Starting phenix.real_space_refine on Thu Feb 5 00:06:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9prw_71814/02_2026/9prw_71814.cif Found real_map, /net/cci-nas-00/data/ceres_data/9prw_71814/02_2026/9prw_71814.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9prw_71814/02_2026/9prw_71814.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9prw_71814/02_2026/9prw_71814.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9prw_71814/02_2026/9prw_71814.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9prw_71814/02_2026/9prw_71814.map" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 12 6.06 5 S 118 5.16 5 C 8618 2.51 5 N 2361 2.21 5 O 2437 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13546 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3490 Classifications: {'peptide': 440} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 417} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2605 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 23, 'TRANS': 306} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 4, 'HIS:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2786 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 23, 'TRANS': 325} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 4601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4601 Classifications: {'peptide': 582} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 551} Chain breaks: 2 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 44 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 194 SG CYS A 494 48.271 32.772 127.527 1.00147.28 S ATOM 214 SG CYS A 497 51.703 34.322 128.523 1.00148.80 S ATOM 336 SG CYS A 514 49.179 34.622 129.920 1.00135.47 S ATOM 359 SG CYS A 517 49.349 35.316 127.460 1.00128.21 S ATOM 527 SG CYS A 537 51.825 35.227 116.190 1.00149.23 S ATOM 548 SG CYS A 540 52.802 32.596 118.811 1.00149.95 S ATOM 685 SG CYS A 559 53.264 31.824 116.050 1.00161.55 S ATOM 707 SG CYS A 562 50.913 30.944 117.593 1.00162.33 S ATOM 611 SG CYS A 549 44.088 34.055 104.892 1.00164.69 S ATOM 645 SG CYS A 554 41.124 36.073 106.877 1.00152.93 S ATOM 858 SG CYS A 583 41.633 33.652 107.956 1.00170.90 S ATOM 884 SG CYS A 586 39.328 34.683 106.378 1.00176.84 S ATOM 3529 SG CYS B 53 52.432 108.856 151.992 1.00228.19 S ATOM 3549 SG CYS B 56 55.935 109.993 150.669 1.00227.06 S ATOM 3676 SG CYS B 73 54.230 108.519 148.079 1.00225.33 S ATOM 3694 SG CYS B 76 54.630 106.940 149.719 1.00219.64 S ATOM 3861 SG CYS B 96 57.475 99.329 158.253 1.00224.96 S ATOM 3881 SG CYS B 99 59.148 101.945 156.776 1.00225.94 S ATOM 4014 SG CYS B 118 60.078 100.467 158.483 1.00225.27 S ATOM 4036 SG CYS B 121 57.007 103.411 158.730 1.00222.47 S ATOM 3939 SG CYS B 108 54.000 90.983 167.255 1.00238.76 S ATOM 3972 SG CYS B 113 52.234 90.319 164.188 1.00232.80 S ATOM 4167 SG CYS B 142 51.053 93.169 166.776 1.00237.20 S ATOM 4193 SG CYS B 145 49.661 90.565 166.284 1.00236.58 S ATOM 6256 SG CYS C 53 40.571 23.677 33.111 1.00211.96 S ATOM 6276 SG CYS C 56 43.835 21.692 33.682 1.00210.28 S ATOM 6403 SG CYS C 73 42.742 23.870 36.571 1.00203.33 S ATOM 6421 SG CYS C 76 43.690 25.166 34.508 1.00196.58 S ATOM 6591 SG CYS C 96 45.824 31.449 25.199 1.00198.43 S ATOM 6611 SG CYS C 99 47.541 28.368 26.632 1.00204.89 S ATOM 6748 SG CYS C 118 48.277 29.882 24.898 1.00202.11 S ATOM 6770 SG CYS C 121 44.778 27.434 25.053 1.00197.29 S ATOM 6673 SG CYS C 108 42.958 40.836 16.498 1.00195.66 S ATOM 6706 SG CYS C 113 41.227 41.684 19.846 1.00183.21 S ATOM 6914 SG CYS C 142 39.838 39.244 18.901 1.00195.34 S ATOM 6940 SG CYS C 145 38.869 41.337 18.451 1.00195.62 S ATOM 10166 SG CYS D 494 48.561 98.834 56.368 1.00106.40 S ATOM 10186 SG CYS D 497 51.614 97.518 54.569 1.00109.06 S ATOM 10308 SG CYS D 514 49.508 95.553 53.372 1.00 87.41 S ATOM 10331 SG CYS D 517 49.626 95.872 56.202 1.00 80.21 S ATOM 10499 SG CYS D 537 51.586 97.250 67.413 1.00109.90 S ATOM 10520 SG CYS D 540 53.476 96.443 63.592 1.00108.61 S ATOM 10657 SG CYS D 559 54.705 98.701 66.380 1.00120.27 S ATOM 10679 SG CYS D 562 52.998 99.815 64.676 1.00124.75 S ATOM 10583 SG CYS D 549 46.535 97.572 78.411 1.00111.43 S ATOM 10617 SG CYS D 554 44.007 96.392 77.118 1.00106.19 S ATOM 10830 SG CYS D 583 45.119 98.842 75.741 1.00114.58 S ATOM 10856 SG CYS D 586 42.254 98.963 78.695 1.00114.48 S Time building chain proxies: 3.07, per 1000 atoms: 0.23 Number of scatterers: 13546 At special positions: 0 Unit cell: (90.52, 127.72, 184.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 12 29.99 S 118 16.00 O 2437 8.00 N 2361 7.00 C 8618 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: 0.90 Conformation dependent library (CDL) restraints added in 432.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 514 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 497 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 517 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 494 " pdb=" ZN A1003 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 559 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 540 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 562 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 537 " pdb=" ZN A1004 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 583 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 554 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 549 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 586 " pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 53 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 73 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 56 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 76 " pdb=" ZN B 502 " pdb="ZN ZN B 502 " - pdb=" SG CYS B 121 " pdb="ZN ZN B 502 " - pdb=" SG CYS B 118 " pdb="ZN ZN B 502 " - pdb=" SG CYS B 99 " pdb="ZN ZN B 502 " - pdb=" SG CYS B 96 " pdb=" ZN B 503 " pdb="ZN ZN B 503 " - pdb=" SG CYS B 145 " pdb="ZN ZN B 503 " - pdb=" SG CYS B 108 " pdb="ZN ZN B 503 " - pdb=" SG CYS B 113 " pdb="ZN ZN B 503 " - pdb=" SG CYS B 142 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 53 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 73 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 56 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 76 " pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 121 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 99 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 118 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 96 " pdb=" ZN C 503 " pdb="ZN ZN C 503 " - pdb=" SG CYS C 113 " pdb="ZN ZN C 503 " - pdb=" SG CYS C 142 " pdb="ZN ZN C 503 " - pdb=" SG CYS C 145 " pdb="ZN ZN C 503 " - pdb=" SG CYS C 108 " pdb=" ZN D1002 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 494 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 497 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 517 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 514 " pdb=" ZN D1003 " pdb="ZN ZN D1003 " - pdb=" SG CYS D 562 " pdb="ZN ZN D1003 " - pdb=" SG CYS D 540 " pdb="ZN ZN D1003 " - pdb=" SG CYS D 537 " pdb="ZN ZN D1003 " - pdb=" SG CYS D 559 " pdb=" ZN D1004 " pdb="ZN ZN D1004 " - pdb=" SG CYS D 583 " pdb="ZN ZN D1004 " - pdb=" SG CYS D 554 " pdb="ZN ZN D1004 " - pdb=" SG CYS D 586 " pdb="ZN ZN D1004 " - pdb=" SG CYS D 549 " Number of angles added : 72 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3168 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 14 sheets defined 38.2% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 489 through 493 Processing helix chain 'A' and resid 515 through 523 removed outlier: 3.531A pdb=" N GLU A 523 " --> pdb=" O ASN A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 566 Processing helix chain 'A' and resid 571 through 578 Processing helix chain 'A' and resid 600 through 611 Processing helix chain 'A' and resid 627 through 631 