Starting phenix.real_space_refine on Fri Sep 19 09:44:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ga4_51173/09_2025/9ga4_51173.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ga4_51173/09_2025/9ga4_51173.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ga4_51173/09_2025/9ga4_51173.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ga4_51173/09_2025/9ga4_51173.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ga4_51173/09_2025/9ga4_51173.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ga4_51173/09_2025/9ga4_51173.map" } resolution = 3.7 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= 0.003 sd= 0.036 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 74 5.49 5 S 71 5.16 5 C 15375 2.51 5 N 4448 2.21 5 O 4928 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24900 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 912, 7031 Classifications: {'peptide': 912} Link IDs: {'CIS': 1, 'PTRANS': 44, 'TRANS': 866} Chain breaks: 4 Chain: "B" Number of atoms: 7035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 913, 7035 Classifications: {'peptide': 913} Link IDs: {'CIS': 2, 'PTRANS': 44, 'TRANS': 866} Chain breaks: 3 Chain: "C" Number of atoms: 4660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4660 Classifications: {'peptide': 589} Link IDs: {'PTRANS': 28, 'TRANS': 560} Chain: "E" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 747 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DC:plan': 1, ' DC:plan2': 1} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 748 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DC:plan': 1, ' DC:plan2': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 4675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4675 Classifications: {'peptide': 591} Link IDs: {'PTRANS': 28, 'TRANS': 562} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5608 SG CYS A 753 83.137 34.949 51.047 1.00268.99 S ATOM 5628 SG CYS A 756 84.424 36.388 47.786 1.00334.38 S ATOM 5686 SG CYS A 776 84.694 32.774 48.113 1.00234.54 S ATOM 5708 SG CYS A 779 81.248 34.423 47.755 1.00219.14 S ATOM 2033 SG CYS A 282 106.483 80.174 67.290 1.00217.09 S ATOM 2055 SG CYS A 285 105.996 78.851 63.852 1.00233.24 S ATOM 3073 SG CYS A 412 103.259 81.076 65.376 1.00246.23 S ATOM 3093 SG CYS A 415 106.612 82.667 64.594 1.00216.11 S ATOM 12548 SG CYS B 753 142.405 77.386 41.859 1.00189.33 S ATOM 12568 SG CYS B 756 140.034 75.570 39.266 1.00206.60 S ATOM 12721 SG CYS B 776 140.393 79.056 38.838 1.00232.72 S ATOM 12743 SG CYS B 779 143.473 76.745 38.396 1.00211.32 S ATOM 8926 SG CYS B 282 120.128 34.847 65.967 1.00156.87 S ATOM 8948 SG CYS B 285 122.652 36.619 64.332 1.00179.36 S ATOM 9966 SG CYS B 412 124.082 33.540 66.098 1.00153.77 S ATOM 9986 SG CYS B 415 121.871 32.968 63.205 1.00155.41 S Time building chain proxies: 6.86, per 1000 atoms: 0.28 Number of scatterers: 24900 At special positions: 0 Unit cell: (227.64, 115.08, 109.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 71 16.00 P 74 15.00 O 4928 8.00 N 4448 7.00 C 15375 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 756 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 779 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 776 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 753 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 282 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 415 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 412 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 285 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 756 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 779 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 776 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 753 " pdb=" ZN B1002 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 285 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 415 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 282 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 412 " Number of angles added : 24 5966 Ramachandran restraints generated. 2983 Oldfield, 0 Emsley, 2983 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5504 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 25 sheets defined 44.6% alpha, 9.9% beta 8 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 3.27 Creating SS restraints... Processing helix chain 'A' and resid 37 through 45 removed outlier: 3.990A pdb=" N THR A 45 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 56 Processing helix chain 'A' and resid 98 through 103 Processing helix chain 'A' and resid 104 through 116 removed outlier: 4.138A pdb=" N TYR A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 142 removed outlier: 4.290A pdb=" N GLN A 139 " --> pdb=" O GLN A 135 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL A 140 " --> pdb=" O ILE A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 174 removed outlier: 3.520A pdb=" N GLN A 173 " --> pdb=" O LYS A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 229 removed outlier: 4.374A pdb=" N ALA A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 281 removed outlier: 3.921A pdb=" N ALA A 281 " --> pdb=" O PRO A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 312 through 317 removed outlier: 3.831A pdb=" N ASN A 317 " --> pdb=" O PRO A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 336 removed outlier: 3.857A pdb=" N TYR A 323 " --> pdb=" O HIS A 319 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N MET A 327 " --> pdb=" O TYR A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 357 Processing helix chain 'A' and resid 381 through 394 Processing helix chain 'A' and resid 398 through 408 removed outlier: 4.828A pdb=" N GLU A 404 " --> pdb=" O LYS A 400 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N PHE A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET A 407 " --> pdb=" O TYR A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 431 removed outlier: 3.790A pdb=" N LEU A 425 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ALA A 426 " --> pdb=" O PRO A 422 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N VAL A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY A 431 " --> pdb=" O VAL A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 448 Processing helix chain 'A' and resid 449 through 458 removed outlier: 4.266A pdb=" N ASN A 458 " --> pdb=" O ALA A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 488 removed outlier: 3.916A pdb=" N ARG A 480 " --> pdb=" O GLU A 476 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU A 481 " --> pdb=" O ILE A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 492 Processing helix chain 'A' and resid 497 through 501 Processing helix chain 'A' and resid 502 through 518 removed outlier: 3.899A pdb=" N ARG A 510 " --> pdb=" O ALA A 506 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU A 511 " --> pdb=" O GLN A 507 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER A 517 " --> pdb=" O THR A 513 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLY A 518 " --> pdb=" O GLN A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 552 removed outlier: 3.581A pdb=" N ARG A 540 " --> pdb=" O ARG A 536 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLU A 543 " --> pdb=" O ARG A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 583 removed outlier: 3.830A pdb=" N GLY A 583 " --> pdb=" O GLU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 607 removed outlier: 3.573A pdb=" N LEU A 606 " --> pdb=" O THR A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 665 Processing helix chain 'A' and resid 667 through 675 Processing helix chain 'A' and resid 691 through 695 removed outlier: 3.602A pdb=" N LEU A 695 " --> pdb=" O LEU A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 730 Processing helix chain 'A' and resid 731 through 737 Processing helix chain 'A' and resid 785 through 790 removed outlier: 3.916A pdb=" N GLU A 790 " --> pdb=" O ARG A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 796 Processing helix chain 'A' and resid 797 through 804 Processing helix chain 'A' and resid 816 through 830 Processing helix chain 'A' and resid 839 through 843 Processing helix chain 'A' and resid 849 through 856 removed outlier: 3.836A pdb=" N SER A 855 " --> pdb=" O VAL A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 895 Processing helix chain 'A' and resid 905 through 910 Processing helix chain 'A' and resid 921 through 925 removed outlier: 3.637A pdb=" N GLY A 925 " --> pdb=" O GLY A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 940 removed outlier: 3.501A pdb=" N VAL A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 952 removed outlier: 3.929A pdb=" N VAL A 952 " --> pdb=" O PHE A 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 45 removed outlier: 3.723A pdb=" N THR B 45 " --> pdb=" O LEU B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 58 removed outlier: 4.488A pdb=" N GLU B 56 " --> pdb=" O ARG B 52 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER B 57 " --> pdb=" O ARG B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 103 removed outlier: 3.883A pdb=" N ILE B 102 " --> pdb=" O THR B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 117 removed outlier: 4.150A pdb=" N ALA B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 143 removed outlier: 4.025A pdb=" N VAL B 140 " --> pdb=" O ILE B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 174 Processing helix chain 'B' and resid 214 through 227 removed outlier: 3.792A pdb=" N ASP B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N THR B 224 " --> pdb=" O ASP B 220 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ALA B 225 " --> pdb=" O SER B 221 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN B 227 " --> pdb=" O GLU B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 249 Processing helix chain 'B' and resid 295 through 300 removed outlier: 4.081A pdb=" N VAL B 299 " --> pdb=" O PRO B 296 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL B 300 " --> pdb=" O GLU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 312 through 317 removed outlier: 4.100A pdb=" N ASN B 317 " --> pdb=" O PRO B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 