Starting phenix.real_space_refine on Sun Jul 5 02:18:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rx6_54359/07_2026/9rx6_54359.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rx6_54359/07_2026/9rx6_54359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rx6_54359/07_2026/9rx6_54359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rx6_54359/07_2026/9rx6_54359.map" model { file = "/net/cci-nas-00/data/ceres_data/9rx6_54359/07_2026/9rx6_54359.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rx6_54359/07_2026/9rx6_54359.cif" } resolution = 3.52 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= 0.001 sd= 0.023 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 5 5.49 5 Mg 2 5.21 5 S 119 5.16 5 C 15293 2.51 5 N 4153 2.21 5 O 4485 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s 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: 24058 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 810, 6564 Classifications: {'peptide': 810} Link IDs: {'CIS': 1, 'PTRANS': 39, 'TRANS': 769} Chain breaks: 2 Chain: "B" Number of atoms: 9520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1197, 9520 Classifications: {'peptide': 1197} Link IDs: {'CIS': 4, 'PCIS': 3, 'PTRANS': 52, 'TRANS': 1137} Chain breaks: 5 Chain: "C" Number of atoms: 3119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3119 Classifications: {'peptide': 379} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 370} Chain breaks: 2 Chain: "D" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3456 Classifications: {'peptide': 423} Link IDs: {'CIS': 3, 'PTRANS': 12, 'TRANS': 407} Chain breaks: 1 Chain: "F" Number of atoms: 1321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1321 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 3, 'TRANS': 164} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 44 Unusual residues: {' MG': 1, 'GDP': 1, 'MYR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16114 SG CYS C 18 42.696 134.244 35.472 1.00219.42 S ATOM 16140 SG CYS C 21 40.975 134.009 36.287 1.00224.01 S ATOM 16611 SG CYS C 137 39.897 136.118 36.921 1.00219.76 S ATOM 16635 SG CYS C 140 42.082 137.673 38.074 1.00231.19 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb="MG MG F 300 " occ=0.70 residue: pdb=" C1' GTP F 301 " occ=0.80 ... (30 atoms not shown) pdb=" PG GTP F 301 " occ=0.80 Time building chain proxies: 5.11, per 1000 atoms: 0.21 Number of scatterers: 24058 At special positions: 0 Unit cell: (104.58, 180.11, 241.53, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 119 16.00 P 5 15.00 Mg 2 11.99 O 4485 8.00 N 4153 7.00 C 15293 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 693 " - pdb=" SG CYS C 165 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 140 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 18 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 21 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 137 " Number of angles added : 6 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5666 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 24 sheets defined 49.7% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 34 through 41 removed outlier: 3.885A pdb=" N VAL A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 47 removed outlier: 3.574A pdb=" N LYS A 45 " --> pdb=" O PRO A 42 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A 47 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 172 through 184 Processing helix chain 'A' and resid 190 through 212 removed outlier: 3.671A pdb=" N ARG A 195 " --> pdb=" O ASP A 191 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LEU A 196 " --> pdb=" O TRP A 192 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLU A 199 " --> pdb=" O ARG A 195 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG A 210 " --> pdb=" O GLU A 206 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER A 211 " --> pdb=" O SER A 207 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 275 removed outlier: 3.515A pdb=" N SER A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS A 270 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG A 275 " --> pdb=" O HIS A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 284 removed outlier: 4.089A pdb=" N HIS A 284 " --> pdb=" O PRO A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 301 Processing helix chain 'A' and resid 309 through 319 removed outlier: 3.586A pdb=" N ASP A 314 " --> pdb=" O TYR A 310 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.597A pdb=" N THR A 324 " --> pdb=" O TYR A 321 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASN A 325 " --> pdb=" O TYR A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 328 No H-bonds generated for 'chain 'A' and resid 327 through 328' Processing helix chain 'A' and resid 329 through 335 removed outlier: 3.645A pdb=" N LYS A 335 " --> pdb=" O THR A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 354 removed outlier: 3.561A pdb=" N GLY A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 368 removed outlier: 3.891A pdb=" N LEU A 364 " --> pdb=" O GLU A 361 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU A 365 " --> pdb=" O ASP A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 388 Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 403 through 406 Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 476 through 484 Processing helix chain 'A' and resid 486 through 502 Processing helix chain 'A' and resid 503 through 510 Processing helix chain 'A' and resid 510 through 529 removed outlier: 3.606A pdb=" N HIS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 561 Processing helix chain 'A' and resid 565 through 578 Processing helix chain 'A' and resid 579 through 584 Processing helix chain 'A' and resid 641 through 660 Processing helix chain 'A' and resid 690 through 697 Processing helix chain 'A' and resid 699 through 708 Processing helix chain 'A' and resid 713 through 717 removed outlier: 3.620A pdb=" N GLY A 716 " --> pdb=" O GLY A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 740 Processing helix chain 'A' and resid 780 through 786 removed outlier: 3.688A pdb=" N VAL A 784 " --> pdb=" O ASN A 780 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY A 786 " --> pdb=" O GLU A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 811 removed outlier: 3.671A pdb=" N GLN A 796 " --> pdb=" O SER A 792 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR A 803 " --> pdb=" O ARG A 799 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR A 804 " --> pdb=" O LYS A 800 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A 805 " --> pdb=" O GLN A 801 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 822 removed outlier: 3.771A pdb=" N ILE A 816 " --> pdb=" O TYR A 812 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 822 " --> pdb=" O ASN A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 844 Processing helix chain 'A' and resid 851 through 868 removed outlier: 3.631A pdb=" N SER A 866 " --> pdb=" O LEU A 862 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HIS A 868 " --> pdb=" O ASP A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 871 No H-bonds generated for 'chain 'A' and resid 869 through 871' Processing helix chain 'B' and resid 64 through 78 removed outlier: 3.978A pdb=" N LYS B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN B 69 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLU B 70 " --> pdb=" O SER B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 115 removed outlier: 4.095A pdb=" N SER B 115 " --> pdb=" O TYR B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 142 removed outlier: 3.782A pdb=" N SER B 142 " --> pdb=" O GLN B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 198 through 200 No H-bonds generated for 'chain 'B' and resid 198 through 200' Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 229 through 233 Processing helix chain 'B' and resid 236 through 239 removed outlier: 3.540A pdb=" N MET B 239 " --> pdb=" O LYS B 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 236 through 239' Processing helix chain 'B' and resid 240 through 253 Processing helix chain 'B' and resid 260 through 269 Processing helix chain 'B' and resid 276 through 281 removed outlier: 3.681A pdb=" N ASN B 279 " --> pdb=" O GLN B 276 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE B 281 " --> pdb=" O LEU B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 294 Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.744A pdb=" N ARG B 301 " --> pdb=" O PRO B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 311 Processing helix chain 'B' and resid 317 through 323 removed outlier: 4.345A pdb=" N TYR B 321 " --> pdb=" O PRO B 317 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE B 323 " --> pdb=" O ILE B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 329 Processing helix chain 'B' and resid 330 through 333 removed outlier: 3.747A pdb=" N LYS B 333 " --> pdb=" O GLN B 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 330 through 333' Processing helix chain 'B' and resid 338 through 349 removed outlier: 3.673A pdb=" N LEU B 344 " --> pdb=" O ASP B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 358 Processing helix chain 'B' and resid 374 through 384 removed outlier: 4.098A pdb=" N LEU B 378 " --> pdb=" O GLY B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 406 Processing helix chain 'B' and resid 407 through 409 No H-bonds generated for 'chain 'B' and resid 407 through 409' Processing helix chain 'B' and resid 410 through 417 Processing helix chain 'B' and resid 418 through 424 Processing helix chain 'B' and resid 430 through 446 Processing helix chain 'B' and resid 463 through 468 Processing helix chain 'B' and resid 469 through 473 Processing helix chain 'B' and resid 475 through 506 removed outlier: 3.729A pdb=" N ARG B 479 " --> pdb=" O ALA B 475 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ALA B 487 " --> pdb=" O ALA B 483 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N LEU B 488 " --> pdb=" O GLU B 484 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU B 502 " --> pdb=" O GLU B 498 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS B 503 " --> pdb=" O LEU B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 545 removed outlier: 3.924A pdb=" N GLN B 531 " --> pdb=" O ASP B 527 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS B 540 " --> pdb=" O MET B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 559 removed outlier: 4.175A pdb=" N LYS B 553 " --> pdb=" O GLU B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 569 removed outlier: 3.746A pdb=" N LEU B 564 " --> pdb=" O GLY B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 576 Processing helix chain 'B' and resid 576 through 581 Processing helix chain 'B' and resid 582 through 587 Processing helix chain 'B' and resid 590 through 600 removed outlier: 4.037A pdb=" N ARG B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 609 removed outlier: 4.243A pdb=" N VAL B 604 " --> pdb=" O SER B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 624 Proline residue: B 618 - end of helix Processing helix chain 'B' and resid 628 through 646 removed outlier: 3.580A pdb=" N ILE B 632 " --> pdb=" O GLU B 628 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 645 " --> pdb=" O CYS B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 661 removed outlier: 3.867A pdb=" N TYR B 654 " --> pdb=" O LYS B 650 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP B 659 " --> pdb=" O GLU B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 666 removed outlier: 3.576A pdb=" N CYS B 665 " --> pdb=" O PRO B 662 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N HIS B 666 " --> pdb=" O PHE B 663 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 662 through 666' Processing helix chain 'B' and resid 668 through 686 removed outlier: 4.081A pdb=" N ARG B 684 " --> pdb=" O THR B 680 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B 686 " --> pdb=" O VAL B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 694 Processing helix chain 'B' and resid 694 through 699 removed outlier: 3.542A pdb=" N TYR B 698 " --> pdb=" O LYS B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 719 removed outlier: 3.548A pdb=" N SER B 718 " --> pdb=" O LEU B 714 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL B 719 " --> pdb=" O VAL B 715 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 714 through 719' Processing helix chain 'B' and resid 725 through 735 removed outlier: 3.711A pdb=" N TYR B 731 " --> pdb=" O SER B 727 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA B 732 " --> pdb=" O ILE B 728 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU B 733 " --> pdb=" O PHE B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 753 Processing helix chain 'B' and resid 764 through 778 Processing helix chain 'B' and resid 780 through 790 Processing helix chain 'B' and resid 790 through 809 Processing helix chain 'B' and resid 810 through 813 removed outlier: 3.725A pdb=" N SER B 813 " --> pdb=" O LEU B 810 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 810 through 813' Processing