Starting phenix.real_space_refine on Tue Jul 7 01:16:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ob1_70289/07_2026/9ob1_70289.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ob1_70289/07_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_70289/07_2026/9ob1_70289.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ob1_70289/07_2026/9ob1_70289.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ob1_70289/07_2026/9ob1_70289.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ob1_70289/07_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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 7.25, per 1000 atoms: 0.18 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: 3.09 Conformation dependent library (CDL) restraints added in 1.6 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: 4.98 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: 10.69 Time building geometry restraints manager: 4.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 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=" C3' DG J 23 " pdb=" C2' DG J 23 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.47e+01 bond pdb=" C3' DG I -58 " pdb=" C2' DG I -58 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.42e+01 bond pdb=" C3' DG J 23 " pdb=" O3' DG J 23 " ideal model delta sigma weight residual 1.435 1.481 -0.046 1.30e-02 5.92e+03 1.27e+01 bond pdb=" C3' DC I -38 " pdb=" C2' DC I -38 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.25e+01 bond pdb=" C3' DT I -17 " pdb=" C2' DT I -17 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.23e+01 ... (remaining 41722 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.87: 57183 3.87 - 7.74: 405 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: 5749 0.075 - 0.149: 859 0.149 - 0.224: 84 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: 7.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 38.670 Find NCS groups from input model: 1.080 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 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 : 0.006 0.095 41727 Z= 0.352 Angle : 0.953 19.353 57675 Z= 0.574 Chirality : 0.054 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/Z covalent geometry : bond 0.00555 / 0.35 (41727) covalent geometry : angle 0.95323 / 0.57 (57675) hydrogen bonds : bond 0.18888 / 20.65 ( 1830) hydrogen bonds : angle 7.27404 / 9.46 ( 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 : 1.207 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: 0.2365 time to fit residues: 115.0282 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 : 1.423 ------------------------------------------------------------------------------- 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: 50.0000 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... R 121 HIS U 441 GLN V 154 ASN W 455 GLN X 190 GLN Y 155 GLN Y 252 GLN D 112 HIS E 55 GLN G 115 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.101224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.069087 restraints weight = 138475.863| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 3.03 r_work: 0.3213 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 41727 Z= 0.159 Angle : 0.643 12.015 57675 Z= 0.339 Chirality : 0.045 0.254 6709 Planarity : 0.005 0.086 6361 Dihedral : 23.353 179.952 8000 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.07 % Allowed : 23.83 % Favored : 74.10 % 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: -0.79 (0.12), residues: 4360 helix: -0.16 (0.11), residues: 2019 sheet: 0.12 (0.21), residues: 592 loop : -1.05 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 53 TYR 0.022 0.001 TYR X 186 PHE 0.017 0.001 PHE H 68 TRP 0.014 0.001 TRP R 214 HIS 0.003 0.001 HIS U 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 (41727) covalent geometry : angle 0.64315 / 0.34 (57675) hydrogen bonds : bond 0.05275 / 5.79 ( 1830) hydrogen bonds : angle 4.49551 / 5.84 ( 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 370 residues out of total 3804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 292 time to evaluate : 1.260 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: 0.8546 (mm110) cc_final: 0.8127 (mp10) REVERT: Q 1293 ARG cc_start: 0.8257 (tmm160) cc_final: 0.7978 (ttp80) REVERT: Q 1331 MET cc_start: 0.8597 (mmt) cc_final: 0.8202 (mmm) REVERT: R 146 GLN cc_start: 0.8185 (tt0) cc_final: 0.7771 (mt0) REVERT: R 212 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8476 (mm) REVERT: R 261 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8596 (pp) REVERT: S 78 LEU cc_start: 0.8997 (mm) cc_final: 0.8711 (pp) REVERT: S 125 TYR cc_start: 0.7693 (OUTLIER) cc_final: 0.7407 (m-80) REVERT: V 182 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7673 (t70) REVERT: W 165 MET cc_start: 0.9130 (ppp) cc_final: 0.8877 (ppp) REVERT: Y 455 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7708 (tm-30) REVERT: A 67 PHE cc_start: 0.7594 (t80) cc_final: 0.7338 (t80) REVERT: G 52 LEU cc_start: 0.8904 (mt) cc_final: 0.8446 (pp) REVERT: H 45 TYR cc_start: 0.7969 (m-10) cc_final: 0.7486 (m-80) outliers start: 78 outliers final: 33 residues processed: 357 average time/residue: 0.2402 time to fit residues: 140.7027 Evaluate side-chains 295 residues out of total 3804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 257 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 965 GLN Chi-restraints excluded: chain Q residue 1102 VAL Chi-restraints excluded: chain Q residue 1149 LEU Chi-restraints excluded: chain R residue 49 LEU 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 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 332 THR Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain V residue 162 THR Chi-restraints excluded: chain V residue 182 ASP 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 X residue 48 PHE 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 Y residue 99 THR 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 455 GLN Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain F residue 87 VAL 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: 9.9990 chunk 364 optimal weight: 3.9990 chunk 306 optimal weight: 0.8980 chunk 232 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 chunk 219 optimal weight: 6.9990 chunk 422 optimal weight: 4.9990 chunk 370 optimal weight: 3.9990 chunk 170 optimal weight: 0.0670 chunk 36 optimal weight: 3.9990 overall best weight: 1.