336 removed outlier: 4.009A pdb=" N TYR B 323 " --> pdb=" O HIS B 319 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N MET B 327 " --> pdb=" O TYR B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 357 Processing helix chain 'B' and resid 384 through 394 removed outlier: 4.085A pdb=" N GLN B 388 " --> pdb=" O LEU B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 405 removed outlier: 4.230A pdb=" N TYR B 403 " --> pdb=" O MET B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 431 removed outlier: 4.122A pdb=" N ALA B 426 " --> pdb=" O PRO B 422 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY B 431 " --> pdb=" O VAL B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 449 through 458 Processing helix chain 'B' and resid 465 through 469 removed outlier: 3.879A pdb=" N ALA B 468 " --> pdb=" O ARG B 465 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE B 469 " --> pdb=" O GLU B 466 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 465 through 469' Processing helix chain 'B' and resid 470 through 488 removed outlier: 4.111A pdb=" N LEU B 474 " --> pdb=" O ALA B 470 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LYS B 475 " --> pdb=" O GLY B 471 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG B 480 " --> pdb=" O GLU B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 501 removed outlier: 3.571A pdb=" N LEU B 501 " --> pdb=" O ALA B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 516 Processing helix chain 'B' and resid 542 through 550 removed outlier: 3.785A pdb=" N ASP B 550 " --> pdb=" O THR B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 597 Processing helix chain 'B' and resid 602 through 607 Processing helix chain 'B' and resid 659 through 665 Processing helix chain 'B' and resid 667 through 676 Processing helix chain 'B' and resid 691 through 695 Processing helix chain 'B' and resid 713 through 719 removed outlier: 3.596A pdb=" N GLY B 719 " --> pdb=" O ALA B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 729 removed outlier: 4.095A pdb=" N LYS B 723 " --> pdb=" O GLY B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 735 removed outlier: 6.229A pdb=" N GLU B 733 " --> pdb=" O ALA B 730 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS B 735 " --> pdb=" O THR B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 745 Processing helix chain 'B' and resid 787 through 791 removed outlier: 3.511A pdb=" N GLU B 790 " --> pdb=" O GLU B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 796 Processing helix chain 'B' and resid 797 through 804 Processing helix chain 'B' and resid 805 through 810 Processing helix chain 'B' and resid 816 through 830 removed outlier: 3.912A pdb=" N TYR B 822 " --> pdb=" O GLY B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 843 removed outlier: 3.533A pdb=" N THR B 842 " --> pdb=" O PRO B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 855 Processing helix chain 'B' and resid 877 through 894 Processing helix chain 'B' and resid 904 through 911 Processing helix chain 'B' and resid 921 through 925 Processing helix chain 'B' and resid 933 through 938 Processing helix chain 'B' and resid 943 through 952 removed outlier: 3.550A pdb=" N GLU B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 952 " --> pdb=" O PHE B 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 30 Processing helix chain 'C' and resid 45 through 58 Processing helix chain 'C' and resid 67 through 82 removed outlier: 3.624A pdb=" N GLN C 73 " --> pdb=" O THR C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 132 Processing helix chain 'C' and resid 142 through 147 Processing helix chain 'C' and resid 151 through 158 removed outlier: 3.798A pdb=" N ARG C 158 " --> pdb=" O SER C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 180 Processing helix chain 'C' and resid 252 through 278 Processing helix chain 'C' and resid 279 through 300 Processing helix chain 'C' and resid 305 through 308 Processing helix chain 'C' and resid 309 through 315 Processing helix chain 'C' and resid 324 through 329 removed outlier: 3.934A pdb=" N TYR C 328 " --> pdb=" O THR C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 363 Proline residue: C 345 - end of helix Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.606A pdb=" N CYS C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 386 Processing helix chain 'C' and resid 397 through 405 Processing helix chain 'C' and resid 431 through 443 Processing helix chain 'C' and resid 444 through 446 No H-bonds generated for 'chain 'C' and resid 444 through 446' Processing helix chain 'C' and resid 455 through 469 removed outlier: 3.687A pdb=" N ALA C 459 " --> pdb=" O THR C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 494 removed outlier: 3.895A pdb=" N ARG C 485 " --> pdb=" O ASP C 481 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU C 488 " --> pdb=" O ARG C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 544 removed outlier: 3.982A pdb=" N LEU C 535 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 582 removed outlier: 3.550A pdb=" N ARG C 562 " --> pdb=" O THR C 558 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA C 581 " --> pdb=" O ALA C 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 32 removed outlier: 4.163A pdb=" N ALA D 22 " --> pdb=" O GLY D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 58 Processing helix chain 'D' and resid 69 through 84 removed outlier: 3.584A pdb=" N ALA D 73 " --> pdb=" O ASN D 69 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N GLN D 75 " --> pdb=" O THR D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 133 Processing helix chain 'D' and resid 144 through 149 Processing helix chain 'D' and resid 153 through 160 Processing helix chain 'D' and resid 171 through 182 Processing helix chain 'D' and resid 254 through 280 Processing helix chain 'D' and resid 281 through 298 removed outlier: 4.011A pdb=" N GLU D 297 " --> pdb=" O ASN D 293 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N MET D 298 " --> pdb=" O TYR D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 310 Processing helix chain 'D' and resid 311 through 317 Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.811A pdb=" N TYR D 330 " --> pdb=" O THR D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 365 Proline residue: D 347 - end of helix Processing helix chain 'D' and resid 370 through 376 removed outlier: 4.084A pdb=" N CYS D 374 " --> pdb=" O LEU D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 388 Processing helix chain 'D' and resid 399 through 407 Processing helix chain 'D' and resid 432 through 446 removed outlier: 3.742A pdb=" N ASP D 436 " --> pdb=" O GLY D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 472 removed outlier: 4.461A pdb=" N MET D 471 " --> pdb=" O TYR D 467 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY D 472 " --> pdb=" O LEU D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 496 removed outlier: 3.865A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 510 removed outlier: 4.068A pdb=" N ARG D 509 " --> pdb=" O ASN D 506 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU D 510 " --> pdb=" O LEU D 507 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 506 through 510' Processing helix chain 'D' and resid 533 through 546 removed outlier: 3.867A pdb=" N ARG D 546 " --> pdb=" O GLY D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 585 removed outlier: 3.790A pdb=" N ARG D 564 " --> pdb=" O THR D 560 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 12 removed outlier: 5.067A pdb=" N VAL A 18 " --> pdb=" O GLY A 9 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ARG A 11 " --> pdb=" O ARG A 16 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ARG A 16 " --> pdb=" O ARG A 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 86 removed outlier: 6.102A pdb=" N VAL A 84 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE A 28 " --> pdb=" O VAL A 557 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL A 572 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 31 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE A 574 " --> pdb=" O THR A 31 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 201 through 204 removed outlier: 4.160A pdb=" N ILE A 201 " --> pdb=" O VAL A 156 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL A 203 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 177 through 180 Processing sheet with id=AA5, first strand: chain 'A' and resid 642 through 645 removed outlier: 3.787A pdb=" N VAL A 630 " --> pdb=" O ARG A 688 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG A 688 " --> pdb=" O VAL A 630 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 698 through 700 removed outlier: 6.823A pdb=" N VAL A 699 " --> pdb=" O ILE A 868 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N TYR A 867 " --> pdb=" O ILE A 899 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ILE A 901 " --> pdb=" O TYR A 867 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU A 869 " --> pdb=" O ILE A 901 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 900 " --> pdb=" O THR A 650 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N SER A 651 " --> pdb=" O ILE A 915 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU A 917 " --> pdb=" O SER A 651 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR A 653 " --> pdb=" O LEU A 917 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA A 930 " --> pdb=" O ASP A 916 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 5 through 10 removed outlier: 5.278A pdb=" N ILE B 6 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N LEU B 22 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N LYS B 8 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LEU B 20 " --> pdb=" O LYS B 8 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA B 10 " --> pdb=" O VAL B 18 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 523 through 526 removed outlier: 6.043A pdb=" N VAL B 29 " --> pdb=" O VAL B 572 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 178 through 180 Processing sheet with id=AB1, first strand: chain 'B' and resid 366 through 367 removed outlier: 3.526A pdb=" N TYR B 