLY U 178 " (cutoff:3.500A) Processing helix chain 'U' and resid 207 through 209 No H-bonds generated for 'chain 'U' and resid 207 through 209' Processing helix chain 'U' and resid 241 through 250 removed outlier: 3.716A pdb=" N ARG U 250 " --> pdb=" O VAL U 246 " (cutoff:3.500A) Processing helix chain 'U' and resid 266 through 283 removed outlier: 3.620A pdb=" N ARG U 270 " --> pdb=" O ARG U 266 " (cutoff:3.500A) Processing helix chain 'U' and resid 302 through 313 Processing helix chain 'U' and resid 340 through 343 Processing helix chain 'U' and resid 344 through 350 removed outlier: 3.510A pdb=" N ARG U 350 " --> pdb=" O ASP U 346 " (cutoff:3.500A) Processing helix chain 'U' and resid 360 through 375 Processing helix chain 'U' and resid 380 through 394 Processing helix chain 'U' and resid 395 through 413 removed outlier: 3.729A pdb=" N SER U 399 " --> pdb=" O SER U 395 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N SER U 404 " --> pdb=" O SER U 400 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL U 405 " --> pdb=" O ASN U 401 " (cutoff:3.500A) Processing helix chain 'U' and resid 419 through 430 removed outlier: 3.655A pdb=" N VAL U 423 " --> pdb=" O GLU U 419 " (cutoff:3.500A) Processing helix chain 'U' and resid 432 through 443 removed outlier: 3.715A pdb=" N ASN U 443 " --> pdb=" O TYR U 439 " (cutoff:3.500A) Processing helix chain 'V' and resid 51 through 67 Processing helix chain 'V' and resid 84 through 97 Processing helix chain 'V' and resid 108 through 111 removed outlier: 3.686A pdb=" N TYR V 111 " --> pdb=" O SER V 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 108 through 111' Processing helix chain 'V' and resid 116 through 128 removed outlier: 3.612A pdb=" N ALA V 128 " --> pdb=" O ASN V 124 " (cutoff:3.500A) Processing helix chain 'V' and resid 182 through 184 No H-bonds generated for 'chain 'V' and resid 182 through 184' Processing helix chain 'V' and resid 185 through 192 Processing helix chain 'V' and resid 249 through 258 Processing helix chain 'V' and resid 264 through 273 removed outlier: 3.516A pdb=" N MET V 268 " --> pdb=" O ASP V 264 " (cutoff:3.500A) Processing helix chain 'V' and resid 281 through 298 removed outlier: 3.519A pdb=" N ARG V 285 " --> pdb=" O THR V 281 " (cutoff:3.500A) Processing helix chain 'V' and resid 312 through 316 Processing helix chain 'V' and resid 317 through 328 Processing helix chain 'V' and resid 360 through 366 removed outlier: 3.653A pdb=" N ARG V 366 " --> pdb=" O ASP V 362 " (cutoff:3.500A) Processing helix chain 'V' and resid 376 through 391 Processing helix chain 'V' and resid 396 through 410 Processing helix chain 'V' and resid 411 through 417 Processing helix chain 'V' and resid 418 through 428 Processing helix chain 'V' and resid 435 through 446 Processing helix chain 'V' and resid 448 through 459 Processing helix chain 'W' and resid 47 through 64 Processing helix chain 'W' and resid 80 through 92 Processing helix chain 'W' and resid 112 through 123 Processing helix chain 'W' and resid 172 through 181 removed outlier: 3.560A pdb=" N LYS W 181 " --> pdb=" O ASP W 177 " (cutoff:3.500A) Processing helix chain 'W' and resid 241 through 250 removed outlier: 3.959A pdb=" N ARG W 250 " --> pdb=" O VAL W 246 " (cutoff:3.500A) Processing helix chain 'W' and resid 252 through 260 removed outlier: 3.649A pdb=" N ALA W 256 " --> pdb=" O GLN W 252 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE W 258 " --> pdb=" O PHE W 254 " (cutoff:3.500A) Processing helix chain 'W' and resid 266 through 283 Processing helix chain 'W' and resid 297 through 301 Processing helix chain 'W' and resid 302 through 313 Processing helix chain 'W' and resid 340 through 343 Processing helix chain 'W' and resid 344 through 350 Processing helix chain 'W' and resid 360 through 375 Processing helix chain 'W' and resid 380 through 394 Processing helix chain 'W' and resid 395 through 413 removed outlier: 4.341A pdb=" N SER W 404 " --> pdb=" O SER W 400 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL W 405 " --> pdb=" O ASN W 401 " (cutoff:3.500A) Processing helix chain 'W' and resid 419 through 430 removed outlier: 3.510A pdb=" N VAL W 423 " --> pdb=" O GLU W 419 " (cutoff:3.500A) Processing helix chain 'W' and resid 432 through 443 Processing helix chain 'W' and resid 444 through 447 Processing helix chain 'X' and resid 51 through 68 removed outlier: 3.743A pdb=" N LYS X 68 " --> pdb=" O LEU X 64 " (cutoff:3.500A) Processing helix chain 'X' and resid 84 through 97 Processing helix chain 'X' and resid 108 through 111 removed outlier: 3.657A pdb=" N TYR X 111 " --> pdb=" O SER X 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 108 through 111' Processing helix chain 'X' and resid 116 through 127 Processing helix chain 'X' and resid 182 through 191 Processing helix chain 'X' and resid 249 through 258 Processing helix chain 'X' and resid 264 through 271 Processing helix chain 'X' and resid 281 through 298 Processing helix chain 'X' and resid 312 through 316 Processing helix chain 'X' and resid 317 through 328 Processing helix chain 'X' and resid 360 through 366 removed outlier: 3.876A pdb=" N ARG X 366 " --> pdb=" O ASP X 362 " (cutoff:3.500A) Processing helix chain 'X' and resid 376 through 391 Processing helix chain 'X' and resid 396 through 410 Processing helix chain 'X' and resid 411 through 417 Processing helix chain 'X' and resid 418 through 429 Processing helix chain 'X' and resid 435 through 446 Processing helix chain 'X' and resid 448 through 458 Processing helix chain 'Y' and resid 47 through 64 Processing helix chain 'Y' and resid 80 through 93 removed outlier: 3.890A pdb=" N GLY Y 93 " --> pdb=" O SER Y 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 112 through 123 Processing helix chain 'Y' and resid 172 through 181 Processing helix chain 'Y' and resid 241 through 249 Processing helix chain 'Y' and resid 255 through 260 Processing helix chain 'Y' and resid 266 through 284 removed outlier: 3.682A pdb=" N ARG Y 270 " --> pdb=" O ARG Y 266 " (cutoff:3.500A) Processing helix chain 'Y' and resid 298 through 301 Processing helix chain 'Y' and resid 302 through 313 Processing helix chain 'Y' and resid 340 through 343 Processing helix chain 'Y' and resid 344 through 350 Processing helix chain 'Y' and resid 360 through 375 Processing helix chain 'Y' and resid 380 through 394 Processing helix chain 'Y' and resid 395 through 413 removed outlier: 4.357A pdb=" N SER Y 404 " --> pdb=" O SER Y 400 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL Y 405 " --> pdb=" O ASN Y 401 " (cutoff:3.500A) Processing helix chain 'Y' and resid 419 through 430 removed outlier: 3.536A pdb=" N VAL Y 423 " --> pdb=" O GLU Y 419 " (cutoff:3.500A) Processing helix chain 'Y' and resid 432 through 443 removed outlier: 3.508A pdb=" N SER Y 436 " --> pdb=" O ASP Y 432 " (cutoff:3.500A) Processing helix chain 'Y' and resid 444 through 447 Processing helix chain 'A' and resid 45 through 57 removed outlier: 3.541A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.562A pdb=" N ILE A 124 " --> pdb=" O GLN A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 40 removed outlier: 3.769A pdb=" N ILE B 35 " --> pdb=" O THR B 31 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 77 removed outlier: 4.123A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN B 65 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP B 69 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA B 77 " --> pdb=" O TYR B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.908A pdb=" N VAL B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 4.284A pdb=" N VAL C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP C 73 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 removed outlier: 3.663A pdb=" N ASN C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'D' and resid 40 through 52 Processing helix chain 'D' and resid 58 through 86 Processing helix chain 'D' and resid 93 through 104 removed outlier: 3.764A pdb=" N ILE D 97 " --> pdb=" O SER D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 127 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.611A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.659A pdb=" N ASP E 106 " --> pdb=" O SER E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.658A pdb=" N ILE E 124 " --> pdb=" O GLN E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 30 removed outlier: 4.154A pdb=" N ILE F 30 " --> pdb=" O ILE F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 43 Processing helix chain 'F' and resid 50 through 63 removed outlier: 4.031A pdb=" N VAL F 61 " --> pdb=" O GLY F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 77 removed outlier: 4.324A pdb=" N ASP F 69 " --> pdb=" O ASN F 65 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR F 72 " --> pdb=" O ARG F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 95 removed outlier: 3.581A pdb=" N VAL F 87 " --> pdb=" O THR F 83 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL F 88 " --> pdb=" O ALA F 84 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TYR F 89 " --> pdb=" O MET F 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 22 removed outlier: 4.149A pdb=" N LYS G 21 " --> pdb=" O SER G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 37 removed outlier: 3.718A pdb=" N VAL G 31 " --> pdb=" O PRO G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 74 removed outlier: 4.402A pdb=" N VAL G 50 " --> pdb=" O SER G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 91 removed outlier: 3.703A pdb=" N LEU G 84 " --> pdb=" O ILE G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'H' and resid 40 through 52 removed outlier: 3.676A pdb=" N THR H 51 " --> pdb=" O VAL H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 87 Processing helix chain 'H' and resid 93 through 105 removed outlier: 3.563A pdb=" N ILE H 97 " --> pdb=" O SER H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 126 Processing sheet with id=AA1, first strand: chain 'Q' and resid 949 through 954 removed outlier: 3.798A pdb=" N LEU Q1422 " --> pdb=" O PHE Q1391 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Q' and resid 1026 through 1027 removed outlier: 5.979A pdb=" N PHE Q1026 " --> pdb=" O SER Q1215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'Q' and resid 1071 through 1073 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 1071 through 1073 current: chain 'X' and resid 163 through 172 removed outlier: 3.518A pdb=" N GLY X 175 " --> pdb=" O SER X 172 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 175 through 181 current: chain 'X' and resid 209 through 215 removed outlier: 6.080A pdb=" N VAL X 230 " --> pdb=" O VAL X 212 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ARG