Starting phenix.real_space_refine on Sun Oct 25 19:51:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11oi_75886/10_2026/11oi_75886.cif Found real_map, /net/cci-nas-00/data/ceres_data/11oi_75886/10_2026/11oi_75886.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/11oi_75886/10_2026/11oi_75886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11oi_75886/10_2026/11oi_75886.map" model { file = "/net/cci-nas-00/data/ceres_data/11oi_75886/10_2026/11oi_75886.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11oi_75886/10_2026/11oi_75886.cif" } 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= 0.003 sd= 0.983 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 149 5.16 5 C 11052 2.51 5 N 3142 2.21 5 O 3156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17511 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 4498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4498 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 539} Chain breaks: 2 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 4, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 32 Chain: "E" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2072 Classifications: {'peptide': 280} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 264} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 260 Unresolved non-hydrogen dihedrals: 174 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLU:plan': 6, 'PHE:plan': 5, 'ASP:plan': 5, 'ARG:plan': 5, 'HIS:plan': 1, 'GLN:plan1': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 121 Chain: "F" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 673 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 7, 'TRANS': 125} Chain breaks: 4 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 428 Unresolved non-hydrogen angles: 553 Unresolved non-hydrogen dihedrals: 367 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'ARG:plan': 12, 'PHE:plan': 9, 'ASP:plan': 8, 'GLN:plan1': 1, 'TYR:plan': 4, 'GLU:plan': 6, 'HIS:plan': 3, 'TRP:plan': 3, 'ASN:plan1': 4} Unresolved non-hydrogen planarities: 248 Chain: "D" Number of atoms: 3333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3333 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 399} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "A" Number of atoms: 2673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2673 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 320} Chain breaks: 2 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 4146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4146 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 539} Chain breaks: 2 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 443 Unresolved non-hydrogen angles: 569 Unresolved non-hydrogen dihedrals: 405 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'PHE:plan': 7, 'GLU:plan': 10, 'TRP:plan': 8, 'ARG:plan': 7, 'ASP:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 5, 'TYR:plan': 3, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 246 Chain: "C" 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: "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} 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: 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 1182 SG CYS C 494 51.675 26.429 118.938 1.00164.89 S ATOM 1202 SG CYS C 497 54.773 27.949 120.168 1.00169.63 S ATOM 1324 SG CYS C 514 51.694 29.916 120.972 1.00160.11 S ATOM 1347 SG CYS C 517 53.277 29.541 117.452 1.00162.78 S ATOM 1515 SG CYS C 537 56.938 26.776 107.546 1.00151.87 S ATOM 1536 SG CYS C 540 58.766 28.672 110.330 1.00157.56 S ATOM 1673 SG CYS C 559 60.314 26.061 108.721 1.00155.79 S ATOM 1695 SG CYS C 562 58.096 24.788 110.926 1.00156.23 S ATOM 1599 SG CYS C 549 53.435 24.500 95.734 1.00161.15 S ATOM 1633 SG CYS C 554 50.326 26.514 97.020 1.00178.09 S ATOM 1846 SG CYS C 583 51.914 23.473 98.782 1.00154.45 S ATOM 1872 SG CYS C 586 49.649 23.384 95.669 1.00154.17 S ATOM 7415 SG CYS D 494 65.586 81.347 106.076 1.00380.38 S ATOM 7435 SG CYS D 497 66.472 78.532 103.680 1.00386.16 S ATOM 7557 SG CYS D 514 62.777 79.051 104.831 1.00404.20 S ATOM 7576 SG CYS D 517 65.356 77.702 107.139 1.00411.37 S ATOM 7744 SG CYS D 537 73.312 77.974 115.045 1.00385.77 S ATOM 7765 SG CYS D 540 72.760 75.810 111.921 1.00386.07 S ATOM 7902 SG CYS D 559 76.148 76.663 112.662 1.00410.27 S ATOM 7924 SG CYS D 562 73.986 79.441 111.492 1.00413.59 S ATOM 7828 SG CYS D 549 76.221 81.104 126.548 1.00380.13 S ATOM 7862 SG CYS D 554 72.488 81.415 127.290 1.00371.45 S ATOM 8075 SG CYS D 583 74.005 83.355 124.336 1.00389.26 S ATOM 8101 SG CYS D 586 