366 " --> pdb=" O ARG B 374 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 626 through 632 removed outlier: 5.069A pdb=" N THR B 628 " --> pdb=" O PHE B 644 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N PHE B 644 " --> pdb=" O THR B 628 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N VAL B 630 " --> pdb=" O VAL B 642 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL B 642 " --> pdb=" O VAL B 630 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 698 through 701 removed outlier: 6.478A pdb=" N VAL B 699 " --> pdb=" O ILE B 868 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N TYR B 867 " --> pdb=" O ILE B 899 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ILE B 901 " --> pdb=" O TYR B 867 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LEU B 869 " --> pdb=" O ILE B 901 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP B 913 " --> pdb=" O LEU B 649 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ILE B 914 " --> pdb=" O GLN B 931 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLN B 931 " --> pdb=" O ILE B 914 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASP B 916 " --> pdb=" O VAL B 929 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 138 through 141 removed outlier: 6.228A pdb=" N THR C 61 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ALA C 141 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N VAL C 63 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LEU C 62 " --> pdb=" O VAL C 336 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ASP C 338 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N MET C 64 " --> pdb=" O ASP C 338 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU C 335 " --> pdb=" O VAL C 390 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU C 392 " --> pdb=" O LEU C 335 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ILE C 337 " --> pdb=" O LEU C 392 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL C 409 " --> pdb=" O VAL C 37 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 94 through 98 removed outlier: 6.298A pdb=" N SER C 115 " --> pdb=" O ASP C 95 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N TYR C 97 " --> pdb=" O ASP C 113 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ASP C 113 " --> pdb=" O TYR C 97 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 101 through 103 Processing sheet with id=AB7, first strand: chain 'C' and resid 160 through 163 Processing sheet with id=AB8, first strand: chain 'C' and resid 183 through 184 removed outlier: 3.582A pdb=" N PHE C 194 " --> pdb=" O THR C 183 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 422 through 426 removed outlier: 6.486A pdb=" N LYS C 422 " --> pdb=" O VAL C 550 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N MET C 552 " --> pdb=" O LYS C 422 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL C 424 " --> pdb=" O MET C 552 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ARG C 448 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ALA C 519 " --> pdb=" O ARG C 448 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU C 450 " --> pdb=" O ALA C 519 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU C 521 " --> pdb=" O LEU C 450 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N VAL C 449 " --> pdb=" O LEU C 500 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 37 through 38 removed outlier: 3.805A pdb=" N VAL D 392 " --> pdb=" O LEU D 337 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU D 64 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ASP D 340 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N MET D 66 " --> pdb=" O ASP D 340 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR D 63 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ALA D 143 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL D 65 " --> pdb=" O ALA D 143 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ALA D 88 " --> pdb=" O VAL D 140 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N VAL D 142 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLU D 90 " --> pdb=" O VAL D 142 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 40 through 41 Processing sheet with id=AC3, first strand: chain 'D' and resid 99 through 100 Processing sheet with id=AC4, first strand: chain 'D' and resid 104 through 105 Processing sheet with id=AC5, first strand: chain 'D' and resid 163 through 165 Processing sheet with id=AC6, first strand: chain 'D' and resid 185 through 186 removed outlier: 7.299A pdb=" N THR D 185 " --> pdb=" O PHE D 196 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N VAL D 198 " --> pdb=" O THR D 185 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N PHE D 219 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ILE D 223 " --> pdb=" O PHE D 219 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N LEU D 226 " --> pdb=" O GLN D 239 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLN D 239 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N TYR D 228 " --> pdb=" O ILE D 237 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 424 through 428 removed outlier: 6.313A pdb=" N VAL D 520 " --> pdb=" O HIS D 553 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N TYR D 555 " --> pdb=" O VAL D 520 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE D 522 " --> pdb=" O TYR D 555 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU D 452 " --> pdb=" O ALA D 521 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N LEU D 523 " --> pdb=" O LEU D 452 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N THR D 454 " --> pdb=" O LEU D 523 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL D 451 " --> pdb=" O LEU D 502 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N GLY D 504 " --> pdb=" O VAL D 451 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL D 453 " --> pdb=" O GLY D 504 " (cutoff:3.500A) 878 hydrogen bonds defined for protein. 2445 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 19 hydrogen bonds 26 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 5.52 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.25: 4063 1.25 - 1.50: 10928 1.50 - 1.75: 10373 1.75 - 2.00: 114 2.00 - 2.25: 1 Bond restraints: 25479 Sorted by residual: bond pdb=" N PRO D 16 " pdb=" CD PRO D 16 " ideal model delta sigma weight residual 1.473 2.251 -0.778 1.40e-02 5.10e+03 3.09e+03 bond pdb=" CB PRO A 119 " pdb=" CG PRO A 119 " ideal model delta sigma weight residual 1.492 0.999 0.493 5.00e-02 4.00e+02 9.71e+01 bond pdb=" CG PRO A 119 " pdb=" CD PRO A 119 " ideal model delta sigma weight residual 1.503 1.226 0.277 3.40e-02 8.65e+02 6.66e+01 bond pdb=" C THR A 118 " pdb=" N PRO A 119 " ideal model delta sigma weight residual 1.332 1.283 0.050 8.90e-03 1.26e+04 3.14e+01 bond pdb=" CG PRO D 16 " pdb=" CD PRO D 16 " ideal model delta sigma weight residual 1.503 1.374 0.129 3.40e-02 8.65e+02 1.43e+01 ... (remaining 25474 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.77: 34830 14.77 - 29.54: 1 29.54 - 44.31: 3 44.31 - 59.08: 0 59.08 - 73.86: 1 Bond angle restraints: 34835 Sorted by residual: angle pdb=" CA PRO D 16 " pdb=" N PRO D 16 " pdb=" CD PRO D 16 " ideal model delta sigma weight residual 112.00 75.35 36.65 1.40e+00 5.10e-01 6.85e+02 angle pdb=" CB PRO A 119 " pdb=" CG PRO A 119 " pdb=" CD PRO A 119 " ideal model delta sigma weight residual 106.10 179.96 -73.86 3.20e+00 9.77e-02 5.33e+02 angle pdb=" N PRO D 16 " pdb=" CD PRO D 16 " pdb=" CG PRO D 16 " ideal model delta sigma weight residual 103.20 73.53 29.67 1.50e+00 4.44e-01 3.91e+02 angle pdb=" N PRO A 119 " pdb=" CD PRO A 119 " pdb=" CG PRO A 119 " ideal model delta sigma weight residual 103.20 75.29 27.91 1.50e+00 4.44e-01 3.46e+02 angle pdb=" CA PRO A 119 " pdb=" CB PRO A 119 " pdb=" CG PRO A 119 " ideal model delta sigma weight residual 104.50 74.93 29.57 1.90e+00 2.77e-01 2.42e+02 ... (remaining 34830 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.27: 14408 34.27 - 68.54: 838 68.54 - 102.81: 35 102.81 - 137.08: 1 137.08 - 171.35: 5 Dihedral angle restraints: 15287 sinusoidal: 6685 harmonic: 8602 Sorted by residual: dihedral pdb=" N PRO A 119 " pdb=" CG PRO A 119 " pdb=" CD PRO A 119 " pdb=" CB PRO A 119 " ideal model delta sinusoidal sigma weight residual 30.00 174.86 -144.86 1 1.50e+01 4.44e-03 7.76e+01 dihedral pdb=" CA PRO A 119 " pdb=" CB PRO A 119 " pdb=" CG PRO A 119 " pdb=" CD PRO A 119 " ideal model delta sinusoidal sigma weight residual 38.00 159.09 -121.09 1 2.00e+01 2.50e-03 3.64e+01 dihedral pdb=" CA ILE A 816 " pdb=" C ILE A 816 " pdb=" N ALA A 817 " pdb=" CA ALA A 817 " ideal model delta harmonic sigma weight residual -180.00 -156.88 -23.12 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 15284 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 3527 0.074 - 0.147: 418 0.147 - 0.221: 13 0.221 - 0.295: 1 0.295 - 0.369: 2 Chirality restraints: 3961 Sorted by residual: chirality pdb=" CG LEU A 109 " pdb=" CB LEU A 109 " pdb=" CD1 LEU A 109 " pdb=" CD2 LEU A 109 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" CB ILE B 531 " pdb=" CA ILE B 531 " pdb=" CG1 ILE B 531 " pdb=" CG2 ILE B 531 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CB ILE A 232 " pdb=" CA ILE A 232 " pdb=" CG1 ILE A 232 " pdb=" CG2 ILE A 232 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 3958 not shown) Planarity restraints: 4330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 15 " -0.197 5.00e-02 4.00e+02 2.24e-01 8.00e+01 pdb=" N PRO D 16 " 0.379 5.00e-02 4.00e+02 pdb=" CA PRO D 16 " -0.113 5.00e-02 4.00e+02 pdb=" CD PRO D 16 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 241 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.86e+00 pdb=" CD GLU A 241 " -0.045 2.00e-02 2.50e+03 pdb=" OE1 GLU A 241 " 0.016 2.00e-02 2.50e+03 pdb=" OE2 GLU A 241 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 302 " 0.038 5.00e-02 4.00e+02 5.74e-02 5.27e+00 pdb=" N PRO A 303 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 303 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 303 " 0.031 5.00e-02 4.00e+02 ... (remaining 4327 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5447 2.79 - 3.32: 25664 3.32 - 3.84: 45289 3.84 - 4.37: 51919 4.37 - 4.90: 81667 Nonbonded interactions: 209986 Sorted by model distance: nonbonded pdb=" OD1 ASP B 696 " pdb=" NH1 ARG B 864 " model vdw 2.261 3.120 nonbonded pdb=" N2 DG E 22 " pdb=" N6 DA F 25 " model vdw 2.273 2.560 nonbonded pdb=" O GLU C 460 " pdb=" OD1 ASP C 464 " model vdw 2.292 3.040 nonbonded pdb=" O PRO C 19 " pdb=" OD1 ASP C 23 " model vdw 2.312 3.040 nonbonded pdb=" OH TYR B 108 " pdb=" CG1 VAL B 473 " model vdw 2.329 3.460 ... (remaining 209981 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 60 or resid 75 through 121 or resid 133 through \ 251 or resid 267 through 1002)) selection = (chain 'B' and (resid 1 through 432 or resid 440 through 762 or resid 774 throug \ h 1002)) } ncs_group { reference = chain 'C' selection = (chain 'D' and resid 3 through 591) } ncs_group { reference = (chain 'E' and (resid 1 through 23 or resid 25 through 37)) selection = (chain 'F' and (resid 1 through 23 or resid 25 through 37)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 7.