X 214 " --> pdb=" O VAL X 230 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Q' and resid 1082 through 1084 removed outlier: 5.718A pdb=" N TYR Q1083 " --> pdb=" O GLU Q1222 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'R' and resid 40 through 41 removed outlier: 6.704A pdb=" N ILE R 40 " --> pdb=" O LEU R 135 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N THR R 137 " --> pdb=" O ILE R 40 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR R 164 " --> pdb=" O ILE R 134 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY R 166 " --> pdb=" O LEU R 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'R' and resid 43 through 44 removed outlier: 3.549A pdb=" N HIS R 61 " --> pdb=" O ALA R 51 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 184 through 189 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 203 through 204 current: chain 'R' and resid 700 through 701 Processing sheet with id=AA8, first strand: chain 'R' and resid 277 through 278 Processing sheet with id=AA9, first strand: chain 'S' and resid 125 through 126 removed outlier: 3.606A pdb=" N TYR S 125 " --> pdb=" O TYR S 134 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'T' and resid 44 through 45 Processing sheet with id=AB2, first strand: chain 'T' and resid 102 through 106 removed outlier: 6.040A pdb=" N CYS T 103 " --> pdb=" O PHE T 309 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ASP T 311 " --> pdb=" O CYS T 103 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU T 105 " --> pdb=" O ASP T 311 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY T 79 " --> pdb=" O SER T 340 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'T' and resid 129 through 143 removed outlier: 6.773A pdb=" N TYR T 201 " --> pdb=" O ARG T 211 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ARG T 211 " --> pdb=" O TYR T 201 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N GLU T 203 " --> pdb=" O VAL T 209 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL T 209 " --> pdb=" O GLU T 203 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N VAL T 230 " --> pdb=" O VAL T 212 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N ARG T 214 " --> pdb=" O VAL T 230 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'T' and resid 146 through 150 removed outlier: 3.822A pdb=" N GLU T 146 " --> pdb=" O GLY T 169 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'T' and resid 344 through 346 Processing sheet with id=AB6, first strand: chain 'T' and resid 394 through 395 removed outlier: 7.342A pdb=" N GLN T 394 " --> pdb=" O ILE T 434 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'U' and resid 40 through 41 removed outlier: 3.585A pdb=" N SER U 41 " --> pdb=" O MET U 44 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'U' and resid 98 through 102 removed outlier: 6.285A pdb=" N THR U 99 " --> pdb=" O PHE U 294 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASP U 296 " --> pdb=" O THR U 99 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE U 101 " --> pdb=" O ASP U 296 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ALA U 70 " --> pdb=" O ILE U 352 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ILE U 354 " --> pdb=" O ALA U 70 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU U 72 " --> pdb=" O ILE U 354 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'U' and resid 125 through 146 removed outlier: 6.638A pdb=" N THR U 159 " --> pdb=" O VAL U 141 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE U 143 " --> pdb=" O LYS U 157 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LYS U 157 " --> pdb=" O ILE U 143 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ILE U 145 " --> pdb=" O GLN U 155 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLN U 155 " --> pdb=" O ILE U 145 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY U 156 " --> pdb=" O LEU U 171 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE U 160 " --> pdb=" O THR U 167 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 166 through 171 current: chain 'U' and resid 199 through 205 removed outlier: 5.224A pdb=" N VAL U 222 " --> pdb=" O LEU U 202 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ARG U 204 " --> pdb=" O VAL U 222 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'U' and resid 330 through 331 Processing sheet with id=AC2, first strand: chain 'V' and resid 102 through 106 removed outlier: 6.191A pdb=" N ILE V 75 " --> pdb=" O LEU V 338 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N SER V 340 " --> pdb=" O ILE V 75 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU V 77 " --> pdb=" O SER V 340 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'V' and resid 129 through 151 removed outlier: 6.552A pdb=" N GLY V 169 " --> pdb=" O THR V 145 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU V 147 " --> pdb=" O ILE V 167 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE V 167 " --> pdb=" O LEU V 147 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N HIS V 165 " --> pdb=" O PRO V 149 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASP V 151 " --> pdb=" O ILE V 163 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE V 163 " --> pdb=" O ASP V 151 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL V 166 " --> pdb=" O LEU V 181 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 176 through 181 current: chain 'V' and resid 211 through 214 Processing sheet with id=AC4, first strand: chain 'V' and resid 344 through 346 Processing sheet with id=AC5, first strand: chain 'V' and resid 394 through 395 removed outlier: 7.198A pdb=" N GLN V 394 " --> pdb=" O ILE V 434 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'W' and resid 40 through 41 Processing sheet with id=AC7, first strand: chain 'W' and resid 98 through 102 removed outlier: 6.378A pdb=" N THR W 99 " --> pdb=" O PHE W 294 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ASP W 296 " --> pdb=" O THR W 99 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE W 101 " --> pdb=" O ASP W 296 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU W 293 " --> pdb=" O ILE W 320 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA W 70 " --> pdb=" O ILE W 352 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ILE W 354 " --> pdb=" O ALA W 70 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU W 72 " --> pdb=" O ILE W 354 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'W' and resid 125 through 147 removed outlier: 6.714A pdb=" N THR W 159 " --> pdb=" O VAL W 141 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE W 143 " --> pdb=" O LYS W 157 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LYS W 157 " --> pdb=" O ILE W 143 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ILE W 145 " --> pdb=" O GLN W 155 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLN W 155 " --> pdb=" O ILE W 145 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY W 156 " --> pdb=" O LEU W 171 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 166 through 171 current: chain 'W' and resid 198 through 204 Processing sheet with id=AC9, first strand: chain 'W' and resid 330 through 331 Processing sheet with id=AD1, first strand: chain 'X' and resid 44 through 45 Processing sheet with id=AD2, first strand: chain 'X' and resid 102 through 106 removed outlier: 7.829A pdb=" N VAL X 370 " --> pdb=" O ALA X 74 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU X 76 " --> pdb=" O VAL X 370 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'X' and resid 344 through 346 Processing sheet with id=AD4, first strand: chain 'X' and resid 394 through 395 removed outlier: 7.616A pdb=" N GLN X 394 " --> pdb=" O ILE X 434 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'Y' and resid 40 through 41 removed outlier: 3.664A pdb=" N SER Y 41 " --> pdb=" O MET Y 44 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Y' and resid 98 through 102 removed outlier: 6.480A pdb=" N THR Y 99 " --> pdb=" O PHE Y 294 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ASP Y 296 " --> pdb=" O THR Y 99 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE Y 101 " --> pdb=" O ASP Y 296 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA Y 70 " --> pdb=" O ILE Y 352 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ILE Y 354 " --> pdb=" O ALA Y 70 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU Y 72 " --> pdb=" O ILE Y 354 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Y' and resid 125 through 146 removed outlier: 6.761A pdb=" N THR Y 159 " --> pdb=" O VAL Y 141 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ILE Y 143 " --> pdb=" O LYS Y 157 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LYS Y 157 " --> pdb=" O ILE Y 143 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ILE Y 145 " --> pdb=" O GLN Y 155 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N GLN Y 155 " --> pdb=" O ILE Y 145 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLY Y 156 " --> pdb=" O LEU Y 171 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 166 through 171 current: chain 'Y' and resid 199 through 204 Processing sheet with id=AD8, first strand: chain 'Y' and resid 330 through 331 Processing sheet with id=AD9, first strand: chain 'C' and resid 43 through 44 removed outlier: 8.053A pdb=" N ARG C 43 " --> pdb=" O ILE D 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AE2, first strand: chain 'E' and resid 83 through 84 removed outlier: 5.965A pdb=" N ARG E 83 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AE4, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.500A pdb=" N ARG G 43 " --> pdb=" O ILE H 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'G' and resid 78 through 79 1501 hydrogen bonds defined for protein. 