helix chain 'B' and resid 821 through 825 Processing helix chain 'B' and resid 940 through 966 removed outlier: 3.560A pdb=" N GLN B 945 " --> pdb=" O LYS B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 1023 through 1025 No H-bonds generated for 'chain 'B' and resid 1023 through 1025' Processing helix chain 'B' and resid 1138 through 1142 removed outlier: 3.513A pdb=" N GLY B1142 " --> pdb=" O LEU B1139 " (cutoff:3.500A) Processing helix chain 'B' and resid 1272 through 1276 removed outlier: 3.599A pdb=" N ARG B1275 " --> pdb=" O TYR B1272 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER B1276 " --> pdb=" O PRO B1273 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1272 through 1276' Processing helix chain 'C' and resid 28 through 33 removed outlier: 3.534A pdb=" N LYS C 32 " --> pdb=" O ASP C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 43 Processing helix chain 'C' and resid 111 through 128 removed outlier: 3.515A pdb=" N ASP C 124 " --> pdb=" O GLY C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 169 removed outlier: 3.579A pdb=" N THR C 143 " --> pdb=" O GLU C 139 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP C 146 " --> pdb=" O ASP C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 176 through 267 removed outlier: 3.942A pdb=" N MET C 182 " --> pdb=" O GLU C 178 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS C 185 " --> pdb=" O GLN C 181 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN C 224 " --> pdb=" O GLU C 220 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP C 245 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 316 removed outlier: 3.510A pdb=" N LEU C 313 " --> pdb=" O THR C 310 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU C 314 " --> pdb=" O VAL C 311 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS C 315 " --> pdb=" O LEU C 312 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA C 316 " --> pdb=" O LEU C 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 310 through 316' Processing helix chain 'C' and resid 317 through 322 removed outlier: 4.312A pdb=" N GLY C 322 " --> pdb=" O ALA C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 336 Processing helix chain 'C' and resid 355 through 362 removed outlier: 3.506A pdb=" N PHE C 359 " --> pdb=" O GLY C 356 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE C 360 " --> pdb=" O LEU C 357 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TRP C 361 " --> pdb=" O ARG C 358 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP C 362 " --> pdb=" O PHE C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 368 removed outlier: 4.130A pdb=" N ASP C 366 " --> pdb=" O ASN C 363 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS C 367 " --> pdb=" O LYS C 364 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA C 368 " --> pdb=" O PHE C 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 363 through 368' Processing helix chain 'C' and resid 369 through 374 removed outlier: 4.156A pdb=" N PHE C 372 " --> pdb=" O MET C 369 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU C 373 " --> pdb=" O VAL C 370 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP C 374 " --> pdb=" O ALA C 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 369 through 374' Processing helix chain 'C' and resid 376 through 381 removed outlier: 3.872A pdb=" N GLU C 381 " --> pdb=" O GLN C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 428 removed outlier: 3.709A pdb=" N GLN C 424 " --> pdb=" O SER C 421 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP C 425 " --> pdb=" O GLU C 422 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N THR C 426 " --> pdb=" O GLU C 423 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LYS C 427 " --> pdb=" O GLN C 424 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA C 428 " --> pdb=" O TRP C 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 421 through 428' Processing helix chain 'C' and resid 429 through 439 removed outlier: 3.994A pdb=" N LEU C 433 " --> pdb=" O LEU C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 443 removed outlier: 3.649A pdb=" N VAL C 443 " --> pdb=" O LEU C 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 440 through 443' Processing helix chain 'D' and resid 41 through 45 removed outlier: 3.632A pdb=" N HIS D 44 " --> pdb=" O ARG D 41 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU D 45 " --> pdb=" O LEU D 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 41 through 45' Processing helix chain 'D' and resid 57 through 61 Processing helix chain 'D' and resid 136 through 138 No H-bonds generated for 'chain 'D' and resid 136 through 138' Processing helix chain 'D' and resid 192 through 224 removed outlier: 3.504A pdb=" N ARG D 198 " --> pdb=" O PHE D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 324 removed outlier: 3.790A pdb=" N LYS D 256 " --> pdb=" O GLU D 252 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS D 267 " --> pdb=" O ALA D 263 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU D 282 " --> pdb=" O ALA D 278 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN D 287 " --> pdb=" O HIS D 283 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU D 291 " --> pdb=" O GLN D 287 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER D 292 " --> pdb=" O LEU D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 329 removed outlier: 3.593A pdb=" N ILE D 328 " --> pdb=" O LEU D 325 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR D 329 " --> pdb=" O SER D 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 325 through 329' Processing helix chain 'D' and resid 351 through 355 removed outlier: 3.719A pdb=" N ALA D 354 " --> pdb=" O ASP D 351 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LYS D 355 " --> pdb=" O PHE D 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 351 through 355' Processing helix chain 'D' and resid 359 through 364 removed outlier: 4.668A pdb=" N ALA D 363 " --> pdb=" O SER D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 378 removed outlier: 4.456A pdb=" N ALA D 368 " --> pdb=" O LEU D 364 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N HIS D 369 " --> pdb=" O GLY D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 392 Processing helix chain 'D' and resid 400 through 404 removed outlier: 3.665A pdb=" N THR D 404 " --> pdb=" O ASP D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 422 No H-bonds generated for 'chain 'D' and resid 420 through 422' Processing helix chain 'D' and resid 423 through 434 removed outlier: 3.718A pdb=" N ALA D 434 " --> pdb=" O ASN D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 439 Processing helix chain 'F' and resid 32 through 42 Processing helix chain 'F' and resid 79 through 86 Processing helix chain 'F' and resid 86 through 91 removed outlier: 3.817A pdb=" N TYR F 90 " --> pdb=" O ALA F 86 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG F 91 " --> pdb=" O PRO F 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 86 through 91' Processing helix chain 'F' and resid 104 through 121 removed outlier: 3.690A pdb=" N PHE F 108 " --> pdb=" O ASN F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 141 removed outlier: 4.442A pdb=" N ASN F 139 " --> pdb=" O ASP F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 155 removed outlier: 3.568A pdb=" N ASP F 154 " --> pdb=" O SER F 150 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN F 155 " --> pdb=" O TYR F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 181 Processing sheet with id=AA1, first strand: chain 'B' and resid 818 through 820 removed outlier: 6.896A pdb=" N CYS A 223 " --> pdb=" O ILE B 819 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL A 224 " --> pdb=" O TYR A 231 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N GLU A 230 " --> pdb=" O LYS A 6 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N HIS A 8 " --> pdb=" O GLU A 230 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 68 through 69 Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 69 removed outlier: 3.837A pdb=" N GLY A 123 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ASP A 112 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N TYR A 114 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ALA A 119 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N THR A 126 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LYS A 144 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 9.951A pdb=" N SER A 128 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 11.970A pdb=" N ASP A 142 " --> pdb=" O SER A 128 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N MET A 215 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TYR A 216 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU A 26 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N MET A 218 " --> pdb=" O GLY A 24 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL A 19 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU A 89 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N SER A 25 " --> pdb=" O TRP A 87 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N TRP A 87 " --> pdb=" O SER A 25 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 591 through 592 removed outlier: 3.723A pdb=" N ILE A 591 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY A 603 " --> pdb=" O LYS A 624 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N PHE A 622 " --> pdb=" O ILE A 605 " (cutoff:3.500A) removed outlier: 9.341A pdb=" N GLU A 607 " --> pdb=" O GLN A 620 " (cutoff:3.500A) removed outlier: 11.311A pdb=" N GLN A 620 " --> pdb=" O GLU A 607 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A 636 " --> pdb=" O GLY A 680 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 688 through 689 Processing sheet with id=AA6, first strand: chain 'B' and resid 31 through 34 removed outlier: 5.863A pdb=" N SER B 31 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ARG B 42 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY B 33 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE B 102 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS B 89 " --> pdb=" O PHE B 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 108 through 109 Processing sheet with id=AA8, first strand: chain 'B' and resid 175 through 176 removed outlier: 6.452A pdb=" N LEU B 175 " --> pdb=" O VAL B 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 998 through 1001 removed outlier: 3.872A pdb=" N ARG B 998 " --> pdb=" O CYS B1011 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1045 through 1050 removed outlier: 3.578A pdb=" N THR B1047 " --> pdb=" O ALA B1060 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA B1060 " --> pdb=" O THR B1047 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER B1061 " --> pdb=" O ALA B1065 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ALA B1065 " --> pdb=" O SER B1061 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1097 through 1103 removed outlier: 3.844A pdb=" N ASP B1100 " --> pdb=" O ALA B1115 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER B1120 " --> pdb=" O THR B1116 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TRP B1133 " --> pdb=" O GLY B1123 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ASP B1125 " --> pdb=" O ASN B1131 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ASN B1131 " --> pdb=" O ASP B1125 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 1144 through 1146 removed outlier: 6.808A pdb=" N GLY B1159 " --> pdb=" O THR B1145 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR B1164 " --> pdb=" O THR B1160 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS B1179 " --> pdb=" O MET B1165 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER B1177 " --> pdb=" O CYS B1167 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N ASP B1169 " --> pdb=" O PRO B1175 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1187 through 1192 removed outlier: 3.794A pdb=" N ARG B1189 " --> pdb=" O ALA B1203 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B1210 " --> pdb=" O LEU B1224 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ASP B1214 " --> pdb=" O ARG B1220 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ARG B1220 " --> pdb=" O ASP B1214 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU B1299 " --> pdb=" O ARG B1221 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1246 through 1247 Processing sheet with id=AB6, first strand: chain 'B' and resid 1332 through 1339 Processing sheet with id=AB7, first strand: chain 'C' and resid 16 through 17 removed outlier: 3.580A pdb=" N PHE C 16 " --> pdb=" O LEU C 25 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 276 through 279 Processing sheet with id=AB9, first strand: chain 'C' and resid 328 through 331 Processing sheet with id=AC1, first strand: chain 'C' and resid 394 through 397 removed outlier: 3.614A pdb=" N LYS C 402 " --> pdb=" O ASP C 397 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 47 through 50 removed outlier: 6.761A pdb=" N TYR D 161 " --> pdb=" O LEU D 141 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 81 through 82 removed outlier: 7.153A pdb=" N PHE D 113 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LYS D 132 " --> pdb=" O PHE D 113 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL D 115 " --> pdb=" O GLU D 130 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N GLU D 130 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE D 117 " --> pdb=" O LEU D 128 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 331 through 332 Processing sheet with id=AC5, first strand: chain 'D' and resid 386 through 387 Processing sheet with id=AC6, first strand: chain 'F' and resid 58 through 64 removed outlier: 3.511A pdb=" N THR F 67 " --> pdb=" O LEU F 64 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N ALA F 95 " --> pdb=" O GLN F 20 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LYS F 22 " --> pdb=" O ALA F 95 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ILE F 97 " --> pdb=" O LYS F 22 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL F 24 " --> pdb=" O ILE F 97 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL F 99 " --> pdb=" O VAL F 24 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU F 26 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N ASP F 101 " --> pdb=" O LEU F 26 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY F 132 " --> pdb=" O MET F 160 " (cutoff:3.500A) 1086 hydrogen bonds defined for protein. 