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 31.670 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.070 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:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5276 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 : 0.007 0.778 25495 Z= 0.387 Angle : 0.908 73.856 34859 Z= 0.456 Chirality : 0.045 0.369 3961 Planarity : 0.006 0.224 4330 Dihedral : 19.303 171.349 9783 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.97 % Favored : 94.00 % Rotamer: Outliers : 0.16 % Allowed : 29.71 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.15), residues: 2983 helix: -0.30 (0.15), residues: 1126 sheet: -0.12 (0.28), residues: 336 loop : -1.57 (0.16), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG B 864 TYR 0.012 0.001 TYR C 226 PHE 0.026 0.001 PHE B 324 TRP 0.016 0.001 TRP D 54 HIS 0.005 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00680 (25479) covalent geometry : angle 0.89318 (34835) hydrogen bonds : bond 0.13063 ( 897) hydrogen bonds : angle 6.87379 ( 2471) metal coordination : bond 0.00719 ( 16) metal coordination : angle 6.19121 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5966 Ramachandran restraints generated. 2983 Oldfield, 0 Emsley, 2983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5966 Ramachandran restraints generated. 2983 Oldfield, 0 Emsley, 2983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 150 time to evaluate : 0.994 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 outliers start: 4 outliers final: 4 residues processed: 150 average time/residue: 0.2057 time to fit residues: 47.3149 Evaluate side-chains 154 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 150 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain D residue 410 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 30.0000 chunk 298 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 GLN A 185 HIS ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 HIS A 703 GLN ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 792 HIS B 94 ASN B 246 HIS B 458 ASN ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 792 HIS C 58 GLN C 98 GLN ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 GLN D 14 HIS ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN D 362 ASN ** D 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 449 GLN D 577 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.087253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.077084 restraints weight = 238088.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.077801 restraints weight = 206967.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.078179 restraints weight = 173791.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.078672 restraints weight = 156916.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.078766 restraints weight = 140534.814| |-----------------------------------------------------------------------------| r_work (final): 0.4237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5703 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.130 25495 Z= 0.227 Angle : 0.787 24.228 34859 Z= 0.399 Chirality : 0.047 0.231 3961 Planarity : 0.006 0.103 4330 Dihedral : 16.430 169.561 4176 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 30.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.98 % Favored : 91.99 % Rotamer: Outliers : 5.41 % Allowed : 26.21 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.15), residues: 2983 helix: -0.58 (0.15), residues: 1138 sheet: -0.65 (0.28), residues: 331 loop : -1.61 (0.16), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 369 TYR 0.023 0.002 TYR A 370 PHE 0.030 0.002 PHE A 728 TRP 0.011 0.002 TRP D 54 HIS 0.007 0.002 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00503 (25479) covalent geometry : angle 0.76231 (34835) hydrogen bonds : bond 0.05935 ( 897) hydrogen bonds : angle 6.09635 ( 2471) metal coordination : bond 0.01179 ( 16) metal coordination : angle 7.50135 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5966 Ramachandran restraints generated. 2983 Oldfield, 0 Emsley, 2983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5966 Ramachandran restraints generated. 2983 Oldfield, 0 Emsley, 2983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 150 time to evaluate : 0.957 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: A 1 MET cc_start: 0.2582 (mmt) cc_final: 0.2361 (mmt) REVERT: A 104 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7275 (pm20) REVERT: A 113 TYR cc_start: 0.6581 (OUTLIER) cc_final: 0.4810 (m-80) REVERT: A 328 MET cc_start: 0.0108 (mmt) cc_final: -0.0130 (mmt) REVERT: A 702 ASP cc_start: 0.6639 (m-30) cc_final: 0.6361 (t0) REVERT: A 790 GLU cc_start: 0.6023 (mm-30) cc_final: 0.5648 (mm-30) REVERT: B 327 MET cc_start: 0.3234 (mmt) cc_final: 0.2827 (ptt) REVERT: B 391 MET cc_start: 0.3839 (mpp) cc_final: 0.3342 (mpp) REVERT: B 617 ILE cc_start: 0.7431 (tp) cc_final: 0.6785 (tp) REVERT: D 510 GLU cc_start: 0.2806 (OUTLIER) cc_final: 0.1558 (pm20) REVERT: D 554 MET cc_start: 0.8247 (mpp) cc_final: 0.6264 (tpt) outliers start: 136 outliers final: 66 residues processed: 271 average time/residue: 0.1734 time to fit residues: 75.1245 Evaluate side-chains 204 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 135 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 746 PHE Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 880 ASP Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 933 THR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 458 ASN Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 658 SER Chi-restraints excluded: chain B residue 660 LYS Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 702 ASP Chi-restraints excluded: chain B residue 706 ILE Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 851 VAL Chi-restraints excluded: chain B residue 857 LEU Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 933 THR Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 475 TYR Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 356 ASP Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 582 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 45 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 105 optimal weight: 20.0000 chunk 58 optimal weight: 8.9990 chunk 195 optimal weight: 0.9990 chunk 217 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 301 optimal weight: 9.9990 chunk 192 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 411 GLN ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.086997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.076444 restraints weight = 237138.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.077279 restraints weight = 205920.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.077679 restraints weight = 171466.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.077969 restraints weight = 154145.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.078509 restraints weight = 143097.537| |-----------------------------------------------------------------------------| r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5705 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 25495 Z= 0.167 Angle : 0.710 14.865 34859 Z= 0.356 Chirality : 0.045 0.223 3961 Planarity : 0.005 0.081 4330 Dihedral : 16.370 169.580 4165 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 26.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.34 % Favored : 92.62 % Rotamer: Outliers : 5.09 % Allowed : 26.97 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.15), residues: 2983 helix: -0.48 (0.15), residues: 1135 sheet: -0.50 (0.29), residues: 315 loop : -1.61 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 618 TYR 0.025 0.002 TYR B 108 PHE 0.017 0.002 PHE B 149 TRP 0.009 0.002 TRP C 379 HIS 0.005 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00368 (25479) covalent geometry : angle 0.68048 (34835) hydrogen bonds : bond 0.05098 ( 897) hydrogen bonds : angle 5.87699 ( 2471) metal coordination : bond 0.01237 ( 16) metal coordination : angle 7.74683 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5966 Ramachandran restraints generated. 2983 Oldfield, 0 Emsley, 2983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5966 Ramachandran restraints generated. 