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q1006 GLN R 23 GLN U 441 GLN A 68 GLN C 32 HIS G 115 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.100361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.068217 restraints weight = 138276.201| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 3.00 r_work: 0.3195 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 41727 Z= 0.158 Angle : 0.608 11.698 57675 Z= 0.320 Chirality : 0.044 0.282 6709 Planarity : 0.004 0.067 6361 Dihedral : 23.261 179.126 8000 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.49 % Allowed : 23.17 % Favored : 74.34 % 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: -0.26 (0.12), residues: 4360 helix: 0.45 (0.11), residues: 2036 sheet: 0.09 (0.21), residues: 595 loop : -0.91 (0.14), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 41 TYR 0.020 0.001 TYR X 186 PHE 0.017 0.001 PHE E 67 TRP 0.013 0.001 TRP R 214 HIS 0.004 0.001 HIS D 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (41727) covalent geometry : angle 0.60805 / 0.32 (57675) hydrogen bonds : bond 0.04560 / 4.99 ( 1830) hydrogen bonds : angle 4.14740 / 5.37 ( 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 370 residues out of total 3804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 276 time to evaluate : 1.353 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: symmetry clash REVERT: Q 1331 MET cc_start: 0.8662 (mmt) cc_final: 0.8300 (mmm) REVERT: R 146 GLN cc_start: 0.8043 (tt0) cc_final: 0.7550 (mt0) REVERT: S 78 LEU cc_start: 0.8990 (mm) cc_final: 0.8715 (pp) REVERT: T 377 LYS cc_start: 0.8590 (tttt) cc_final: 0.8309 (ptpp) REVERT: U 44 MET cc_start: 0.7629 (ttm) cc_final: 0.7406 (mtp) REVERT: V 48 PHE cc_start: 0.8537 (OUTLIER) cc_final: 0.6836 (t80) REVERT: V 182 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7687 (t0) REVERT: W 165 MET cc_start: 0.9137 (ppp) cc_final: 0.8931 (ppp) REVERT: Z 301 ASN cc_start: 0.8738 (t0) cc_final: 0.8411 (t0) REVERT: A 67 PHE cc_start: 0.7609 (t80) cc_final: 0.7302 (t80) REVERT: A 113 HIS cc_start: 0.5554 (OUTLIER) cc_final: 0.5077 (t70) REVERT: D 83 LEU cc_start: 0.9154 (mm) cc_final: 0.8280 (tp) REVERT: F 85 MET cc_start: 0.9278 (mpp) cc_final: 0.8722 (mmp) REVERT: G 52 LEU cc_start: 0.8964 (mt) cc_final: 0.8514 (pp) REVERT: G 69 ASN cc_start: 0.8706 (t0) cc_final: 0.8479 (t0) outliers start: 94 outliers final: 50 residues processed: 356 average time/residue: 0.2258 time to fit residues: 133.2906 Evaluate side-chains 311 residues out of total 3804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 258 time to evaluate : 1.321 ------------------------------------------------------------------------------- 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 1221 ILE 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 213 ASN 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 118 VAL 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 V residue 48 PHE Chi-restraints excluded: chain V residue 162 THR Chi-restraints excluded: chain V residue 182 ASP Chi-restraints excluded: chain V residue 355 SER Chi-restraints excluded: chain V residue 443 LYS Chi-restraints excluded: chain W residue 58 LEU 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 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 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 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 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 62 ILE Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 74 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 144 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 412 optimal weight: 9.9990 chunk 434 optimal weight: 40.0000 chunk 322 optimal weight: 7.9990 chunk 285 optimal weight: 2.9990 chunk 227 optimal weight: 10.0000 chunk 382 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 200 optimal weight: 0.9980 chunk 392 optimal weight: 7.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** T 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.100481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.068352 restraints weight = 137100.701| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.99 r_work: 0.3199 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 41727 Z= 0.137 Angle : 0.579 11.382 57675 Z= 0.306 Chirality : 0.043 0.262 6709 Planarity : 0.004 0.056 6361 Dihedral : 23.193 178.261 7998 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.49 % Allowed : 23.83 % Favored : 73.67 % 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: 0.01 (0.13), residues: 4360 helix: 0.77 (0.12), residues: 2023 sheet: 0.05 (0.21), residues: 599 loop : -0.83 (0.15), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG W 232 TYR 0.024 0.001 TYR D 124 PHE 0.024 0.001 PHE V 125 TRP 0.011 0.001 TRP R 214 HIS 0.004 0.001 HIS Q1342 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (41727) covalent geometry : angle 0.57917 / 0.31 (57675) hydrogen bonds : bond 0.03954 / 4.31 ( 1830) hydrogen bonds : angle 3.99431 / 5.16 ( 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 373 residues out of total 3804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 279 time to evaluate : 1.328 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: 0.8547 (mm110) cc_final: 0.8150 (mp10) REVERT: Q 1331 MET cc_start: 0.8650 (mmt) cc_final: 0.8383 (mmt) REVERT: R 100 PHE cc_start: 0.6751 (OUTLIER) cc_final: 0.6209 (m-80) REVERT: R 146 GLN cc_start: 0.8008 (tt0) cc_final: 0.7734 (tt0) REVERT: R 259 GLU cc_start: 0.8761 (pm20) cc_final: 0.8271 (pm20) REVERT: R 261 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8581 (pp) REVERT: R 670 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7994 (pp) REVERT: S 78 LEU cc_start: 0.8992 (mm) cc_final: 0.8696 (pp) REVERT: S 147 MET cc_start: 0.7134 (mmp) cc_final: 0.5632 (mtt) REVERT: T 377 LYS cc_start: 0.8588 (tttt) cc_final: 0.8275 (ptpp) REVERT: U 44 MET cc_start: 0.7697 (ttm) cc_final: 0.7495 (mtp) REVERT: V 48 PHE cc_start: 0.8601 (OUTLIER) cc_final: 0.6956 (t80) REVERT: V 182 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7675 (t70) REVERT: X 312 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8269 (mp0) REVERT: X 463 LEU cc_start: 0.7093 (OUTLIER) cc_final: 0.6039 (tm) REVERT: A 67 PHE cc_start: 0.7604 (t80) cc_final: 0.7257 (t80) REVERT: A 113 HIS cc_start: 0.5609 (OUTLIER) cc_final: 0.5128 (t70) REVERT: B 28 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.7463 (tp40) REVERT: C 52 LEU cc_start: 0.9451 (mt) cc_final: 0.8923 (pp) REVERT: D 83 LEU cc_start: 0.9169 (mm) cc_final: 0.8655 (tp) REVERT: E 79 LYS cc_start: 0.4918 (ptpp) cc_final: 0.4661 (pttt) REVERT: F 85 MET cc_start: 0.9221 (mpp) cc_final: 0.8893 (mmp) REVERT: G 52 LEU cc_start: 0.8975 (mt) cc_final: 0.8511 (pp) REVERT: G 69 ASN cc_start: 0.8776 (t0) cc_final: 0.8550 (t0) REVERT: G 72 ARG cc_start: 0.8207 (tmm-80) cc_final: 0.7994 (tmm-80) REVERT: H 82 LYS cc_start: 0.9461 (OUTLIER) cc_final: 0.9187 (tmtt) REVERT: H 86 TYR cc_start: 0.8772 (m-80) cc_final: 0.8417 (m-80) outliers start: 94 outliers final: 58 residues processed: 360 average time/residue: 0.2276 time to fit residues: 136.5538 Evaluate side-chains 325 residues out of total 3804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 257 time to evaluate : 1.251 ------------------------------------------------------------------------------- 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 1400 ILE Chi-restraints excluded: chain R residue 18 ASP 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 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 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 179 LEU 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 22 THR Chi-restraints excluded: chain V residue 48 PHE Chi-restraints excluded: chain V residue 162 THR Chi-restraints excluded: chain V residue 182 ASP Chi-restraints excluded: chain V residue 195 SER 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 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 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 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 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 B residue 88 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 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 87 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 82 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 152 optimal weight: 1.9990 chunk 343 optimal weight: 0.9980 chunk 422 optimal weight: 10.0000 chunk 129 optimal weight: 1.9990 chunk 373 optimal weight: 6.9990 chunk 80 optimal weight: 0.0970 chunk 108 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 367 optimal weight: 4.9990 chunk 301 optimal weight: 0.8980 chunk 457 optimal weight: 9.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 121 HIS ** T 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 29 HIS Y 155 GLN A 120 GLN C 39 ASN D 59 GLN E 55 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.100202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.068926 restraints weight = 136124.272| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.95 r_work: 0.3207 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 41727 Z= 0.124 Angle : 0.578 11.574 57675 Z= 0.302 Chirality : 0.043 0.258 6709 Planarity : 0.004 0.052 6361 Dihedral : 23.124 177.869 7998 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.71 % Allowed : 23.73 % Favored : 73.57 % 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: 0.17 (0.13), residues: 4360 helix: 0.92 (0.12), residues: 2027 sheet: 0.06 (0.21), residues: 599 loop : -0.76 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG W 232 TYR 0.017 0.001 TYR X 186 PHE 0.016 0.001 PHE S 32 TRP 0.009 0.001 TRP R 214 HIS 0.003 0.001 HIS X 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (41727) covalent geometry : angle 0.57792 / 0.30 (57675) hydrogen bonds : bond 0.03764 / 4.09 ( 1830) hydrogen bonds : angle 3.88894 / 5.02 ( 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 382 residues out of total 3804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 280 time to evaluate : 1.350 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: 0.8520 (mm110) cc_final: 0.8145 (mp10) REVERT: R 100 PHE cc_start: 0.6671 (OUTLIER) cc_final: 0.6068 (m-80) REVERT: R 259 GLU cc_start: 0.8729 (pm20) cc_final: 0.8235 (pm20) REVERT: R 261 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8578 (pp) REVERT: R 670 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.8009 (pp) REVERT: S 69 ASP cc_start: 0.8764 (p0) cc_final: 0.8491 (p0) REVERT: S 78 LEU cc_start: 0.8963 (mm) cc_final: 0.8688 (pp) REVERT: T 377 LYS cc_start: 0.8607 (tttt) cc_final: 0.8305 (ptpp) REVERT: V 48 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.6953 (t80) REVERT: V 182 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7686 (t70) REVERT: X 312 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8292 (mp0) REVERT: X 463 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6150 (tm) REVERT: A 67 PHE cc_start: 0.7566 (t80) cc_final: 0.7221 (t80) REVERT: A 113 HIS cc_start: 0.5684 (OUTLIER) cc_final: 0.5214 (t70) REVERT: B 28 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7433 (tp40) REVERT: C 52 LEU cc_start: 0.9439 (mt) cc_final: 0.8965 (pp) REVERT: D 83 LEU cc_start: 0.9117 (mm) cc_final: 0.8576 (tp) REVERT: E 79 LYS cc_start: 0.4864 (ptpp) cc_final: 0.4642 (pttt) REVERT: G 52 LEU cc_start: 0.8989 (mt) cc_final: 0.8523 (pp) REVERT: G 69 ASN cc_start: 0.8647 (t0) cc_final: 0.8372 (t0) REVERT: G 72 ARG cc_start: 0.8149 (tmm-80) cc_final: 0.7913 (tmm-80) REVERT: H 86 TYR cc_start: 0.8724 (m-80) cc_final: 0.8293 (m-80) outliers start: 102 outliers final: 61 residues processed: 368 average time/residue: 0.2235 time to fit residues: 135.8611 Evaluate side-chains 332 residues out of total 3804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 262 time to evaluate : 1.547 ------------------------------------------------------------------------------- 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 1001 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 1434 ASP Chi-restraints excluded: chain R residue 18 ASP Chi-restraints excluded: chain R residue 100 PHE Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 164 THR 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 125 TYR 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 179 LEU Chi-restraints excluded: chain U residue 215 MET 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 182 ASP Chi-restraints excluded: chain V residue 195 SER 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 456 ILE Chi-restraints excluded: chain X residue 93 SER 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 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 463 LEU Chi-restraints excluded: chain Y residue 18 SER Chi-restraints excluded: chain Y residue 44 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 191 SER 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 87 SER 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 57 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain H residue 51 THR Chi-restraints excluded: chain H residue 69 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 408 optimal weight: 5.9990 chunk 181 optimal weight: 0.0470 chunk 189 optimal weight: 4.9990 chunk 191 optimal weight: 0.6980 chunk 320 optimal weight: 5.9990 chunk 300 optimal weight: 8.9990 chunk 172 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 358 optimal weight: 4.9990 chunk 165 optimal weight: 0.1980 chunk 348 optimal weight: 2.9990 overall best weight: 1.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 121 HIS ** T 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 144 GLN G 115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.100312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.068582 restraints weight = 139171.564| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.99 r_work: 0.3204 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 41727 Z= 0.122 Angle : 0.572 11.582 57675 Z= 0.299 Chirality : 0.043 0.251 6709 Planarity : 0.003 0.053 6361 Dihedral : 23.078 177.114 7998 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.73 % Allowed : 23.78 % Favored : 73.49 % 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: 0.24 (0.13), residues: 4360 helix: 0.99 (0.12), residues: 2028 sheet: 0.08 (0.21), residues: 601 loop : -0.73 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 36 TYR 0.016 0.001 TYR X 186 PHE 0.025 0.001 PHE V 125 TRP 0.010 0.001 TRP R 214 HIS 0.005 0.001 HIS R 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (41727) covalent geometry : angle 0.57203 / 0.30 (57675) hydrogen bonds : bond 0.03645 / 3.97 ( 1830) hydrogen bonds : angle 3.80703 / 4.91 ( 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 383 residues out of total 3804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 280 time to evaluate : 1.463 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: 0.8525 (mm110) cc_final: 0.8135 (mp10) REVERT: Q 1335 LEU cc_start: 0.9043 (mm) cc_final: 0.8841 (mm) REVERT: R 261 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8586 (pp) REVERT: R 670 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.8024 (pp) REVERT: S 69 ASP cc_start: 0.8870 (p0) cc_final: 0.8575 (p0) REVERT: S 78 LEU cc_start: 0.8966 (mm) cc_final: 0.8726 (pp) REVERT: S 147 MET cc_start: 0.7044 (mmp) cc_final: 0.5688 (mtt) REVERT: T 377 LYS cc_start: 0.8599 (tttt) cc_final: 0.8307 (ptpp) REVERT: V 48 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.6929 (t80) REVERT: V 182 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7651 (t70) REVERT: X 312 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8276 (mp0) REVERT: X 406 MET cc_start: 0.8779 (tpp) cc_final: 0.8300 (tpp) REVERT: X 463 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6172 (tm) REVERT: A 67 PHE cc_start: 0.7573 (t80) cc_final: 0.7292 (t80) REVERT: A 113 HIS cc_start: 0.5664 (OUTLIER) cc_final: 0.5208 (t70) REVERT: B 28 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7437 (tp40) REVERT: C 52 LEU cc_start: 0.9432 (mt) cc_final: 0.8984 (pp) REVERT: D 83 LEU cc_start: 0.9113 (mm) cc_final: 0.8564 (tp) REVERT: E 79 LYS cc_start: 0.4832 (ptpp) cc_final: 0.4629 (pttt) REVERT: F 85 MET cc_start: 0.9201 (mpp) cc_final: 0.8689 (mmp) REVERT: G 52 LEU cc_start: 0.8991 (mt) cc_final: 0.8539 (pp) REVERT: G 69 ASN cc_start: 0.8663 (t0) cc_final: 0.8347 (t0) REVERT: G 72 ARG cc_start: 0.8129 (tmm-80) cc_final: 0.7914 (tmm-80) REVERT: H 82 LYS cc_start: 0.9481 (OUTLIER) cc_final: 0.9209 (tmtt) REVERT: H 86 TYR cc_start: 0.8753 (m-80) cc_final: 0.8450 (m-80) outliers start: 103 outliers final: 69 residues processed: 368 average time/residue: 0.2206 time to fit residues: 135.1361 Evaluate side-chains 340 residues out of total 3804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 262 time to evaluate : 1.273 ------------------------------------------------------------------------------- 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 1001 ILE Chi-restraints excluded: chain Q residue 1092 ASP 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 100 PHE Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 164 THR 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 614 LEU 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 125 TYR 