4383 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 329 hydrogen bonds 654 hydrogen bond angles 0 basepair planarities 131 basepair parallelities 257 stacking parallelities Total time for adding SS restraints: 11.51 Time building geometry restraints manager: 4.37 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: 12130 1.34 - 1.46: 10208 1.46 - 1.58: 18619 1.58 - 1.71: 596 1.71 - 1.83: 174 Bond restraints: 41727 Sorted by residual: bond pdb=" N SER Q1183 " pdb=" CA SER Q1183 " ideal model delta sigma weight residual 1.454 1.484 -0.030 1.17e-02 7.31e+03 6.78e+00 bond pdb=" N ASP U 95 " pdb=" CA ASP U 95 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.25e+00 bond pdb=" N VAL Q1186 " pdb=" CA VAL Q1186 " ideal model delta sigma weight residual 1.463 1.490 -0.027 1.14e-02 7.69e+03 5.80e+00 bond pdb=" N TYR S 125 " pdb=" CA TYR S 125 " ideal model delta sigma weight residual 1.454 1.483 -0.029 1.27e-02 6.20e+03 5.12e+00 bond pdb=" CB LYS X 294 " pdb=" CG LYS X 294 " ideal model delta sigma weight residual 1.520 1.587 -0.067 3.00e-02 1.11e+03 5.05e+00 ... (remaining 41722 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.87: 57190 3.87 - 7.74: 398 7.74 - 11.61: 69 11.61 - 15.48: 11 15.48 - 19.35: 7 Bond angle restraints: 57675 Sorted by residual: angle pdb=" CA PRO S 45 " pdb=" N PRO S 45 " pdb=" CD PRO S 45 " ideal model delta sigma weight residual 112.00 102.81 9.19 1.40e+00 5.10e-01 4.30e+01 angle pdb=" CB MET T 70 " pdb=" CG MET T 70 " pdb=" SD MET T 70 " ideal model delta sigma weight residual 112.70 131.23 -18.53 3.00e+00 1.11e-01 3.81e+01 angle pdb=" CA LYS H 111 " pdb=" CB LYS H 111 " pdb=" CG LYS H 111 " ideal model delta sigma weight residual 114.10 126.38 -12.28 2.00e+00 2.50e-01 3.77e+01 angle pdb=" CA ARG F 41 " pdb=" CB ARG F 41 " pdb=" CG ARG F 41 " ideal model delta sigma weight residual 114.10 126.00 -11.90 2.00e+00 2.50e-01 3.54e+01 angle pdb=" CA TYR B 89 " pdb=" CB TYR B 89 " pdb=" CG TYR B 89 " ideal model delta sigma weight residual 113.90 124.57 -10.67 1.80e+00 3.09e-01 3.51e+01 ... (remaining 57670 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 22486 35.30 - 70.60: 2146 70.60 - 105.90: 81 105.90 - 141.20: 4 141.20 - 176.50: 1 Dihedral angle restraints: 24718 sinusoidal: 11960 harmonic: 12758 Sorted by residual: dihedral pdb=" C5' ADP W 501 " pdb=" O5' ADP W 501 " pdb=" PA ADP W 501 " pdb=" O2A ADP W 501 " ideal model delta sinusoidal sigma weight residual -60.00 -162.69 102.70 1 2.00e+01 2.50e-03 2.93e+01 dihedral pdb=" O1B ADP W 501 " pdb=" O3A ADP W 501 " pdb=" PB ADP W 501 " pdb=" PA ADP W 501 " ideal model delta sinusoidal sigma weight residual -60.00 -148.60 88.60 1 2.00e+01 2.50e-03 2.34e+01 dihedral pdb=" C5' ADP X 501 " pdb=" O5' ADP X 501 " pdb=" PA ADP X 501 " pdb=" O2A ADP X 501 " ideal model delta sinusoidal sigma weight residual -60.00 -147.21 87.21 1 2.00e+01 2.50e-03 2.28e+01 ... (remaining 24715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 5825 0.075 - 0.149: 788 0.149 - 0.224: 79 0.224 - 0.299: 15 0.299 - 0.373: 2 Chirality restraints: 6709 Sorted by residual: chirality pdb=" CA SER Q1183 " pdb=" N SER Q1183 " pdb=" C SER Q1183 " pdb=" CB SER Q1183 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CB THR W 40 " pdb=" CA THR W 40 " pdb=" OG1 THR W 40 " pdb=" CG2 THR W 40 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CB ILE B 30 " pdb=" CA ILE B 30 " pdb=" CG1 ILE B 30 " pdb=" CG2 ILE B 30 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 6706 not shown) Planarity restraints: 6361 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL R 125 " -0.103 5.00e-02 4.00e+02 1.52e-01 3.70e+01 pdb=" N PRO R 126 " 0.263 5.00e-02 4.00e+02 pdb=" CA PRO R 126 " -0.083 5.00e-02 4.00e+02 pdb=" CD PRO R 126 " -0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE S 44 " 0.064 5.00e-02 4.00e+02 9.28e-02 1.38e+01 pdb=" N PRO S 45 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO S 45 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO S 45 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 40 " 0.017 2.00e-02 2.50e+03 2.59e-02 1.34e+01 pdb=" CG TYR G 40 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR G 40 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR G 40 " 0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR G 40 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR G 40 " -0.017 2.00e-02 2.50e+03 pdb=" CZ TYR G 40 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR G 40 " -0.000 2.00e-02 2.50e+03 ... (remaining 6358 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 9228 2.79 - 3.32: 36473 3.32 - 3.84: 75421 3.84 - 4.37: 84924 4.37 - 4.90: 137193 Nonbonded interactions: 343239 Sorted by model distance: nonbonded pdb=" OG1 THR W 162 " pdb=" O PRO W 225 " model vdw 2.258 3.040 nonbonded pdb=" OG SER Y 380 " pdb=" OD1 ASP Y 382 " model vdw 2.266 3.040 nonbonded pdb=" O ALA V 26 " pdb=" O3' ADP V 501 " model vdw 2.274 3.040 nonbonded pdb=" OG1 THR T 248 " pdb=" OD1 ASP T 251 " model vdw 2.276 3.040 nonbonded pdb=" O ALA T 449 " pdb=" OG1 THR T 453 " model vdw 2.278 3.040 ... (remaining 343234 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 38 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 134)) selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 25 through 91 or (resid 92 and (name N or name CA or name \ C or name O or name CB )) or resid 93 through 103)) selection = (chain 'F' and (resid 25 through 66 or (resid 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 through 103)) } ncs_group { reference = (chain 'C' and (resid 16 through 62 or (resid 63 and (name N or name CA or name \ C or name O or name CB )) or resid 64 through 87 or (resid 88 and (name N or nam \ e CA or name C or name O or name CB )) or resid 89 through 120)) selection = (chain 'G' and resid 16 through 120) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'T' and (resid 22 through 462 or (resid 463 and (name N or name CA or nam \ e C or name O or name CB )) or resid 501)) selection = (chain 'V' and (resid 22 through 43 or (resid 44 and (name N or name CA or name \ C or name O or name CB )) or resid 45 through 74 or (resid 75 and (name N or nam \ e CA or name C or name O or name CB )) or resid 76 through 154 or (resid 161 thr \ ough 163 and (name N or name CA or name C or name O or name CB )) or resid 164 t \ hrough 501)) selection = (chain 'X' and (resid 22 through 43 or (resid 44 and (name N or name CA or name \ C or name O or name CB )) or resid 45 through 74 or (resid 75 and (name N or nam \ e CA or name C or name O or name CB )) or resid 76 through 154 or (resid 161 thr \ ough 163 and (name N or name CA or name C or name O or name CB )) or resid 164 t \ hrough 462 or (resid 463 and (name N or name CA or name C or name O or name CB ) \ ) or resid 501)) } ncs_group { reference = (chain 'U' and (resid 18 through 167 or (resid 168 and (name N or name CA or nam \ e C or name O or name CB )) or resid 169 through 210 or resid 221 through 459 or \ resid 501)) selection = (chain 'W' and (resid 18 through 167 or (resid 168 and (name N or name CA or nam \ e C or name O or name CB )) or resid 169 through 210 or resid 221 through 501)) selection = (chain 'Y' and (resid 18 through 459 or resid 501)) } 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: 5.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.650 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 42.460 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 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 : 0.005 0.095 41727 Z= 0.224 Angle : 0.915 19.353 57675 Z= 0.473 Chirality : 0.052 0.373 6709 Planarity : 0.007 0.152 6361 Dihedral : 22.201 176.497 16478 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.03 % Allowed : 26.99 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.11), residues: 4360 helix: -1.59 (0.09), residues: 2008 sheet: 0.09 (0.21), residues: 593 loop : -1.23 (0.14), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 53 TYR 0.056 0.002 TYR G 40 PHE 0.056 0.002 PHE R 104 TRP 0.045 0.004 TRP R 108 HIS 0.006 0.001 HIS H 112 Details of bonding type rmsd covalent geometry : bond 0.00498 (41727) covalent geometry : angle 0.91480 (57675) hydrogen bonds : bond 0.18888 ( 1830) hydrogen bonds : angle 7.27404 ( 5037) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 296 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1293 ARG cc_start: 0.8410 (tmm160) cc_final: 0.8167 (ttp80) REVERT: Q 1331 MET cc_start: 0.8576 (mmt) cc_final: 0.8227 (mmm) REVERT: S 147 MET cc_start: 0.7279 (mmp) cc_final: 0.5845 (mtt) REVERT: D 83 LEU cc_start: 0.9110 (mm) cc_final: 0.8122 (tp) REVERT: G 52 LEU cc_start: 0.8859 (mt) cc_final: 0.8349 (pp) REVERT: H 45 TYR cc_start: 0.7854 (m-10) cc_final: 0.7269 (m-80) outliers start: 1 outliers final: 1 residues processed: 297 average time/residue: 0.2587 time to fit residues: 125.3526 Evaluate side-chains 280 residues out of total 3804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 279 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 125 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 432 optimal weight: 8.9990 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 0.8980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 40.0000 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1006 GLN Q1397 ASN R 23 GLN R 121 HIS U 441 GLN V 154 ASN ** W 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 190 GLN Y 155 GLN Y 252 GLN C 32 HIS D 112 HIS E 55 GLN G 115 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.100803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.068734 restraints weight = 138042.660| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 3.01 r_work: 0.3208 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 41727 Z= 0.161 Angle : 0.603 12.693 57675 Z= 0.321 Chirality : 0.041 0.256 6709 Planarity : 0.004 0.087 6361 Dihedral : 23.084 172.123 8000 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.31 % Allowed : 23.57 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.12), residues: 4360 helix: -0.00 (0.11), residues: 2019 sheet: 0.14 (0.21), residues: 605 loop : -0.97 (0.14), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Y 350 TYR 0.022 0.001 TYR X 186 PHE 0.016 0.001 PHE V 48 TRP 0.014 0.001 TRP R 214 HIS 0.003 0.001 HIS T 165 Details of bonding type rmsd covalent geometry : bond 0.00355 (41727) covalent geometry : angle 0.60341 (57675) hydrogen bonds : bond 0.04214 ( 1830) hydrogen bonds : angle 4.21722 ( 5037) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 294 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 958 GLN cc_start: 0.8554 (mm110) cc_final: 0.8142 (mp10) REVERT: Q 1293 ARG cc_start: 0.8177 (tmm160) cc_final: 0.7937 (ttp80) REVERT: Q 1331 MET cc_start: 0.8616 (mmt) cc_final: 0.8264 (mmm) REVERT: R 146 GLN cc_start: 0.8068 (tt0) cc_final: 0.7640 (mt0) REVERT: R 212 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8489 (mm) REVERT: R 261 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8592 (pp) REVERT: S 78 LEU cc_start: 0.9001 (mm) cc_final: 0.8731 (pp) REVERT: S 125 TYR cc_start: 0.7690 (OUTLIER) cc_final: 0.7405 (m-80) REVERT: U 44 MET cc_start: 0.7628 (ttm) cc_final: 0.7371 (mtp) REVERT: V 48 PHE cc_start: 0.8602 (OUTLIER) cc_final: 0.6749 (t80) REVERT: V 269 MET cc_start: 0.9355 (mmm) cc_final: 0.9113 (mmm) REVERT: W 165 MET cc_start: 0.9126 (ppp) cc_final: 0.8895 (ppp) REVERT: A 67 PHE cc_start: 0.7633 (t80) cc_final: 0.7375 (t80) REVERT: G 52 LEU cc_start: 0.8951 (mt) cc_final: 0.8518 (pp) outliers start: 87 outliers final: 39 residues processed: 369 average time/residue: 0.2538 time to fit residues: 153.9848 Evaluate side-chains 299 residues out of total 3804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 