2983 Oldfield, 0 Emsley, 2983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 149 time to evaluate : 0.946 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: A 104 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7128 (pm20) REVERT: A 113 TYR cc_start: 0.6611 (OUTLIER) cc_final: 0.4834 (m-80) REVERT: A 152 LEU cc_start: 0.1330 (OUTLIER) cc_final: -0.0133 (mp) REVERT: A 294 VAL cc_start: 0.2741 (OUTLIER) cc_final: 0.2442 (p) REVERT: A 501 LEU cc_start: 0.5961 (OUTLIER) cc_final: 0.5705 (tp) REVERT: A 702 ASP cc_start: 0.6467 (m-30) cc_final: 0.6187 (t70) REVERT: B 294 VAL cc_start: 0.6207 (OUTLIER) cc_final: 0.5982 (p) REVERT: B 327 MET cc_start: 0.3246 (mmt) cc_final: 0.2798 (ptt) REVERT: B 328 MET cc_start: 0.2826 (ppp) cc_final: 0.2248 (ppp) REVERT: B 409 ASP cc_start: 0.7544 (t0) cc_final: 0.7127 (m-30) REVERT: C 200 THR cc_start: 0.2513 (OUTLIER) cc_final: 0.2092 (m) REVERT: D 75 GLN cc_start: 0.9127 (OUTLIER) cc_final: 0.8634 (pm20) REVERT: D 83 MET cc_start: 0.7111 (mpp) cc_final: 0.6870 (mpp) REVERT: D 510 GLU cc_start: 0.3144 (OUTLIER) cc_final: 0.1877 (pm20) outliers start: 128 outliers final: 73 residues processed: 264 average time/residue: 0.1843 time to fit residues: 76.6345 Evaluate side-chains 219 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 137 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 746 PHE Chi-restraints excluded: chain A residue 783 ARG Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 880 ASP Chi-restraints excluded: chain A residue 933 THR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 376 TYR Chi-restraints excluded: chain B residue 412 CYS Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 658 SER Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 945 THR Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 457 LYS Chi-restraints excluded: chain C residue 475 TYR Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 356 ASP Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 582 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 73 optimal weight: 9.9990 chunk 189 optimal weight: 5.9990 chunk 150 optimal weight: 0.0040 chunk 271 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 chunk 246 optimal weight: 8.9990 chunk 273 optimal weight: 7.9990 chunk 225 optimal weight: 30.0000 chunk 241 optimal weight: 10.0000 chunk 171 optimal weight: 6.9990 chunk 230 optimal weight: 5.9990 overall best weight: 3.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 677 ASN ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.085024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.074408 restraints weight = 239396.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.075157 restraints weight = 208971.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.075539 restraints weight = 177056.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.076040 restraints weight = 159624.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.076450 restraints weight = 144453.528| |-----------------------------------------------------------------------------| r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5857 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 25495 Z= 0.195 Angle : 0.746 17.389 34859 Z= 0.376 Chirality : 0.047 0.273 3961 Planarity : 0.005 0.062 4330 Dihedral : 16.492 171.340 4165 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 30.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.85 % Favored : 91.12 % Rotamer: Outliers : 6.32 % Allowed : 26.77 % Favored : 66.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.15), residues: 2983 helix: -0.58 (0.15), residues: 1136 sheet: -0.67 (0.29), residues: 319 loop : -1.63 (0.16), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 369 TYR 0.023 0.002 TYR B 108 PHE 0.021 0.002 PHE A 337 TRP 0.009 0.002 TRP A 343 HIS 0.006 0.002 HIS D 250 Details of bonding type rmsd covalent geometry : bond 0.00428 (25479) covalent geometry : angle 0.71659 (34835) hydrogen bonds : bond 0.05571 ( 897) hydrogen bonds : angle 5.97820 ( 2471) metal coordination : bond 0.00958 ( 16) metal coordination : angle 7.87128 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5966 Ramachandran restraints generated. 2983 Oldfield, 0 Emsley, 2983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5966 Ramachandran restraints generated. 2983 Oldfield, 0 Emsley, 2983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 143 time to evaluate : 1.023 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: A 104 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7198 (pm20) REVERT: A 113 TYR cc_start: 0.6547 (OUTLIER) cc_final: 0.4588 (m-80) REVERT: A 294 VAL cc_start: 0.3346 (OUTLIER) cc_final: 0.2998 (p) REVERT: A 399 MET cc_start: 0.3316 (tmm) cc_final: 0.3083 (tmm) REVERT: A 634 GLU cc_start: 0.2746 (OUTLIER) cc_final: 0.1782 (tt0) REVERT: A 702 ASP cc_start: 0.6540 (m-30) cc_final: 0.6286 (t70) REVERT: B 109 LEU cc_start: 0.7970 (mm) cc_final: 0.7412 (tt) REVERT: B 327 MET cc_start: 0.3432 (mmt) cc_final: 0.3201 (ptt) REVERT: B 366 TYR cc_start: 0.7325 (m-80) cc_final: 0.7072 (m-80) REVERT: B 566 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7861 (pt0) REVERT: B 821 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8234 (ptt180) REVERT: B 873 THR cc_start: 0.7158 (OUTLIER) cc_final: 0.6936 (p) REVERT: C 147 TYR cc_start: 0.2315 (OUTLIER) cc_final: 0.2085 (m-80) REVERT: C 200 THR cc_start: 0.2479 (OUTLIER) cc_final: 0.2038 (m) REVERT: D 268 GLU cc_start: -0.3091 (OUTLIER) cc_final: -0.3740 (mm-30) REVERT: D 451 VAL cc_start: 0.9155 (t) cc_final: 0.8805 (t) REVERT: D 510 GLU cc_start: 0.3066 (OUTLIER) cc_final: 0.1915 (pm20) REVERT: D 512 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9115 (mm) REVERT: D 524 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.8007 (t0) REVERT: D 554 MET cc_start: 0.8325 (mpp) cc_final: 0.6500 (tpt) outliers start: 159 outliers final: 103 residues processed: 285 average time/residue: 0.1762 time to fit residues: 79.1377 Evaluate side-chains 252 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 136 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 746 PHE Chi-restraints excluded: chain A residue 783 ARG Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 864 ARG Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 880 ASP Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 933 THR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 376 TYR Chi-restraints excluded: chain B residue 412 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 566 GLU Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 658 SER Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 700 ARG Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 702 ASP Chi-restraints excluded: chain B residue 706 ILE Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 821 ARG Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 857 LEU Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 940 VAL Chi-restraints excluded: chain B residue 945 THR Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 448 ARG Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 457 LYS Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 475 TYR Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 356 ASP Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 524 ASP Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 582 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 204 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 222 optimal weight: 9.9990 chunk 252 optimal weight: 0.9990 chunk 229 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 244 optimal weight: 10.0000 chunk 273 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 535 GLN ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.085264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.074575 restraints weight = 238766.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.075340 restraints weight = 211166.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.075709 restraints weight = 180330.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.076265 restraints weight = 162392.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.076432 restraints weight = 145591.545| |-----------------------------------------------------------------------------| r_work (final): 0.4197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5835 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 25495 Z= 0.167 Angle : 0.718 13.240 34859 Z= 0.362 Chirality : 0.046 0.338 3961 Planarity : 0.005 0.063 4330 Dihedral : 16.544 170.524 4165 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 28.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.98 % Favored : 91.99 % Rotamer: Outliers : 6.01 % Allowed : 27.96 % Favored : 66.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.15), residues: 2983 helix: -0.57 (0.15), residues: 1134 sheet: -0.65 (0.29), residues: 307 loop : -1.62 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 486 TYR 0.018 0.002 TYR A 370 PHE 0.021 0.002 PHE B 149 TRP 0.009 0.002 TRP B 913 HIS 0.006 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00374 (25479) covalent geometry : angle 0.69411 (34835) hydrogen bonds : bond 0.05151 ( 897) hydrogen bonds : angle 5.91832 ( 2471) metal coordination : bond 0.00796 ( 16) metal coordination : angle 7.10688 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5966 Ramachandran restraints generated. 2983 Oldfield, 0 Emsley, 2983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5966 Ramachandran restraints generated. 2983 Oldfield, 0 Emsley, 2983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 148 time to evaluate : 0.936 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: A 104 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7179 (pm20) REVERT: A 113 TYR cc_start: 0.6587 (OUTLIER) cc_final: 0.4470 (m-80) REVERT: A 152 LEU cc_start: 0.1344 (OUTLIER) cc_final: -0.0166 (mp) REVERT: A 294 VAL cc_start: 0.3396 (OUTLIER) cc_final: 0.3061 (p) REVERT: A 399 MET cc_start: 0.3400 (tmm) cc_final: 0.3170 (tmm) REVERT: A 612 ILE cc_start: 0.2661 (OUTLIER) cc_final: 0.2300 (mm) REVERT: A 634 GLU cc_start: 0.3031 (OUTLIER) cc_final: 0.1844 (tt0) REVERT: A 804 MET cc_start: 0.4872 (tpt) cc_final: 0.4119 (tpt) REVERT: A 864 ARG cc_start: 0.5506 (OUTLIER) cc_final: 0.5256 (tmm160) REVERT: B 327 MET cc_start: 0.3468 (mmt) cc_final: 0.3240 (ptt) REVERT: B 366 TYR cc_start: 0.7282 (m-80) cc_final: 0.7015 (m-80) REVERT: B 566 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7885 (pt0) REVERT: C 81 MET cc_start: 0.7024 (tmm) cc_final: 0.6348 (ppp) REVERT: C 200 THR cc_start: 0.2524 (OUTLIER) cc_final: 0.2168 (m) REVERT: D 268 GLU cc_start: -0.3187 (OUTLIER) cc_final: -0.3803 (mm-30) REVERT: D 483 ASP cc_start: 0.9240 (OUTLIER) cc_final: 0.9039 (t70) REVERT: D 510 GLU cc_start: 0.3513 (OUTLIER) cc_final: 0.2224 (pm20) REVERT: D 512 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9155 (mm) REVERT: D 554 MET cc_start: 0.8333 (mpp) cc_final: 0.6474 (tpt) outliers start: 151 outliers final: 103 residues processed: 286 average time/residue: 0.1845 time to fit residues: 82.1402 Evaluate side-chains 