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 T residue 418 LEU Chi-restraints excluded: chain U residue 179 LEU 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 22 THR Chi-restraints excluded: chain V residue 48 PHE Chi-restraints excluded: chain V residue 162 THR Chi-restraints excluded: chain V residue 182 ASP 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 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 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 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 463 LEU Chi-restraints excluded: chain Y residue 44 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 191 SER 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 87 SER 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 92 ILE Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 103 ILE 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 423 optimal weight: 6.9990 chunk 440 optimal weight: 5.9990 chunk 294 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 263 optimal weight: 0.0060 chunk 21 optimal weight: 50.0000 chunk 6 optimal weight: 50.0000 chunk 455 optimal weight: 9.9990 chunk 453 optimal weight: 10.0000 chunk 410 optimal weight: 0.4980 chunk 265 optimal weight: 7.9990 overall best weight: 3.9002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q1279 ASN Q1281 ASN Q1397 ASN ** R 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 451 GLN W 326 ASN ** W 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 27 HIS ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.097393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.065410 restraints weight = 139940.386| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.96 r_work: 0.3130 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 41727 Z= 0.248 Angle : 0.667 12.358 57675 Z= 0.347 Chirality : 0.044 0.253 6709 Planarity : 0.004 0.059 6361 Dihedral : 23.218 176.578 7998 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.97 % Allowed : 23.73 % 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: 0.09 (0.13), residues: 4360 helix: 0.89 (0.12), residues: 2025 sheet: -0.14 (0.20), residues: 629 loop : -0.78 (0.15), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Q1293 TYR 0.031 0.002 TYR X 186 PHE 0.025 0.002 PHE V 125 TRP 0.018 0.002 TRP R 214 HIS 0.011 0.001 HIS D 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.25 (41727) covalent geometry : angle 0.66652 / 0.35 (57675) hydrogen bonds : bond 0.04638 / 5.13 ( 1830) hydrogen bonds : angle 4.04653 / 5.23 ( 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 375 residues out of total 3804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 263 time to evaluate : 1.702 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: 0.8573 (mm110) cc_final: 0.8153 (mp10) REVERT: Q 1291 MET cc_start: 0.8957 (tpp) cc_final: 0.8688 (tpp) REVERT: R 74 LYS cc_start: 0.6817 (OUTLIER) cc_final: 0.6237 (pttm) REVERT: R 100 PHE cc_start: 0.7031 (OUTLIER) cc_final: 0.6282 (m-80) REVERT: R 261 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8602 (pp) REVERT: R 670 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.8034 (pp) REVERT: S 69 ASP cc_start: 0.8875 (p0) cc_final: 0.8552 (p0) REVERT: S 78 LEU cc_start: 0.8959 (mm) cc_final: 0.8687 (pp) REVERT: S 147 MET cc_start: 0.7189 (mmp) cc_final: 0.5737 (mtt) REVERT: T 315 MET cc_start: 0.8785 (mmm) cc_final: 0.8559 (mmm) REVERT: T 377 LYS cc_start: 0.8631 (tttt) cc_final: 0.8333 (ptpp) REVERT: U 105 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8042 (mp0) REVERT: V 48 PHE cc_start: 0.8600 (OUTLIER) cc_final: 0.7027 (t80) REVERT: V 182 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.7741 (t70) REVERT: X 268 MET cc_start: 0.9083 (mmm) cc_final: 0.8454 (mmm) REVERT: X 312 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8022 (mm-30) REVERT: Y 351 SER cc_start: 0.9189 (OUTLIER) cc_final: 0.8899 (p) REVERT: A 67 PHE cc_start: 0.7661 (t80) cc_final: 0.7372 (t80) REVERT: A 113 HIS cc_start: 0.5693 (OUTLIER) cc_final: 0.5287 (t-90) REVERT: C 24 LEU cc_start: 0.6290 (OUTLIER) cc_final: 0.5933 (pp) REVERT: C 52 LEU cc_start: 0.9435 (mt) cc_final: 0.8945 (pp) REVERT: D 49 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.7395 (mtmt) REVERT: D 83 LEU cc_start: 0.9165 (mm) cc_final: 0.8780 (tp) REVERT: F 85 MET cc_start: 0.9188 (mpp) cc_final: 0.8727 (mmp) REVERT: G 52 LEU cc_start: 0.9010 (mt) cc_final: 0.8564 (pp) REVERT: G 69 ASN cc_start: 0.8621 (t0) cc_final: 0.8378 (t0) REVERT: H 82 LYS cc_start: 0.9489 (OUTLIER) cc_final: 0.9190 (tmtt) REVERT: H 86 TYR cc_start: 0.8740 (m-80) cc_final: 0.8412 (m-80) outliers start: 112 outliers final: 76 residues processed: 357 average time/residue: 0.2617 time to fit residues: 153.3453 Evaluate side-chains 345 residues out of total 3804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 256 time to evaluate : 1.860 ------------------------------------------------------------------------------- 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 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 137 THR 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 614 LEU 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 T residue 424 ILE Chi-restraints excluded: chain U residue 105 GLU Chi-restraints excluded: chain U residue 179 LEU 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 156 LEU Chi-restraints excluded: chain V residue 162 THR Chi-restraints excluded: chain V residue 182 ASP Chi-restraints excluded: chain V residue 195 SER Chi-restraints excluded: chain V residue 355 SER 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 257 LEU Chi-restraints excluded: chain W residue 456 ILE Chi-restraints excluded: chain X residue 48 PHE Chi-restraints excluded: chain X residue 93 SER Chi-restraints excluded: chain X residue 117 LYS 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 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 Y residue 44 MET Chi-restraints excluded: chain Y residue 