256 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 965 GLN Chi-restraints excluded: chain Q residue 1001 ILE Chi-restraints excluded: chain Q residue 1102 VAL Chi-restraints excluded: chain Q residue 1434 ASP Chi-restraints excluded: chain R residue 18 ASP Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 213 ASN Chi-restraints excluded: chain R residue 261 ILE Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 616 VAL Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 125 TYR Chi-restraints excluded: chain S residue 127 SER Chi-restraints excluded: chain T residue 230 VAL Chi-restraints excluded: chain T residue 279 GLU Chi-restraints excluded: chain T residue 390 VAL Chi-restraints excluded: chain U residue 215 MET Chi-restraints excluded: chain V residue 48 PHE Chi-restraints excluded: chain V residue 162 THR Chi-restraints excluded: chain V residue 279 GLU Chi-restraints excluded: chain V residue 355 SER Chi-restraints excluded: chain W residue 239 VAL Chi-restraints excluded: chain W residue 379 LEU Chi-restraints excluded: chain W residue 456 ILE Chi-restraints excluded: chain X residue 93 SER Chi-restraints excluded: chain X residue 330 SER Chi-restraints excluded: chain X residue 341 ASN Chi-restraints excluded: chain X residue 373 LEU Chi-restraints excluded: chain Y residue 44 MET Chi-restraints excluded: chain Y residue 99 THR Chi-restraints excluded: chain Y residue 191 SER Chi-restraints excluded: chain Y residue 255 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain H residue 69 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 357 optimal weight: 20.0000 chunk 359 optimal weight: 8.9990 chunk 364 optimal weight: 4.9990 chunk 306 optimal weight: 0.8980 chunk 232 optimal weight: 9.9990 chunk 94 optimal weight: 0.5980 chunk 219 optimal weight: 3.9990 chunk 422 optimal weight: 5.9990 chunk 370 optimal weight: 6.9990 chunk 170 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 121 HIS U 441 GLN V 29 HIS W 455 GLN C 115 ASN G 115 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.099077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.067305 restraints weight = 139442.100| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.97 r_work: 0.3172 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 41727 Z= 0.184 Angle : 0.596 11.749 57675 Z= 0.314 Chirality : 0.041 0.184 6709 Planarity : 0.004 0.069 6361 Dihedral : 22.953 179.084 8000 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.95 % Allowed : 23.33 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.12), residues: 4360 helix: 0.55 (0.11), residues: 2024 sheet: 0.12 (0.21), residues: 603 loop : -0.87 (0.15), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 41 TYR 0.023 0.001 TYR X 186 PHE 0.016 0.001 PHE W 308 TRP 0.013 0.001 TRP R 214 HIS 0.003 0.001 HIS R 121 Details of bonding type rmsd covalent geometry : bond 0.00414 (41727) covalent geometry : angle 0.59645 (57675) hydrogen bonds : bond 0.04219 ( 1830) hydrogen bonds : angle 4.06002 ( 5037) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 274 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1331 MET cc_start: 0.8611 (mmt) cc_final: 0.8342 (mmt) REVERT: R 74 LYS cc_start: 0.6948 (OUTLIER) cc_final: 0.6514 (pptt) REVERT: R 100 PHE cc_start: 0.6803 (OUTLIER) cc_final: 0.6273 (m-80) REVERT: R 146 GLN cc_start: 0.7999 (tt0) cc_final: 0.7663 (tt0) REVERT: R 261 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8635 (pp) REVERT: S 69 ASP cc_start: 0.8803 (p0) cc_final: 0.8550 (p0) REVERT: S 78 LEU cc_start: 0.9006 (mm) cc_final: 0.8730 (pp) REVERT: S 147 MET cc_start: 0.7130 (mmp) cc_final: 0.5714 (mtt) REVERT: T 377 LYS cc_start: 0.8625 (tttt) cc_final: 0.8341 (ptpp) REVERT: U 165 MET cc_start: 0.8695 (pmm) cc_final: 0.8449 (pmm) REVERT: V 48 PHE cc_start: 0.8560 (OUTLIER) cc_final: 0.6938 (t80) REVERT: W 29 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8836 (mp) REVERT: X 312 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8258 (mp0) REVERT: A 67 PHE cc_start: 0.7591 (t80) cc_final: 0.7256 (t80) REVERT: A 113 HIS cc_start: 0.5656 (OUTLIER) cc_final: 0.5210 (t70) REVERT: B 28 GLN cc_start: 0.7574 (OUTLIER) cc_final: 0.7286 (tp40) REVERT: F 85 MET cc_start: 0.9261 (mpp) cc_final: 0.8689 (mmp) REVERT: G 52 LEU cc_start: 0.8966 (mt) cc_final: 0.8509 (pp) outliers start: 111 outliers final: 62 residues processed: 366 average time/residue: 0.2529 time to fit residues: 151.7493 Evaluate side-chains 319 residues out of total 3804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 249 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 954 CYS Chi-restraints excluded: chain Q residue 965 GLN Chi-restraints excluded: chain Q residue 1001 ILE Chi-restraints excluded: chain Q residue 1102 VAL Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1342 HIS Chi-restraints excluded: chain Q residue 1434 ASP Chi-restraints excluded: chain R residue 18 ASP Chi-restraints excluded: chain R residue 74 LYS Chi-restraints excluded: chain R residue 100 PHE Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 213 ASN Chi-restraints excluded: chain R residue 261 ILE Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 616 VAL Chi-restraints excluded: chain R residue 629 THR Chi-restraints excluded: chain S residue 53 TYR Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 127 SER Chi-restraints excluded: chain T residue 230 VAL Chi-restraints excluded: chain T residue 279 GLU Chi-restraints excluded: chain T residue 380 ILE Chi-restraints excluded: chain T residue 390 VAL Chi-restraints excluded: chain U residue 215 MET Chi-restraints excluded: chain U residue 332 THR Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain V residue 48 PHE Chi-restraints excluded: chain V residue 162 THR Chi-restraints excluded: chain V residue 279 GLU Chi-restraints excluded: chain V residue 355 SER Chi-restraints excluded: chain W residue 29 LEU Chi-restraints excluded: chain W residue 58 LEU Chi-restraints excluded: chain W residue 239 VAL Chi-restraints excluded: chain W residue 456 ILE Chi-restraints excluded: chain X residue 48 PHE Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 93 SER Chi-restraints excluded: chain X residue 181 LEU Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain X residue 330 SER Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 341 ASN Chi-restraints excluded: chain X residue 355 SER Chi-restraints excluded: chain X residue 373 LEU Chi-restraints excluded: chain Y residue 44 MET Chi-restraints excluded: chain Y residue 99 THR Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 118 THR Chi-restraints excluded: chain Y residue 129 ILE Chi-restraints excluded: chain Y residue 191 SER Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 255 LEU Chi-restraints excluded: chain Y residue 271 ASP Chi-restraints excluded: chain Y residue 373 GLN Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain B residue 28 GLN Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 69 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 144 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 chunk 412 optimal weight: 6.9990 chunk 434 optimal weight: 30.0000 chunk 322 optimal weight: 5.9990 chunk 285 optimal weight: 4.9990 chunk 227 optimal weight: 8.9990 chunk 382 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 200 optimal weight: 0.8980 chunk 392 optimal weight: 6.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 121 HIS ** R 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 451 GLN W 144 GLN W 326 ASN ** W 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.097366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.065040 restraints weight = 137469.239| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.97 r_work: 0.3120 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 41727 Z= 0.237 Angle : 0.636 12.609 57675 Z= 0.333 Chirality : 0.042 0.172 6709 Planarity : 0.004 0.061 6361 Dihedral : 23.049 179.678 7998 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.69 % Allowed : 23.30 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.13), residues: 4360 helix: 0.64 (0.11), residues: 2041 sheet: -0.07 (0.21), residues: 602 loop : -0.84 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG V 191 TYR 0.027 0.002 TYR X 186 PHE 0.021 0.002 PHE V 125 TRP 0.017 0.002 TRP R 214 HIS 0.006 0.001 HIS T 27 Details of bonding type rmsd covalent geometry : bond 0.00535 (41727) covalent geometry : angle 0.63607 (57675) hydrogen bonds : bond 0.04329 ( 1830) hydrogen bonds : angle 4.11800 ( 5037) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 282 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 958 GLN cc_start: 0.8553 (mm110) cc_final: 0.8109 (mp10) REVERT: Q 1191 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9125 (tt) REVERT: Q 1331 MET cc_start: 0.8668 (mmt) cc_final: 0.8461 (mmt) REVERT: R 74 LYS cc_start: 0.6930 (OUTLIER) cc_final: 0.6447 (pptt) REVERT: R 100 PHE cc_start: 0.7138 (OUTLIER) cc_final: 0.6222 (m-80) REVERT: R 261 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8554 (pp) REVERT: R 623 GLU cc_start: 0.8401 (tp30) cc_final: 0.8146 (tm-30) REVERT: R 647 LEU cc_start: 0.9122 (mp) cc_final: 0.8910 (mp) REVERT: R 670 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.8103 (pp) REVERT: S 64 ARG cc_start: 0.8707 (tpt90) cc_final: 0.8500 (tpt90) REVERT: S 78 LEU cc_start: 0.9009 (mm) cc_final: 0.8776 (pp) REVERT: T 315 MET cc_start: 0.8855 (mmm) cc_final: 0.8588 (mmm) REVERT: T 377 LYS cc_start: 0.8665 (tttt) cc_final: 0.8329 (ptpp) REVERT: U 105 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8023 (mp0) REVERT: U 165 MET cc_start: 0.8535 (pmm) cc_final: 0.8271 (pmm) REVERT: V 48 PHE cc_start: 0.8635 (OUTLIER) cc_final: 0.7018 (t80) REVERT: V 315 MET cc_start: 0.8555 (tpp) cc_final: 0.8215 (tpp) REVERT: V 406 MET cc_start: 0.8327 (mmm) cc_final: 0.8084 (tpp) REVERT: X 312 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8045 (mm-30) REVERT: X 463 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6221 (tm) REVERT: A 67 PHE cc_start: 0.7646 (t80) cc_final: 0.7307 (t80) REVERT: A 113 HIS cc_start: 0.5681 (OUTLIER) cc_final: 0.5252 (t70) REVERT: C 24 LEU cc_start: 0.6392 (OUTLIER) cc_final: 0.6005 (pp) REVERT: F 85 MET cc_start: 0.9173 (mpp) cc_final: 0.8856 (mmm) REVERT: G 52 LEU cc_start: 0.8994 (mt) cc_final: 0.8555 (pp) REVERT: H 82 LYS cc_start: 0.9493 (OUTLIER) cc_final: 0.9185 (tmtt) outliers start: 139 outliers final: 80 residues processed: 401 average time/residue: 0.2537 time to fit residues: 166.2212 Evaluate side-chains 348 residues out of total 3804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 256 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 954 CYS Chi-restraints