256 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 140 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 680 ARG Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 746 PHE Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 783 ARG Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 864 ARG Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 880 ASP Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 931 GLN Chi-restraints excluded: chain A residue 933 THR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 376 TYR Chi-restraints excluded: chain B residue 412 CYS Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 566 GLU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 658 SER Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 857 LEU Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 940 VAL Chi-restraints excluded: chain B residue 945 THR Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain C residue 448 ARG Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 457 LYS Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 475 TYR Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 127 HIS Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 339 ILE Chi-restraints excluded: chain D residue 356 ASP Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 582 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 55 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 227 optimal weight: 7.9990 chunk 53 optimal weight: 20.0000 chunk 45 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 chunk 37 optimal weight: 20.0000 chunk 271 optimal weight: 3.9990 chunk 222 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 256 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 553 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.083859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.073262 restraints weight = 238878.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.073988 restraints weight = 211018.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.074385 restraints weight = 180000.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.074923 restraints weight = 161706.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.075047 restraints weight = 143896.917| |-----------------------------------------------------------------------------| r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5914 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 25495 Z= 0.182 Angle : 0.752 14.071 34859 Z= 0.377 Chirality : 0.047 0.327 3961 Planarity : 0.005 0.056 4330 Dihedral : 16.628 171.590 4165 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 31.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.29 % Favored : 90.68 % Rotamer: Outliers : 6.68 % Allowed : 28.76 % Favored : 64.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.15), residues: 2983 helix: -0.65 (0.15), residues: 1129 sheet: -0.89 (0.28), residues: 315 loop : -1.70 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 369 TYR 0.017 0.002 TYR A 370 PHE 0.022 0.002 PHE B 149 TRP 0.010 0.002 TRP B 913 HIS 0.006 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00406 (25479) covalent geometry : angle 0.72458 (34835) hydrogen bonds : bond 0.05397 ( 897) hydrogen bonds : angle 5.97015 ( 2471) metal coordination : bond 0.00878 ( 16) metal coordination : angle 7.70093 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5966 Ramachandran restraints generated. 2983 Oldfield, 0 Emsley, 2983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5966 Ramachandran restraints generated. 2983 Oldfield, 0 Emsley, 2983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 143 time to evaluate : 0.868 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: A 104 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7107 (pm20) REVERT: A 113 TYR cc_start: 0.6473 (OUTLIER) cc_final: 0.4352 (m-80) REVERT: A 152 LEU cc_start: 0.1561 (OUTLIER) cc_final: 0.0502 (mt) REVERT: A 294 VAL cc_start: 0.3739 (OUTLIER) cc_final: 0.3433 (p) REVERT: A 612 ILE cc_start: 0.2753 (OUTLIER) cc_final: 0.2365 (mm) REVERT: A 634 GLU cc_start: 0.3201 (OUTLIER) cc_final: 0.2015 (tt0) REVERT: A 722 ASP cc_start: -0.0828 (OUTLIER) cc_final: -0.1755 (m-30) REVERT: A 804 MET cc_start: 0.4936 (tpt) cc_final: 0.4119 (tpt) REVERT: B 1 MET cc_start: 0.6565 (pmm) cc_final: 0.4758 (ppp) REVERT: B 327 MET cc_start: 0.3596 (mmt) cc_final: 0.3169 (ptt) REVERT: B 419 ARG cc_start: 0.5789 (OUTLIER) cc_final: 0.5277 (mmt-90) REVERT: B 566 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7900 (pt0) REVERT: B 821 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8410 (ptt180) REVERT: B 873 THR cc_start: 0.7207 (OUTLIER) cc_final: 0.6997 (p) REVERT: C 81 MET cc_start: 0.6992 (tmm) cc_final: 0.6399 (ppp) REVERT: C 200 THR cc_start: 0.2429 (OUTLIER) cc_final: 0.1993 (m) REVERT: C 309 TYR cc_start: 0.6692 (OUTLIER) cc_final: 0.6182 (m-80) REVERT: C 530 ARG cc_start: 0.4727 (OUTLIER) cc_final: 0.4440 (tpp80) REVERT: D 268 GLU cc_start: -0.3262 (OUTLIER) cc_final: -0.3815 (mm-30) REVERT: D 483 ASP cc_start: 0.9245 (OUTLIER) cc_final: 0.9032 (t70) REVERT: D 510 GLU cc_start: 0.3469 (OUTLIER) cc_final: 0.2201 (pm20) REVERT: D 512 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9134 (mm) REVERT: D 554 MET cc_start: 0.8439 (mpp) cc_final: 0.6662 (tpt) outliers start: 168 outliers final: 117 residues processed: 294 average time/residue: 0.1697 time to fit residues: 78.2160 Evaluate side-chains 273 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 138 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 746 PHE Chi-restraints excluded: chain A residue 776 CYS Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 783 ARG Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 864 ARG Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 880 ASP Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 931 GLN Chi-restraints excluded: chain A residue 933 THR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 227 ASN Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 351 ARG Chi-restraints excluded: chain B residue 376 TYR Chi-restraints excluded: chain B residue 412 CYS Chi-restraints excluded: chain B residue 419 ARG Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 566 GLU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 658 SER Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 702 ASP Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 798 VAL Chi-restraints excluded: chain B residue 821 ARG Chi-restraints excluded: chain B residue 857 LEU Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 945 THR Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 309 TYR Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain C residue 448 ARG Chi-restraints excluded: chain C residue 457 LYS Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 475 TYR Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 530 ARG Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 356 ASP Chi-restraints excluded: chain D residue 388 ILE Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 582 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 298 optimal weight: 8.9990 chunk 227 optimal weight: 0.9990 chunk 98 optimal weight: 0.3980 chunk 7 optimal weight: 20.0000 chunk 121 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 208 optimal weight: 3.9990 chunk 294 optimal weight: 0.1980 chunk 262 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN ** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.087170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.076533 restraints weight = 234303.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.077315 restraints weight = 205029.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.077702 restraints weight = 173675.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.078042 restraints weight = 155315.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.078451 restraints weight = 143556.549| |-----------------------------------------------------------------------------| r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5704 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25495 Z= 0.132 Angle : 0.701 13.712 34859 Z= 0.350 Chirality : 0.046 0.335 3961 Planarity : 0.005 0.061 4330 Dihedral : 16.435 170.311 4165 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 22.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.97 % Favored : 92.99 % Rotamer: Outliers : 4.42 % Allowed : 30.71 % Favored : 64.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.15), residues: 2983 helix: -0.42 (0.15), residues: 1129 sheet: -0.69 (0.28), residues: 321 loop : -1.65 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 486 TYR 0.016 0.001 TYR B 108 PHE 0.019 0.001 PHE B 149 TRP 0.017 0.002 TRP C 379 HIS 0.006 0.001 HIS C 125 Details of bonding type rmsd covalent geometry : bond 0.00293 (25479) covalent geometry : angle 0.68174 (34835) hydrogen bonds : bond 0.04434 ( 897) hydrogen bonds : angle 5.66844 ( 2471) metal coordination : bond 0.00694 ( 16) metal coordination : angle 6.24391 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5966 Ramachandran restraints generated. 2983 Oldfield, 0 Emsley, 2983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5966 Ramachandran restraints generated. 