60 MET Chi-restraints excluded: chain Y residue 89 SER 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 255 LEU Chi-restraints excluded: chain Y residue 271 ASP Chi-restraints excluded: chain Y residue 351 SER Chi-restraints excluded: chain Y residue 373 GLN 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 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 49 LYS 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 87 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 103 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 348 optimal weight: 0.9980 chunk 432 optimal weight: 8.9990 chunk 63 optimal weight: 7.9990 chunk 396 optimal weight: 10.0000 chunk 319 optimal weight: 0.3980 chunk 231 optimal weight: 5.9990 chunk 420 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 27 optimal weight: 50.0000 chunk 415 optimal weight: 5.9990 chunk 151 optimal weight: 0.9980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 121 HIS ** R 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 326 ASN D 112 HIS ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.098800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.066891 restraints weight = 138011.019| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.96 r_work: 0.3162 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 41727 Z= 0.145 Angle : 0.598 11.821 57675 Z= 0.312 Chirality : 0.043 0.261 6709 Planarity : 0.004 0.057 6361 Dihedral : 23.205 175.992 7998 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.57 % Allowed : 24.10 % Favored : 73.33 % 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: 0.22 (0.13), residues: 4360 helix: 0.99 (0.12), residues: 2031 sheet: -0.07 (0.21), residues: 619 loop : -0.70 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Y 220 TYR 0.020 0.001 TYR X 186 PHE 0.021 0.001 PHE V 125 TRP 0.013 0.001 TRP R 214 HIS 0.010 0.001 HIS D 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (41727) covalent geometry : angle 0.59804 / 0.31 (57675) hydrogen bonds : bond 0.03772 / 4.13 ( 1830) hydrogen bonds : angle 3.88823 / 5.01 ( 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 364 residues out of total 3804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 267 time to evaluate : 1.515 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: 0.8546 (mm110) cc_final: 0.8149 (mp10) REVERT: R 121 HIS cc_start: 0.6248 (OUTLIER) cc_final: 0.5781 (m-70) REVERT: R 261 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8557 (pp) REVERT: R 670 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.8061 (pp) REVERT: S 69 ASP cc_start: 0.8849 (p0) cc_final: 0.8524 (p0) REVERT: S 78 LEU cc_start: 0.8960 (mm) cc_final: 0.8719 (pp) REVERT: S 147 MET cc_start: 0.7064 (mmp) cc_final: 0.5767 (mtt) REVERT: T 377 LYS cc_start: 0.8626 (tttt) cc_final: 0.8311 (ptpp) REVERT: V 48 PHE cc_start: 0.8604 (OUTLIER) cc_final: 0.7032 (t80) REVERT: V 182 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.7745 (t70) REVERT: X 312 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8025 (mm-30) REVERT: X 463 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6166 (tm) REVERT: A 67 PHE cc_start: 0.7670 (t80) cc_final: 0.7377 (t80) REVERT: A 113 HIS cc_start: 0.5638 (OUTLIER) cc_final: 0.5250 (t-90) REVERT: B 28 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.7393 (tp40) REVERT: C 52 LEU cc_start: 0.9440 (mt) cc_final: 0.8987 (pp) REVERT: D 49 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7435 (mtmt) REVERT: D 83 LEU cc_start: 0.9132 (mm) cc_final: 0.8605 (tp) REVERT: F 85 MET cc_start: 0.9232 (mpp) cc_final: 0.8784 (mmp) REVERT: G 52 LEU cc_start: 0.8982 (mt) cc_final: 0.8542 (pp) REVERT: H 82 LYS cc_start: 0.9489 (OUTLIER) cc_final: 0.9224 (tmtt) REVERT: H 86 TYR cc_start: 0.8758 (m-80) cc_final: 0.8450 (m-80) outliers start: 97 outliers final: 68 residues processed: 351 average time/residue: 0.2401 time to fit residues: 138.8577 Evaluate side-chains 335 residues out of total 3804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 256 time to evaluate : 1.494 ------------------------------------------------------------------------------- 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 1001 ILE 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 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 258 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 614 LEU 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 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 215 MET Chi-restraints excluded: chain U residue 332 THR Chi-restraints excluded: chain U residue 418 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 182 ASP 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 239 VAL Chi-restraints excluded: chain W residue 257 LEU Chi-restraints excluded: chain W residue 456 ILE Chi-restraints excluded: chain X residue 48 PHE 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 336 VAL Chi-restraints excluded: chain X residue 341 ASN Chi-restraints excluded: chain X residue 355 SER Chi-restraints excluded: chain X residue 463 LEU Chi-restraints excluded: chain Y residue 44 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 191 SER 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 87 SER 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 49 LYS Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 87 VAL 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 51 THR Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 82 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 459 random chunks: chunk 446 optimal weight: 6.9990 chunk 330 optimal weight: 2.9990 chunk 243 optimal weight: 3.9990 chunk 428 optimal weight: 5.9990 chunk 370 optimal weight: 1.9990 chunk 248 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 225 optimal weight: 8.9990 chunk 229 optimal weight: 0.7980 chunk 339 optimal weight: 0.9980 chunk 230 optimal weight: 0.0970 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q1342 HIS ** R 