3099 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.88 Time building geometry restraints manager: 2.54 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: 7731 1.34 - 1.46: 4044 1.46 - 1.58: 12576 1.58 - 1.69: 8 1.69 - 1.81: 186 Bond restraints: 24545 Sorted by residual: bond pdb=" C THR B 419 " pdb=" N PRO B 420 " ideal model delta sigma weight residual 1.335 1.394 -0.059 1.28e-02 6.10e+03 2.13e+01 bond pdb=" C ALA F 86 " pdb=" N PRO F 87 " ideal model delta sigma weight residual 1.337 1.381 -0.044 1.11e-02 8.12e+03 1.60e+01 bond pdb=" C LEU B 464 " pdb=" N PRO B 465 " ideal model delta sigma weight residual 1.334 1.366 -0.032 8.40e-03 1.42e+04 1.48e+01 bond pdb=" C LYS B 650 " pdb=" N PRO B 651 " ideal model delta sigma weight residual 1.337 1.373 -0.037 1.11e-02 8.12e+03 1.09e+01 bond pdb=" CG LEU A 265 " pdb=" CD1 LEU A 265 " ideal model delta sigma weight residual 1.521 1.432 0.089 3.30e-02 9.18e+02 7.24e+00 ... (remaining 24540 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 32909 3.05 - 6.10: 218 6.10 - 9.15: 37 9.15 - 12.19: 9 12.19 - 15.24: 3 Bond angle restraints: 33176 Sorted by residual: angle pdb=" C HIS A 141 " pdb=" N ASP A 142 " pdb=" CA ASP A 142 " ideal model delta sigma weight residual 121.70 135.51 -13.81 1.80e+00 3.09e-01 5.88e+01 angle pdb=" C ILE B 456 " pdb=" N ASN B 457 " pdb=" CA ASN B 457 " ideal model delta sigma weight residual 121.70 134.69 -12.99 1.80e+00 3.09e-01 5.21e+01 angle pdb=" CA TYR A 11 " pdb=" C TYR A 11 " pdb=" O TYR A 11 " ideal model delta sigma weight residual 119.10 112.38 6.72 1.26e+00 6.30e-01 2.85e+01 angle pdb=" C LEU F 85 " pdb=" N ALA F 86 " pdb=" CA ALA F 86 " ideal model delta sigma weight residual 120.58 127.23 -6.65 1.32e+00 5.74e-01 2.54e+01 angle pdb=" C GLN B 649 " pdb=" N LYS B 650 " pdb=" CA LYS B 650 " ideal model delta sigma weight residual 121.80 133.69 -11.89 2.44e+00 1.68e-01 2.37e+01 ... (remaining 33171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.09: 14444 32.09 - 64.19: 431 64.19 - 96.28: 53 96.28 - 128.37: 2 128.37 - 160.47: 2 Dihedral angle restraints: 14932 sinusoidal: 6200 harmonic: 8732 Sorted by residual: dihedral pdb=" CB CYS B 693 " pdb=" SG CYS B 693 " pdb=" SG CYS C 165 " pdb=" CB CYS C 165 " ideal model delta sinusoidal sigma weight residual 93.00 174.44 -81.44 1 1.00e+01 1.00e-02 8.17e+01 dihedral pdb=" O3B GTP F 301 " pdb=" O3A GTP F 301 " pdb=" PB GTP F 301 " pdb=" PA GTP F 301 " ideal model delta sinusoidal sigma weight residual 291.08 130.61 160.47 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" C8 GTP F 301 " pdb=" C1' GTP F 301 " pdb=" N9 GTP F 301 " pdb=" O4' GTP F 301 " ideal model delta sinusoidal sigma weight residual 104.59 -52.11 156.70 1 2.00e+01 2.50e-03 4.60e+01 ... (remaining 14929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 3129 0.062 - 0.124: 497 0.124 - 0.185: 52 0.185 - 0.247: 6 0.247 - 0.309: 2 Chirality restraints: 3686 Sorted by residual: chirality pdb=" CB VAL A 588 " pdb=" CA VAL A 588 " pdb=" CG1 VAL A 588 " pdb=" CG2 VAL A 588 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CA LYS B 650 " pdb=" N LYS B 650 " pdb=" C LYS B 650 " pdb=" CB LYS B 650 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CB VAL B 986 " pdb=" CA VAL B 986 " pdb=" CG1 VAL B 986 " pdb=" CG2 VAL B 986 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 3683 not shown) Planarity restraints: 4248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 666 " -0.057 5.00e-02 4.00e+02 8.68e-02 1.21e+01 pdb=" N PRO B 667 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO B 667 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 667 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 259 " 0.016 2.00e-02 2.50e+03 3.05e-02 9.33e+00 pdb=" C GLN A 259 " -0.053 2.00e-02 2.50e+03 pdb=" O GLN A 259 " 0.020 2.00e-02 2.50e+03 pdb=" N MET A 260 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET B 696 " 0.049 5.00e-02 4.00e+02 7.32e-02 8.58e+00 pdb=" N PRO B 697 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 697 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 697 " 0.041 5.00e-02 4.00e+02 ... (remaining 4245 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 182 2.60 - 3.17: 18308 3.17 - 3.75: 36169 3.75 - 4.32: 48283 4.32 - 4.90: 80312 Nonbonded interactions: 183254 Sorted by model distance: nonbonded pdb=" O1A GDP B1402 " pdb="MG MG B1403 " model vdw 2.024 2.170 nonbonded pdb="MG MG F 300 " pdb=" O1G GTP F 301 " model vdw 2.070 2.170 nonbonded pdb=" O1B GDP B1402 " pdb="MG MG B1403 " model vdw 2.072 2.170 nonbonded pdb=" OD1 ASN B 153 " pdb="MG MG B1403 " model vdw 2.080 2.170 nonbonded pdb="MG MG F 300 " pdb=" O2B GTP F 301 " model vdw 2.085 2.170 ... (remaining 183249 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.70 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.370 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: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 24.870 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 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 : 0.004 0.163 24551 Z= 0.212 Angle : 0.954 59.284 33184 Z= 0.449 Chirality : 0.046 0.309 3686 Planarity : 0.006 0.087 4248 Dihedral : 15.406 160.466 9263 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.94 % Favored : 95.93 % Rotamer: Outliers : 0.08 % Allowed : 8.72 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.28 % 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: -1.72 (0.14), residues: 2947 helix: -1.20 (0.12), residues: 1293 sheet: -0.40 (0.25), residues: 390 loop : -1.14 (0.16), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 210 TYR 0.029 0.002 TYR A 58 PHE 0.037 0.002 PHE F 48 TRP 0.016 0.001 TRP B 670 HIS 0.031 0.001 HIS B 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.20 (24545) covalent geometry : angle 0.77067 / 0.44 (33176) SS BOND : bond 0.00380 / 0.20 ( 1) SS BOND : angle 0.74851 / 0.50 ( 2) hydrogen bonds : bond 0.20035 / 13.18 ( 1084) hydrogen bonds : angle 6.46197 / 4.40 ( 3099) metal coordination : bond 0.09915 / 5.01 ( 4) metal coordination : angle 41.85300 / 22.60 ( 6) Misc. bond : bond 0.10357 / 5.45 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 2650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 591 time to evaluate : 0.844 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: 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: A 306 LYS cc_start: 0.8669 (tttt) cc_final: 0.8423 (tttp) REVERT: A 394 MET cc_start: 0.8249 (mtm) cc_final: 0.7974 (mtp) REVERT: A 396 LEU cc_start: 0.8318 (tp) cc_final: 0.7979 (tp) REVERT: A 397 LEU cc_start: 0.7672 (tp) cc_final: 0.7410 (tp) REVERT: A 475 LEU cc_start: 0.8670 (tp) cc_final: 0.8328 (tt) REVERT: A 481 SER cc_start: 0.8256 (t) cc_final: 0.8053 (p) REVERT: A 503 ASP cc_start: 0.7200 (t0) cc_final: 0.6475 (t0) REVERT: A 506 THR cc_start: 0.7840 (m) cc_final: 0.7570 (t) REVERT: A 510 ASP cc_start: 0.7550 (t0) cc_final: 0.6973 (t0) REVERT: A 513 THR cc_start: 0.8819 (m) cc_final: 0.8420 (p) REVERT: A 552 LEU cc_start: 0.8651 (tp) cc_final: 0.8264 (tp) REVERT: A 554 HIS cc_start: 0.8822 (t70) cc_final: 0.8527 (m90) REVERT: A 572 ARG cc_start: 0.8722 (tpt170) cc_final: 0.8450 (mmm-85) REVERT: A 617 MET cc_start: 0.6585 (mtm) cc_final: 0.6291 (mtp) REVERT: A 636 LYS cc_start: 0.7854 (mttt) cc_final: 0.7414 (mppt) REVERT: A 654 MET cc_start: 0.7574 (mtt) cc_final: 0.7313 (mtm) REVERT: A 681 PHE cc_start: 0.6973 (m-80) cc_final: 0.6735 (m-80) REVERT: A 682 MET cc_start: 0.7574 (ttm) cc_final: 0.7257 (tmm) REVERT: A 702 ASN cc_start: 0.8573 (m-40) cc_final: 0.8322 (t0) REVERT: A 707 TYR cc_start: 0.7052 (m-80) cc_final: 0.6775 (m-80) REVERT: A 711 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8379 (pm20) REVERT: A 743 ASP cc_start: 0.7408 (t0) cc_final: 0.6421 (t0) REVERT: A 747 ASP cc_start: 0.8335 (m-30) cc_final: 0.7847 (t0) REVERT: A 751 LEU cc_start: 0.6297 (tp) cc_final: 0.5652 (pp) REVERT: A 753 LYS cc_start: 0.8760 (mttt) cc_final: 0.8402 (mmtm) REVERT: A 761 ASP cc_start: 0.7922 (t0) cc_final: 0.7356 (m-30) REVERT: A 771 LYS cc_start: 0.8275 (mtmm) cc_final: 0.7851 (pttm) REVERT: A 773 LEU cc_start: 0.8450 (mt) cc_final: 0.8147 (tp) REVERT: A 785 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8351 (pp20) REVERT: A 797 GLU cc_start: 0.8768 (tp30) cc_final: 0.8516 (tm-30) REVERT: A 847 ARG cc_start: 0.7970 (mmm-85) cc_final: 0.7589 (tpp80) REVERT: A 850 LEU cc_start: 0.8725 (mt) cc_final: 0.8068 (mt) REVERT: A 859 MET cc_start: 0.8906 (tpt) cc_final: 0.8357 (tpp) REVERT: A 860 GLN cc_start: 0.8833 (mt0) cc_final: 0.8241 (mm-40) REVERT: B 4 GLN cc_start: 0.7805 (mm-40) cc_final: 0.7315 (pp30) REVERT: B 17 GLU cc_start: 0.7826 (tt0) cc_final: 0.7429 (pp20) REVERT: B 64 LEU cc_start: 0.8329 (mt) cc_final: 0.8084 (tt) REVERT: B 73 GLU cc_start: 0.8311 (tt0) cc_final: 0.7680 (tp30) REVERT: B 100 MET cc_start: 0.7684 (mtt) cc_final: 0.7213 (mpp) REVERT: B 108 ASP cc_start: 0.7175 (m-30) cc_final: 0.6811 (t0) REVERT: B 111 TYR cc_start: 0.8501 (t80) cc_final: 0.8180 (t80) REVERT: B 155 MET cc_start: 0.7190 (mmt) cc_final: 0.6458 (mmt) REVERT: B 239 MET cc_start: 0.8338 (mtt) cc_final: 0.8133 (mtm) REVERT: B 276 GLN cc_start: 0.8567 (tt0) cc_final: 0.8219 (tm-30) REVERT: B 297 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8233 (mp0) REVERT: B 300 LYS cc_start: 0.8783 (mttt) cc_final: 0.8532 (mtmm) REVERT: B 565 CYS cc_start: 0.4614 (m) cc_final: 0.4397 (m) REVERT: B 748 ARG cc_start: 0.8519 (mtp85) cc_final: 0.8247 (ttp-110) REVERT: B 779 MET cc_start: 0.8378 (tmm) cc_final: 0.8012 (ppp) REVERT: B 785 ASP cc_start: 0.8671 (m-30) cc_final: 0.8308 (t0) REVERT: B 951 LYS cc_start: 0.8704 (tttt) cc_final: 0.8417 (mmtm) REVERT: B 959 ARG cc_start: 0.8107 (mtt-85) cc_final: 0.7875 (mmt180) REVERT: B 965 MET cc_start: 0.8195 (tmm) cc_final: 0.7498 (tpp) REVERT: B 1020 TRP cc_start: 0.7255 (m100) cc_final: 0.6626 (m100) REVERT: B 1147 PHE cc_start: 0.6112 (m-80) cc_final: 0.5672 (m-10) REVERT: B 1200 VAL cc_start: 0.8822 (t) cc_final: 0.8578 (m) REVERT: B 1215 MET cc_start: 0.7077 (mmt) cc_final: 0.6607 (ttt) REVERT: C 40 GLN cc_start: 0.9134 (mt0) cc_final: 0.8548 (mt0) REVERT: C 122 LEU cc_start: 0.8963 (mt) cc_final: 0.8566 (tp) REVERT: C 126 MET cc_start: 0.8669 (mtm) cc_final: 0.8366 (mtm) REVERT: C 222 LEU cc_start: 0.8438 (mm) cc_final: 0.8024 (tt) REVERT: C 223 ASP cc_start: 0.8466 (m-30) cc_final: 0.8245 (m-30) REVERT: C 254 MET cc_start: 0.8097 (tpt) cc_final: 0.7621 (mtp) REVERT: D 63 ASP cc_start: 0.7938 (m-30) cc_final: 0.7554 (m-30) REVERT: D 69 HIS cc_start: 0.6351 (m90) cc_final: 0.5901 (m-70) REVERT: D 126 GLN cc_start: 0.8111 (mm110) cc_final: 0.7799 (mm-40) REVERT: D 138 LEU cc_start: 0.8228 (mt) cc_final: 0.8008 (mt) REVERT: D 194 PHE cc_start: 0.7964 (t80) cc_final: 0.7595 (t80) REVERT: D 204 CYS cc_start: 0.7709 (m) cc_final: 0.6958 (p) REVERT: D 290 LYS cc_start: 0.9237 (mttt) cc_final: 0.8627 (mmmt) REVERT: D 294 ASN cc_start: 0.8900 (m-40) cc_final: 0.8359 (m-40) REVERT: D 307 PHE cc_start: 0.8755 (t80) cc_final: 0.8258 (t80) REVERT: D 377 PHE cc_start: 0.9051 (m-80) cc_final: 0.8635 (m-80) REVERT: D 378 LEU cc_start: 0.8932 (mt) cc_final: 0.8718 (tp) REVERT: F 44 GLN cc_start: 0.7395 (mt0) cc_final: 0.7182 (tt0) REVERT: F 70 LYS cc_start: 0.7379 (mmmm) cc_final: 0.6632 (mmmm) REVERT: F 89 TYR cc_start: 0.3872 (m-80) cc_final: 0.3293 (m-10) REVERT: F 114 TRP cc_start: 0.5368 (m100) cc_final: 0.4861 (m100) REVERT: F 143 VAL cc_start: 0.5919 (t) cc_final: 0.5044 (t) REVERT: F 147 GLU cc_start: 0.6582 (mt-10) cc_final: 0.6374 (pt0) outliers start: 2 outliers final: 1 residues processed: 593 average time/residue: 0.2127 time to fit residues: 183.6471 Evaluate side-chains 451 residues out of total 2650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 450 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.2980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.0060 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 overall best weight: 1.