74.493 84.400 127.792 1.00385.94 S ATOM 10748 SG CYS A 494 83.378 40.775 61.185 1.00427.37 S ATOM 10768 SG CYS A 497 81.766 43.478 63.336 1.00427.56 S ATOM 10890 SG CYS A 514 79.504 41.424 61.058 1.00430.18 S ATOM 10909 SG CYS A 517 81.896 43.913 59.641 1.00422.71 S ATOM 11077 SG CYS A 537 91.160 48.109 55.309 1.00414.59 S ATOM 11098 SG CYS A 540 88.799 49.392 57.975 1.00409.18 S ATOM 11235 SG CYS A 559 92.354 50.223 58.385 1.00415.71 S ATOM 11257 SG CYS A 562 91.425 46.664 58.943 1.00411.96 S ATOM 11161 SG CYS A 549 99.749 48.004 46.193 1.00425.79 S ATOM 11195 SG CYS A 554 97.225 46.102 44.051 1.00428.13 S ATOM 11408 SG CYS A 583 98.209 44.749 47.570 1.00427.65 S ATOM 11434 SG CYS A 586 100.435 44.422 44.718 1.00417.25 S ATOM 14079 SG CYS B 494 53.524 84.730 37.949 1.00230.67 S ATOM 14099 SG CYS B 497 57.046 84.714 37.771 1.00234.15 S ATOM 14221 SG CYS B 514 55.480 81.644 36.378 1.00219.63 S ATOM 14244 SG CYS B 517 55.512 82.427 40.214 1.00222.60 S ATOM 14412 SG CYS B 537 53.624 85.515 50.513 1.00215.28 S ATOM 14433 SG CYS B 540 56.990 84.889 48.693 1.00224.41 S ATOM 14570 SG CYS B 559 56.750 87.761 50.625 1.00234.51 S ATOM 14592 SG CYS B 562 54.818 88.050 47.705 1.00233.28 S ATOM 14496 SG CYS B 549 45.354 85.470 60.291 1.00210.09 S ATOM 14530 SG CYS B 554 44.397 82.219 58.372 1.00200.23 S ATOM 14743 SG CYS B 583 44.845 85.629 56.500 1.00211.82 S ATOM 14769 SG CYS B 586 41.957 84.625 58.635 1.00203.81 S Time building chain proxies: 3.82, per 1000 atoms: 0.22 Number of scatterers: 17511 At special positions: 0 Unit cell: (131.623, 113.378, 212.422, 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 149 16.00 O 3156 8.00 N 3142 7.00 C 11052 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: 1.64 Conformation dependent library (CDL) restraints added in 693.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 517 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 497 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 514 " 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 586 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 554 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 583 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 549 " pdb=" ZN B1002 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 497 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 494 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 517 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 514 " pdb=" ZN B1003 " pdb="ZN ZN B1003 " - pdb=" SG CYS B 559 " pdb="ZN ZN B1003 " - pdb=" SG CYS B 540 " pdb="ZN ZN B1003 " - pdb=" SG CYS B 562 " pdb="ZN ZN B1003 " - pdb=" SG CYS B 537 " pdb=" ZN B1004 " pdb="ZN ZN B1004 " - pdb=" SG CYS B 586 " pdb="ZN ZN B1004 " - pdb=" SG CYS B 583 " pdb="ZN ZN B1004 " - pdb=" SG CYS B 554 " pdb="ZN ZN B1004 " - pdb=" SG CYS B 549 " pdb=" ZN C1002 " pdb="ZN ZN C1002 " - pdb=" SG CYS C 497 " pdb="ZN ZN C1002 " - pdb=" SG CYS C 517 " pdb="ZN ZN C1002 " - pdb=" SG CYS C 494 " pdb="ZN ZN C1002 " - pdb=" SG CYS C 514 " pdb=" ZN C1003 " pdb="ZN ZN C1003 " - pdb=" SG CYS C 559 " pdb="ZN ZN C1003 " - pdb=" SG CYS C 540 " pdb="ZN ZN C1003 " - pdb=" SG CYS C 562 " pdb="ZN ZN C1003 " - pdb=" SG CYS C 537 " pdb=" ZN C1004 " pdb="ZN ZN C1004 " - pdb=" SG CYS C 583 " pdb="ZN ZN C1004 " - pdb=" SG CYS C 586 " pdb="ZN ZN C1004 " - pdb=" SG CYS C 549 " pdb="ZN ZN C1004 " - pdb=" SG CYS C 554 " pdb=" ZN D1002 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 517 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 494 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 514 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 497 " pdb=" ZN D1003 " pdb="ZN ZN D1003 " - pdb=" SG CYS D 540 " pdb="ZN ZN D1003 " - pdb=" SG CYS D 559 " pdb="ZN ZN D1003 " - pdb=" SG CYS D 562 " pdb="ZN ZN D1003 " - pdb=" SG CYS D 537 " pdb=" ZN D1004 " pdb="ZN ZN D1004 " - pdb=" SG CYS D 586 " pdb="ZN ZN D1004 " - pdb=" SG CYS D 554 " pdb="ZN ZN D1004 " - pdb=" SG CYS D 583 " pdb="ZN ZN D1004 " - pdb=" SG CYS D 549 " Number of angles added : 72 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4264 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 14 sheets defined 39.0% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'C' and resid 312 through 317 removed outlier: 3.726A pdb=" N GLY C 317 " --> pdb=" O TRP C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 342 No H-bonds generated for 'chain 'C' and resid 340 through 342' Processing helix chain 'C' and resid 349 through 354 removed outlier: 3.976A pdb=" N ALA C 353 " --> pdb=" O SER C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 