removed outlier: 3.748A pdb=" N ARG A 631 " --> pdb=" O ALA A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 654 removed outlier: 3.829A pdb=" N LEU A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 676 Processing helix chain 'A' and resid 686 through 690 Processing helix chain 'A' and resid 691 through 699 Processing helix chain 'A' and resid 728 through 742 removed outlier: 4.112A pdb=" N PHE A 732 " --> pdb=" O GLY A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 774 Processing helix chain 'A' and resid 783 through 785 No H-bonds generated for 'chain 'A' and resid 783 through 785' Processing helix chain 'A' and resid 835 through 839 Processing helix chain 'A' and resid 842 through 847 removed outlier: 4.766A pdb=" N GLN A 846 " --> pdb=" O GLN A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 868 Processing helix chain 'A' and resid 881 through 890 Processing helix chain 'A' and resid 894 through 909 Proline residue: A 904 - end of helix removed outlier: 4.333A pdb=" N GLU A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR A 908 " --> pdb=" O PRO A 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 83 removed outlier: 3.677A pdb=" N ALA B 83 " --> pdb=" O LYS B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 125 Processing helix chain 'B' and resid 129 through 137 removed outlier: 3.673A pdb=" N LYS B 133 " --> pdb=" O GLY B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 172 removed outlier: 4.194A pdb=" N GLN B 163 " --> pdb=" O LYS B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 206 removed outlier: 3.565A pdb=" N LEU B 203 " --> pdb=" O ILE B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 227 Processing helix chain 'B' and resid 228 through 236 Processing helix chain 'B' and resid 256 through 270 removed outlier: 3.868A pdb=" N LEU B 260 " --> pdb=" O PRO B 256 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE B 263 " --> pdb=" O TYR B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 303 Processing helix chain 'B' and resid 330 through 334 Processing helix chain 'B' and resid 339 through 353 removed outlier: 3.785A pdb=" N LEU B 343 " --> pdb=" O SER B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'C' and resid 37 through 44 Processing helix chain 'C' and resid 73 through 83 Processing helix chain 'C' and resid 118 through 126 Processing helix chain 'C' and resid 129 through 137 removed outlier: 3.810A pdb=" N LYS C 133 " --> pdb=" O GLY C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 171 removed outlier: 3.771A pdb=" N GLN C 163 " --> pdb=" O LYS C 159 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS C 165 " --> pdb=" O ARG C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 187 removed outlier: 3.638A pdb=" N ARG C 187 " --> pdb=" O VAL C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 206 Processing helix chain 'C' and resid 214 through 216 No H-bonds generated for 'chain 'C' and resid 214 through 216' Processing helix chain 'C' and resid 228 through 236 removed outlier: 3.836A pdb=" N GLY C 236 " --> pdb=" O VAL C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 270 removed outlier: 3.891A pdb=" N PHE C 263 " --> pdb=" O TYR C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 303 Processing helix chain 'C' and resid 339 through 353 Processing helix chain 'C' and resid 360 through 366 removed outlier: 3.705A pdb=" N VAL C 364 " --> pdb=" O PRO C 360 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN C 366 " --> pdb=" O LYS C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 374 Proline residue: C 370 - end of helix Processing helix chain 'D' and resid 340 through 342 No H-bonds generated for 'chain 'D' and resid 340 through 342' Processing helix chain 'D' and resid 355 through 362 removed outlier: 3.806A pdb=" N TYR D 359 " --> pdb=" O HIS D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 381 removed outlier: 3.936A pdb=" N ARG D 366 " --> pdb=" O GLN D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 413 removed outlier: 4.427A pdb=" N LYS D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) Proline residue: D 405 - end of helix Processing helix chain 'D' and resid 418 through 423 removed outlier: 3.586A pdb=" N LEU D 422 " --> pdb=" O PRO D 419 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU D 423 " --> pdb=" O LYS D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 484 removed outlier: 3.684A pdb=" N TYR D 481 " --> pdb=" O GLU D 477 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG D 484 " --> pdb=" O VAL D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 493 Processing helix chain 'D' and resid 514 through 524 Processing helix chain 'D' and resid 560 through 567 Processing helix chain 'D' and resid 570 through 578 removed outlier: 3.536A pdb=" N GLU D 578 " --> pdb=" O ALA D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 612 Processing helix chain 'D' and resid 627 through 631 removed outlier: 4.136A pdb=" N ARG D 631 " --> pdb=" O ALA D 628 " (cutoff:3.500A) Processing helix chain 'D' and resid 644 through 653 Processing helix chain 'D' and resid 666 through 677 removed outlier: 3.759A pdb=" N HIS D 677 " --> pdb=" O GLY D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 691 through 699 Processing helix chain 'D' and resid 725 through 727 No H-bonds generated for 'chain 'D' and resid 725 through 727' Processing helix chain 'D' and resid 728 through 742 removed outlier: 4.251A pdb=" N PHE D 732 " --> pdb=" O GLY D 728 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU D 733 " --> pdb=" O ARG D 729 " (cutoff:3.500A) Processing helix chain 'D' and resid 762 through 773 Processing helix chain 'D' and resid 781 through 785 Processing helix chain 'D' and resid 815 through 819 Processing helix chain 'D' and resid 835 through 839 Processing helix chain 'D' and resid 860 through 868 removed outlier: 3.604A pdb=" N MET D 864 " --> pdb=" O TRP D 860 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU D 865 " --> pdb=" O CYS D 861 " (cutoff:3.500A) Processing helix chain 'D' and resid 881 through 890 Processing helix chain 'D' and resid 894 through 909 Proline residue: D 904 - end of helix removed outlier: 3.960A pdb=" N GLU D 907 " --> pdb=" O ALA D 903 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 502 through 505 removed outlier: 3.714A pdb=" N LEU A 504 " --> pdb=" O MET A 513 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 591 through 592 removed outlier: 3.778A pdb=" N LEU A 595 " --> pdb=" O TYR A 592 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 682 through 683 removed outlier: 8.867A pdb=" N MET A 682 " --> pdb=" O ASP A 658 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TYR A 660 " --> pdb=" O MET A 682 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE A 634 " --> pdb=" O ASP A 658 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N TYR A 660 " --> pdb=" O ILE A 634 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL A 636 " --> pdb=" O TYR A 660 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ALA A 662 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER A 638 " --> pdb=" O ALA A 662 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ARG A 635 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE A 705 " --> pdb=" O ARG A 635 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU A 637 " --> pdb=" O ILE A 705 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL A 704 " --> pdb=" O LEU A 754 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLU A 756 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLY A 706 " --> pdb=" O GLU A 756 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N VAL A 758 " --> pdb=" O GLY A 706 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 824 through 825 removed outlier: 3.885A pdb=" N VAL A 850 " --> pdb=" O