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 GLN A 271 HIS A 504 GLN A 598 GLN A 794 GLN A 827 ASN A 843 GLN B 504 ASN B 534 HIS B 539 GLN B 798 ASN B 803 ASN ** B1193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1329 HIS C 228 GLN C 253 GLN D 203 GLN ** D 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 HIS F 146 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.145018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.121313 restraints weight = 109621.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.121705 restraints weight = 70272.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.121616 restraints weight = 51579.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.121858 restraints weight = 48474.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.122010 restraints weight = 41094.934| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3926 r_free = 0.3926 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3927 r_free = 0.3927 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (15 function evaluations) r_final: 0.3927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 24551 Z= 0.188 Angle : 0.772 42.214 33184 Z= 0.362 Chirality : 0.045 0.208 3686 Planarity : 0.005 0.073 4248 Dihedral : 7.742 167.203 3261 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.53 % Favored : 96.40 % Rotamer: Outliers : 1.70 % Allowed : 12.08 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.28 % 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: -0.56 (0.15), residues: 2947 helix: 0.19 (0.14), residues: 1323 sheet: -0.45 (0.25), residues: 388 loop : -0.84 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 551 TYR 0.023 0.002 TYR D 81 PHE 0.025 0.002 PHE B 102 TRP 0.018 0.002 TRP B1199 HIS 0.015 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.19 (24545) covalent geometry : angle 0.68954 / 0.36 (33176) SS BOND : bond 0.00347 / 0.18 ( 1) SS BOND : angle 1.48961 / 0.99 ( 2) hydrogen bonds : bond 0.04422 / 2.87 ( 1084) hydrogen bonds : angle 4.60425 / 3.17 ( 3099) metal coordination : bond 0.01094 / 0.52 ( 4) metal coordination : angle 25.87085 / 14.50 ( 6) Misc. bond : bond 0.00065 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 461 time to evaluate : 0.963 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 TYR cc_start: 0.7053 (m-10) cc_final: 0.6449 (m-80) REVERT: A 198 PHE cc_start: 0.8845 (m-80) cc_final: 0.8643 (m-80) REVERT: A 354 LYS cc_start: 0.7851 (tppt) cc_final: 0.7327 (ttmt) REVERT: A 358 MET cc_start: 0.6896 (ttt) cc_final: 0.6457 (mtp) REVERT: A 394 MET cc_start: 0.7613 (mtm) cc_final: 0.7395 (mtp) REVERT: A 396 LEU cc_start: 0.8392 (tp) cc_final: 0.8122 (tp) REVERT: A 475 LEU cc_start: 0.8722 (tp) cc_final: 0.8369 (tt) REVERT: A 497 VAL cc_start: 0.7647 (m) cc_final: 0.7361 (m) REVERT: A 510 ASP cc_start: 0.7533 (t0) cc_final: 0.7083 (t0) REVERT: A 513 THR cc_start: 0.9054 (m) cc_final: 0.8724 (p) REVERT: A 552 LEU cc_start: 0.8463 (tp) cc_final: 0.8148 (tp) REVERT: A 557 LYS cc_start: 0.8130 (mmtm) cc_final: 0.7628 (mmtt) REVERT: A 560 GLN cc_start: 0.8003 (mm-40) cc_final: 0.7044 (mp10) REVERT: A 617 MET cc_start: 0.7054 (mtm) cc_final: 0.6706 (ptm) REVERT: A 635 PHE cc_start: 0.6625 (t80) cc_final: 0.6108 (t80) REVERT: A 636 LYS cc_start: 0.8131 (mttt) cc_final: 0.7717 (ttpp) REVERT: A 676 SER cc_start: 0.7731 (t) cc_final: 0.7432 (p) REVERT: A 681 PHE cc_start: 0.6908 (m-80) cc_final: 0.6493 (m-80) REVERT: A 683 GLN cc_start: 0.8145 (tt0) cc_final: 0.7035 (mt0) REVERT: A 743 ASP cc_start: 0.7482 (t0) cc_final: 0.6923 (t70) REVERT: A 812 TYR cc_start: 0.7135 (m-10) cc_final: 0.6895 (m-10) REVERT: A 840 LYS cc_start: 0.8250 (tppt) cc_final: 0.7990 (tttm) REVERT: A 854 GLU cc_start: 0.7768 (tp30) cc_final: 0.7459 (tp30) REVERT: A 859 MET cc_start: 0.8345 (tpt) cc_final: 0.8145 (tpp) REVERT: A 860 GLN cc_start: 0.8292 (mt0) cc_final: 0.7978 (mm-40) REVERT: B 64 LEU cc_start: 0.8578 (mt) cc_final: 0.8360 (tt) REVERT: B 73 GLU cc_start: 0.7623 (tt0) cc_final: 0.7423 (tp30) REVERT: B 100 MET cc_start: 0.7039 (mtt) cc_final: 0.6796 (mpp) REVERT: B 111 TYR cc_start: 0.8161 (t80) cc_final: 0.7936 (t80) REVERT: B 127 TRP cc_start: 0.7038 (t-100) cc_final: 0.6803 (t-100) REVERT: B 155 MET cc_start: 0.6516 (mmt) cc_final: 0.5765 (mmt) REVERT: B 421 TYR cc_start: 0.7672 (m-80) cc_final: 0.7418 (m-80) REVERT: B 499 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8169 (mm) REVERT: B 536 MET cc_start: 0.6199 (OUTLIER) cc_final: 0.5360 (mpp) REVERT: B 748 ARG cc_start: 0.8578 (mtp85) cc_final: 0.8347 (ttp-110) REVERT: B 779 MET cc_start: 0.8282 (tmm) cc_final: 0.8005 (ppp) REVERT: B 959 ARG cc_start: 0.7977 (mtt-85) cc_final: 0.7742 (mtp85) REVERT: B 964 MET cc_start: 0.9020 (tmm) cc_final: 0.8667 (tmm) REVERT: B 965 MET cc_start: 0.8204 (tmm) cc_final: 0.7440 (tpt) REVERT: B 1020 TRP cc_start: 0.7297 (m100) cc_final: 0.6698 (m100) REVERT: B 1038 TYR cc_start: 0.6049 (t80) cc_final: 0.5806 (t80) REVERT: B 1147 PHE cc_start: 0.5771 (m-80) cc_final: 0.5086 (m-10) REVERT: B 1200 VAL cc_start: 0.8418 (t) cc_final: 0.7928 (m) REVERT: B 1212 MET cc_start: 0.8115 (mpp) cc_final: 0.7715 (mpp) REVERT: C 16 PHE cc_start: 0.6663 (m-10) cc_final: 0.6335 (m-10) REVERT: C 26 LYS cc_start: 0.6775 (tttm) cc_final: 0.6518 (mtmm) REVERT: C 36 ARG cc_start: 0.7426 (ttp80) cc_final: 0.7000 (tmm160) REVERT: C 40 GLN cc_start: 0.8885 (mt0) cc_final: 0.8204 (mt0) REVERT: C 122 LEU cc_start: 0.8883 (mt) cc_final: 0.8465 (tp) REVERT: C 126 MET cc_start: 0.8477 (mtm) cc_final: 0.8182 (mtm) REVERT: C 222 LEU cc_start: 0.8554 (mm) cc_final: 0.8298 (tt) REVERT: C 237 LYS cc_start: 0.9207 (tptp) cc_final: 0.8911 (ptmt) REVERT: C 238 ARG cc_start: 0.8309 (ttm170) cc_final: 0.7880 (ttp80) REVERT: C 254 MET cc_start: 0.8049 (tpt) cc_final: 0.7677 (mtp) REVERT: C 269 VAL cc_start: -0.0364 (OUTLIER) cc_final: -0.0592 (t) REVERT: D 65 TYR cc_start: 0.8244 (p90) cc_final: 0.7924 (p90) REVERT: D 69 HIS cc_start: 0.6967 (m90) cc_final: 0.6661 (m90) REVERT: D 138 LEU cc_start: 0.8451 (mt) cc_final: 0.8244 (mt) REVERT: D 194 PHE cc_start: 0.7825 (t80) cc_final: 0.6907 (t80) REVERT: D 214 GLN cc_start: 0.8554 (mt0) cc_final: 0.8291 (mp10) REVERT: D 279 PHE cc_start: 0.8393 (t80) cc_final: 0.7999 (t80) REVERT: D 290 LYS cc_start: 0.9381 (mttt) cc_final: 0.9156 (pttm) REVERT: D 294 ASN cc_start: 0.8908 (m-40) cc_final: 0.8505 (t0) REVERT: D 297 ARG cc_start: 0.8901 (ttp-110) cc_final: 0.8680 (mtm110) REVERT: D 303 LYS cc_start: 0.8719 (mttt) cc_final: 0.8365 (ptpt) REVERT: D 307 PHE cc_start: 0.8716 (t80) cc_final: 0.7915 (t80) REVERT: D 329 TYR cc_start: 0.6976 (m-80) cc_final: 0.6728 (t80) REVERT: D 378 LEU cc_start: 0.8850 (mt) cc_final: 0.8648 (tt) outliers start: 45 outliers final: 19 residues processed: 490 average time/residue: 0.1894 time to fit residues: 136.3528 Evaluate side-chains 413 residues out of total 2650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 391 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 TRP Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 868 HIS Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 459 TYR Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 536 MET Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 806 ASP Chi-restraints excluded: chain B residue 1179 HIS Chi-restraints excluded: chain B residue 1204 VAL Chi-restraints excluded: chain B residue 1346 VAL Chi-restraints excluded: chain B residue 1356 VAL Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 57 ASN Chi-restraints excluded: chain D residue 327 TYR Chi-restraints excluded: chain F residue 69 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 277 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 198 optimal weight: 7.9990 chunk 147 optimal weight: 0.9980 chunk 266 optimal weight: 0.0270 chunk 152 optimal weight: 0.9990 chunk 211 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 chunk 210 optimal weight: 4.9990 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 HIS A 32 GLN A 62 GLN ** A 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 GLN A 645 GLN ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 830 GLN ** B1103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 ASN F 44 GLN F 146 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.143313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.118793 restraints weight = 108150.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.119079 restraints weight = 67580.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.119718 restraints weight = 51781.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.119901 restraints weight = 41115.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.119799 restraints weight = 36841.489| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3892 r_free = 0.3892 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3892 r_free = 0.3892 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24551 Z= 0.153 Angle : 0.708 35.931 33184 Z= 0.342 Chirality : 0.044 0.202 3686 Planarity : 0.005 0.103 4248 Dihedral : 7.552 165.179 3260 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.53 % Favored : 96.40 % Rotamer: Outliers : 1.96 % Allowed : 13.55 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.28 % 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: -0.18 (0.15), residues: 2947 helix: 0.60 (0.14), residues: 1333 sheet: -0.36 (0.25), residues: 397 loop : -0.74 (0.17), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 110 TYR 0.017 0.002 TYR A 58 PHE 0.024 0.002 PHE F 71 TRP 0.034 0.001 TRP B1199 HIS 0.011 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (24545) covalent geometry : angle 0.65668 / 0.34 (33176) SS BOND : bond 0.00279 / 0.15 ( 1) SS BOND : angle 1.10738 / 0.74 ( 2) hydrogen bonds : bond 0.04115 / 2.66 ( 1084) hydrogen bonds : angle 4.44162 / 3.08 ( 3099) metal coordination : bond 0.01180 / 0.45 ( 4) metal coordination : angle 19.65970 / 11.16 ( 6) Misc. bond : bond 0.00017 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 415 time to evaluate : 0.876 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7522 (tp30) cc_final: 0.6917 (tp30) REVERT: A 198 PHE cc_start: 0.8906 (m-80) cc_final: 0.8682 (m-80) REVERT: A 394 MET cc_start: 0.7545 (mtm) cc_final: 0.7327 (mtp) REVERT: A 396 LEU cc_start: 0.8437 (tp) cc_final: 0.8177 (tp) REVERT: A 475 LEU cc_start: 0.8721 (tp) cc_final: 0.8381 (tt) REVERT: A 500 GLU cc_start: 0.7669 (mm-30) cc_final: 0.6885 (mm-30) REVERT: A 510 ASP cc_start: 0.7533 (t0) cc_final: 0.7060 (t0) REVERT: A 513 THR cc_start: 0.8979 (m) cc_final: 0.8720 (p) REVERT: A 552 LEU cc_start: 0.8470 (tp) cc_final: 0.8032 (tp) REVERT: A 556 MET cc_start: 0.8448 (mmm) cc_final: 0.8112 (mtp) REVERT: A 560 GLN cc_start: 0.7853 (mm-40) cc_final: 0.7149 (mp10) REVERT: A 617 MET cc_start: 0.7023 (mtm) cc_final: 0.6801 (ptm) REVERT: A 635 PHE cc_start: 0.6813 (t80) cc_final: 0.5705 (t80) REVERT: A 636 LYS cc_start: 0.8220 (mttt) cc_final: 0.7755 (ttpp) REVERT: A 676 SER cc_start: 0.7872 (t) cc_final: 0.7589 (p) REVERT: A 688 VAL cc_start: 0.8020 (t) cc_final: 0.7794 (m) REVERT: A 743 ASP cc_start: 0.7593 (t0) cc_final: 0.6894 (t70) REVERT: A 751 LEU cc_start: 0.6734 (mt) cc_final: 0.6124 (pp) REVERT: A 777 MET cc_start: 0.6874 (mmm) cc_final: 0.6558 (ttm) REVERT: A 785 GLU cc_start: 0.7603 (pp20) cc_final: 0.6779 (pp20) REVERT: A 795 TYR cc_start: 0.8539 (t80) cc_final: 0.8338 (t80) REVERT: A 854 GLU cc_start: 0.7621 (tp30) cc_final: 0.7409 (tp30) REVERT: B 35 THR cc_start: 0.7557 (p) cc_final: 0.7196 (p) REVERT: B 155 MET cc_start: 0.6589 (mmt) cc_final: 0.5747 (mmt) REVERT: B 421 TYR cc_start: 0.7729 (m-80) cc_final: 0.7374 (m-80) REVERT: B 572 LYS cc_start: 0.5796 (mmtt) cc_final: 0.5319 (mmtt) REVERT: B 650 LYS cc_start: 0.8290 (mmmt) cc_final: 0.8034 (mmmt) REVERT: B 779 MET cc_start: 0.8346 (tmm) cc_final: 0.8127 (ppp) REVERT: B 941 LYS cc_start: 0.7627 (ptmm) cc_final: 0.7394 (ttpp) REVERT: B 965 MET cc_start: 0.8212 (tmm) cc_final: 0.7485 (tpt) REVERT: B 1020 TRP cc_start: 0.7348 (m100) cc_final: 0.6750 (m100) REVERT: B 1102 HIS cc_start: 0.6611 (m90) cc_final: 0.6405 (m-70) REVERT: B 1212 MET cc_start: 0.7847 (mpp) cc_final: 0.7411 (mpp) REVERT: B 1215 MET cc_start: 0.7170 (mmp) cc_final: 0.6562 (ttt) REVERT: C 36 ARG cc_start: 0.7388 (ttp80) cc_final: 0.7007 (tmm160) REVERT: C 40 GLN cc_start: 0.8918 (mt0) cc_final: 0.8358 (mt0) REVERT: C 122 LEU cc_start: 0.8935 (mt) cc_final: 0.8521 (tp) REVERT: C 126 MET cc_start: 0.8497 (mtm) cc_final: 0.8165 (mtm) REVERT: C 235 GLU cc_start: 0.8879 (tp30) cc_final: 0.8155 (mp0) REVERT: C 238 ARG cc_start: 0.8290 (ttm170) cc_final: 0.8019 (ttp80) REVERT: C 248 LYS cc_start: 0.9119 (tptp) cc_final: 0.8792 (tptp) REVERT: D 65 TYR cc_start: 0.8399 (p90) cc_final: 0.8026 (p90) REVERT: D 69 HIS cc_start: 0.7191 (m90) cc_final: 0.6892 (m90) REVERT: D 121 LYS cc_start: 0.7779 (mmtt) cc_final: 0.7555 (mmtt) REVERT: D 138 LEU cc_start: 