2983 Oldfield, 0 Emsley, 2983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 149 time to evaluate : 0.996 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: A 1 MET cc_start: 0.2754 (mmt) cc_final: 0.0575 (ppp) REVERT: A 104 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7038 (pm20) REVERT: A 113 TYR cc_start: 0.6340 (OUTLIER) cc_final: 0.4227 (m-80) REVERT: A 294 VAL cc_start: 0.3183 (OUTLIER) cc_final: 0.2880 (p) REVERT: A 612 ILE cc_start: 0.2581 (OUTLIER) cc_final: 0.2320 (mm) REVERT: A 634 GLU cc_start: 0.2083 (OUTLIER) cc_final: 0.0848 (tt0) REVERT: A 672 LEU cc_start: 0.7481 (mp) cc_final: 0.7163 (mt) REVERT: A 804 MET cc_start: 0.4636 (tpt) cc_final: 0.3941 (tpt) REVERT: B 1 MET cc_start: 0.6476 (pmm) cc_final: 0.4731 (ppp) REVERT: B 327 MET cc_start: 0.3527 (mmt) cc_final: 0.3241 (ptt) REVERT: B 366 TYR cc_start: 0.7264 (m-80) cc_final: 0.6956 (m-80) REVERT: B 391 MET cc_start: 0.3531 (mpp) cc_final: 0.2914 (mpp) REVERT: B 566 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7881 (pt0) REVERT: B 637 LEU cc_start: 0.8613 (mm) cc_final: 0.8215 (mt) REVERT: B 873 THR cc_start: 0.7200 (OUTLIER) cc_final: 0.6956 (p) REVERT: C 200 THR cc_start: 0.2257 (OUTLIER) cc_final: 0.1767 (m) REVERT: D 268 GLU cc_start: -0.3263 (OUTLIER) cc_final: -0.3942 (mm-30) REVERT: D 510 GLU cc_start: 0.3386 (OUTLIER) cc_final: 0.1834 (pm20) REVERT: D 554 MET cc_start: 0.8397 (mpp) cc_final: 0.6621 (tpt) outliers start: 111 outliers final: 83 residues processed: 250 average time/residue: 0.1868 time to fit residues: 73.1196 Evaluate side-chains 232 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 139 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 776 CYS Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 783 ARG Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 864 ARG Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 911 SER Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 376 TYR Chi-restraints excluded: chain B residue 412 CYS Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 566 GLU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 779 CYS Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 945 THR Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 457 LYS Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 475 TYR Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 127 HIS Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 165 LYS Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 339 ILE Chi-restraints excluded: chain D residue 356 ASP Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 582 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 99 optimal weight: 8.9990 chunk 163 optimal weight: 0.9980 chunk 304 optimal weight: 7.9990 chunk 210 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 230 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.083915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.073283 restraints weight = 236848.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.074083 restraints weight = 208757.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.074450 restraints weight = 176946.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.074831 restraints weight = 157892.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.075306 restraints weight = 145144.755| |-----------------------------------------------------------------------------| r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5887 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 25495 Z= 0.186 Angle : 0.761 14.134 34859 Z= 0.382 Chirality : 0.047 0.343 3961 Planarity : 0.005 0.066 4330 Dihedral : 16.537 172.030 4165 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 31.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.32 % Favored : 90.58 % Rotamer: Outliers : 5.41 % Allowed : 30.35 % Favored : 64.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.78 (0.15), residues: 2983 helix: -0.62 (0.15), residues: 1129 sheet: -0.91 (0.28), residues: 317 loop : -1.66 (0.16), residues: 1537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 752 TYR 0.022 0.002 TYR B 108 PHE 0.022 0.002 PHE B 149 TRP 0.011 0.002 TRP B 913 HIS 0.007 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00418 (25479) covalent geometry : angle 0.73842 (34835) hydrogen bonds : bond 0.05226 ( 897) hydrogen bonds : angle 5.90774 ( 2471) metal coordination : bond 0.00898 ( 16) metal coordination : angle 7.12828 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5966 Ramachandran restraints generated. 2983 Oldfield, 0 Emsley, 2983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5966 Ramachandran restraints generated. 2983 Oldfield, 0 Emsley, 2983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 143 time to evaluate : 1.183 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: A 1 MET cc_start: 0.2731 (mmt) cc_final: 0.0607 (ppp) REVERT: A 104 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7108 (pm20) REVERT: A 113 TYR cc_start: 0.6562 (OUTLIER) cc_final: 0.4503 (m-80) REVERT: A 143 MET cc_start: -0.0364 (OUTLIER) cc_final: -0.0785 (mtp) REVERT: A 152 LEU cc_start: 0.1796 (OUTLIER) cc_final: 0.0716 (mt) REVERT: A 294 VAL cc_start: 0.3751 (OUTLIER) cc_final: 0.3443 (p) REVERT: A 612 ILE cc_start: 0.2811 (OUTLIER) cc_final: 0.2458 (mm) REVERT: A 634 GLU cc_start: 0.3157 (OUTLIER) cc_final: 0.1972 (tt0) REVERT: A 728 PHE cc_start: 0.7281 (OUTLIER) cc_final: 0.6746 (t80) REVERT: A 804 MET cc_start: 0.4788 (tpt) cc_final: 0.4062 (tpt) REVERT: B 1 MET cc_start: 0.6541 (pmm) cc_final: 0.4675 (ppp) REVERT: B 327 MET cc_start: 0.3701 (mmt) cc_final: 0.3255 (ptt) REVERT: B 391 MET cc_start: 0.3628 (mpp) cc_final: 0.2993 (mpp) REVERT: B 419 ARG cc_start: 0.5704 (OUTLIER) cc_final: 0.4904 (mpt180) REVERT: B 566 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7854 (pt0) REVERT: C 200 THR cc_start: 0.2240 (OUTLIER) cc_final: 0.1845 (m) REVERT: C 309 TYR cc_start: 0.6597 (OUTLIER) cc_final: 0.6190 (m-80) REVERT: C 530 ARG cc_start: 0.4441 (OUTLIER) cc_final: 0.4205 (tpp80) REVERT: D 29 ARG cc_start: 0.9169 (mmt180) cc_final: 0.8932 (mmp80) REVERT: D 268 GLU cc_start: -0.3209 (OUTLIER) cc_final: -0.3807 (mm-30) REVERT: D 510 GLU cc_start: 0.3597 (OUTLIER) cc_final: 0.2350 (pm20) REVERT: D 512 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9138 (mm) REVERT: D 554 MET cc_start: 0.8489 (mpp) cc_final: 0.6785 (tpt) outliers start: 136 outliers final: 96 residues processed: 266 average time/residue: 0.1804 time to fit residues: 75.9041 Evaluate side-chains 251 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 139 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 756 CYS Chi-restraints excluded: chain A residue 776 CYS Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 783 ARG Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 864 ARG Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 880 ASP Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 911 SER Chi-restraints excluded: chain A residue 933 THR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 54 TYR Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 376 TYR Chi-restraints excluded: chain B residue 412 CYS Chi-restraints excluded: chain B residue 419 ARG Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 566 GLU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 700 ARG Chi-restraints excluded: chain B residue 702 ASP Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 779 CYS Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 309 TYR Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 457 LYS Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 475 TYR Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 530 ARG Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 127 HIS Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 165 LYS Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 339 ILE Chi-restraints excluded: chain D residue 356 ASP Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 582 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 143 optimal weight: 20.0000 chunk 198 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 125 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 224 optimal weight: 20.0000 chunk 195 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.084091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.073516 restraints weight = 235725.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.074278 restraints weight = 207505.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.074588 restraints weight = 175611.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.075041 restraints weight = 158705.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.075198 restraints weight = 146059.570| |-----------------------------------------------------------------------------| r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5891 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 25495 Z= 0.170 Angle : 0.758 16.535 34859 Z= 0.377 Chirality : 0.047 0.331 3961 Planarity : 0.005 0.053 4330 Dihedral : 16.554 171.446 4165 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 30.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.28 % Favored : 91.62 % Rotamer: Outliers : 5.09 % Allowed : 30.55 % Favored : 64.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.15), residues: 2983 helix: -0.65 (0.15), residues: 1130 sheet: -0.97 (0.29), residues: 299 loop : -1.65 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 486 TYR 0.030 0.002 TYR D 96 PHE 0.023 0.002 PHE B 149 TRP 0.010 0.002 TRP B 913 HIS 0.007 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00385 (25479) covalent geometry : angle 0.73507 (34835) hydrogen bonds : bond 0.05021 ( 897) hydrogen bonds : angle 5.92325 ( 2471) metal coordination : bond 0.00811 ( 16) metal coordination : angle 7.16267 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5966 Ramachandran restraints generated. 2983 Oldfield, 0 Emsley, 2983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5966 Ramachandran restraints generated. 