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 326 ASN ** 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 = 0.4089 r_free = 0.4089 target = 0.099038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.067218 restraints weight = 139208.953| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.96 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: 0.8319 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 41727 Z= 0.133 Angle : 0.601 12.072 57675 Z= 0.311 Chirality : 0.043 0.281 6709 Planarity : 0.003 0.058 6361 Dihedral : 23.159 175.912 7998 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.44 % Allowed : 24.20 % Favored : 73.35 % 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: 0.29 (0.13), residues: 4360 helix: 1.03 (0.12), residues: 2032 sheet: 0.04 (0.21), residues: 613 loop : -0.68 (0.15), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Q1293 TYR 0.018 0.001 TYR X 186 PHE 0.025 0.001 PHE V 125 TRP 0.010 0.001 TRP R 214 HIS 0.039 0.001 HIS R 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (41727) covalent geometry : angle 0.60092 / 0.31 (57675) hydrogen bonds : bond 0.03669 / 4.01 ( 1830) hydrogen bonds : angle 3.86112 / 4.97 ( 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 360 residues out of total 3804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 268 time to evaluate : 1.478 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: 0.8540 (mm110) cc_final: 0.8143 (mp10) REVERT: Q 1335 LEU cc_start: 0.8883 (mm) cc_final: 0.8674 (pp) REVERT: R 74 LYS cc_start: 0.6829 (OUTLIER) cc_final: 0.6323 (pttm) REVERT: R 261 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8629 (pp) REVERT: R 670 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.8061 (pp) REVERT: S 69 ASP cc_start: 0.8838 (p0) cc_final: 0.8513 (p0) REVERT: S 78 LEU cc_start: 0.8978 (mm) cc_final: 0.8719 (pp) REVERT: S 147 MET cc_start: 0.7055 (mmp) cc_final: 0.5810 (mtt) REVERT: T 377 LYS cc_start: 0.8636 (tttt) cc_final: 0.8343 (ptpp) REVERT: V 48 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.7038 (t80) REVERT: V 182 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7735 (t70) REVERT: W 165 MET cc_start: 0.9166 (ppp) cc_final: 0.8946 (ppp) REVERT: X 312 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8286 (mp0) REVERT: X 463 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.6188 (tm) REVERT: A 67 PHE cc_start: 0.7660 (t80) cc_final: 0.7362 (t80) REVERT: A 113 HIS cc_start: 0.5622 (OUTLIER) cc_final: 0.5215 (t-90) REVERT: B 28 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.7391 (tp40) REVERT: C 24 LEU cc_start: 0.6293 (OUTLIER) cc_final: 0.5895 (pp) REVERT: C 52 LEU cc_start: 0.9434 (mt) cc_final: 0.9025 (pp) REVERT: D 49 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7456 (mtmt) REVERT: D 83 LEU cc_start: 0.9148 (mm) cc_final: 0.8610 (tp) REVERT: F 85 MET cc_start: 0.9192 (mpp) cc_final: 0.8760 (mmp) REVERT: G 52 LEU cc_start: 0.9011 (mt) cc_final: 0.8548 (pp) REVERT: H 82 LYS cc_start: 0.9494 (OUTLIER) cc_final: 0.9222 (tmtt) REVERT: H 86 TYR cc_start: 0.8758 (m-80) cc_final: 0.8442 (m-80) outliers start: 92 outliers final: 74 residues processed: 348 average time/residue: 0.2526 time to fit residues: 145.3740 Evaluate side-chains 348 residues out of total 3804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 262 time to evaluate : 1.512 ------------------------------------------------------------------------------- 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 1001 ILE 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 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 100 PHE Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 164 THR 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 614 LEU 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 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 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 332 THR Chi-restraints excluded: chain U residue 418 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 182 ASP 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 184 VAL Chi-restraints excluded: chain W residue 210 ARG Chi-restraints excluded: chain W residue 239 VAL Chi-restraints excluded: chain W residue 326 ASN Chi-restraints excluded: chain W residue 456 ILE Chi-restraints excluded: chain X residue 48 PHE 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 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 463 LEU Chi-restraints excluded: chain Y residue 44 MET Chi-restraints excluded: chain Y residue 89 SER Chi-restraints excluded: chain Y residue 99 THR Chi-restraints excluded: chain Y residue 112 SER 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 373 GLN 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 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 68 GLN Chi-restraints excluded: chain F residue 87 VAL 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 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 222 optimal weight: 1.9990 chunk 413 optimal weight: 20.0000 chunk 417 optimal weight: 3.9990 chunk 352 optimal weight: 0.9980 chunk 149 optimal weight: 0.7980 chunk 112 optimal weight: 8.9990 chunk 454 optimal weight: 3.9990 chunk 402 optimal weight: 6.9990 chunk 435 optimal weight: 7.9990 chunk 200 optimal weight: 0.6980 chunk 153 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** T 51 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 = 0.4096 r_free = 0.4096 target = 0.099412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.067641 restraints weight = 137668.732| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.96 r_work: 0.3183 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 41727 Z= 0.122 Angle : 0.604 12.765 57675 Z= 0.312 Chirality : 0.043 0.253 6709 Planarity : 0.004 0.058 6361 Dihedral : 23.138 175.848 7998 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.12 % Allowed : 24.73 % Favored : 73.14 % 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: 