ASP A 857 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 150 through 151 Processing sheet with id=AA6, first strand: chain 'B' and resid 218 through 221 removed outlier: 7.589A pdb=" N VAL B 192 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N VAL B 221 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N SER B 194 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ALA B 244 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL B 241 " --> pdb=" O MET B 283 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL B 285 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLY B 243 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN B 318 " --> pdb=" O ASP B 311 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ASP B 311 " --> pdb=" O GLN B 318 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ALA B 320 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE B 309 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ARG B 322 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL B 307 " --> pdb=" O ARG B 322 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 63 through 64 removed outlier: 4.056A pdb=" N THR C 63 " --> pdb=" O ILE C 72 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 150 through 151 Processing sheet with id=AA9, first strand: chain 'C' and resid 218 through 221 removed outlier: 3.551A pdb=" N LYS C 219 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL C 241 " --> pdb=" O MET C 283 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N VAL C 285 " --> pdb=" O VAL C 241 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLY C 243 " --> pdb=" O VAL C 285 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LEU C 317 " --> pdb=" O HIS C 313 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N HIS C 313 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN C 319 " --> pdb=" O ASP C 311 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 336 through 339 removed outlier: 3.771A pdb=" N SER D 337 " --> pdb=" O VAL D 328 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TRP D 297 " --> pdb=" O MET D 345 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET D 345 " --> pdb=" O TRP D 297 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 504 through 505 removed outlier: 3.528A pdb=" N LEU D 504 " --> pdb=" O MET D 513 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 546 through 547 removed outlier: 3.678A pdb=" N PHE D 558 " --> pdb=" O LEU D 547 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 657 through 663 removed outlier: 6.210A pdb=" N ILE D 634 " --> pdb=" O VAL D 657 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG D 659 " --> pdb=" O ILE D 634 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY D 707 " --> pdb=" O LEU D 639 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL D 704 " --> pdb=" O LEU D 754 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N GLU D 756 " --> pdb=" O VAL D 704 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLY D 706 " --> pdb=" O GLU D 756 " (cutoff:3.500A) removed outlier: 9.202A pdb=" N VAL D 758 " --> pdb=" O GLY D 706 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 824 through 825 removed outlier: 4.151A pdb=" N VAL D 850 " --> pdb=" O ASP D 857 " (cutoff:3.500A) 416 hydrogen bonds defined for protein. 1128 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.29 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4434 1.34 - 1.46: 2901 1.46 - 1.58: 6406 1.58 - 1.70: 0 1.70 - 1.82: 154 Bond restraints: 13895 Sorted by residual: bond pdb=" N ILE A 833 " pdb=" CA ILE A 833 " ideal model delta sigma weight residual 1.459 1.496 -0.037 9.10e-03 1.21e+04 1.69e+01 bond pdb=" N VAL A 830 " pdb=" CA VAL A 830 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.32e-02 5.74e+03 9.65e+00 bond pdb=" N ILE A 840 " pdb=" CA ILE A 840 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.96e+00 bond pdb=" N ASP A 845 " pdb=" CA ASP A 845 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.58e+00 bond pdb=" N LYS A 844 " pdb=" CA LYS A 844 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.32e-02 5.74e+03 6.08e+00 ... (remaining 13890 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 18305 1.71 - 3.43: 425 3.43 - 5.14: 92 5.14 - 6.86: 19 6.86 - 8.57: 6 Bond angle restraints: 18847 Sorted by residual: angle pdb=" N ILE A 833 " pdb=" CA ILE A 833 " pdb=" C ILE A 833 " ideal model delta sigma weight residual 113.47 109.33 4.14 1.01e+00 9.80e-01 1.68e+01 angle pdb=" CA LYS A 844 " pdb=" C LYS A 844 " pdb=" O LYS A 844 " ideal model delta sigma weight residual 121.87 117.50 4.37 1.10e+00 8.26e-01 1.58e+01 angle pdb=" CA SER A 839 " pdb=" C SER A 839 " pdb=" N ILE A 840 " ideal model delta sigma weight residual 119.63 116.42 3.21 8.10e-01 1.52e+00 1.57e+01 angle pdb=" CA ASP A 845 " pdb=" CB ASP A 845 " pdb=" CG ASP A 845 " ideal model delta sigma weight residual 112.60 116.39 -3.79 1.00e+00 1.00e+00 1.44e+01 angle pdb=" N ARG A 831 " pdb=" CA ARG A 831 " pdb=" C ARG A 831 " ideal model delta sigma weight residual 113.89 108.13 5.76 1.58e+00 4.01e-01 1.33e+01 ... (remaining 18842 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 7458 17.92 - 35.83: 638 35.83 - 53.75: 116 53.75 - 71.67: 26 71.67 - 89.59: 9 Dihedral angle restraints: 8247 sinusoidal: 3327 harmonic: 4920 Sorted by residual: dihedral pdb=" CA MET C 137 " pdb=" C MET C 137 " pdb=" N SER C 138 " pdb=" CA SER C 138 " ideal model delta harmonic sigma weight residual -180.00 -151.82 -28.18 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA GLN D 362 " pdb=" C GLN D 362 " pdb=" N PRO D 363 " pdb=" CA PRO D 363 " ideal model delta harmonic sigma weight residual -180.00 -152.68 -27.32 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA GLU C 234 " pdb=" C GLU C 234 " pdb=" N TRP C 235 " pdb=" CA TRP C 235 " ideal model delta harmonic sigma weight residual 180.00 154.75 25.25 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 8244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1535 0.047 - 0.094: 366 0.094 - 0.142: 91 0.142 - 0.189: 6 0.189 - 0.236: 1 Chirality restraints: 1999 Sorted by residual: chirality pdb=" CA ILE A 840 " pdb=" N ILE A 840 " pdb=" C ILE A 840 " pdb=" CB ILE A 840 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA ILE A 833 " pdb=" N ILE A 833 " pdb=" C ILE A 833 " pdb=" CB ILE A 833 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.40e-01 chirality pdb=" CB VAL C 224 " pdb=" CA VAL C 224 " pdb=" CG1 VAL C 224 " pdb=" CG2 VAL C 224 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.17 2.00e-01 2.50e+01 7.64e-01 ... (remaining 1996 not shown) Planarity restraints: 2449 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 235 " -0.032 2.00e-02 2.50e+03 2.82e-02 1.99e+01 pdb=" CG TRP C 235 " 0.076 2.00e-02 2.50e+03 pdb=" CD1 TRP C 235 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP C 235 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 235 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 235 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 235 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 235 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 235 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 235 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 297 " 0.025 2.00e-02 2.50e+03 2.35e-02 1.38e+01 pdb=" CG TRP D 297 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP D 297 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP D 297 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 297 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 297 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 297 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 297 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 297 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP D 297 