2983 Oldfield, 0 Emsley, 2983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 140 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: A 1 MET cc_start: 0.2606 (mmt) cc_final: 0.0544 (ppp) REVERT: A 104 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7167 (pm20) REVERT: A 113 TYR cc_start: 0.6521 (OUTLIER) cc_final: 0.4317 (m-80) REVERT: A 143 MET cc_start: -0.0207 (OUTLIER) cc_final: -0.0569 (mtp) REVERT: A 294 VAL cc_start: 0.3862 (OUTLIER) cc_final: 0.3583 (p) REVERT: A 612 ILE cc_start: 0.2800 (OUTLIER) cc_final: 0.2490 (mm) REVERT: A 634 GLU cc_start: 0.2947 (OUTLIER) cc_final: 0.1754 (tt0) REVERT: A 728 PHE cc_start: 0.7340 (OUTLIER) cc_final: 0.7011 (t80) REVERT: A 804 MET cc_start: 0.4738 (tpt) cc_final: 0.3984 (tpt) REVERT: A 902 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6600 (tp30) REVERT: B 1 MET cc_start: 0.6574 (pmm) cc_final: 0.4624 (ppp) REVERT: B 327 MET cc_start: 0.3713 (mmt) cc_final: 0.3293 (ptt) REVERT: B 391 MET cc_start: 0.3724 (mpp) cc_final: 0.3172 (mpp) REVERT: B 419 ARG cc_start: 0.5665 (OUTLIER) cc_final: 0.4753 (mpt180) REVERT: B 566 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7849 (pt0) REVERT: B 783 ARG cc_start: 0.0769 (OUTLIER) cc_final: 0.0473 (pmt170) REVERT: C 81 MET cc_start: 0.7103 (tmm) cc_final: 0.6587 (ppp) REVERT: C 200 THR cc_start: 0.2244 (OUTLIER) cc_final: 0.1836 (m) REVERT: C 309 TYR cc_start: 0.6495 (OUTLIER) cc_final: 0.6086 (m-80) REVERT: C 530 ARG cc_start: 0.4319 (OUTLIER) cc_final: 0.4058 (tpp80) REVERT: D 268 GLU cc_start: -0.3198 (OUTLIER) cc_final: -0.3770 (mm-30) REVERT: D 510 GLU cc_start: 0.3749 (OUTLIER) cc_final: 0.2378 (pm20) REVERT: D 512 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9106 (mm) REVERT: D 554 MET cc_start: 0.8478 (mpp) cc_final: 0.6816 (tpt) outliers start: 128 outliers final: 100 residues processed: 254 average time/residue: 0.1641 time to fit residues: 65.6571 Evaluate side-chains 256 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 139 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 776 CYS Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 783 ARG Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 864 ARG Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 880 ASP Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 911 SER Chi-restraints excluded: chain A residue 933 THR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 54 TYR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 376 TYR Chi-restraints excluded: chain B residue 412 CYS Chi-restraints excluded: chain B residue 419 ARG Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 566 GLU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 658 SER Chi-restraints excluded: chain B residue 702 ASP Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 779 CYS Chi-restraints excluded: chain B residue 783 ARG Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 309 TYR Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 457 LYS Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 475 TYR Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 530 ARG Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 127 HIS Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 165 LYS Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 339 ILE Chi-restraints excluded: chain D residue 356 ASP Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 582 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 168 optimal weight: 0.0070 chunk 180 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 264 optimal weight: 4.9990 chunk 157 optimal weight: 9.9990 chunk 302 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 214 optimal weight: 3.9990 chunk 200 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 overall best weight: 4.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 551 HIS ** D 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.082813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.072150 restraints weight = 239514.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.072870 restraints weight = 211318.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.073227 restraints weight = 180070.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.073626 restraints weight = 161034.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.073981 restraints weight = 147153.500| |-----------------------------------------------------------------------------| r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5971 moved from start: 0.5214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 25495 Z= 0.193 Angle : 0.794 15.262 34859 Z= 0.397 Chirality : 0.048 0.339 3961 Planarity : 0.006 0.058 4330 Dihedral : 16.677 172.628 4165 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 33.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.55 % Favored : 90.31 % Rotamer: Outliers : 5.13 % Allowed : 30.35 % Favored : 64.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.94 (0.15), residues: 2983 helix: -0.76 (0.15), residues: 1127 sheet: -1.05 (0.28), residues: 311 loop : -1.73 (0.16), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 486 TYR 0.025 0.002 TYR D 96 PHE 0.025 0.002 PHE B 149 TRP 0.031 0.002 TRP A 315 HIS 0.007 0.002 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00432 (25479) covalent geometry : angle 0.76817 (34835) hydrogen bonds : bond 0.05417 ( 897) hydrogen bonds : angle 6.05619 ( 2471) metal coordination : bond 0.00873 ( 16) metal coordination : angle 7.68062 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5966 Ramachandran restraints generated. 2983 Oldfield, 0 Emsley, 2983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5966 Ramachandran restraints generated. 2983 Oldfield, 0 Emsley, 2983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 145 time to evaluate : 0.996 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: A 104 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7129 (pm20) REVERT: A 113 TYR cc_start: 0.6396 (OUTLIER) cc_final: 0.4336 (m-80) REVERT: A 143 MET cc_start: -0.0064 (OUTLIER) cc_final: -0.0488 (mtp) REVERT: A 294 VAL cc_start: 0.4132 (OUTLIER) cc_final: 0.3857 (p) REVERT: A 328 MET cc_start: -0.0530 (mmt) cc_final: -0.0962 (mmt) REVERT: A 612 ILE cc_start: 0.2946 (OUTLIER) cc_final: 0.2630 (mm) REVERT: A 634 GLU cc_start: 0.3616 (OUTLIER) cc_final: 0.2322 (tt0) REVERT: A 804 MET cc_start: 0.4698 (tpt) cc_final: 0.3922 (tpt) REVERT: A 902 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6690 (tp30) REVERT: A 911 SER cc_start: 0.6016 (OUTLIER) cc_final: 0.5623 (p) REVERT: B 1 MET cc_start: 0.6608 (pmm) cc_final: 0.5448 (ppp) REVERT: B 327 MET cc_start: 0.3784 (mmt) cc_final: 0.3353 (ptt) REVERT: B 419 ARG cc_start: 0.5752 (OUTLIER) cc_final: 0.4938 (mpt180) REVERT: B 566 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7857 (pt0) REVERT: C 81 MET cc_start: 0.7326 (tmm) cc_final: 0.6803 (ppp) REVERT: C 200 THR cc_start: 0.2289 (OUTLIER) cc_final: 0.1893 (m) REVERT: C 309 TYR cc_start: 0.6633 (OUTLIER) cc_final: 0.6196 (m-80) REVERT: C 530 ARG cc_start: 0.4481 (OUTLIER) cc_final: 0.4270 (tpp80) REVERT: D 268 GLU cc_start: -0.3122 (OUTLIER) cc_final: -0.3612 (mm-30) REVERT: D 510 GLU cc_start: 0.3687 (OUTLIER) cc_final: 0.2532 (pm20) REVERT: D 512 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9113 (mm) REVERT: D 554 MET cc_start: 0.8491 (mpp) cc_final: 0.6887 (tpt) outliers start: 129 outliers final: 101 residues processed: 258 average time/residue: 0.1837 time to fit residues: 75.0733 Evaluate side-chains 256 residues out of total 2514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 139 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 600 SER Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 776 CYS Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 783 ARG Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 864 ARG Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 880 ASP Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 911 SER Chi-restraints excluded: chain A residue 933 THR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 54 TYR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 376 TYR Chi-restraints excluded: chain B residue 412 CYS Chi-restraints excluded: chain B residue 419 ARG Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 566 GLU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 627 LEU Chi-restraints excluded: chain B residue 658 SER Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 702 ASP Chi-restraints excluded: chain B residue 706 ILE Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 779 CYS Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain B residue 927 THR Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 309 TYR Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 457 LYS Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 475 TYR Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 530 ARG Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 127 HIS Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 165 LYS Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 339 ILE Chi-restraints excluded: chain D residue 356 ASP Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 514 LEU Chi-restraints excluded: chain D residue 555 TYR Chi-restraints excluded: chain D residue 582 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 170 optimal weight: 0.8980 chunk 129 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 246 optimal weight: 30.0000 chunk 73 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 283 optimal weight: 2.9990 chunk 272 optimal weight: 10.0000 chunk 203 optimal weight: 0.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.085287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.074652 restraints weight = 235663.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.075348 restraints weight = 205416.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.075905 restraints weight = 178518.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.076134 restraints weight = 156762.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.076631 restraints weight = 144827.158| |-----------------------------------------------------------------------------| r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5823 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 25495 Z= 0.144 Angle : 0.752 14.332 34859 Z= 0.372 Chirality : 0.046 0.328 3961 Planarity : 0.005 0.061 4330 Dihedral : 16.567 172.215 4165 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 26.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.44 % Favored : 92.46 % Rotamer: Outliers : 4.10 % Allowed : 31.50 % Favored : 64.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.15), residues: 2983 helix: -0.68 (0.15), residues: 1140 sheet: -0.96 (0.29), residues: 293 loop : -1.66 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 486 TYR 0.022 0.002 TYR C 147 PHE 0.020 0.002 PHE B 149 TRP 0.014 0.002 TRP C 379 HIS 0.006 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00326 (25479) covalent geometry : angle 0.73110 (34835) hydrogen bonds : bond 0.04611 ( 897) hydrogen bonds : angle 5.84401 ( 2471) metal coordination : bond 0.00785 ( 16) metal coordination : angle 6.73605 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5246.28 seconds wall clock time: 91 minutes 33.73 seconds (5493.73 seconds total)