excluded: chain Q residue 965 GLN Chi-restraints excluded: chain Q residue 978 ILE Chi-restraints excluded: chain Q residue 1001 ILE Chi-restraints excluded: chain Q residue 1102 VAL Chi-restraints excluded: chain Q residue 1191 LEU Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain R residue 18 ASP Chi-restraints excluded: chain R residue 74 LYS Chi-restraints excluded: chain R residue 100 PHE Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 213 ASN Chi-restraints excluded: chain R residue 260 ASP Chi-restraints excluded: chain R residue 261 ILE Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 616 VAL Chi-restraints excluded: chain R residue 629 THR Chi-restraints excluded: chain R residue 670 ILE Chi-restraints excluded: chain S residue 53 TYR Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 127 SER Chi-restraints excluded: chain T residue 230 VAL Chi-restraints excluded: chain T residue 279 GLU Chi-restraints excluded: chain T residue 380 ILE Chi-restraints excluded: chain T residue 390 VAL Chi-restraints excluded: chain U residue 105 GLU Chi-restraints excluded: chain U residue 215 MET Chi-restraints excluded: chain U residue 332 THR Chi-restraints excluded: chain U residue 418 VAL Chi-restraints excluded: chain U residue 440 VAL Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 48 PHE Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 162 THR Chi-restraints excluded: chain V residue 195 SER Chi-restraints excluded: chain V residue 355 SER Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 58 LEU Chi-restraints excluded: chain W residue 210 ARG Chi-restraints excluded: chain W residue 224 CYS Chi-restraints excluded: chain W residue 239 VAL Chi-restraints excluded: chain W residue 456 ILE Chi-restraints excluded: chain X residue 48 PHE Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 93 SER Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 163 ILE Chi-restraints excluded: chain X residue 168 VAL Chi-restraints excluded: chain X residue 181 LEU Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 341 ASN Chi-restraints excluded: chain X residue 355 SER Chi-restraints excluded: chain X residue 373 LEU Chi-restraints excluded: chain X residue 463 LEU Chi-restraints excluded: chain Y residue 44 MET Chi-restraints excluded: chain Y residue 95 ASP Chi-restraints excluded: chain Y residue 99 THR Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 129 ILE Chi-restraints excluded: chain Y residue 191 SER Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 255 LEU Chi-restraints excluded: chain Y residue 271 ASP Chi-restraints excluded: chain Y residue 373 GLN Chi-restraints excluded: chain Y residue 428 LEU Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain B residue 28 GLN Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain H residue 43 TYR Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 109 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 152 optimal weight: 3.9990 chunk 343 optimal weight: 0.7980 chunk 422 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 373 optimal weight: 0.9980 chunk 80 optimal weight: 8.9990 chunk 108 optimal weight: 0.0000 chunk 101 optimal weight: 0.9990 chunk 367 optimal weight: 0.8980 chunk 301 optimal weight: 0.8980 chunk 457 optimal weight: 8.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 121 HIS S 82 ASN S 135 HIS ** T 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 326 ASN Z 301 ASN C 74 ASN E 55 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.099483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.067809 restraints weight = 137573.397| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.94 r_work: 0.3186 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 41727 Z= 0.117 Angle : 0.564 12.804 57675 Z= 0.295 Chirality : 0.040 0.180 6709 Planarity : 0.003 0.056 6361 Dihedral : 22.923 179.586 7998 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.44 % Allowed : 24.26 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.13), residues: 4360 helix: 0.92 (0.12), residues: 2041 sheet: 0.04 (0.21), residues: 599 loop : -0.71 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Y 220 TYR 0.013 0.001 TYR X 186 PHE 0.021 0.001 PHE V 125 TRP 0.006 0.001 TRP R 214 HIS 0.006 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00254 (41727) covalent geometry : angle 0.56413 (57675) hydrogen bonds : bond 0.03353 ( 1830) hydrogen bonds : angle 3.82058 ( 5037) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 288 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 958 GLN cc_start: 0.8525 (mm110) cc_final: 0.8135 (mp10) REVERT: Q 1291 MET cc_start: 0.8652 (tpp) cc_final: 0.8357 (tpp) REVERT: R 121 HIS cc_start: 0.6241 (OUTLIER) cc_final: 0.5891 (m90) REVERT: R 670 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.8002 (pp) REVERT: S 78 LEU cc_start: 0.8990 (mm) cc_final: 0.8741 (pp) REVERT: S 147 MET cc_start: 0.7163 (mmp) cc_final: 0.5980 (mtt) REVERT: T 125 PHE cc_start: 0.8849 (OUTLIER) cc_final: 0.8585 (m-80) REVERT: T 315 MET cc_start: 0.8569 (mmm) cc_final: 0.8352 (mmm) REVERT: T 377 LYS cc_start: 0.8610 (tttt) cc_final: 0.8310 (ptpp) REVERT: U 99 THR cc_start: 0.9249 (m) cc_final: 0.8798 (p) REVERT: U 165 MET cc_start: 0.8549 (pmm) cc_final: 0.8306 (pmm) REVERT: V 48 PHE cc_start: 0.8582 (OUTLIER) cc_final: 0.6974 (t80) REVERT: V 268 MET cc_start: 0.8181 (mtt) cc_final: 0.7830 (mtt) REVERT: V 406 MET cc_start: 0.8363 (mmm) cc_final: 0.8113 (tpp) REVERT: W 218 ASP cc_start: 0.8077 (t0) cc_final: 0.7869 (t0) REVERT: X 312 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8275 (mp0) REVERT: X 463 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6387 (tm) REVERT: A 67 PHE cc_start: 0.7561 (t80) cc_final: 0.7284 (t80) REVERT: A 113 HIS cc_start: 0.5637 (OUTLIER) cc_final: 0.5257 (t-90) REVERT: B 28 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7429 (tp40) REVERT: C 24 LEU cc_start: 0.6290 (OUTLIER) cc_final: 0.5921 (pp) REVERT: G 52 LEU cc_start: 0.8986 (mt) cc_final: 0.8543 (pp) REVERT: H 82 LYS cc_start: 0.9487 (OUTLIER) cc_final: 0.9201 (tmtt) REVERT: H 86 TYR cc_start: 0.8732 (m-80) cc_final: 0.8420 (m-80) outliers start: 92 outliers final: 54 residues processed: 367 average time/residue: 0.2508 time to fit residues: 151.4173 Evaluate side-chains 326 residues out of total 3804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 262 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 950 ILE Chi-restraints excluded: chain Q residue 965 GLN Chi-restraints excluded: chain Q residue 1102 VAL Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain R residue 18 ASP Chi-restraints excluded: chain R residue 100 PHE Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 246 MET Chi-restraints excluded: chain R residue 260 ASP Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 670 ILE Chi-restraints excluded: chain S residue 53 TYR Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 125 TYR Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 230 VAL Chi-restraints excluded: chain T residue 380 ILE Chi-restraints excluded: chain T residue 390 VAL Chi-restraints excluded: chain U residue 215 MET Chi-restraints excluded: chain U residue 332 THR Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain V residue 48 PHE Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 279 GLU Chi-restraints excluded: chain V residue 355 SER Chi-restraints excluded: chain W residue 58 LEU Chi-restraints excluded: chain W residue 239 VAL Chi-restraints excluded: chain W residue 255 LEU Chi-restraints excluded: chain W residue 456 ILE Chi-restraints excluded: chain X residue 48 PHE Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 117 LYS Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 181 LEU Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 341 ASN Chi-restraints excluded: chain X residue 355 SER Chi-restraints excluded: chain X residue 373 LEU Chi-restraints excluded: chain X residue 463 LEU Chi-restraints excluded: chain Y residue 89 SER Chi-restraints excluded: chain Y residue 99 THR Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 129 ILE Chi-restraints excluded: chain Y residue 255 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain B residue 28 GLN Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain H residue 43 TYR Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 108 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 408 optimal weight: 20.0000 chunk 181 optimal weight: 0.0070 chunk 189 optimal weight: 8.9990 chunk 191 optimal weight: 0.5980 chunk 320 optimal weight: 7.9990 chunk 300 optimal weight: 10.0000 chunk 172 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 358 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 348 optimal weight: 0.9990 overall best weight: 1.1204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 82 ASN ** T 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 326 ASN A 120 GLN D 70 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.099306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.067626 restraints weight = 138801.041| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.95 r_work: 0.3184 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 41727 Z= 0.125 Angle : 0.562 12.808 57675 Z= 0.293 Chirality : 0.040 0.186 6709 Planarity : 0.003 0.057 6361 Dihedral : 22.824 179.759 7998 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.76 % Allowed : 24.20 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.13), residues: 4360 helix: 1.05 (0.12), residues: 2040 sheet: 0.10 (0.21), residues: 601 loop : -0.66 (0.15), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG W 210 TYR 0.017 0.001 TYR X 186 PHE 0.019 0.001 PHE V 125 TRP 0.008 0.001 TRP R 214 HIS 0.022 0.001 HIS R 121 Details of bonding type rmsd covalent geometry : bond 0.00278 (41727) covalent geometry : angle 0.56222 (57675) hydrogen bonds : bond 0.03354 ( 1830) hydrogen bonds : angle 3.75798 ( 5037) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 278 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 958 GLN cc_start: 0.8535 (mm110) cc_final: 0.8145 (mp10) REVERT: Q 1291 MET cc_start: 0.8722 (tpp) cc_final: 0.8426 (tpp) REVERT: R 74 LYS cc_start: 0.6818 (OUTLIER) cc_final: 0.6348 (pptt) REVERT: R 259 GLU cc_start: 0.8703 (pm20) cc_final: 0.8244 (pm20) REVERT: R 261 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8603 (pp) REVERT: R 670 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.8009 (pp) REVERT: S 78 LEU cc_start: 0.8971 (mm) cc_final: 0.8743 (pp) REVERT: S 147 MET cc_start: 0.7189 (mmp) cc_final: 0.5953 (mtt) REVERT: T 125 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.8619 (m-80) REVERT: T 377 LYS cc_start: 0.8612 (tttt) cc_final: 0.8319 (ptpp) REVERT: U 165 MET cc_start: 0.8543 (pmm) cc_final: 0.8280 (pmm) REVERT: V 48 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.7001 (t80) REVERT: W 218 ASP cc_start: 0.8065 (t0) cc_final: 0.7799 (t0) REVERT: X 312 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8277 (mp0) REVERT: X 463 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.6237 (tm) REVERT: A 67 PHE cc_start: 0.7640 (t80) cc_final: 0.7328 (t80) REVERT: A 113 HIS cc_start: 0.5653 (OUTLIER) cc_final: 0.5273 (t-90) REVERT: B 28 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7454 (tp40) REVERT: B 35 ILE cc_start: 0.5638 (OUTLIER) cc_final: 0.5426 (mp) REVERT: C 24 LEU cc_start: 0.6324 (OUTLIER) cc_final: 0.5908 (pp) REVERT: C 52 LEU cc_start: 0.9456 (mt) cc_final: 0.8873 (pp) REVERT: D 83 LEU cc_start: 0.9188 (mm) cc_final: 0.8973 (tp) REVERT: F 85 MET cc_start: 0.9193 (mpp) cc_final: 0.8692 (mmp) REVERT: G 52 LEU cc_start: 0.9004 (mt) cc_final: 0.8542 (pp) REVERT: H 82 LYS cc_start: 0.9501 (OUTLIER) cc_final: 0.9230 (tmtt) REVERT: H 86 TYR cc_start: 0.8776 (m-80) cc_final: 0.8488 (m-80) outliers start: 104 outliers final: 65 residues processed: 369 average time/residue: 0.2595 time to fit residues: 157.0024 Evaluate side-chains 337 residues out of total 3804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 260 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 954 CYS Chi-restraints excluded: chain Q residue 965 GLN Chi-restraints excluded: chain Q residue 1092 ASP Chi-restraints excluded: chain Q residue 1102 VAL Chi-restraints excluded: chain Q residue 1206 ILE Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1400 ILE Chi-restraints excluded: chain Q residue 1434 ASP Chi-restraints excluded: chain R residue 18 ASP Chi-restraints excluded: chain R residue 74 LYS Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 246 MET Chi-restraints excluded: chain R residue 260 ASP Chi-restraints excluded: chain R residue 261 ILE Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 606 ILE Chi-restraints excluded: chain R residue 629 THR Chi-restraints excluded: chain R residue 670 ILE Chi-restraints excluded: chain S residue 53 TYR Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 125 TYR Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 230 VAL Chi-restraints excluded: chain T residue 380 ILE Chi-restraints excluded: chain T residue 390 VAL Chi-restraints excluded: chain U residue 215 MET Chi-restraints excluded: chain U residue 332 THR Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain V residue 48 PHE Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 355 SER Chi-restraints excluded: chain W residue 58 LEU Chi-restraints excluded: chain W residue 239 VAL Chi-restraints excluded: chain W residue 411 MET Chi-restraints excluded: chain W residue 456 ILE Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 117 LYS Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 168 VAL Chi-restraints excluded: chain X residue 181 LEU Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 341 ASN Chi-restraints excluded: chain X residue 355 SER Chi-restraints excluded: chain X residue 373 LEU Chi-restraints excluded: chain X residue 390 VAL Chi-restraints excluded: chain X residue 463 LEU Chi-restraints excluded: chain Y residue 89 SER Chi-restraints excluded: chain Y residue 99 THR Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 129 ILE Chi-restraints excluded: chain Y residue 191 SER Chi-restraints excluded: chain Y residue 255 LEU Chi-restraints excluded: chain Y residue 271 ASP Chi-restraints excluded: chain Y residue 428 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain B residue 28 GLN Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain H residue 43 TYR Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 108 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 423 optimal weight: 0.0870 chunk 440 optimal weight: 0.0040 chunk 294 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 263 optimal weight: 0.3980 chunk 21 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 455 optimal weight: 10.0000 chunk 453 optimal weight: 5.9990 chunk 410 optimal weight: 0.0050 chunk 265 optimal weight: 0.1980 overall best weight: 0.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1342 HIS S 82 ASN ** T 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 190 GLN V 190 GLN W 326 ASN Y 155 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.100903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.069469 restraints weight = 138370.185| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.98 r_work: 0.3232 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 41727 Z= 0.110 Angle : 0.565 13.811 57675 Z= 0.292 Chirality : 0.040 0.188 6709 Planarity : 0.003 0.057 6361 Dihedral : 22.682 179.553 7998 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.55 % Allowed : 24.44 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.13), residues: 4360 helix: 1.16 (0.12), residues: 2042 sheet: 0.23 (0.21), residues: 594 loop : -0.62 (0.15), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG W 232 TYR 0.013 0.001 TYR T 201 PHE 0.024 0.001 PHE S 32 TRP 0.008 0.001 TRP Y 280 HIS 0.004 0.001 HIS X 357 Details of bonding type rmsd covalent geometry : bond 0.00236 (41727) covalent geometry : angle 0.56505 (57675) hydrogen bonds : bond 0.03154 ( 1830) hydrogen bonds : angle 3.61597 ( 5037) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 295 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 958 GLN cc_start: 0.8522 (mm110) cc_final: 0.8114 (mp10) REVERT: Q 1291 MET cc_start: 0.8701 (tpp) cc_final: 0.8385 (tpp) REVERT: Q 1335 LEU cc_start: 0.8891 (mm) cc_final: 0.8678 (pp) REVERT: R 74 LYS cc_start: 0.6753 (OUTLIER) cc_final: 0.6279 (pptt) REVERT: R 259 GLU cc_start: 0.8720 (pm20) cc_final: 0.8208 (pm20) REVERT: R 261 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8623 (pp) REVERT: R 670 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.7996 (pp) REVERT: S 78 LEU cc_start: 0.8995 (mm) cc_final: 0.8738 (pp) REVERT: T 125 PHE cc_start: 0.8792 (OUTLIER) cc_final: 0.8529 (m-80) REVERT: T 377 LYS cc_start: 0.8577 (tttt) cc_final: 0.8302 (ptpp) REVERT: U 165 MET cc_start: 0.8544 (pmm) cc_final: 0.8298 (pmm) REVERT: V 48 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.6953 (t80) REVERT: W 165 MET cc_start: 0.9170 (ppp) cc_final: 0.8961 (ppp) REVERT: W 218 ASP cc_start: 0.8180 (t0) cc_final: 0.7867 (t0) REVERT: W 310 ASN cc_start: 0.8695 (m-40) cc_final: 0.8462 (m110) REVERT: W 395 SER cc_start: 0.6566 (OUTLIER) cc_final: 0.6316 (t) REVERT: X 463 LEU cc_start: 0.7120 (OUTLIER) cc_final: 0.6194 (tm) REVERT: A 67 PHE cc_start: 0.7668 (t80) cc_final: 0.7339 (t80) REVERT: A 113 HIS cc_start: 0.5694 (OUTLIER) cc_final: 0.5241 (t-90) REVERT: C 24 LEU cc_start: 0.6191 (OUTLIER) cc_final: 0.5783 (pp) REVERT: C 52 LEU cc_start: 0.9456 (mt) cc_final: 0.8975 (pp) REVERT: D 49 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7473 (mtmt) REVERT: D 83 LEU cc_start: 0.9155 (mm) cc_final: 0.8784 (tp) REVERT: F 85 MET cc_start: 0.9125 (mpp) cc_final: 0.8802 (mmp) REVERT: G 52 LEU cc_start: 0.9002 (mt) cc_final: 0.8548 (pp) REVERT: H 82 LYS cc_start: 0.9514 (OUTLIER) cc_final: 0.9271 (tmtt) REVERT: H 86 TYR cc_start: 0.8712 (m-80) cc_final: 0.8462 (m-80) outliers start: 96 outliers final: 59 residues processed: 380 average time/residue: 0.2458 time to fit residues: 154.1256 Evaluate side-chains 339 residues out of total 3804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 269 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 950 ILE Chi-restraints excluded: chain Q residue 954 CYS Chi-restraints excluded: chain Q residue 965 GLN Chi-restraints excluded: chain Q residue 978 ILE Chi-restraints excluded: chain Q residue 1092 ASP Chi-restraints excluded: chain Q residue 1342 HIS Chi-restraints excluded: chain Q residue 1400 ILE Chi-restraints excluded: chain Q residue 1434 ASP Chi-restraints excluded: chain R residue 18 ASP Chi-restraints excluded: chain R residue 74 LYS Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 246 MET Chi-restraints excluded: chain R residue 260 ASP Chi-restraints excluded: chain R residue 261 ILE Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 606 ILE Chi-restraints excluded: chain R residue 616 VAL Chi-restraints excluded: chain R residue 670 ILE Chi-restraints excluded: chain S residue 53 TYR Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 125 TYR Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 230 VAL Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 380 ILE Chi-restraints excluded: chain T residue 390 VAL Chi-restraints excluded: chain T residue 418 LEU Chi-restraints excluded: chain U residue 215 MET Chi-restraints excluded: chain V residue 48 PHE Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 279 GLU Chi-restraints excluded: chain V residue 355 SER Chi-restraints excluded: chain W residue 136 ILE Chi-restraints excluded: chain W residue 239 VAL Chi-restraints excluded: chain W residue 326 ASN Chi-restraints excluded: chain W residue 395 SER Chi-restraints excluded: chain W residue 456 ILE Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 93 SER Chi-restraints excluded: chain X residue 117 LYS Chi-restraints excluded: chain X residue 168 VAL Chi-restraints excluded: chain X residue 181 LEU Chi-restraints excluded: chain X residue 330 SER Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 341 ASN Chi-restraints excluded: chain X residue 373 LEU Chi-restraints excluded: chain X residue 463 LEU Chi-restraints excluded: chain Y residue 99 THR Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 191 SER Chi-restraints excluded: chain Y residue 255 LEU Chi-restraints excluded: chain Y residue 304 GLU Chi-restraints excluded: chain Y residue 345 LEU Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain G residue 115 ASN Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 108 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 348 optimal weight: 1.9990 chunk 432 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 396 optimal weight: 10.0000 chunk 319 optimal weight: 4.9990 chunk 231 optimal weight: 3.9990 chunk 420 optimal weight: 3.9990 chunk 223 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 415 optimal weight: 10.0000 chunk 151 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 190 GLN V 190 GLN W 326 ASN A 68 GLN C 111 ASN D 112 HIS ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.097520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.066167 restraints weight = 137574.264| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.87 r_work: 0.3145 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 41727 Z= 0.217 Angle : 0.628 13.584 57675 Z= 0.325 Chirality : 0.042 0.196 6709 Planarity : 0.004 0.062 6361 Dihedral : 22.801 179.799 7998 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.92 % Allowed : 24.39 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.13), residues: 4360 helix: 1.11 (0.12), residues: 2042 sheet: 0.06 (0.21), residues: 610 loop : -0.68 (0.15), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG Y 350 TYR 0.027 0.002 TYR X 186 PHE 0.029 0.002 PHE V 125 TRP 0.017 0.002 TRP R 214 HIS 0.025 0.001 HIS Q1342 Details of bonding type rmsd covalent geometry : bond 0.00487 (41727) covalent geometry : angle 0.62808 (57675) hydrogen bonds : bond 0.04021 ( 1830) hydrogen bonds : angle 3.86463 ( 5037) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 266 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 958 GLN cc_start: 0.8584 (mm110) cc_final: 0.8182 (mp10) REVERT: Q 1291 MET cc_start: 0.8798 (tpp) cc_final: 0.8505 (tpp) REVERT: Q 1335 LEU cc_start: 0.8990 (mm) cc_final: 0.8789 (pp) REVERT: R 74 LYS cc_start: 0.6790 (OUTLIER) cc_final: 0.6187 (pttm) REVERT: R 259 GLU cc_start: 0.8709 (pm20) cc_final: 0.8202 (pm20) REVERT: R 261 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8580 (pp) REVERT: R 670 ILE cc_start: 0.8265 (OUTLIER) cc_final: 0.7981 (pp) REVERT: S 78 LEU cc_start: 0.8981 (mm) cc_final: 0.8715 (pp) REVERT: S 147 MET cc_start: 0.7094 (mmp) cc_final: 0.5865 (mtt) REVERT: T 125 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8710 (m-80) REVERT: T 377 LYS cc_start: 0.8638 (tttt) cc_final: 0.8334 (ptpp) REVERT: U 165 MET cc_start: 0.8553 (pmm) cc_final: 0.8270 (pmm) REVERT: V 48 PHE cc_start: 0.8561 (OUTLIER) cc_final: 0.6984 (t80) REVERT: V 315 MET cc_start: 0.8472 (tpp) cc_final: 0.8247 (tpp) REVERT: W 165 MET cc_start: 0.9163 (ppp) cc_final: 0.8911 (ppp) REVERT: W 218 ASP cc_start: 0.8173 (t0) cc_final: 0.7884 (t0) REVERT: W 395 SER cc_start: 0.6905 (OUTLIER) cc_final: 0.6626 (t) REVERT: X 312 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8282 (mp0) REVERT: X 463 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6245 (tm) REVERT: Y 134 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7517 (mm-30) REVERT: A 67 PHE cc_start: 0.7718 (t80) cc_final: 0.7399 (t80) REVERT: A 113 HIS cc_start: 0.5716 (OUTLIER) cc_final: 0.5280 (t-90) REVERT: B 28 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7462 (tp40) REVERT: C 24 LEU cc_start: 0.6341 (OUTLIER) cc_final: 0.5898 (pp) REVERT: C 52 LEU cc_start: 0.9479 (mt) cc_final: 0.8999 (pp) REVERT: D 49 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7509 (mtmt) REVERT: F 85 MET cc_start: 0.9164 (mpp) cc_final: 0.8712 (mmp) REVERT: G 52 LEU cc_start: 0.9003 (mt) cc_final: 0.8555 (pp) REVERT: H 82 LYS cc_start: 0.9518 (OUTLIER) cc_final: 0.9257 (tmtt) REVERT: H 86 TYR cc_start: 0.8761 (m-80) cc_final: 0.8491 (m-80) outliers start: 110 outliers final: 77 residues processed: 363 average time/residue: 0.2562 time to fit residues: 153.2306 Evaluate side-chains 346 residues out of total 3804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 255 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 950 ILE Chi-restraints excluded: chain Q residue 954 CYS Chi-restraints excluded: chain Q residue 965 GLN Chi-restraints excluded: chain Q residue 978 ILE Chi-restraints excluded: chain Q residue 1092 ASP Chi-restraints excluded: chain Q residue 1102 VAL Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1342 HIS Chi-restraints excluded: chain Q residue 1400 ILE Chi-restraints excluded: chain R residue 18 ASP Chi-restraints excluded: chain R residue 74 LYS Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 246 MET Chi-restraints excluded: chain R residue 260 ASP Chi-restraints excluded: chain R residue 261 ILE Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 606 ILE Chi-restraints excluded: chain R residue 616 VAL Chi-restraints excluded: chain R residue 629 THR Chi-restraints excluded: chain R residue 670 ILE Chi-restraints excluded: chain S residue 53 TYR Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 230 VAL Chi-restraints excluded: chain T residue 279 GLU Chi-restraints excluded: chain T residue 380 ILE Chi-restraints excluded: chain T residue 390 VAL Chi-restraints excluded: chain T residue 418 LEU Chi-restraints excluded: chain U residue 66 ILE Chi-restraints excluded: chain U residue 215 MET Chi-restraints excluded: chain V residue 48 PHE Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 279 GLU Chi-restraints excluded: chain V residue 355 SER Chi-restraints excluded: chain W residue 58 LEU Chi-restraints excluded: chain W residue 136 ILE Chi-restraints excluded: chain W residue 239 VAL Chi-restraints excluded: chain W residue 326 ASN Chi-restraints excluded: chain W residue 395 SER Chi-restraints excluded: chain W residue 411 MET Chi-restraints excluded: chain W residue 456 ILE Chi-restraints excluded: chain X residue 48 PHE Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 93 SER Chi-restraints excluded: chain X residue 117 LYS Chi-restraints excluded: chain X residue 168 VAL Chi-restraints excluded: chain X residue 181 LEU Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain X residue 330 SER Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 341 ASN Chi-restraints excluded: chain X residue 355 SER Chi-restraints excluded: chain X residue 373 LEU Chi-restraints excluded: chain X residue 390 VAL Chi-restraints excluded: chain X residue 463 LEU Chi-restraints excluded: chain Y residue 60 MET Chi-restraints excluded: chain Y residue 89 SER Chi-restraints excluded: chain Y residue 99 THR Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 129 ILE Chi-restraints excluded: chain Y residue 134 GLU Chi-restraints excluded: chain Y residue 191 SER Chi-restraints excluded: chain Y residue 255 LEU Chi-restraints excluded: chain Y residue 271 ASP Chi-restraints excluded: chain Y residue 304 GLU Chi-restraints excluded: chain Y residue 345 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain B residue 28 GLN Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain G residue 115 ASN Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 108 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 446 optimal weight: 0.8980 chunk 330 optimal weight: 0.6980 chunk 243 optimal weight: 3.9990 chunk 428 optimal weight: 8.9990 chunk 370 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 225 optimal weight: 6.9990 chunk 229 optimal weight: 6.9990 chunk 339 optimal weight: 0.8980 chunk 230 optimal weight: 9.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1342 HIS ** R 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 190 GLN ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.098530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.066761 restraints weight = 138993.776| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.94 r_work: 0.3161 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 41727 Z= 0.154 Angle : 0.597 12.925 57675 Z= 0.309 Chirality : 0.041 0.182 6709 Planarity : 0.004 0.060 6361 Dihedral : 22.838 179.406 7998 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.39 % Allowed : 24.89 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.13), residues: 4360 helix: 1.13 (0.12), residues: 2040 sheet: 0.11 (0.21), residues: 606 loop : -0.64 (0.15), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q1293 TYR 0.019 0.001 TYR X 186 PHE 0.020 0.001 PHE V 125 TRP 0.011 0.001 TRP R 214 HIS 0.003 0.001 HIS T 27 Details of bonding type rmsd covalent geometry : bond 0.00346 (41727) covalent geometry : angle 0.59715 (57675) hydrogen bonds : bond 0.03505 ( 1830) hydrogen bonds : angle 3.79780 ( 5037) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 273 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 958 GLN cc_start: 0.8572 (mm110) cc_final: 0.8200 (mp10) REVERT: Q 1291 MET cc_start: 0.8708 (tpp) cc_final: 0.8403 (tpp) REVERT: Q 1335 LEU cc_start: 0.8977 (mm) cc_final: 0.8766 (pp) REVERT: R 74 LYS cc_start: 0.6803 (OUTLIER) cc_final: 0.6204 (pttm) REVERT: R 259 GLU cc_start: 0.8740 (pm20) cc_final: 0.8198 (pm20) REVERT: R 261 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8556 (pp) REVERT: R 670 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.8012 (pp) REVERT: S 78 LEU cc_start: 0.8951 (mm) cc_final: 0.8691 (pp) REVERT: S 125 TYR cc_start: 0.7989 (OUTLIER) cc_final: 0.7363 (m-80) REVERT: S 147 MET cc_start: 0.7006 (mmp) cc_final: 0.5817 (mtt) REVERT: T 125 PHE cc_start: 0.8850 (OUTLIER) cc_final: 0.8606 (m-80) REVERT: T 377 LYS cc_start: 0.8650 (tttt) cc_final: 0.8351 (ptpp) REVERT: U 99 THR cc_start: 0.9281 (m) cc_final: 0.8823 (p) REVERT: U 165 MET cc_start: 0.8479 (pmm) cc_final: 0.8215 (pmm) REVERT: V 37 GLU cc_start: 0.9267 (tm-30) cc_final: 0.8967 (tm-30) REVERT: V 48 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.6992 (t80) REVERT: V 315 MET cc_start: 0.8412 (tpp) cc_final: 0.8184 (tpp) REVERT: V 344 MET cc_start: 0.8826 (mmt) cc_final: 0.8569 (mmt) REVERT: W 165 MET cc_start: 0.9194 (ppp) cc_final: 0.8947 (ppp) REVERT: W 218 ASP cc_start: 0.8190 (t0) cc_final: 0.7887 (t0) REVERT: W 395 SER cc_start: 0.6842 (OUTLIER) cc_final: 0.6595 (t) REVERT: X 312 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8282 (mp0) REVERT: X 463 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.6258 (tm) REVERT: Y 134 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7932 (mm-30) REVERT: A 67 PHE cc_start: 0.7692 (t80) cc_final: 0.7361 (t80) REVERT: A 113 HIS cc_start: 0.5787 (OUTLIER) cc_final: 0.5324 (t-90) REVERT: C 24 LEU cc_start: 0.6373 (OUTLIER) cc_final: 0.5939 (pp) REVERT: C 52 LEU cc_start: 0.9462 (mt) cc_final: 0.8999 (pp) REVERT: D 49 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7570 (mtmt) REVERT: E 99 TYR cc_start: 0.7804 (t80) cc_final: 0.7384 (t80) REVERT: F 85 MET cc_start: 0.9167 (mpp) cc_final: 0.8866 (mmp) REVERT: G 52 LEU cc_start: 0.8992 (mt) cc_final: 0.8531 (pp) REVERT: H 82 LYS cc_start: 0.9515 (OUTLIER) cc_final: 0.9267 (tmtt) REVERT: H 86 TYR cc_start: 0.8766 (m-80) cc_final: 0.8498 (m-80) REVERT: H 124 TYR cc_start: 0.8303 (t80) cc_final: 0.7938 (t80) outliers start: 90 outliers final: 69 residues processed: 353 average time/residue: 0.2539 time to fit residues: 147.8161 Evaluate side-chains 347 residues out of total 3804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 264 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 950 ILE Chi-restraints excluded: chain Q residue 954 CYS Chi-restraints excluded: chain Q residue 965 GLN Chi-restraints excluded: chain Q residue 978 ILE Chi-restraints excluded: chain Q residue 1092 ASP Chi-restraints excluded: chain Q residue 1102 VAL Chi-restraints excluded: chain Q residue 1400 ILE Chi-restraints excluded: chain R residue 18 ASP Chi-restraints