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 831 " 0.204 9.50e-02 1.11e+02 9.13e-02 5.12e+00 pdb=" NE ARG A 831 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 831 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 831 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 831 " 0.007 2.00e-02 2.50e+03 ... (remaining 2446 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.91: 5302 2.91 - 3.41: 14099 3.41 - 3.91: 22471 3.91 - 4.40: 25337 4.40 - 4.90: 40596 Nonbonded interactions: 107805 Sorted by model distance: nonbonded pdb=" O ALA B 347 " pdb=" OE1 GLN B 351 " model vdw 2.416 3.040 nonbonded pdb=" O ASN A 552 " pdb=" OD1 ASN A 553 " model vdw 2.464 3.040 nonbonded pdb=" O MET A 852 " pdb=" OD1 ASN A 853 " model vdw 2.479 3.040 nonbonded pdb=" N GLU C 341 " pdb=" OE1 GLU C 341 " model vdw 2.522 3.120 nonbonded pdb=" O ASN A 612 " pdb=" OD1 ASN A 612 " model vdw 2.531 3.040 ... (remaining 107800 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 'B' and (resid 49 through 277 or (resid 278 and (name N or name CA or nam \ e C or name O or name CB )) or resid 279 through 503)) selection = (chain 'C' and (resid 49 through 89 or (resid 90 and (name N or name CA or name \ C or name O or name CB )) or resid 91 through 102 or (resid 103 and (name N or n \ ame CA or name C or name O or name CB )) or resid 104 through 129 or (resid 130 \ through 131 and (name N or name CA or name C or name O or name CB )) or (resid 1 \ 32 through 137 and (name N or name CA or name C or name O or name CB )) or resid \ 138 through 158 or (resid 159 and (name N or name CA or name C or name O or nam \ e CB )) or resid 160 through 172 or (resid 173 through 174 and (name N or name C \ A or name C or name O or name CB )) or resid 175 or (resid 176 through 177 and ( \ name N or name CA or name C or name O or name CB )) or resid 178 through 378 or \ resid 501 through 503)) } 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: 1.080 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: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.710 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 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 : 0.010 0.447 13943 Z= 0.359 Angle : 1.807 56.596 18919 Z= 0.466 Chirality : 0.043 0.236 1999 Planarity : 0.005 0.091 2449 Dihedral : 13.840 89.587 5079 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.14 % Allowed : 0.41 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.21), residues: 1689 helix: -0.16 (0.23), residues: 529 sheet: -1.03 (0.44), residues: 146 loop : -0.32 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 885 TYR 0.017 0.001 TYR A 724 PHE 0.017 0.001 PHE A 755 TRP 0.076 0.002 TRP C 235 HIS 0.011 0.001 HIS D 739 Details of bonding type rmsd covalent geometry : bond 0.00291 (13895) covalent geometry : angle 0.66145 (18847) hydrogen bonds : bond 0.15725 ( 416) hydrogen bonds : angle 7.28957 ( 1128) metal coordination : bond 0.16066 ( 48) metal coordination : angle 27.26727 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 268 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 ASN cc_start: 0.7096 (t0) cc_final: 0.6749 (t0) REVERT: A 513 MET cc_start: 0.7354 (ttt) cc_final: 0.5410 (ptm) REVERT: A 585 MET cc_start: 0.7227 (mpp) cc_final: 0.6923 (mpp) REVERT: A 779 MET cc_start: 0.6998 (ttt) cc_final: 0.6779 (ttt) REVERT: A 783 LYS cc_start: 0.8726 (ttpt) cc_final: 0.8325 (ttpp) REVERT: A 872 VAL cc_start: 0.8227 (t) cc_final: 0.7870 (m) REVERT: A 883 LEU cc_start: 0.7847 (tp) cc_final: 0.7412 (mp) REVERT: B 155 GLN cc_start: 0.7155 (tp-100) cc_final: 0.6672 (tp40) REVERT: B 230 LYS cc_start: 0.8553 (tptt) cc_final: 0.8169 (mmmt) REVERT: C 55 CYS cc_start: 0.9082 (m) cc_final: 0.8602 (m) REVERT: C 64 GLN cc_start: 0.8516 (pt0) cc_final: 0.7700 (pm20) REVERT: C 115 ARG cc_start: 0.7997 (mmp80) cc_final: 0.7613 (mmm160) REVERT: C 137 MET cc_start: 0.3790 (ppp) cc_final: 0.0417 (mtm) REVERT: C 139 ASN cc_start: 0.7925 (p0) cc_final: 0.6888 (p0) REVERT: C 226 ASP cc_start: 0.7745 (t0) cc_final: 0.7445 (t0) REVERT: D 326 ARG cc_start: 0.6284 (mmp-170) cc_final: 0.5713 (mmp-170) REVERT: D 420 LYS cc_start: 0.9199 (tptp) cc_final: 0.8974 (tptp) REVERT: D 761 MET cc_start: 0.7661 (ppp) cc_final: 0.6948 (ptt) REVERT: D 779 MET cc_start: 0.8853 (ttp) cc_final: 0.7722 (ttp) REVERT: D 864 MET cc_start: 0.7275 (mpp) cc_final: 0.6981 (mtm) outliers start: 2 outliers final: 0 residues processed: 270 average time/residue: 0.1249 time to fit residues: 49.4084 Evaluate side-chains 212 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 98 optimal weight: 0.0050 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.0070 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.0070 chunk 103 optimal weight: 0.0870 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.1208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 GLN A 873 HIS B 262 GLN ** C 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 ASN ** D 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 677 HIS D 739 HIS D 776 ASN D 821 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.235205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.193423 restraints weight = 17689.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.191223 restraints weight = 23856.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.194151 restraints weight = 21167.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.194526 restraints weight = 12096.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.195465 restraints weight = 11211.624| |-----------------------------------------------------------------------------| r_work (final): 0.4327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13943 Z= 0.123 Angle : 0.907 28.441 18919 Z= 0.337 Chirality : 0.042 0.156 1999 Planarity : 0.004 0.049 2449 Dihedral : 4.323 41.536 1872 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.28 % Allowed : 9.10 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.21), residues: 1689 helix: 0.23 (0.23), residues: 536 sheet: -1.08 (0.44), residues: 140 loop : -0.37 (0.20), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 831 TYR 0.019 0.001 TYR A 724 PHE 0.015 0.001 PHE D 608 TRP 0.044 0.002 TRP C 235 HIS 0.007 0.001 HIS D 900 Details of bonding type rmsd covalent geometry : bond 0.00268 (13895) covalent geometry : angle 0.62499 (18847) hydrogen bonds : bond 0.03477 ( 416) hydrogen bonds : angle 5.41157 ( 1128) metal coordination : bond 0.01343 ( 48) metal coordination : angle 10.68051 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 243 time to evaluate : 0.577 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: A 481 TYR cc_start: 0.7251 (t80) cc_final: 0.7015 (t80) REVERT: A 501 ASN cc_start: 0.7074 (t0) cc_final: 0.6797 (t0) REVERT: A 872 VAL cc_start: 0.7981 (t) cc_final: 0.7620 (m) REVERT: A 883 LEU cc_start: 0.8135 (tp) cc_final: 0.7727 (mp) REVERT: B 155 GLN cc_start: 0.7620 (tp-100) cc_final: 0.7418 (tp40) REVERT: C 55 CYS cc_start: 0.7035 (m) cc_final: 0.6486 (m) REVERT: C 64 GLN cc_start: 0.7413 (pt0) cc_final: 0.7151 (pm20) REVERT: C 219 LYS cc_start: 0.7573 (tppt) cc_final: 0.7355 (tppt) REVERT: C 226 ASP cc_start: 0.7284 (t0) cc_final: 0.6967 (t0) REVERT: D 420 LYS cc_start: 0.9094 (tptp) cc_final: 0.8783 (tptp) REVERT: D 761 MET cc_start: 0.7815 (ppp) cc_final: 0.6935 (ptt) REVERT: D 779 MET cc_start: 0.8758 (ttp) cc_final: 0.7630 (ttp) REVERT: D 864 MET cc_start: 0.7117 (mpp) cc_final: 0.6801 (mtm) outliers start: 4 outliers final: 3 residues processed: 244 average time/residue: 0.1290 time to fit residues: 45.8532 Evaluate side-chains 219 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 216 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 694 HIS Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain D residue 314 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 46 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 23 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 164 optimal weight: 0.5980 chunk 151 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 chunk 19 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 ASN A 789 HIS B 262 GLN C 287 ASN C 326 ASN D 677 HIS D 739 HIS D 821 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.231540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.188474 restraints weight = 17670.