0.32 (0.13), residues: 4360 helix: 1.05 (0.12), residues: 2032 sheet: 0.05 (0.21), residues: 601 loop : -0.65 (0.15), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Q1293 TYR 0.017 0.001 TYR X 186 PHE 0.022 0.001 PHE V 125 TRP 0.009 0.001 TRP R 214 HIS 0.030 0.001 HIS Q1342 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (41727) covalent geometry : angle 0.60374 / 0.31 (57675) hydrogen bonds : bond 0.03596 / 3.91 ( 1830) hydrogen bonds : angle 3.83766 / 4.93 ( 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 349 residues out of total 3804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 269 time to evaluate : 1.567 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: symmetry clash revert: symmetry clash REVERT: Q 958 GLN cc_start: 0.8538 (mm110) cc_final: 0.8134 (mp10) REVERT: Q 1335 LEU cc_start: 0.8852 (mm) cc_final: 0.8651 (pp) REVERT: R 74 LYS cc_start: 0.6800 (OUTLIER) cc_final: 0.6275 (pttm) REVERT: R 261 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8612 (pp) REVERT: R 670 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.8045 (pp) REVERT: S 69 ASP cc_start: 0.8861 (p0) cc_final: 0.8534 (p0) REVERT: S 78 LEU cc_start: 0.8975 (mm) cc_final: 0.8706 (pp) REVERT: S 147 MET cc_start: 0.7002 (mmp) cc_final: 0.5746 (mtt) REVERT: T 377 LYS cc_start: 0.8629 (tttt) cc_final: 0.8332 (ptpp) REVERT: V 48 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.7003 (t80) REVERT: V 182 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.7717 (t70) REVERT: V 406 MET cc_start: 0.8155 (mmm) cc_final: 0.7483 (mmm) REVERT: W 165 MET cc_start: 0.9163 (ppp) cc_final: 0.8940 (ppp) REVERT: X 312 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8277 (mp0) REVERT: X 463 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.6183 (tm) REVERT: Y 323 MET cc_start: 0.9127 (mtm) cc_final: 0.8870 (mtt) REVERT: A 67 PHE cc_start: 0.7657 (t80) cc_final: 0.7352 (t80) REVERT: A 113 HIS cc_start: 0.5597 (OUTLIER) cc_final: 0.5182 (t-90) REVERT: B 28 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.7463 (tp40) REVERT: C 24 LEU cc_start: 0.6294 (OUTLIER) cc_final: 0.5886 (pp) REVERT: C 52 LEU cc_start: 0.9437 (mt) cc_final: 0.9003 (pp) REVERT: D 49 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7429 (mtmt) REVERT: D 83 LEU cc_start: 0.9141 (mm) cc_final: 0.8262 (tp) REVERT: F 85 MET cc_start: 0.9156 (mpp) cc_final: 0.8739 (mmp) REVERT: G 16 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7408 (tp40) REVERT: G 52 LEU cc_start: 0.9015 (mt) cc_final: 0.8553 (pp) REVERT: H 82 LYS cc_start: 0.9491 (OUTLIER) cc_final: 0.9166 (tmtt) REVERT: H 86 TYR cc_start: 0.8756 (m-80) cc_final: 0.8325 (m-80) outliers start: 80 outliers final: 63 residues processed: 338 average time/residue: 0.2391 time to fit residues: 133.6876 Evaluate side-chains 340 residues out of total 3804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 264 time to evaluate : 1.465 ------------------------------------------------------------------------------- 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 1001 ILE Chi-restraints excluded: chain Q residue 1102 VAL Chi-restraints excluded: chain Q residue 1206 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 100 PHE Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 164 THR 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 125 TYR 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 215 MET Chi-restraints excluded: chain U residue 332 THR Chi-restraints excluded: chain U residue 418 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 182 ASP 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 239 VAL Chi-restraints excluded: chain W residue 456 ILE Chi-restraints excluded: chain X residue 48 PHE 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 336 VAL Chi-restraints excluded: chain X residue 341 ASN Chi-restraints excluded: chain X residue 355 SER Chi-restraints excluded: chain X residue 463 LEU Chi-restraints excluded: chain Y residue 44 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 191 SER Chi-restraints excluded: chain Y residue 255 LEU Chi-restraints excluded: chain Y residue 271 ASP 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 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 68 GLN Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain G residue 16 GLN Chi-restraints excluded: chain G residue 103 ILE 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: 0.0370 chunk 174 optimal weight: 8.9990 chunk 25 optimal weight: 50.0000 chunk 347 optimal weight: 3.9990 chunk 76 optimal weight: 0.1980 chunk 106 optimal weight: 0.9980 chunk 309 optimal weight: 7.9990 chunk 419 optimal weight: 10.0000 chunk 279 optimal weight: 0.9980 chunk 314 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q1342 HIS ** T 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.100018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.068355 restraints weight = 138922.110| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.98 r_work: 0.3198 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 41727 Z= 0.115 Angle : 0.596 13.656 57675 Z= 0.308 Chirality : 0.043 0.250 6709 Planarity : 0.003 0.058 6361 Dihedral : 23.052 175.716 7998 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.15 % Allowed : 24.87 % 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: 0.40 (0.13), residues: 4360 helix: 1.12 (0.12), residues: 2027 sheet: 0.12 (0.21), residues: 600 loop : -0.63 (0.15), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 64 TYR 0.014 0.001 TYR X 186 PHE 0.017 0.001 PHE V 125 TRP 0.007 0.001 TRP R 711 HIS 0.004 0.001 HIS R 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (41727) covalent geometry : angle 0.59607 / 0.31 (57675) hydrogen bonds : bond 0.03490 / 3.77 ( 1830) hydrogen bonds : angle 3.78257 / 4.85 ( 5037) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10305.64 seconds wall clock time: 177 minutes 21.00 seconds (10641.00 seconds total)