excluded: chain R residue 74 LYS Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 246 MET Chi-restraints excluded: chain R residue 260 ASP Chi-restraints excluded: chain R residue 261 ILE Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 606 ILE Chi-restraints excluded: chain R residue 616 VAL Chi-restraints excluded: chain R residue 670 ILE Chi-restraints excluded: chain S residue 53 TYR Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 125 TYR Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 230 VAL Chi-restraints excluded: chain T residue 380 ILE Chi-restraints excluded: chain T residue 390 VAL Chi-restraints excluded: chain T residue 418 LEU Chi-restraints excluded: chain U residue 66 ILE Chi-restraints excluded: chain U residue 215 MET Chi-restraints excluded: chain U residue 418 VAL Chi-restraints excluded: chain V residue 48 PHE Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 279 GLU Chi-restraints excluded: chain V residue 355 SER Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 58 LEU Chi-restraints excluded: chain W residue 136 ILE Chi-restraints excluded: chain W residue 184 VAL Chi-restraints excluded: chain W residue 224 CYS Chi-restraints excluded: chain W residue 239 VAL Chi-restraints excluded: chain W residue 395 SER Chi-restraints excluded: chain W residue 456 ILE Chi-restraints excluded: chain X residue 48 PHE Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 93 SER Chi-restraints excluded: chain X residue 117 LYS Chi-restraints excluded: chain X residue 168 VAL Chi-restraints excluded: chain X residue 181 LEU Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain X residue 330 SER Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 341 ASN Chi-restraints excluded: chain X residue 355 SER Chi-restraints excluded: chain X residue 373 LEU Chi-restraints excluded: chain X residue 390 VAL Chi-restraints excluded: chain X residue 463 LEU Chi-restraints excluded: chain Y residue 60 MET Chi-restraints excluded: chain Y residue 89 SER Chi-restraints excluded: chain Y residue 99 THR Chi-restraints excluded: chain Y residue 129 ILE Chi-restraints excluded: chain Y residue 134 GLU Chi-restraints excluded: chain Y residue 191 SER Chi-restraints excluded: chain Y residue 255 LEU Chi-restraints excluded: chain Y residue 304 GLU Chi-restraints excluded: chain Y residue 345 LEU Chi-restraints excluded: chain Y residue 428 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 108 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 222 optimal weight: 1.9990 chunk 413 optimal weight: 7.9990 chunk 417 optimal weight: 0.8980 chunk 352 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 chunk 112 optimal weight: 9.9990 chunk 454 optimal weight: 5.9990 chunk 402 optimal weight: 6.9990 chunk 435 optimal weight: 7.9990 chunk 200 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 326 ASN Y 248 ASN ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.099006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.067307 restraints weight = 137819.109| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.94 r_work: 0.3176 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 41727 Z= 0.134 Angle : 0.600 13.504 57675 Z= 0.308 Chirality : 0.041 0.373 6709 Planarity : 0.004 0.061 6361 Dihedral : 22.781 179.505 7998 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.28 % Allowed : 25.27 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.13), residues: 4360 helix: 1.16 (0.12), residues: 2039 sheet: 0.14 (0.21), residues: 601 loop : -0.60 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG W 232 TYR 0.019 0.001 TYR R 252 PHE 0.018 0.001 PHE H 68 TRP 0.009 0.001 TRP R 214 HIS 0.008 0.001 HIS R 121 Details of bonding type rmsd covalent geometry : bond 0.00301 (41727) covalent geometry : angle 0.59955 (57675) hydrogen bonds : bond 0.03414 ( 1830) hydrogen bonds : angle 3.76687 ( 5037) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 272 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 958 GLN cc_start: 0.8576 (mm110) cc_final: 0.8186 (mp10) REVERT: Q 1291 MET cc_start: 0.8735 (tpp) cc_final: 0.8437 (tpp) REVERT: R 74 LYS cc_start: 0.6803 (OUTLIER) cc_final: 0.6217 (pttm) REVERT: R 259 GLU cc_start: 0.8731 (pm20) cc_final: 0.8167 (pm20) REVERT: R 261 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8578 (pp) REVERT: R 670 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7987 (pp) REVERT: S 78 LEU cc_start: 0.8969 (mm) cc_final: 0.8701 (pp) REVERT: S 147 MET cc_start: 0.6976 (mmp) cc_final: 0.5762 (mtt) REVERT: T 70 MET cc_start: 0.8172 (mmm) cc_final: 0.7971 (mmm) REVERT: T 125 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.8606 (m-80) REVERT: T 377 LYS cc_start: 0.8643 (tttt) cc_final: 0.8352 (ptpp) REVERT: U 165 MET cc_start: 0.8486 (pmm) cc_final: 0.8220 (pmm) REVERT: V 37 GLU cc_start: 0.9293 (tm-30) cc_final: 0.8997 (tm-30) REVERT: V 48 PHE cc_start: 0.8574 (OUTLIER) cc_final: 0.7005 (t80) REVERT: V 315 MET cc_start: 0.8371 (tpp) cc_final: 0.8135 (tpp) REVERT: V 344 MET cc_start: 0.8825 (mmt) cc_final: 0.8562 (mmt) REVERT: W 165 MET cc_start: 0.9189 (ppp) cc_final: 0.8948 (ppp) REVERT: W 218 ASP cc_start: 0.8252 (t0) cc_final: 0.7972 (t0) REVERT: W 395 SER cc_start: 0.6775 (OUTLIER) cc_final: 0.6534 (t) REVERT: X 312 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8316 (mp0) REVERT: X 463 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6218 (tm) REVERT: Y 134 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7721 (mm-30) REVERT: A 67 PHE cc_start: 0.7726 (t80) cc_final: 0.7380 (t80) REVERT: A 113 HIS cc_start: 0.5708 (OUTLIER) cc_final: 0.5309 (t70) REVERT: C 24 LEU cc_start: 0.6366 (OUTLIER) cc_final: 0.5905 (pp) REVERT: C 52 LEU cc_start: 0.9450 (mt) cc_final: 0.9030 (pp) REVERT: D 49 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7535 (mtmt) REVERT: E 99 TYR cc_start: 0.7767 (t80) cc_final: 0.7344 (t80) REVERT: F 85 MET cc_start: 0.9169 (mpp) cc_final: 0.8865 (mmp) REVERT: G 52 LEU cc_start: 0.8975 (mt) cc_final: 0.8508 (pp) REVERT: H 82 LYS cc_start: 0.9509 (OUTLIER) cc_final: 0.9215 (tmtt) REVERT: H 86 TYR cc_start: 0.8758 (m-80) cc_final: 0.8334 (m-80) REVERT: H 124 TYR cc_start: 0.8308 (t80) cc_final: 0.7944 (t80) outliers start: 86 outliers final: 68 residues processed: 349 average time/residue: 0.2513 time to fit residues: 145.0321 Evaluate side-chains 344 residues out of total 3804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 263 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 950 ILE Chi-restraints excluded: chain Q residue 954 CYS Chi-restraints excluded: chain Q residue 965 GLN Chi-restraints excluded: chain Q residue 978 ILE Chi-restraints excluded: chain Q residue 1092 ASP Chi-restraints excluded: chain Q residue 1102 VAL Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1400 ILE Chi-restraints excluded: chain R residue 18 ASP Chi-restraints excluded: chain R residue 74 LYS Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 246 MET Chi-restraints excluded: chain R residue 260 ASP Chi-restraints excluded: chain R residue 261 ILE Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 606 ILE Chi-restraints excluded: chain R residue 616 VAL Chi-restraints excluded: chain R residue 629 THR Chi-restraints excluded: chain R residue 670 ILE Chi-restraints excluded: chain S residue 53 TYR Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 230 VAL Chi-restraints excluded: chain T residue 380 ILE Chi-restraints excluded: chain T residue 390 VAL Chi-restraints excluded: chain T residue 418 LEU Chi-restraints excluded: chain U residue 215 MET Chi-restraints excluded: chain U residue 418 VAL Chi-restraints excluded: chain V residue 48 PHE Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 279 GLU Chi-restraints excluded: chain V residue 355 SER Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 58 LEU Chi-restraints excluded: chain W residue 136 ILE Chi-restraints excluded: chain W residue 224 CYS Chi-restraints excluded: chain W residue 239 VAL Chi-restraints excluded: chain W residue 326 ASN Chi-restraints excluded: chain W residue 395 SER Chi-restraints excluded: chain W residue 456 ILE Chi-restraints excluded: chain X residue 48 PHE Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 93 SER Chi-restraints excluded: chain X residue 117 LYS Chi-restraints excluded: chain X residue 168 VAL Chi-restraints excluded: chain X residue 181 LEU Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain X residue 330 SER Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 341 ASN Chi-restraints excluded: chain X residue 355 SER Chi-restraints excluded: chain X residue 373 LEU Chi-restraints excluded: chain X residue 390 VAL Chi-restraints excluded: chain X residue 463 LEU Chi-restraints excluded: chain Y residue 60 MET Chi-restraints excluded: chain Y residue 89 SER Chi-restraints excluded: chain Y residue 99 THR Chi-restraints excluded: chain Y residue 129 ILE Chi-restraints excluded: chain Y residue 134 GLU Chi-restraints excluded: chain Y residue 191 SER Chi-restraints excluded: chain Y residue 255 LEU Chi-restraints excluded: chain Y residue 304 GLU Chi-restraints excluded: chain Y residue 345 LEU Chi-restraints excluded: chain Y residue 428 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 82 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 213 optimal weight: 0.1980 chunk 174 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 347 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 309 optimal weight: 7.9990 chunk 419 optimal weight: 9.9990 chunk 279 optimal weight: 7.9990 chunk 314 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.098934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.067263 restraints weight = 138652.548| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.94 r_work: 0.3175 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.179 41727 Z= 0.177 Angle : 0.687 59.196 57675 Z= 0.379 Chirality : 0.042 0.783 6709 Planarity : 0.004 0.061 6361 Dihedral : 22.782 179.508 7998 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.44 % Allowed : 25.19 % Favored : 72.37 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.13), residues: 4360 helix: 1.15 (0.12), residues: 2039 sheet: 0.14 (0.21), residues: 601 loop : -0.60 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG W 232 TYR 0.022 0.001 TYR G 58 PHE 0.017 0.001 PHE V 125 TRP 0.009 0.001 TRP R 214 HIS 0.003 0.001 HIS U 25 Details of bonding type rmsd covalent geometry : bond 0.00368 (41727) covalent geometry : angle 0.68652 (57675) hydrogen bonds : bond 0.03427 ( 1830) hydrogen bonds : angle 3.76748 ( 5037) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11997.57 seconds wall clock time: 205 minutes 41.70 seconds (12341.70 seconds total)