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.185848 restraints weight = 25294.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.189190 restraints weight = 21975.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.189640 restraints weight = 12291.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.190821 restraints weight = 11218.771| |-----------------------------------------------------------------------------| r_work (final): 0.4287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13943 Z= 0.130 Angle : 0.744 14.330 18919 Z= 0.313 Chirality : 0.042 0.162 1999 Planarity : 0.004 0.033 2449 Dihedral : 4.283 44.686 1872 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.52 % Allowed : 11.59 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.21), residues: 1689 helix: 0.44 (0.23), residues: 533 sheet: -1.05 (0.44), residues: 132 loop : -0.44 (0.20), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 885 TYR 0.021 0.001 TYR D 481 PHE 0.018 0.001 PHE D 608 TRP 0.025 0.002 TRP D 314 HIS 0.007 0.001 HIS D 506 Details of bonding type rmsd covalent geometry : bond 0.00303 (13895) covalent geometry : angle 0.60583 (18847) hydrogen bonds : bond 0.03226 ( 416) hydrogen bonds : angle 5.14621 ( 1128) metal coordination : bond 0.00980 ( 48) metal coordination : angle 7.02416 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 232 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 ASN cc_start: 0.7045 (t0) cc_final: 0.6675 (t0) REVERT: A 513 MET cc_start: 0.5745 (ttt) cc_final: 0.5075 (ptm) REVERT: A 531 ASP cc_start: 0.7405 (m-30) cc_final: 0.7050 (t0) REVERT: A 872 VAL cc_start: 0.8299 (t) cc_final: 0.7890 (m) REVERT: A 883 LEU cc_start: 0.8154 (tp) cc_final: 0.7746 (mp) REVERT: B 155 GLN cc_start: 0.7654 (tp-100) cc_final: 0.7285 (tp-100) REVERT: B 262 GLN cc_start: 0.7101 (OUTLIER) cc_final: 0.6840 (mp10) REVERT: C 55 CYS cc_start: 0.7226 (m) cc_final: 0.6665 (m) REVERT: C 64 GLN cc_start: 0.7588 (pt0) cc_final: 0.7199 (pm20) REVERT: C 226 ASP cc_start: 0.7429 (t0) cc_final: 0.7120 (t0) REVERT: D 297 TRP cc_start: 0.6195 (m-90) cc_final: 0.5754 (m-90) REVERT: D 374 GLN cc_start: 0.8457 (mt0) cc_final: 0.8235 (mt0) REVERT: D 779 MET cc_start: 0.8909 (ttp) cc_final: 0.7886 (ttp) REVERT: D 836 ARG cc_start: 0.7499 (ttm170) cc_final: 0.7214 (ttm170) REVERT: D 880 MET cc_start: 0.8225 (mmm) cc_final: 0.7790 (mtt) outliers start: 22 outliers final: 12 residues processed: 243 average time/residue: 0.1226 time to fit residues: 43.4487 Evaluate side-chains 225 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 212 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 CYS Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 694 HIS Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 911 CYS Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain D residue 314 TRP Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 674 MET Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 872 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 71 optimal weight: 7.9990 chunk 12 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 131 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 ASN A 717 ASN B 250 HIS C 287 ASN C 326 ASN C 366 ASN D 677 HIS ** D 821 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.229655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.186459 restraints weight = 17650.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.187457 restraints weight = 25676.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.189192 restraints weight = 22418.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.190217 restraints weight = 13189.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.191147 restraints weight = 11620.291| |-----------------------------------------------------------------------------| r_work (final): 0.4286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13943 Z= 0.142 Angle : 0.724 11.817 18919 Z= 0.317 Chirality : 0.042 0.148 1999 Planarity : 0.004 0.057 2449 Dihedral : 4.389 46.059 1872 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.52 % Allowed : 13.72 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.21), residues: 1689 helix: 0.47 (0.23), residues: 533 sheet: -1.19 (0.43), residues: 134 loop : -0.42 (0.20), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 115 TYR 0.015 0.001 TYR D 908 PHE 0.031 0.001 PHE B 280 TRP 0.027 0.002 TRP D 313 HIS 0.012 0.001 HIS D 821 Details of bonding type rmsd covalent geometry : bond 0.00334 (13895) covalent geometry : angle 0.61992 (18847) hydrogen bonds : bond 0.03052 ( 416) hydrogen bonds : angle 5.05222 ( 1128) metal coordination : bond 0.00977 ( 48) metal coordination : angle 6.09425 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 231 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 ASN cc_start: 0.7113 (t0) cc_final: 0.6813 (t0) REVERT: A 531 ASP cc_start: 0.7505 (m-30) cc_final: 0.7232 (t0) REVERT: A 585 MET cc_start: 0.7249 (mpp) cc_final: 0.7029 (mpp) REVERT: A 872 VAL cc_start: 0.8415 (t) cc_final: 0.8027 (m) REVERT: B 178 MET cc_start: 0.0053 (ppp) cc_final: -0.0410 (ppp) REVERT: C 55 CYS cc_start: 0.6994 (m) cc_final: 0.6493 (m) REVERT: C 64 GLN cc_start: 0.7503 (pt0) cc_final: 0.7175 (pm20) REVERT: C 226 ASP cc_start: 0.7471 (t0) cc_final: 0.7179 (t0) REVERT: C 268 GLN cc_start: 0.8037 (mm-40) cc_final: 0.7361 (mm-40) REVERT: D 297 TRP cc_start: 0.6213 (m-90) cc_final: 0.5928 (m-90) REVERT: D 374 GLN cc_start: 0.8348 (mt0) cc_final: 0.8111 (mt0) REVERT: D 420 LYS cc_start: 0.9062 (tptp) cc_final: 0.8735 (tptp) REVERT: D 761 MET cc_start: 0.8256 (ppp) cc_final: 0.6547 (ppp) outliers start: 22 outliers final: 15 residues processed: 242 average time/residue: 0.1105 time to fit residues: 39.3572 Evaluate side-chains 234 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 219 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 CYS Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 694 HIS Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 911 CYS Chi-restraints excluded: chain C residue 235 TRP Chi-restraints excluded: chain D residue 314 TRP Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 548 MET Chi-restraints excluded: chain D residue 674 MET Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 832 THR Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 872 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 59 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 151 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 162 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 ASN B 262 GLN C 287 ASN C 366 ASN D 677 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.224688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.172330 restraints weight = 17288.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.173696 restraints weight = 20735.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.169060 restraints weight = 11788.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.169414 restraints weight = 11658.