0.8484 (mt) cc_final: 0.8268 (mt) REVERT: D 153 ILE cc_start: 0.8583 (tt) cc_final: 0.8266 (tp) REVERT: D 214 GLN cc_start: 0.8538 (mt0) cc_final: 0.8283 (mp10) REVERT: D 279 PHE cc_start: 0.8327 (t80) cc_final: 0.7947 (t80) REVERT: D 290 LYS cc_start: 0.9402 (mttt) cc_final: 0.8761 (mmmt) REVERT: D 294 ASN cc_start: 0.8947 (m-40) cc_final: 0.8455 (m110) REVERT: D 297 ARG cc_start: 0.8895 (ttp-110) cc_final: 0.8681 (mtm110) REVERT: D 329 TYR cc_start: 0.7087 (m-80) cc_final: 0.6817 (t80) REVERT: D 377 PHE cc_start: 0.8503 (m-10) cc_final: 0.8293 (m-10) REVERT: D 378 LEU cc_start: 0.8905 (mt) cc_final: 0.8670 (tt) REVERT: F 29 SER cc_start: 0.6704 (m) cc_final: 0.6206 (t) REVERT: F 70 LYS cc_start: 0.6800 (mmmm) cc_final: 0.6441 (mmmm) REVERT: F 83 HIS cc_start: 0.6997 (OUTLIER) cc_final: 0.6470 (t-90) REVERT: F 104 ASN cc_start: 0.6872 (p0) cc_final: 0.6641 (p0) REVERT: F 110 ARG cc_start: 0.6103 (tpt90) cc_final: 0.5311 (tpt90) REVERT: F 126 ILE cc_start: 0.7969 (tt) cc_final: 0.7573 (mt) REVERT: F 181 LEU cc_start: 0.7372 (tt) cc_final: 0.7128 (tp) outliers start: 52 outliers final: 24 residues processed: 443 average time/residue: 0.1863 time to fit residues: 123.5760 Evaluate side-chains 407 residues out of total 2650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 382 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 192 TRP Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 868 HIS Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 806 ASP Chi-restraints excluded: chain B residue 1155 TRP Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 327 TYR Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 83 HIS Chi-restraints excluded: chain F residue 97 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 105 optimal weight: 0.8980 chunk 218 optimal weight: 0.9990 chunk 134 optimal weight: 0.6980 chunk 201 optimal weight: 9.9990 chunk 185 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 191 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 198 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 241 optimal weight: 0.0770 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 745 HIS ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN B 292 GLN ** B 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 830 GLN B 990 HIS ** B1103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN C 240 GLN C 253 GLN ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 HIS F 44 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.142031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.116956 restraints weight = 107411.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.117283 restraints weight = 65819.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.118776 restraints weight = 51293.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.117849 restraints weight = 41516.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.118189 restraints weight = 34921.612| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3896 r_free = 0.3896 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3896 r_free = 0.3896 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24551 Z= 0.143 Angle : 0.651 16.627 33184 Z= 0.329 Chirality : 0.043 0.215 3686 Planarity : 0.005 0.072 4248 Dihedral : 7.512 166.858 3260 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.04 % Favored : 95.89 % Rotamer: Outliers : 2.19 % Allowed : 14.87 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.28 % 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: -0.06 (0.15), residues: 2947 helix: 0.76 (0.14), residues: 1341 sheet: -0.27 (0.26), residues: 375 loop : -0.78 (0.17), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 602 TYR 0.017 0.001 TYR A 50 PHE 0.025 0.002 PHE B1104 TRP 0.036 0.002 TRP B1199 HIS 0.010 0.001 HIS B 666 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (24545) covalent geometry : angle 0.64144 / 0.33 (33176) SS BOND : bond 0.00319 / 0.17 ( 1) SS BOND : angle 1.03818 / 0.69 ( 2) hydrogen bonds : bond 0.03875 / 2.50 ( 1084) hydrogen bonds : angle 4.38068 / 3.05 ( 3099) metal coordination : bond 0.00826 / 0.34 ( 4) metal coordination : angle 8.44224 / 4.57 ( 6) Misc. bond : bond 0.00029 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 403 time to evaluate : 0.959 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: 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: A 43 MET cc_start: 0.8610 (mmm) cc_final: 0.8372 (tpt) REVERT: A 172 MET cc_start: 0.8418 (mmm) cc_final: 0.8142 (mmm) REVERT: A 198 PHE cc_start: 0.8952 (m-80) cc_final: 0.8712 (m-80) REVERT: A 203 MET cc_start: 0.8816 (ppp) cc_final: 0.7789 (ppp) REVERT: A 370 HIS cc_start: 0.7149 (t-90) cc_final: 0.6871 (t-90) REVERT: A 396 LEU cc_start: 0.8394 (tp) cc_final: 0.8149 (tp) REVERT: A 475 LEU cc_start: 0.8736 (tp) cc_final: 0.8408 (tt) REVERT: A 510 ASP cc_start: 0.7368 (t0) cc_final: 0.7043 (t0) REVERT: A 513 THR cc_start: 0.8929 (m) cc_final: 0.8702 (p) REVERT: A 546 GLN cc_start: 0.7456 (tp-100) cc_final: 0.7212 (tp-100) REVERT: A 589 GLU cc_start: 0.8069 (pp20) cc_final: 0.7867 (pp20) REVERT: A 590 LEU cc_start: 0.7272 (tp) cc_final: 0.6843 (tp) REVERT: A 635 PHE cc_start: 0.6939 (t80) cc_final: 0.6231 (t80) REVERT: A 636 LYS cc_start: 0.8204 (mttt) cc_final: 0.7872 (ttpt) REVERT: A 676 SER cc_start: 0.7784 (t) cc_final: 0.7430 (p) REVERT: A 743 ASP cc_start: 0.7543 (t0) cc_final: 0.6874 (t70) REVERT: A 751 LEU cc_start: 0.6801 (mt) cc_final: 0.6254 (pp) REVERT: A 777 MET cc_start: 0.7006 (mmm) cc_final: 0.6672 (ttm) REVERT: A 854 GLU cc_start: 0.7594 (tp30) cc_final: 0.7388 (tp30) REVERT: B 100 MET cc_start: 0.6658 (mtm) cc_final: 0.6429 (mpp) REVERT: B 155 MET cc_start: 0.6535 (mmt) cc_final: 0.5702 (mmt) REVERT: B 207 MET cc_start: 0.8192 (ptm) cc_final: 0.7988 (ptp) REVERT: B 305 GLU cc_start: 0.7190 (pm20) cc_final: 0.6929 (pm20) REVERT: B 349 ASP cc_start: 0.6978 (t70) cc_final: 0.6577 (t0) REVERT: B 421 TYR cc_start: 0.7723 (m-80) cc_final: 0.7358 (m-80) REVERT: B 536 MET cc_start: 0.6005 (tpp) cc_final: 0.5423 (tpp) REVERT: B 557 MET cc_start: 0.7808 (mmp) cc_final: 0.7171 (mmm) REVERT: B 959 ARG cc_start: 0.8147 (mtp180) cc_final: 0.7797 (mmt180) REVERT: B 964 MET cc_start: 0.9043 (tmm) cc_final: 0.8668 (tmm) REVERT: B 965 MET cc_start: 0.8214 (tmm) cc_final: 0.7451 (tpt) REVERT: B 1020 TRP cc_start: 0.7388 (m100) cc_final: 0.6901 (m100) REVERT: B 1038 TYR cc_start: 0.5899 (t80) cc_final: 0.5616 (t80) REVERT: B 1102 HIS cc_start: 0.7090 (m90) cc_final: 0.6822 (m-70) REVERT: B 1215 MET cc_start: 0.6997 (mmp) cc_final: 0.6495 (ttt) REVERT: C 122 LEU cc_start: 0.8939 (mt) cc_final: 0.8510 (tp) REVERT: C 126 MET cc_start: 0.8559 (mtm) cc_final: 0.8223 (mtm) REVERT: C 235 GLU cc_start: 0.8902 (tp30) cc_final: 0.8012 (mm-30) REVERT: C 236 PHE cc_start: 0.8697 (t80) cc_final: 0.8484 (t80) REVERT: C 237 LYS cc_start: 0.9198 (tptp) cc_final: 0.8796 (tppt) REVERT: C 238 ARG cc_start: 0.8361 (ttm170) cc_final: 0.8069 (ttp80) REVERT: C 248 LYS cc_start: 0.9170 (tptp) cc_final: 0.8844 (tptp) REVERT: C 266 LYS cc_start: 0.8270 (mttt) cc_final: 0.8060 (mttt) REVERT: D 69 HIS cc_start: 0.7076 (m90) cc_final: 0.6846 (m90) REVERT: D 121 LYS cc_start: 0.7834 (mmtt) cc_final: 0.7571 (mmtt) REVERT: D 138 LEU cc_start: 0.8449 (mt) cc_final: 0.8237 (mt) REVERT: D 214 GLN cc_start: 0.8543 (mt0) cc_final: 0.8291 (mp10) REVERT: D 279 PHE cc_start: 0.8449 (t80) cc_final: 0.8059 (t80) REVERT: D 294 ASN cc_start: 0.8993 (m-40) cc_final: 0.8709 (m110) REVERT: D 329 TYR cc_start: 0.7286 (m-80) cc_final: 0.6982 (t80) REVERT: D 378 LEU cc_start: 0.8950 (mt) cc_final: 0.8728 (tt) REVERT: F 29 SER cc_start: 0.6810 (m) cc_final: 0.6457 (t) REVERT: F 38 LEU cc_start: 0.7542 (mt) cc_final: 0.7159 (mt) REVERT: F 70 LYS cc_start: 0.6868 (mmmm) cc_final: 0.6541 (mmmm) REVERT: F 110 ARG cc_start: 0.5983 (tpt90) cc_final: 0.5511 (tpt90) REVERT: F 126 ILE cc_start: 0.8257 (tt) cc_final: 0.7800 (mt) REVERT: F 133 ASN cc_start: 0.6862 (t0) cc_final: 0.6643 (m-40) REVERT: F 181 LEU cc_start: 0.7580 (tt) cc_final: 0.7352 (tt) outliers start: 58 outliers final: 30 residues processed: 436 average time/residue: 0.1877 time to fit residues: 122.3953 Evaluate side-chains 398 residues out of total 2650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 368 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 192 TRP Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 868 HIS Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 806 ASP Chi-restraints excluded: chain B residue 1147 PHE Chi-restraints excluded: chain B residue 1356 VAL Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 327 TYR Chi-restraints excluded: chain F residue 66 ASP Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 97 ILE Chi-restraints excluded: chain F residue 130 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 280 optimal weight: 0.9980 chunk 274 optimal weight: 50.0000 chunk 159 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 220 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 38 optimal weight: 0.0670 chunk 103 optimal weight: 0.1980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 182 HIS ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 GLN A 598 GLN A 759 HIS B1021 ASN B1103 HIS C 147 GLN C 240 GLN D 126 GLN D 283 HIS D 311 ASN F 44 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.141632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.116115 restraints weight = 106498.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.117105 restraints weight = 65768.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.118591 restraints weight = 46445.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.117758 restraints weight = 38815.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.118246 restraints weight = 32068.690| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3888 r_free = 0.3888 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3889 r_free = 0.3889 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.5161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24551 Z= 0.130 Angle : 0.651 13.093 33184 Z= 0.327 Chirality : 0.043 0.260 3686 Planarity : 0.004 0.065 4248 Dihedral : 7.401 170.854 3260 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.97 % Favored : 96.00 % Rotamer: Outliers : 2.00 % Allowed : 16.11 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.28 % 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: 0.05 (0.15), residues: 2947 helix: 0.86 (0.14), residues: 1345 sheet: -0.39 (0.26), residues: 371 loop : -0.67 (0.17), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 347 TYR 0.020 0.001 TYR F 151 PHE 0.026 0.001 PHE A 548 TRP 0.030 0.001 TRP B1199 HIS 0.013 0.001 HIS B 666 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (24545) covalent geometry : angle 0.64477 / 0.33 (33176) SS BOND : bond 0.00335 / 0.18 ( 1) SS BOND : angle 0.96598 / 0.64 ( 2) hydrogen bonds : bond 0.03752 / 2.44 ( 1084) hydrogen bonds : angle 4.28531 / 2.97 ( 3099) metal coordination : bond 0.00712 / 0.26 ( 4) metal coordination : angle 6.74995 / 3.87 ( 6) Misc. bond : bond 0.00011 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 380 time to evaluate : 0.924 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.8577 (mmm) cc_final: 0.8359 (tpt) REVERT: A 198 PHE cc_start: 0.8932 (m-80) cc_final: 0.8676 (m-80) REVERT: A 394 MET cc_start: 0.7294 (mtp) cc_final: 0.6618 (tpt) REVERT: A 396 LEU cc_start: 0.8403 (tp) cc_final: 0.8159 (tp) REVERT: A 475 LEU cc_start: 0.8769 (tp) cc_final: 0.8424 (tt) REVERT: A 510 ASP cc_start: 0.7267 (t0) cc_final: 0.6835 (t0) REVERT: A 513 THR cc_start: 0.8886 (m) cc_final: 0.8568 (p) REVERT: A 546 GLN cc_start: 0.7503 (tp-100) cc_final: 0.7291 (tp-100) REVERT: A 560 GLN cc_start: 0.7687 (mm-40) cc_final: 0.7445 (mp10) REVERT: A 635 PHE cc_start: 0.6856 (t80) cc_final: 0.6444 (t80) REVERT: A 636 LYS cc_start: 0.8191 (mttt) cc_final: 0.7686 (ttpp) REVERT: A 676 SER cc_start: 0.7754 (t) cc_final: 0.7417 (p) REVERT: A 681 PHE cc_start: 0.6833 (m-80) cc_final: 0.6458 (m-80) REVERT: A 751 LEU cc_start: 0.6884 (mt) cc_final: 0.6299 (pp) REVERT: A 777 MET cc_start: 0.7062 (mmm) cc_final: 0.6806 (ttm) REVERT: A 854 GLU cc_start: 0.7671 (tp30) cc_final: 0.7462 (tp30) REVERT: B 30 LYS cc_start: 0.8278 (ptpt) cc_final: 0.8042 (ptpp) REVERT: B 100 MET cc_start: 0.6639 (mtm) cc_final: 0.6394 (mpp) REVERT: B 155 MET cc_start: 0.6576 (mmt) cc_final: 0.5685 (mmt) REVERT: B 241 ILE cc_start: 0.7476 (OUTLIER) cc_final: 0.7229 (tt) REVERT: B 349 ASP cc_start: 0.6982 (t70) cc_final: 0.6596 (t70) REVERT: B 421 TYR cc_start: 0.7688 (m-80) cc_final: 0.7202 (m-80) REVERT: B 536 MET cc_start: 0.6197 (tpp) cc_final: 0.5771 (tpp) REVERT: B 561 ILE cc_start: 0.5398 (OUTLIER) cc_final: 0.4630 (tt) REVERT: B 951 LYS cc_start: 0.8661 (mmtm) cc_final: 0.8426 (mmtm) REVERT: B 952 ARG cc_start: 0.8454 (mmp80) cc_final: 0.8236 (mmp80) REVERT: B 959 ARG cc_start: 0.8177 (mtp180) cc_final: 0.7833 (mtp180) REVERT: B 965 MET cc_start: 0.8202 (tmm) cc_final: 0.7459 (tpt) REVERT: B 1020 TRP cc_start: 0.7457 (m100) cc_final: 0.6941 (m100) REVERT: B 1102 HIS cc_start: 0.6988 (m90) cc_final: 0.6758 (m-70) REVERT: B 1171 ARG cc_start: 0.7605 (mpp80) cc_final: 0.7100 (mpp80) REVERT: B 1215 MET cc_start: 0.7029 (mmp) cc_final: 0.6583 (ttt) REVERT: C 40 GLN cc_start: 0.9015 (mt0) cc_final: 0.8573 (mt0) REVERT: C 122 LEU cc_start: 0.8944 (mt) cc_final: 0.8545 (tp) REVERT: C 126 MET cc_start: 0.8503 (mtm) cc_final: 0.8197 (mtm) REVERT: C 206 LYS cc_start: 0.8814 (mmtm) cc_final: 0.8607 (mmtt) REVERT: C 235 GLU cc_start: 0.8865 (tp30) cc_final: 0.8040 (mm-30) REVERT: C 237 LYS cc_start: 0.9199 (tptp) cc_final: 0.8784 (tppt) REVERT: C 238 ARG cc_start: 0.8310 (ttm170) cc_final: 0.8042 (ttp80) REVERT: C 248 LYS cc_start: 0.9167 (tptp) cc_final: 0.8804 (tptp) REVERT: D 69 HIS cc_start: 0.7062 (m90) cc_final: 0.6797 (m90) REVERT: D 121 LYS cc_start: 0.7813 (mmtt) cc_final: 0.7567 (mmtt) REVERT: D 214 GLN cc_start: 0.8550 (mt0) cc_final: 0.8298 (mp10) REVERT: D 279 PHE cc_start: 0.8437 (t80) cc_final: 0.8021 (t80) REVERT: D 294 ASN cc_start: 0.8923 (m-40) cc_final: 0.8712 (m110) REVERT: D 311 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.8147 (m110) REVERT: D 329 TYR cc_start: 0.7295 (m-80) cc_final: 0.7019 (t80) REVERT: D 377 PHE cc_start: 0.8068 (m-10) cc_final: 0.7853 (m-10) REVERT: D 378 LEU cc_start: 0.8934 (mt) cc_final: 0.8699 (tt) REVERT: F 90 TYR cc_start: 0.4277 (p90) cc_final: 0.3933 (p90) REVERT: F 94 GLN cc_start: 0.8032 (tm-30) cc_final: 0.7665 (tm-30) REVERT: F 133 ASN cc_start: 0.7091 (t0) cc_final: 0.6887 (m-40) REVERT: F 181 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7387 (tt) outliers start: 53 outliers final: 33 residues processed: 411 average time/residue: 0.1857 time to fit residues: 115.1916 Evaluate side-chains 391 residues out of total 2650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 354 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 192 TRP Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 841 LYS Chi-restraints excluded: chain A residue 868 HIS Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 806 ASP Chi-restraints excluded: chain B residue 1147 PHE Chi-restraints excluded: chain B residue 1155 TRP Chi-restraints excluded: chain B residue 1356 VAL Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 457 PHE Chi-restraints excluded: chain F residue 44 GLN Chi-restraints excluded: chain F residue 66 ASP Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 97 ILE Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 181 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 271 optimal weight: 1.9990 chunk 205 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 4 optimal weight: 0.2980 chunk 173 optimal weight: 8.9990 chunk 155 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 199 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 GLN B 310 GLN C 253 GLN D 283 HIS F 49 GLN F 146 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.130957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.106294 restraints weight = 88597.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.108828 restraints weight = 44281.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.110489 restraints weight = 27281.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.111583 restraints weight = 19273.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.112289 restraints weight = 15143.476| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3897 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3897 r_free = 0.3897 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3896 r_free = 0.3896 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.5657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24551 Z= 0.168 Angle : 0.693 13.039 33184 Z= 0.348 Chirality : 0.044 0.192 3686 Planarity : 0.004 0.064 4248 Dihedral : 7.449 178.907 3260 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.55 % Favored : 95.42 % Rotamer: Outliers : 2.19 % Allowed : 16.04 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.28 % 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 (0.15), residues: 2947 helix: 0.81 (0.14), residues: 1347 sheet: -0.45 (0.26), residues: 369 loop : -0.65 (0.17), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 200 TYR 0.018 0.002 TYR C 256 PHE 0.024 0.002 PHE C 82 TRP 0.023 0.001 TRP B1199 HIS 0.008 0.001 HIS F 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (24545) covalent geometry : angle 0.68857 / 0.35 (33176) SS BOND : bond 0.00373 / 0.20 ( 1) SS BOND : angle 1.10712 / 0.74 ( 2) hydrogen bonds : bond 0.03916 / 2.53 ( 1084) hydrogen bonds : angle 4.38360 / 3.03 ( 3099) metal coordination : bond 0.00744 / 0.28 ( 4) metal coordination : angle 5.54855 / 3.22 ( 6) Misc. bond : bond 0.00043 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 392 time to evaluate : 1.024 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 LYS cc_start: 0.8550 (mttt) cc_final: 0.8123 (mttp) REVERT: A 338 ASN cc_start: 0.8346 (t0) cc_final: 0.7821 (p0) REVERT: A 344 GLU cc_start: 0.6148 (tp30) cc_final: 0.5920 (mm-30) REVERT: A 358 MET cc_start: 0.6543 (tpp) cc_final: 0.5375 (mmp) REVERT: A 396 LEU cc_start: 0.8414 (tp) cc_final: 0.8175 (tp) REVERT: A 404 LYS cc_start: 0.8268 (mttp) cc_final: 0.7862 (mttt) REVERT: A 475 LEU cc_start: 0.8754 (tp) cc_final: 0.8389 (tt) REVERT: A 500 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7148 (mm-30) REVERT: A 510 ASP cc_start: 0.7194 (t0) cc_final: 0.6765 (t0) REVERT: A 513 THR cc_start: 0.8874 (m) cc_final: 0.8400 (p) REVERT: A 556 MET cc_start: 0.7970 (mmm) cc_final: 0.7721 (mmp) REVERT: A 635 PHE cc_start: 0.6836 (t80) cc_final: 0.6444 (t80) REVERT: A 636 LYS cc_start: 0.8145 (mttt) cc_final: 0.7754 (ttpp) REVERT: A 676 SER cc_start: 0.7860 (t) cc_final: 0.7305 (m) REVERT: A 681 PHE cc_start: 0.6856 (m-80) cc_final: 0.6543 (m-80) REVERT: A 751 LEU cc_start: 0.6973 (mt) cc_final: 0.6465 (pp) REVERT: A 854 GLU cc_start: 0.7556 (tp30) cc_final: 0.7352 (tp30) REVERT: B 8 ILE cc_start: 0.7949 (mm) cc_final: 0.7606 (mm) REVERT: B 155 MET cc_start: 0.6540 (mmt) cc_final: 0.5714 (mmt) REVERT: B 241 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.7264 (tt) REVERT: B 349 ASP cc_start: 0.7068 (t70) cc_final: 0.6749 (t70) REVERT: B 421 TYR cc_start: 0.7778 (m-80) cc_final: 0.7227 (m-80) REVERT: B 557 MET cc_start: 0.7721 (mmp) cc_final: 0.7141 (mmm) REVERT: B 748 ARG cc_start: 0.8282 (mpp80) cc_final: 0.7988 (mpp80) REVERT: B 951 LYS cc_start: 0.8673 (mmtm) cc_final: 0.8422 (mmtm) REVERT: B 959 ARG cc_start: 0.7924 (mtp180) cc_final: 0.7504 (mtp85) REVERT: B 964 MET cc_start: 0.8549 (tmm) cc_final: 0.8149 (tmm) REVERT: B 1020 TRP cc_start: 0.7217 (m100) cc_final: 0.6448 (m100) REVERT: B 1171 ARG cc_start: 0.7495 (mpp80) cc_final: 0.6981 (mpp80) REVERT: C 122 LEU cc_start: 0.8702 (mt) cc_final: 0.8416 (tp) REVERT: C 206 LYS cc_start: 0.8798 (mmtm) cc_final: 0.8525 (mmtt) REVERT: C 221 ARG cc_start: 0.8752 (tpp-160) cc_final: 0.8544 (tpm170) REVERT: C 235 GLU cc_start: 0.8335 (tp30) cc_final: 0.7934 (mm-30) REVERT: C 237 LYS cc_start: 0.8994 (tptp) cc_final: 0.8574 (tppt) REVERT: C 238 ARG cc_start: 0.7813 (ttm170) cc_final: 0.7442 (ttp80) REVERT: C 248 LYS cc_start: 0.8862 (tptp) cc_final: 0.8473 (tptp) REVERT: D 38 GLN cc_start: 0.8249 (tp-100) cc_final: 0.8018 (tp-100) REVERT: D 279 PHE cc_start: 0.7897 (t80) cc_final: 0.7604 (t80) REVERT: D 311 ASN cc_start: 0.8678 (OUTLIER) cc_final: 0.8166 (m-40) REVERT: D 378 LEU cc_start: 0.8815 (mt) cc_final: 0.8588 (tt) REVERT: F 41 VAL cc_start: 0.8691 (t) cc_final: 0.8144 (m) REVERT: F 168 MET cc_start: 0.7733 (tmm) cc_final: 0.7275 (tmm) REVERT: F 181 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7555 (tt) outliers start: 58 outliers final: 39 residues processed: 427 average time/residue: 0.1874 time to fit residues: 121.0973 Evaluate side-chains 408 residues out of total 2650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 366 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 192 TRP Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 868 HIS Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 1137 HIS Chi-restraints excluded: chain B residue 1147 PHE Chi-restraints excluded: chain B residue 1155 TRP Chi-restraints excluded: chain B residue 1356 VAL Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain F residue 66 ASP Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 97 ILE Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 181 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 63 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 244 optimal weight: 0.9980 chunk 175 optimal weight: 0.0970 chunk 94 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 162 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 148 optimal weight: 0.0050 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 182 HIS ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN A 598 GLN B 506 ASN B 777 GLN B1102 HIS B1329 HIS C 240 GLN C 253 GLN ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.139993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.114545 restraints weight = 106324.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.115290 restraints weight = 66534.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.115321 restraints weight = 48744.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.115615 restraints weight = 44639.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.115566 restraints weight = 39674.511| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3811 r_free = 0.3811 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3812 r_free = 0.3812 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.5896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24551 Z= 0.131 Angle : 0.691 13.370 33184 Z= 0.343 Chirality : 0.044 0.209 3686 Planarity : 0.004 0.065 4248 Dihedral : 7.329 175.071 3260 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.97 % Favored : 96.00 % Rotamer: Outliers : 2.08 % Allowed : 17.28 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.28 % 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: 0.14 (0.15), residues: 2947 helix: 0.94 (0.14), residues: 1349 sheet: -0.25 (0.27), residues: 361 loop : -0.65 (0.18), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 117 TYR 0.021 0.001 TYR C 256 PHE 0.027 0.001 PHE C 82 TRP 0.020 0.001 TRP B1199 HIS 0.011 0.001 HIS B 666 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (24545) covalent geometry : angle 0.68736 / 0.34 (33176) SS BOND : bond 0.00408 / 0.21 ( 1) SS BOND : angle 1.01721 / 0.68 ( 2) hydrogen bonds : bond 0.03703 / 2.39 ( 1084) hydrogen bonds : angle 4.30066 / 2.97 ( 3099) metal coordination : bond 0.00623 / 0.24 ( 4) metal coordination : angle 5.30485 / 3.10 ( 6) Misc. bond : bond 0.00005 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 377 time to evaluate : 1.028 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: A 43 MET cc_start: 0.8572 (tpt) cc_final: 0.8238 (tpp) REVERT: A 172 MET cc_start: 0.8342 (mmm) cc_final: 0.7951 (mmm) REVERT: A 203 MET cc_start: 0.8451 (ppp) cc_final: 0.8177 (ppp) REVERT: A 335 LYS cc_start: 0.8559 (mttt) cc_final: 0.8066 (mttp) REVERT: A 338 ASN cc_start: 0.8410 (t0) cc_final: 0.7751 (p0) REVERT: A 344 GLU cc_start: 0.6602 (tp30) cc_final: 0.6367 (mm-30) REVERT: A 394 MET cc_start: 0.7431 (mmm) cc_final: 0.6793 (tpt) REVERT: A 396 LEU cc_start: 0.8420 (tp) cc_final: 0.8210 (tp) REVERT: A 404 LYS cc_start: 0.8195 (mttp) cc_final: 0.7827 (mttt) REVERT: A 475 LEU cc_start: 0.8701 (tp) cc_final: 0.8329 (tt) REVERT: A 500 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7212 (mm-30) REVERT: A 510 ASP cc_start: 0.7465 (t0) cc_final: 0.6880 (t0) REVERT: A 513 THR cc_start: 0.8939 (m) cc_final: 0.8479 (p) REVERT: A 545 GLN cc_start: 0.8226 (mt0) cc_final: 0.7965 (mm-40) REVERT: A 557 LYS cc_start: 0.8127 (mmtm) cc_final: 0.7803 (mmtm) REVERT: A 560 GLN cc_start: 0.7188 (mp-120) cc_final: 0.6692 (mp10) REVERT: A 635 PHE cc_start: 0.6905 (t80) cc_final: 0.6512 (t80) REVERT: A 636 LYS cc_start: 0.8162 (mttt) cc_final: 0.7644 (ttpp) REVERT: A 641 LEU cc_start: 0.8220 (mt) cc_final: 0.7586 (tt) REVERT: A 676 SER cc_start: 0.7805 (t) cc_final: 0.7263 (m) REVERT: A 681 PHE cc_start: 0.6852 (m-80) cc_final: 0.6522 (m-80) REVERT: A 743 ASP cc_start: 0.7492 (t0) cc_final: 0.6646 (t70) REVERT: A 751 LEU cc_start: 0.6971 (mt) cc_final: 0.6454 (pp) REVERT: A 854 GLU cc_start: 0.7962 (tp30) cc_final: 0.7620 (tp30) REVERT: B 8 ILE cc_start: 0.7877 (mm) cc_final: 0.7501 (mm) REVERT: B 30 LYS cc_start: 0.8298 (ptpt) cc_final: 0.8053 (ptpp) REVERT: B 73 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6596 (tm-30) REVERT: B 155 MET cc_start: 0.6459 (mmt) cc_final: 0.5561 (mmt) REVERT: B 196 TYR cc_start: 0.7396 (m-80) cc_final: 0.7017 (m-80) REVERT: B 207 MET cc_start: 0.8123 (ptt) cc_final: 0.7571 (mpp) REVERT: B 349 ASP cc_start: 0.7009 (t70) cc_final: 0.6667 (t70) REVERT: B 421 TYR cc_start: 0.7739 (m-80) cc_final: 0.7143 (m-80) REVERT: B 557 MET cc_start: 0.7707 (mmp) cc_final: 0.7157 (mmm) REVERT: B 561 ILE cc_start: 0.5562 (OUTLIER) cc_final: 0.4727 (mm) REVERT: B 748 ARG cc_start: 0.8642 (mpp80) cc_final: 0.8195 (mpp80) REVERT: B 951 LYS cc_start: 0.8751 (mmtm) cc_final: 