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.169836 restraints weight = 10690.688| |-----------------------------------------------------------------------------| r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13943 Z= 0.213 Angle : 0.761 12.674 18919 Z= 0.345 Chirality : 0.044 0.162 1999 Planarity : 0.005 0.053 2449 Dihedral : 4.671 52.220 1872 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.55 % Allowed : 15.38 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.20), residues: 1689 helix: 0.35 (0.23), residues: 538 sheet: -1.27 (0.41), residues: 132 loop : -0.56 (0.20), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 885 TYR 0.037 0.002 TYR C 374 PHE 0.024 0.002 PHE C 167 TRP 0.030 0.002 TRP D 313 HIS 0.008 0.001 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00511 (13895) covalent geometry : angle 0.67089 (18847) hydrogen bonds : bond 0.03406 ( 416) hydrogen bonds : angle 5.13006 ( 1128) metal coordination : bond 0.01098 ( 48) metal coordination : angle 5.86912 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 230 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 ASN cc_start: 0.7306 (t0) cc_final: 0.6957 (t0) REVERT: A 513 MET cc_start: 0.6271 (ttt) cc_final: 0.5264 (ptm) REVERT: A 559 CYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7623 (p) REVERT: A 585 MET cc_start: 0.7519 (mpp) cc_final: 0.7178 (mpp) REVERT: A 588 HIS cc_start: 0.7374 (t70) cc_final: 0.6966 (t-90) REVERT: A 637 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8089 (tp) REVERT: C 64 GLN cc_start: 0.7920 (pt0) cc_final: 0.7297 (pm20) REVERT: C 226 ASP cc_start: 0.7576 (t0) cc_final: 0.7338 (t0) REVERT: C 268 GLN cc_start: 0.8162 (mm-40) cc_final: 0.7570 (mm-40) REVERT: D 297 TRP cc_start: 0.6691 (m-90) cc_final: 0.6199 (m-10) REVERT: D 374 GLN cc_start: 0.8438 (mt0) cc_final: 0.8067 (mt0) REVERT: D 536 TYR cc_start: 0.6390 (m-10) cc_final: 0.6109 (m-80) REVERT: D 779 MET cc_start: 0.8900 (ttp) cc_final: 0.8557 (ttt) REVERT: D 864 MET cc_start: 0.7230 (mtm) cc_final: 0.6818 (mtm) outliers start: 37 outliers final: 27 residues processed: 252 average time/residue: 0.0963 time to fit residues: 36.5524 Evaluate side-chains 242 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 213 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 CYS Chi-restraints excluded: chain A residue 559 CYS Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 694 HIS Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 911 CYS Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain C residue 235 TRP Chi-restraints excluded: chain D residue 314 TRP Chi-restraints excluded: chain D residue 315 MET Chi-restraints excluded: chain D residue 364 MET Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 669 SER Chi-restraints excluded: chain D residue 674 MET Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 832 THR Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 872 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 8 optimal weight: 0.9980 chunk 53 optimal weight: 20.0000 chunk 149 optimal weight: 3.9990 chunk 48 optimal weight: 20.0000 chunk 90 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 151 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 153 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 ASN B 262 GLN ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 366 ASN D 677 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.233949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.166759 restraints weight = 19686.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.168647 restraints weight = 13625.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.169944 restraints weight = 9496.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.169738 restraints weight = 8554.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.169999 restraints weight = 8553.769| |-----------------------------------------------------------------------------| r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13943 Z= 0.138 Angle : 0.695 11.461 18919 Z= 0.315 Chirality : 0.042 0.147 1999 Planarity : 0.004 0.041 2449 Dihedral : 4.569 52.505 1872 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.00 % Allowed : 17.03 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.21), residues: 1689 helix: 0.48 (0.23), residues: 538 sheet: -1.48 (0.40), residues: 147 loop : -0.43 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 887 TYR 0.022 0.001 TYR C 374 PHE 0.021 0.001 PHE A 909 TRP 0.037 0.002 TRP D 297 HIS 0.005 0.001 HIS D 739 Details of bonding type rmsd covalent geometry : bond 0.00324 (13895) covalent geometry : angle 0.62042 (18847) hydrogen bonds : bond 0.02984 ( 416) hydrogen bonds : angle 4.94030 ( 1128) metal coordination : bond 0.00726 ( 48) metal coordination : angle 5.10962 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 218 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 ASN cc_start: 0.7312 (t0) cc_final: 0.6877 (t0) REVERT: A 513 MET cc_start: 0.7024 (ttt) cc_final: 0.5374 (ptm) REVERT: A 559 CYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7427 (p) REVERT: A 585 MET cc_start: 0.7550 (mpp) cc_final: 0.7028 (mpp) REVERT: A 588 HIS cc_start: 0.7779 (t70) cc_final: 0.7263 (t-90) REVERT: B 155 GLN cc_start: 0.6553 (tp40) cc_final: 0.6338 (tp40) REVERT: B 304 MET cc_start: 0.6303 (tpp) cc_final: 0.6050 (tpp) REVERT: C 64 GLN cc_start: 0.8630 (pt0) cc_final: 0.7541 (pm20) REVERT: C 226 ASP cc_start: 0.7784 (t0) cc_final: 0.7573 (t0) REVERT: D 297 TRP cc_start: 0.8023 (m-90) cc_final: 0.7503 (m-90) REVERT: D 374 GLN cc_start: 0.8877 (mt0) cc_final: 0.8464 (mt0) REVERT: D 420 LYS cc_start: 0.9264 (tptp) cc_final: 0.8809 (tptp) REVERT: D 544 ARG cc_start: 0.7068 (mmm-85) cc_final: 0.6532 (mmm-85) REVERT: D 548 MET cc_start: 0.7792 (mmp) cc_final: 0.7549 (mmp) REVERT: D 757 ASN cc_start: 0.8495 (t0) cc_final: 0.8178 (m-40) REVERT: D 864 MET cc_start: 0.7360 (mtm) cc_final: 0.6778 (mtm) outliers start: 29 outliers final: 25 residues processed: 234 average time/residue: 0.1208 time to fit residues: 41.7380 Evaluate side-chains 232 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 206 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 CYS Chi-restraints excluded: chain A residue 559 CYS Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 694 HIS Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 911 CYS Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain C residue 235 TRP Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain D residue 314 TRP Chi-restraints excluded: chain D residue 315 MET Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 364 MET Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 579 ASP Chi-restraints excluded: chain D residue 607 MET Chi-restraints excluded: chain D residue 669 SER Chi-restraints excluded: chain D residue 674 MET Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 832 THR Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 872 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 88 optimal weight: 0.0970 chunk 13 optimal weight: 0.6980 chunk 53 optimal weight: 0.0040 chunk 51 optimal weight: 7.9990 chunk 104 optimal weight: 0.1980 chunk 157 optimal weight: 0.7980 chunk 85 optimal weight: 10.0000 chunk 147 optimal weight: 3.9990 chunk 110 optimal weight: 0.4980 chunk 55 optimal weight: 7.9990 chunk 37 optimal weight: 0.0050 overall best weight: 0.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 886 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 366 ASN D 677 HIS D 776 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.237951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.172929 restraints weight = 19832.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.174922 restraints weight = 13106.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.175973 restraints weight = 8780.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.176821 restraints weight = 8216.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.177078 restraints weight = 7735.687| |-----------------------------------------------------------------------------| r_work (final): 0.4279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13943 Z= 0.108 Angle : 0.653 9.886 18919 Z= 0.302 Chirality : 0.041 0.139 1999 Planarity : 0.004 0.036 2449 Dihedral : 4.383 50.591 1872 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.86 % Allowed : 17.79 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.21), residues: 1689 helix: 0.56 (0.23), residues: 542 sheet: -1.36 (0.42), residues: 145 loop : -0.37 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 887 TYR 0.018 0.001 TYR D 481 PHE 0.022 0.001 PHE A 731 TRP 0.027 0.002 TRP C 235 HIS 0.006 0.001 HIS D 900 Details of bonding type rmsd covalent geometry : bond 0.00241 (13895) covalent geometry : angle 0.59691 (18847) hydrogen bonds : bond 0.02679 ( 416) hydrogen bonds : angle 4.72735 ( 1128) metal coordination : bond 0.00628 ( 48) metal coordination : angle 4.34984 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 228 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 ASN cc_start: 0.7283 (t0) cc_final: 0.6842 (t0) REVERT: A 585 MET cc_start: 0.7570 (mpp) cc_final: 0.7037 (mpp) REVERT: A 588 HIS cc_start: 0.7737 (t70) cc_final: 0.7260 (t-90) REVERT: A 887 ARG cc_start: 0.7566 (tmm-80) cc_final: 0.7356 (tmm-80) REVERT: B 155 GLN cc_start: 0.6760 (tp40) cc_final: 0.6361 (tp40) REVERT: B 235 TRP cc_start: 0.6185 (m-10) cc_final: 0.5530 (m-10) REVERT: C 64 GLN cc_start: 0.8483 (pt0) cc_final: 0.7457 (pm20) REVERT: C 65 HIS cc_start: 0.8022 (t70) cc_final: 0.7751 (t70) REVERT: C 226 ASP cc_start: 0.7640 (t0) cc_final: 0.7424 (t0) REVERT: D 297 TRP cc_start: 0.7948 (m-90) cc_final: 0.6906 (m-10) REVERT: D 374 GLN cc_start: 0.8754 (mt0) cc_final: 0.8242 (mt0) REVERT: D 420 LYS cc_start: 0.9206 (tptp) cc_final: 0.8994 (tptp) REVERT: D 544 ARG cc_start: 0.7076 (mmm-85) cc_final: 0.6455 (mmm-85) REVERT: D 761 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.6684 (ppp) REVERT: D 864 MET cc_start: 0.7341 (mtm) cc_final: 0.6746 (mtm) REVERT: D 880 MET cc_start: 0.8161 (mmm) cc_final: 0.7461 (mtt) outliers start: 27 outliers final: 21 residues processed: 242 average time/residue: 0.1062 time to fit residues: 37.9299 Evaluate side-chains 236 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 214 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 CYS Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 694 HIS Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain C residue 235 TRP Chi-restraints excluded: chain D residue 314 TRP Chi-restraints excluded: chain D residue 315 MET Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 364 MET Chi-restraints excluded: chain D residue 579 ASP Chi-restraints excluded: chain D residue 669 SER Chi-restraints excluded: chain D residue 674 MET Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 761 MET Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 832 THR Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 872 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 106 optimal weight: 0.3980 chunk 38 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 164 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 50 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 GLN ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 366 ASN D 677 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.235296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.170929 restraints weight = 19725.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.171619 restraints weight = 12328.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.171769 restraints weight = 8958.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.172553 restraints weight = 8810.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.172689 restraints weight = 8170.911| |-----------------------------------------------------------------------------| r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13943 Z= 0.132 Angle : 0.664 9.245 18919 Z= 0.308 Chirality : 0.042 0.157 1999 Planarity : 0.004 0.035 2449 Dihedral : 4.433 53.323 1872 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.07 % Allowed : 18.48 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.21), residues: 1689 helix: 0.60 (0.23), residues: 544 sheet: -1.43 (0.41), residues: 147 loop : -0.38 (0.21), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 115 TYR 0.018 0.001 TYR C 374 PHE 0.037 0.001 PHE A 909 TRP 0.040 0.002 TRP B 160 HIS 0.004 0.001 HIS D 900 Details of bonding type rmsd covalent geometry : bond 0.00314 (13895) covalent geometry : angle 0.60647 (18847) hydrogen bonds : bond 0.02775 ( 416) hydrogen bonds : angle 4.72351 ( 1128) metal coordination : bond 0.00636 ( 48) metal coordination : angle 4.40767 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 210 time to evaluate : 0.497 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 501 ASN cc_start: 0.7313 (t0) cc_final: 0.6869 (t0) REVERT: A 513 MET cc_start: 0.6555 (ttt) cc_final: 0.4932 (ptm) REVERT: A 585 MET cc_start: 0.7697 (mpp) cc_final: 0.7087 (mpp) REVERT: A 588 HIS cc_start: 0.7760 (t70) cc_final: 0.7274 (t-90) REVERT: A 887 ARG cc_start: 0.7605 (tmm-80) cc_final: 0.7294 (tmm-80) REVERT: B 155 GLN cc_start: 0.6985 (tp40) cc_final: 0.6681 (tp40) REVERT: C 64 GLN cc_start: 0.8545 (pt0) cc_final: 0.7390 (pm20) REVERT: C 137 MET cc_start: 0.3871 (ppp) cc_final: 0.3606 (ppp) REVERT: C 226 ASP cc_start: 0.7711 (t0) cc_final: 0.7492 (t0) REVERT: D 297 TRP cc_start: 0.7919 (m-90) cc_final: 0.7001 (m-10) REVERT: D 374 GLN cc_start: 0.8776 (mt0) cc_final: 0.8270 (mt0) REVERT: D 420 LYS cc_start: 0.9249 (tptp) cc_final: 0.9016 (tptp) REVERT: D 757 ASN cc_start: 0.8379 (t0) cc_final: 0.8096 (m-40) REVERT: D 761 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.6871 (ppp) outliers start: 30 outliers final: 27 residues processed: 228 average time/residue: 0.1055 time to fit residues: 35.9307 Evaluate side-chains 234 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 206 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 CYS Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 694 HIS Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain C residue 235 TRP Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 314 TRP Chi-restraints excluded: chain D residue 315 MET Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 364 MET Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 579 ASP Chi-restraints excluded: chain D residue 669 SER Chi-restraints excluded: chain D residue 674 MET Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 761 MET Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 832 THR Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 872 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 99 optimal weight: 0.1980 chunk 122 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 GLN ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 366 ASN D 677 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.222396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.168071 restraints weight = 17462.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.168030 restraints weight = 19890.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.165336 restraints weight = 15300.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.165126 restraints weight = 12072.