0.8549 (mmtm) REVERT: B 959 ARG cc_start: 0.8237 (mtp180) cc_final: 0.7820 (mtp85) REVERT: B 964 MET cc_start: 0.9031 (tmm) cc_final: 0.8769 (tmm) REVERT: B 965 MET cc_start: 0.7450 (mmt) cc_final: 0.6748 (tmm) REVERT: B 1020 TRP cc_start: 0.7650 (m100) cc_final: 0.7106 (m100) REVERT: B 1097 CYS cc_start: 0.2679 (OUTLIER) cc_final: 0.1308 (m) REVERT: B 1147 PHE cc_start: 0.6114 (OUTLIER) cc_final: 0.5455 (m-10) REVERT: B 1171 ARG cc_start: 0.7523 (mpp80) cc_final: 0.7045 (mpp80) REVERT: B 1292 ARG cc_start: 0.8193 (tmm160) cc_final: 0.7885 (tpt90) REVERT: C 16 PHE cc_start: 0.7030 (m-10) cc_final: 0.6767 (m-10) REVERT: C 36 ARG cc_start: 0.7530 (ttp80) cc_final: 0.7130 (tmm-80) REVERT: C 40 GLN cc_start: 0.9065 (mt0) cc_final: 0.8713 (pt0) REVERT: C 221 ARG cc_start: 0.8851 (tpp-160) cc_final: 0.8627 (tpm170) REVERT: C 235 GLU cc_start: 0.8859 (tp30) cc_final: 0.8141 (mm-30) REVERT: C 237 LYS cc_start: 0.9152 (tptp) cc_final: 0.8732 (tppt) REVERT: C 238 ARG cc_start: 0.8322 (ttm170) cc_final: 0.7828 (ttp80) REVERT: C 247 LEU cc_start: 0.9082 (tp) cc_final: 0.8844 (pp) REVERT: C 248 LYS cc_start: 0.9152 (tptp) cc_final: 0.8739 (tptp) REVERT: D 38 GLN cc_start: 0.8399 (tp-100) cc_final: 0.8147 (tp-100) REVERT: D 65 TYR cc_start: 0.8261 (p90) cc_final: 0.7935 (p90) REVERT: D 118 TRP cc_start: 0.8107 (m100) cc_final: 0.7439 (m100) REVERT: D 121 LYS cc_start: 0.7744 (mmtt) cc_final: 0.7374 (mmpt) REVERT: D 162 TYR cc_start: 0.7239 (m-80) cc_final: 0.6688 (m-10) REVERT: D 279 PHE cc_start: 0.8523 (t80) cc_final: 0.8035 (t80) REVERT: D 311 ASN cc_start: 0.8811 (OUTLIER) cc_final: 0.8254 (m110) REVERT: D 329 TYR cc_start: 0.6908 (t80) cc_final: 0.6367 (t80) REVERT: D 373 MET cc_start: 0.7912 (tpp) cc_final: 0.7552 (tpp) REVERT: D 377 PHE cc_start: 0.8071 (m-10) cc_final: 0.7014 (m-10) REVERT: D 378 LEU cc_start: 0.8927 (mt) cc_final: 0.8675 (tt) REVERT: F 41 VAL cc_start: 0.8760 (t) cc_final: 0.8526 (m) REVERT: F 42 LYS cc_start: 0.8587 (mmtm) cc_final: 0.8212 (mmtm) REVERT: F 94 GLN cc_start: 0.8225 (tm-30) cc_final: 0.7629 (tm-30) REVERT: F 181 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7335 (tt) outliers start: 55 outliers final: 34 residues processed: 410 average time/residue: 0.1991 time to fit residues: 121.8863 Evaluate side-chains 398 residues out of total 2650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 358 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 192 TRP Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 868 HIS Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 1097 CYS Chi-restraints excluded: chain B residue 1137 HIS Chi-restraints excluded: chain B residue 1147 PHE Chi-restraints excluded: chain B residue 1155 TRP Chi-restraints excluded: chain B residue 1356 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 97 ILE Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 181 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 23 optimal weight: 3.9990 chunk 150 optimal weight: 0.5980 chunk 248 optimal weight: 3.9990 chunk 169 optimal weight: 8.9990 chunk 293 optimal weight: 0.4980 chunk 108 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 259 optimal weight: 10.0000 chunk 161 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 ASN ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 HIS B 310 GLN ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 554 GLN B1179 HIS ** B1193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 240 GLN ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 GLN ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.136803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.110677 restraints weight = 104459.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.111690 restraints weight = 62316.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.113283 restraints weight = 43332.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.112332 restraints weight = 40430.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.112249 restraints weight = 33916.971| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3762 r_free = 0.3762 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3763 r_free = 0.3763 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.6588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 24551 Z= 0.238 Angle : 0.808 16.067 33184 Z= 0.406 Chirality : 0.048 0.271 3686 Planarity : 0.005 0.063 4248 Dihedral : 7.534 173.772 3260 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.06 % Favored : 94.91 % Rotamer: Outliers : 2.34 % Allowed : 18.34 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.15), residues: 2947 helix: 0.61 (0.14), residues: 1351 sheet: -0.52 (0.26), residues: 382 loop : -0.74 (0.18), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 561 TYR 0.032 0.002 TYR B 482 PHE 0.045 0.002 PHE A 198 TRP 0.021 0.002 TRP B1213 HIS 0.012 0.002 HIS B 666 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.24 (24545) covalent geometry : angle 0.80554 / 0.41 (33176) SS BOND : bond 0.00469 / 0.25 ( 1) SS BOND : angle 1.00862 / 0.67 ( 2) hydrogen bonds : bond 0.04519 / 2.96 ( 1084) hydrogen bonds : angle 4.69217 / 3.24 ( 3099) metal coordination : bond 0.00948 / 0.37 ( 4) metal coordination : angle 5.11878 / 3.01 ( 6) Misc. bond : bond 0.00103 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 397 time to evaluate : 0.955 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.8369 (mmm) cc_final: 0.7972 (mmm) REVERT: A 203 MET cc_start: 0.8449 (ppp) cc_final: 0.8138 (ppp) REVERT: A 302 TYR cc_start: 0.8463 (m-80) cc_final: 0.8140 (m-80) REVERT: A 335 LYS cc_start: 0.8541 (mttt) cc_final: 0.8104 (mttp) REVERT: A 338 ASN cc_start: 0.8375 (t0) cc_final: 0.7751 (p0) REVERT: A 394 MET cc_start: 0.7365 (mmm) cc_final: 0.6766 (tpt) REVERT: A 396 LEU cc_start: 0.8532 (tp) cc_final: 0.8236 (tp) REVERT: A 404 LYS cc_start: 0.8446 (mttp) cc_final: 0.8006 (mtmm) REVERT: A 475 LEU cc_start: 0.8724 (tp) cc_final: 0.8334 (tt) REVERT: A 510 ASP cc_start: 0.7463 (t0) cc_final: 0.6844 (t0) REVERT: A 513 THR cc_start: 0.8951 (m) cc_final: 0.8487 (p) REVERT: A 545 GLN cc_start: 0.8240 (mt0) cc_final: 0.7983 (mm-40) REVERT: A 617 MET cc_start: 0.6550 (ptm) cc_final: 0.5627 (ppp) REVERT: A 635 PHE cc_start: 0.7031 (t80) cc_final: 0.5991 (t80) REVERT: A 636 LYS cc_start: 0.8236 (mttt) cc_final: 0.7875 (ttpp) REVERT: A 676 SER cc_start: 0.7813 (t) cc_final: 0.7210 (m) REVERT: A 681 PHE cc_start: 0.6884 (m-80) cc_final: 0.6266 (m-10) REVERT: A 751 LEU cc_start: 0.7124 (mt) cc_final: 0.6732 (pp) REVERT: A 783 MET cc_start: 0.7415 (tpp) cc_final: 0.7055 (mpp) REVERT: A 799 ARG cc_start: 0.8483 (mtp-110) cc_final: 0.8121 (ttm-80) REVERT: A 840 LYS cc_start: 0.8510 (ttpt) cc_final: 0.8281 (ttpp) REVERT: A 849 ASP cc_start: 0.8248 (p0) cc_final: 0.8014 (p0) REVERT: B 8 ILE cc_start: 0.8092 (mm) cc_final: 0.7676 (pt) REVERT: B 73 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6566 (tm-30) REVERT: B 91 SER cc_start: 0.8193 (m) cc_final: 0.7847 (t) REVERT: B 127 TRP cc_start: 0.6905 (t-100) cc_final: 0.6705 (t-100) REVERT: B 155 MET cc_start: 0.6614 (mmt) cc_final: 0.5694 (mmt) REVERT: B 196 TYR cc_start: 0.7410 (m-80) cc_final: 0.7117 (m-80) REVERT: B 349 ASP cc_start: 0.7061 (t70) cc_final: 0.6761 (t70) REVERT: B 421 TYR cc_start: 0.7851 (m-80) cc_final: 0.7237 (m-80) REVERT: B 451 VAL cc_start: 0.8702 (t) cc_final: 0.7534 (p) REVERT: B 557 MET cc_start: 0.7589 (mmp) cc_final: 0.7332 (mmp) REVERT: B 561 ILE cc_start: 0.5926 (OUTLIER) cc_final: 0.5173 (tt) REVERT: B 684 ARG cc_start: 0.7847 (ttm110) cc_final: 0.7251 (mtm180) REVERT: B 748 ARG cc_start: 0.8520 (mpp80) cc_final: 0.8098 (mpp80) REVERT: B 959 ARG cc_start: 0.8162 (mtp180) cc_final: 0.7708 (mtp85) REVERT: B 964 MET cc_start: 0.9032 (tmm) cc_final: 0.8773 (tmm) REVERT: B 965 MET cc_start: 0.7480 (mmt) cc_final: 0.6904 (tmm) REVERT: B 1020 TRP cc_start: 0.7837 (m100) cc_final: 0.7592 (m100) REVERT: B 1292 ARG cc_start: 0.8215 (tmm160) cc_final: 0.7912 (tpt90) REVERT: C 16 PHE cc_start: 0.6954 (m-10) cc_final: 0.6742 (m-10) REVERT: C 121 ASP cc_start: 0.8523 (m-30) cc_final: 0.8274 (m-30) REVERT: C 221 ARG cc_start: 0.8918 (tpp-160) cc_final: 0.8692 (tpm170) REVERT: C 240 GLN cc_start: 0.9155 (OUTLIER) cc_final: 0.8541 (pt0) REVERT: C 248 LYS cc_start: 0.9157 (tptp) cc_final: 0.8750 (tptp) REVERT: D 65 TYR cc_start: 0.8266 (p90) cc_final: 0.7776 (p90) REVERT: D 125 TYR cc_start: 0.7133 (m-80) cc_final: 0.6886 (m-80) REVERT: D 279 PHE cc_start: 0.8507 (t80) cc_final: 0.8103 (t80) REVERT: D 311 ASN cc_start: 0.8838 (OUTLIER) cc_final: 0.8345 (m-40) REVERT: D 329 TYR cc_start: 0.7061 (t80) cc_final: 0.6545 (t80) REVERT: D 373 MET cc_start: 0.8063 (tpp) cc_final: 0.7614 (tpp) REVERT: D 377 PHE cc_start: 0.8012 (m-10) cc_final: 0.6912 (m-10) REVERT: F 145 PHE cc_start: 0.5818 (t80) cc_final: 0.5370 (t80) REVERT: F 149 GLN cc_start: 0.6608 (pp30) cc_final: 0.6368 (tt0) outliers start: 62 outliers final: 42 residues processed: 430 average time/residue: 0.1966 time to fit residues: 126.5119 Evaluate side-chains 420 residues out of total 2650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 374 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 192 TRP Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 554 HIS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 841 LYS Chi-restraints excluded: chain A residue 868 HIS Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 806 ASP Chi-restraints excluded: chain B residue 1137 HIS Chi-restraints excluded: chain B residue 1147 PHE Chi-restraints excluded: chain B residue 1155 TRP Chi-restraints excluded: chain B residue 1171 ARG Chi-restraints excluded: chain B residue 1356 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 97 ILE Chi-restraints excluded: chain F residue 130 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 22 optimal weight: 0.9980 chunk 216 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 186 optimal weight: 10.0000 chunk 290 optimal weight: 1.9990 chunk 197 optimal weight: 10.0000 chunk 196 optimal weight: 9.9990 chunk 36 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 chunk 281 optimal weight: 0.6980 chunk 151 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 182 HIS ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN A 745 HIS A 794 GLN ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 554 GLN ** B1193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 240 GLN ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 GLN ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.137435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.110385 restraints weight = 105109.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.113346 restraints weight = 61249.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.112060 restraints weight = 41913.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.112748 restraints weight = 36366.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.112707 restraints weight = 30961.545| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3768 r_free = 0.3768 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3767 r_free = 0.3767 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.6735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24551 Z= 0.151 Angle : 0.760 13.355 33184 Z= 0.379 Chirality : 0.044 0.210 3686 Planarity : 0.004 0.067 4248 Dihedral : 7.452 176.885 3260 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.34 % Favored : 95.62 % Rotamer: Outliers : 1.92 % Allowed : 19.13 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.28 % 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: 0.03 (0.15), residues: 2947 helix: 0.86 (0.14), residues: 1343 sheet: -0.29 (0.26), residues: 374 loop : -0.73 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 30 TYR 0.026 0.001 TYR C 256 PHE 0.026 0.002 PHE F 21 TRP 0.067 0.002 TRP B1213 HIS 0.007 0.001 HIS B 666 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (24545) covalent geometry : angle 0.75687 / 0.38 (33176) SS BOND : bond 0.00388 / 0.20 ( 1) SS BOND : angle 0.97929 / 0.65 ( 2) hydrogen bonds : bond 0.04022 / 2.62 ( 1084) hydrogen bonds : angle 4.48838 / 3.11 ( 3099) metal coordination : bond 0.00968 / 0.39 ( 4) metal coordination : angle 4.88720 / 2.84 ( 6) Misc. bond : bond 0.00010 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 386 time to evaluate : 0.919 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 MET cc_start: 0.8363 (mmm) cc_final: 0.8114 (mmm) REVERT: A 187 MET cc_start: 0.5576 (pmm) cc_final: 0.5138 (pmm) REVERT: A 203 MET cc_start: 0.8444 (ppp) cc_final: 0.8148 (ppp) REVERT: A 302 TYR cc_start: 0.8398 (m-80) cc_final: 0.8155 (m-80) REVERT: A 335 LYS cc_start: 0.8515 (mttt) cc_final: 0.8103 (mttp) REVERT: A 338 ASN cc_start: 0.8309 (t0) cc_final: 0.7881 (t0) REVERT: A 394 MET cc_start: 0.7291 (mmm) cc_final: 0.6740 (tpt) REVERT: A 396 LEU cc_start: 0.8416 (tp) cc_final: 0.8148 (tp) REVERT: A 475 LEU cc_start: 0.8731 (tp) cc_final: 0.8345 (tt) REVERT: A 545 GLN cc_start: 0.8209 (mt0) cc_final: 0.7951 (mm-40) REVERT: A 635 PHE cc_start: 0.6985 (t80) cc_final: 0.6010 (t80) REVERT: A 641 LEU cc_start: 0.8268 (mt) cc_final: 0.7564 (tt) REVERT: A 676 SER cc_start: 0.7778 (t) cc_final: 0.7221 (m) REVERT: A 681 PHE cc_start: 0.6889 (m-80) cc_final: 0.6303 (m-10) REVERT: A 751 LEU cc_start: 0.7059 (mt) cc_final: 0.6646 (pp) REVERT: A 799 ARG cc_start: 0.8400 (mtp-110) cc_final: 0.8119 (ttm-80) REVERT: A 840 LYS cc_start: 0.8478 (ttpt) cc_final: 0.8168 (ttpp) REVERT: A 849 ASP cc_start: 0.8252 (p0) cc_final: 0.8024 (p0) REVERT: A 859 MET cc_start: 0.8008 (tpp) cc_final: 0.7621 (tmm) REVERT: B 8 ILE cc_start: 0.8030 (mm) cc_final: 0.7586 (pt) REVERT: B 30 LYS cc_start: 0.8329 (ptpt) cc_final: 0.8096 (ptpp) REVERT: B 73 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6540 (tm-30) REVERT: B 91 SER cc_start: 0.8161 (m) cc_final: 0.7804 (t) REVERT: B 155 MET cc_start: 0.6524 (mmt) cc_final: 0.5610 (mmt) REVERT: B 207 MET cc_start: 0.7904 (ptt) cc_final: 0.7569 (ppp) REVERT: B 349 ASP cc_start: 0.6992 (t70) cc_final: 0.6696 (t70) REVERT: B 421 TYR cc_start: 0.7771 (m-80) cc_final: 0.7106 (m-80) REVERT: B 451 VAL cc_start: 0.8360 (t) cc_final: 0.8077 (p) REVERT: B 557 MET cc_start: 0.7567 (mmp) cc_final: 0.7019 (mmp) REVERT: B 561 ILE cc_start: 0.6051 (OUTLIER) cc_final: 0.5156 (tt) REVERT: B 684 ARG cc_start: 0.7809 (ttm110) cc_final: 0.7407 (mtm-85) REVERT: B 748 ARG cc_start: 0.8405 (mpp80) cc_final: 0.7992 (mpp80) REVERT: B 959 ARG cc_start: 0.8163 (mtp180) cc_final: 0.7706 (mtp85) REVERT: B 964 MET cc_start: 0.9032 (tmm) cc_final: 0.8789 (tmm) REVERT: B 965 MET cc_start: 0.7456 (mmt) cc_final: 0.6741 (tmm) REVERT: B 1020 TRP cc_start: 0.7831 (m100) cc_final: 0.7624 (m100) REVERT: B 1171 ARG cc_start: 0.7619 (mpp80) cc_final: 0.7168 (mpp80) REVERT: B 1181 HIS cc_start: 0.7968 (t-90) cc_final: 0.7757 (t-90) REVERT: B 1192 MET cc_start: 0.5150 (mpp) cc_final: 0.4163 (mtm) REVERT: B 1292 ARG cc_start: 0.8218 (tmm160) cc_final: 0.7761 (tpt90) REVERT: B 1330 ASP cc_start: 0.6305 (t0) cc_final: 0.6053 (t0) REVERT: B 1346 VAL cc_start: 0.6146 (t) cc_final: 0.5933 (p) REVERT: C 121 ASP cc_start: 0.8475 (m-30) cc_final: 0.8215 (m-30) REVERT: C 221 ARG cc_start: 0.8909 (tpp-160) cc_final: 0.8701 (tpm170) REVERT: C 237 LYS cc_start: 0.9155 (tptp) cc_final: 0.8771 (tppt) REVERT: C 248 LYS cc_start: 0.9170 (tptp) cc_final: 0.8758 (tptp) REVERT: D 65 TYR cc_start: 0.8143 (p90) cc_final: 0.7678 (p90) REVERT: D 121 LYS cc_start: 0.7696 (mmtt) cc_final: 0.7318 (mmpt) REVERT: D 125 TYR cc_start: 0.7071 (m-80) cc_final: 0.6830 (m-80) REVERT: D 279 PHE cc_start: 0.8487 (t80) cc_final: 0.8028 (t80) REVERT: D 298 LYS cc_start: 0.9421 (pptt) cc_final: 0.9160 (pptt) REVERT: D 311 ASN cc_start: 0.8757 (OUTLIER) cc_final: 0.8277 (m110) REVERT: D 329 TYR cc_start: 0.7103 (t80) cc_final: 0.6579 (t80) REVERT: D 377 PHE cc_start: 0.7826 (m-10) cc_final: 0.7555 (m-10) REVERT: F 145 PHE cc_start: 0.5934 (t80) cc_final: 0.5631 (t80) outliers start: 51 outliers final: 35 residues processed: 415 average time/residue: 0.1931 time to fit residues: 120.6300 Evaluate side-chains 411 residues out of total 2650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 373 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 192 TRP Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 841 LYS Chi-restraints excluded: chain A residue 868 HIS Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 806 ASP Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1137 HIS Chi-restraints excluded: chain B residue 1147 PHE Chi-restraints excluded: chain B residue 1155 TRP Chi-restraints excluded: chain B residue 1356 VAL Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 97 ILE Chi-restraints excluded: chain F residue 130 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 31 optimal weight: 1.9990 chunk 138 optimal weight: 0.0010 chunk 274 optimal weight: 40.0000 chunk 25 optimal weight: 0.8980 chunk 212 optimal weight: 0.7980 chunk 207 optimal weight: 0.0470 chunk 67 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 227 optimal weight: 20.0000 chunk 27 optimal weight: 0.9990 chunk 286 optimal weight: 0.2980 overall best weight: 0.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN B 504 ASN B 622 GLN B 777 GLN ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 GLN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.137695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.109323 restraints weight = 105241.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.110870 restraints weight = 56644.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.112091 restraints weight = 35500.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.112758 restraints weight = 26558.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.112955 restraints weight = 22295.545| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3843 r_free = 0.3843 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3843 r_free = 0.3843 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.6833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24551 Z= 0.139 Angle : 0.768 13.137 33184 Z= 0.381 Chirality : 0.044 0.244 3686 Planarity : 0.004 0.068 4248 Dihedral : 7.330 178.654 3260 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.38 % Favored : 95.59 % Rotamer: Outliers : 1.36 % Allowed : 19.70 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.15), residues: 2947 helix: 0.90 (0.14), residues: 1352 sheet: -0.15 (0.27), residues: 368 loop : -0.70 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 117 TYR 0.057 0.001 TYR C 256 PHE 0.036 0.001 PHE B 102 TRP 0.075 0.002 TRP B1213 HIS 0.007 0.001 HIS B 666 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (24545) covalent geometry : angle 0.76543 / 0.38 (33176) SS BOND : bond 0.00325 / 0.17 ( 1) SS BOND : angle 1.04416 / 0.70 ( 2) hydrogen bonds : bond 0.03881 / 2.55 ( 1084) hydrogen bonds : angle 4.41109 / 3.06 ( 3099) metal coordination : bond 0.00768 / 0.32 ( 4) metal coordination : angle 4.55275 / 2.63 ( 6) Misc. bond : bond 0.00010 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5894 Ramachandran restraints generated. 2947 Oldfield, 0 Emsley, 2947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 383 time to evaluate : 0.979 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: 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: A 172 MET cc_start: 0.8219 (mmm) cc_final: 0.7914 (mmm) REVERT: A 203 MET cc_start: 0.8460 (ppp) cc_final: 0.8136 (ppp) REVERT: A 302 TYR cc_start: 0.8427 (m-80) cc_final: 0.8170 (m-80) REVERT: A 335 LYS cc_start: 0.8520 (mttt) cc_final: 0.8114 (mttp) REVERT: A 338 ASN cc_start: 0.8274 (t0) cc_final: 0.7875 (t0) REVERT: A 394 MET cc_start: 0.7262 (mmm) cc_final: 0.6758 (tpt) REVERT: A 475 LEU cc_start: 0.8739 (tp) cc_final: 0.8371 (tt) REVERT: A 510 ASP cc_start: 0.7310 (t0) cc_final: 0.6772 (t0) REVERT: A 545 GLN cc_start: 0.8106 (mt0) cc_final: 0.7890 (mm-40) REVERT: A 617 MET cc_start: 0.6385 (ptm) cc_final: 0.5395 (ppp) REVERT: A 635 PHE cc_start: 0.6912 (t80) cc_final: 0.5976 (t80) REVERT: A 676 SER cc_start: 0.7753 (t) cc_final: 0.7204 (m) REVERT: A 681 PHE cc_start: 0.6818 (m-80) cc_final: 0.6294 (m-10) REVERT: A 693 VAL cc_start: 0.8106 (t) cc_final: 0.7869 (t) REVERT: A 751 LEU cc_start: 0.6957 (mt) cc_final: 0.6560 (pp) REVERT: A 795 TYR cc_start: 0.8349 (t80) cc_final: 0.8083 (t80) REVERT: A 799 ARG cc_start: 0.8343 (mtp-110) cc_final: 0.8006 (ttm-80) REVERT: A 847 ARG cc_start: 0.7894 (mmm-85) cc_final: 0.7564 (mtm-85) REVERT: B 8 ILE cc_start: 0.7965 (mm) cc_final: 0.7505 (pt) REVERT: B 30 LYS cc_start: 0.8320 (ptpt) cc_final: 0.8099 (ptpp) REVERT: B 73 GLU cc_start: 0.6737 (OUTLIER) cc_final: 0.6459 (tm-30) REVERT: B 91 SER cc_start: 0.8070 (m) cc_final: 0.7760 (t) REVERT: B 155 MET cc_start: 0.6513 (mmt) cc_final: 0.5791 (mmt) REVERT: B 196 TYR cc_start: 0.7383 (m-80) cc_final: 0.6993 (m-80) REVERT: B 296 ARG cc_start: 0.7787 (tpt90) cc_final: 0.7535 (mmm160) REVERT: B 349 ASP cc_start: 0.6815 (t70) cc_final: 0.6586 (t70) REVERT: B 421 TYR cc_start: 0.7660 (m-80) cc_final: 0.7052 (m-80) REVERT: B 451 VAL cc_start: 0.8381 (t) cc_final: 0.8137 (p) REVERT: B 557 MET cc_start: 0.7626 (mmp) cc_final: 0.7375 (mmp) REVERT: B 561 ILE cc_start: 0.5927 (OUTLIER) cc_final: 0.5202 (mm) REVERT: B 684 ARG cc_start: 0.7746 (ttm110) cc_final: 0.7153 (mtm180) REVERT: B 959 ARG cc_start: 0.8162 (mtp180) cc_final: 0.7688 (mtp85) REVERT: B 964 MET cc_start: 0.9013 (tmm) cc_final: 0.8631 (tmm) REVERT: B 965 MET cc_start: 0.7431 (mmt) cc_final: 0.6857 (mmt) REVERT: B 1020 TRP cc_start: 0.7689 (m100) cc_final: 0.7425 (m100) REVERT: B 1025 MET cc_start: 0.3048 (mtp) cc_final: 0.2847 (mtp) REVERT: B 1171 ARG cc_start: 0.7666 (mpp80) cc_final: 0.7179 (mpp80) REVERT: B 1192 MET cc_start: 0.4766 (mpp) cc_final: 0.3964 (mtt) REVERT: B 1292 ARG cc_start: 0.8100 (tmm160) cc_final: 0.7589 (tpt90) REVERT: C 121 ASP cc_start: 0.8253 (m-30) cc_final: 0.7997 (m-30) REVERT: C 206 LYS cc_start: 0.8758 (mmtm) cc_final: 0.8480 (mmtt) REVERT: C 235 GLU cc_start: 0.9032 (tp30) cc_final: 0.8013 (mm-30) REVERT: C 237 LYS cc_start: 0.9143 (tptp) cc_final: 0.8760 (tppt) REVERT: C 247 LEU cc_start: 0.8966 (tt) cc_final: 0.8665 (mm) REVERT: C 248 LYS cc_start: 0.9251 (tptp) cc_final: 0.8945 (tptp) REVERT: D 65 TYR cc_start: 0.7760 (p90) cc_final: 0.7375 (p90) REVERT: D 121 LYS cc_start: 0.7571 (mmtt) cc_final: 0.7253 (mmpt) REVERT: D 194 PHE cc_start: 0.7943 (t80) cc_final: 0.7664 (t80) REVERT: D 198 ARG cc_start: 0.7529 (ptt-90) cc_final: 0.6860 (ptt-90) REVERT: D 279 PHE cc_start: 0.8362 (t80) cc_final: 0.7891 (t80) REVERT: D 298 LYS cc_start: 0.9463 (pptt) cc_final: 0.9229 (pptt) REVERT: D 307 PHE cc_start: 0.9181 (t80) cc_final: 0.8966 (t80) REVERT: D 311 ASN cc_start: 0.8614 (OUTLIER) cc_final: 0.8279 (m110) REVERT: D 329 TYR cc_start: 0.7196 (t80) cc_final: 0.6738 (t80) REVERT: F 119 GLN cc_start: 0.7927 (mt0) cc_final: 0.7206 (mp10) outliers start: 36 outliers final: 30 residues processed: 405 average time/residue: 0.1910 time to fit residues: 116.5006 Evaluate side-chains 400 residues out of total 2650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 367 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 192 TRP Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 295 GLN Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 868 HIS Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 496 PHE Chi-restraints excluded: chain B residue 501 GLN Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1137 HIS Chi-restraints excluded: chain B residue 1147 PHE Chi-restraints excluded: chain B residue 1155 TRP Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 253 GLN Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 97 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 250 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 256 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 184 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 71 optimal weight: 0.2980 chunk 176 optimal weight: 8.9990 chunk 211 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 chunk 141 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 182 HIS ** A 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 ASN ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 GLN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.137548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.111753 restraints weight = 105502.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.112468 restraints weight = 63628.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.113170 restraints weight = 46082.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.113079 restraints weight = 39735.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.113279 restraints weight = 33614.304| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3792 r_free = 0.3792 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3792 r_free = 0.3792 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.6879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.333 24551 Z= 0.275 Angle : 0.929 59.200 33184 Z= 0.511 Chirality : 0.047 0.741 3686 Planarity : 0.006 0.215 4248 Dihedral : 7.332 178.639 3260 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.38 % Favored : 95.55 % Rotamer: Outliers : 1.40 % Allowed : 20.04 % Favored : 78.57 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.28 % 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: 0.10 (0.15), residues: 2947 helix: 0.88 (0.14), residues: 1352 sheet: -0.16 (0.27), residues: 368 loop : -0.70 (0.18), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B 734 TYR 0.045 0.001 TYR C 256 PHE 0.029 0.002 PHE B 102 TRP 0.060 0.002 TRP B1213 HIS 0.010 0.001 HIS B1181 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.27 (24545) covalent geometry : angle 0.92744 / 0.51 (33176) SS BOND : bond 0.00327 / 0.17 ( 1) SS BOND : angle 1.05101 / 0.70 ( 2) hydrogen bonds : bond 0.03885 / 2.54 ( 1084) hydrogen bonds : angle 4.41514 / 3.07 ( 3099) metal coordination : bond 0.00745 / 0.31 ( 4) metal coordination : angle 4.53365 / 2.62 ( 6) Misc. bond : bond 0.00013 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5961.44 seconds wall clock time: 103 minutes 17.14 seconds (6197.14 seconds total)