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.165500 restraints weight = 11002.895| |-----------------------------------------------------------------------------| r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13943 Z= 0.196 Angle : 0.727 9.867 18919 Z= 0.337 Chirality : 0.044 0.162 1999 Planarity : 0.004 0.044 2449 Dihedral : 4.696 59.226 1872 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.48 % Allowed : 17.93 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.21), residues: 1689 helix: 0.46 (0.23), residues: 554 sheet: -1.68 (0.40), residues: 147 loop : -0.47 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 115 TYR 0.023 0.002 TYR C 374 PHE 0.051 0.002 PHE A 909 TRP 0.028 0.002 TRP C 185 HIS 0.005 0.001 HIS D 677 Details of bonding type rmsd covalent geometry : bond 0.00473 (13895) covalent geometry : angle 0.66230 (18847) hydrogen bonds : bond 0.03229 ( 416) hydrogen bonds : angle 4.87690 ( 1128) metal coordination : bond 0.00808 ( 48) metal coordination : angle 4.90399 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 216 time to evaluate : 0.526 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: A 501 ASN cc_start: 0.7090 (t0) cc_final: 0.6764 (t0) REVERT: A 559 CYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7418 (p) REVERT: A 588 HIS cc_start: 0.7587 (t70) cc_final: 0.7171 (t-90) REVERT: B 155 GLN cc_start: 0.7439 (tp40) cc_final: 0.7020 (tp40) REVERT: C 64 GLN cc_start: 0.8068 (pt0) cc_final: 0.7301 (pm20) REVERT: C 226 ASP cc_start: 0.7666 (t0) cc_final: 0.7459 (t0) REVERT: D 297 TRP cc_start: 0.6792 (m-90) cc_final: 0.6341 (m-10) REVERT: D 761 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.7035 (ppp) outliers start: 36 outliers final: 28 residues processed: 237 average time/residue: 0.1068 time to fit residues: 38.4327 Evaluate side-chains 238 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 208 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 CYS Chi-restraints excluded: chain A residue 559 CYS Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 694 HIS Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain C residue 235 TRP Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 314 TRP Chi-restraints excluded: chain D residue 315 MET Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 364 MET Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 579 ASP Chi-restraints excluded: chain D residue 669 SER Chi-restraints excluded: chain D residue 674 MET Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 761 MET Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 832 THR Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 872 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 29 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 124 optimal weight: 0.0770 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 101 optimal weight: 0.2980 chunk 119 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 GLN ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 366 ASN D 677 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.233457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.181085 restraints weight = 19598.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.178370 restraints weight = 15518.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.180587 restraints weight = 13968.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.180808 restraints weight = 10126.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.181674 restraints weight = 9040.053| |-----------------------------------------------------------------------------| r_work (final): 0.4312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13943 Z= 0.129 Angle : 0.694 14.919 18919 Z= 0.322 Chirality : 0.042 0.151 1999 Planarity : 0.004 0.036 2449 Dihedral : 4.598 58.114 1872 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.14 % Allowed : 18.83 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.21), residues: 1689 helix: 0.54 (0.23), residues: 549 sheet: -1.51 (0.41), residues: 145 loop : -0.43 (0.20), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 115 TYR 0.020 0.001 TYR C 374 PHE 0.033 0.001 PHE A 909 TRP 0.028 0.002 TRP C 235 HIS 0.005 0.001 HIS D 739 Details of bonding type rmsd covalent geometry : bond 0.00304 (13895) covalent geometry : angle 0.63390 (18847) hydrogen bonds : bond 0.02869 ( 416) hydrogen bonds : angle 4.74486 ( 1128) metal coordination : bond 0.00766 ( 48) metal coordination : angle 4.62740 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 213 time to evaluate : 0.532 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: A 501 ASN cc_start: 0.7169 (t0) cc_final: 0.6807 (t0) REVERT: A 513 MET cc_start: 0.6517 (ttt) cc_final: 0.5154 (ptm) REVERT: A 588 HIS cc_start: 0.7769 (t70) cc_final: 0.7283 (t-90) REVERT: A 887 ARG cc_start: 0.7918 (tmm-80) cc_final: 0.7673 (ttp-110) REVERT: B 155 GLN cc_start: 0.7389 (tp40) cc_final: 0.6986 (tp40) REVERT: C 64 GLN cc_start: 0.8273 (pt0) cc_final: 0.7339 (pm20) REVERT: C 137 MET cc_start: 0.3671 (ppp) cc_final: 0.3055 (tmm) REVERT: C 226 ASP cc_start: 0.7791 (t0) cc_final: 0.7587 (t0) REVERT: D 297 TRP cc_start: 0.7235 (m-90) cc_final: 0.6506 (m-10) REVERT: D 374 GLN cc_start: 0.8736 (mt0) cc_final: 0.8157 (mt0) REVERT: D 757 ASN cc_start: 0.8402 (t0) cc_final: 0.8009 (m-40) REVERT: D 761 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.6801 (ppp) outliers start: 31 outliers final: 27 residues processed: 232 average time/residue: 0.1074 time to fit residues: 37.2938 Evaluate side-chains 239 residues out of total 1502 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 211 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 CYS Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 694 HIS Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 250 HIS Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain C residue 235 TRP Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 314 TRP Chi-restraints excluded: chain D residue 315 MET Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 364 MET Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 579 ASP Chi-restraints excluded: chain D residue 669 SER Chi-restraints excluded: chain D residue 674 MET Chi-restraints excluded: chain D residue 684 VAL Chi-restraints excluded: chain D residue 761 MET Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 832 THR Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 872 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 107 optimal weight: 0.6980 chunk 161 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 116 optimal weight: 0.0870 chunk 36 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 115 optimal weight: 8.9990 chunk 88 optimal weight: 0.3980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 GLN ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 366 ASN D 677 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.225635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.180613 restraints weight = 17464.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.180073 restraints weight = 24445.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.182106 restraints weight = 22492.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.182537 restraints weight = 14484.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.186696 restraints weight = 12098.216| |-----------------------------------------------------------------------------| r_work (final): 0.4233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13943 Z= 0.128 Angle : 0.690 11.476 18919 Z= 0.322 Chirality : 0.042 0.192 1999 Planarity : 0.004 0.043 2449 Dihedral : 4.549 58.687 1872 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.14 % Allowed : 18.90 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.21), residues: 1689 helix: 0.61 (0.23), residues: 547 sheet: -1.63 (0.40), residues: 155 loop : -0.38 (0.21), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 556 TYR 0.019 0.001 TYR C 374 PHE 0.030 0.001 PHE A 909 TRP 0.028 0.002 TRP C 185 HIS 0.004 0.001 HIS D 739 Details of bonding type rmsd covalent geometry : bond 0.00303 (13895) covalent geometry : angle 0.64149 (18847) hydrogen bonds : bond 0.02820 ( 416) hydrogen bonds : angle 4.67152 ( 1128) metal coordination : bond 0.00705 ( 48) metal coordination : angle 4.19018 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2298.00 seconds wall clock time: 40 minutes 31.73 seconds (2431.73 seconds total)