362 Processing helix chain 'C' and resid 362 through 381 Processing helix chain 'C' and resid 396 through 412 Proline residue: C 405 - end of helix Processing helix chain 'C' and resid 419 through 423 removed outlier: 3.734A pdb=" N GLU C 423 " --> pdb=" O LYS C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 485 Processing helix chain 'C' and resid 514 through 525 removed outlier: 3.686A pdb=" N CYS C 524 " --> pdb=" O CYS C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 567 Processing helix chain 'C' and resid 570 through 578 Processing helix chain 'C' and resid 600 through 611 Processing helix chain 'C' and resid 627 through 631 Processing helix chain 'C' and resid 644 through 653 Processing helix chain 'C' and resid 666 through 677 Processing helix chain 'C' and resid 691 through 698 Processing helix chain 'C' and resid 728 through 742 removed outlier: 3.855A pdb=" N PHE C 732 " --> pdb=" O GLY C 728 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 774 Processing helix chain 'C' and resid 783 through 785 No H-bonds generated for 'chain 'C' and resid 783 through 785' Processing helix chain 'C' and resid 814 through 819 removed outlier: 3.510A pdb=" N LEU C 819 " --> pdb=" O GLN C 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 860 through 868 Processing helix chain 'C' and resid 881 through 890 Processing helix chain 'C' and resid 894 through 903 Processing helix chain 'C' and resid 904 through 909 removed outlier: 3.778A pdb=" N PHE C 909 " --> pdb=" O LYS C 906 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 631 removed outlier: 3.918A pdb=" N ARG E 631 " --> pdb=" O ALA E 628 " (cutoff:3.500A) Processing helix chain 'E' and resid 644 through 653 Processing helix chain 'E' and resid 666 through 677 Processing helix chain 'E' and resid 691 through 699 Processing helix chain 'E' and resid 728 through 742 removed outlier: 4.106A pdb=" N PHE E 732 " --> pdb=" O GLY E 728 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU E 733 " --> pdb=" O ARG E 729 " (cutoff:3.500A) Processing helix chain 'E' and resid 762 through 774 Processing helix chain 'E' and resid 783 through 785 No H-bonds generated for 'chain 'E' and resid 783 through 785' Processing helix chain 'E' and resid 814 through 819 removed outlier: 3.953A pdb=" N CYS E 818 " --> pdb=" O GLU E 814 " (cutoff:3.500A) Processing helix chain 'E' and resid 860 through 869 Processing helix chain 'E' and resid 881 through 890 Processing helix chain 'E' and resid 894 through 903 Processing helix chain 'E' and resid 904 through 909 removed outlier: 4.045A pdb=" N TYR E 908 " --> pdb=" O PRO E 904 " (cutoff:3.500A) Processing helix chain 'F' and resid 644 through 654 Processing helix chain 'F' and resid 730 through 742 Processing helix chain 'F' and resid 762 through 774 Processing helix chain 'F' and resid 783 through 785 No H-bonds generated for 'chain 'F' and resid 783 through 785' Processing helix chain 'F' and resid 894 through 903 Processing helix chain 'F' and resid 904 through 906 No H-bonds generated for 'chain 'F' and resid 904 through 906' Processing helix chain 'D' and resid 476 through 485 Processing helix chain 'D' and resid 489 through 493 removed outlier: 3.534A pdb=" N ILE D 493 " --> pdb=" O ILE D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 524 Processing helix chain 'D' and resid 559 through 567 Processing helix chain 'D' and resid 570 through 578 Processing helix chain 'D' and resid 600 through 609 Processing helix chain 'D' and resid 644 through 653 removed outlier: 3.531A pdb=" N LEU D 648 " --> pdb=" O ALA D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 677 Processing helix chain 'D' and resid 691 through 699 Processing helix chain 'D' and resid 728 through 742 Processing helix chain 'D' and resid 762 through 774 Processing helix chain 'D' and resid 783 through 785 No H-bonds generated for 'chain 'D' and resid 783 through 785' Processing helix chain 'D' and resid 835 through 839 Processing helix chain 'D' and resid 860 through 868 removed outlier: 3.778A pdb=" N PHE D 868 " --> pdb=" O MET D 864 " (cutoff:3.500A) Processing helix chain 'D' and resid 881 through 890 Processing helix chain 'D' and resid 894 through 903 Processing helix chain 'D' and resid 904 through 909 removed outlier: 3.789A pdb=" N TYR D 908 " --> pdb=" O PRO D 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 485 Processing helix chain 'A' and resid 489 through 493 Processing helix chain 'A' and resid 514 through 524 Processing helix chain 'A' and resid 559 through 567 Processing helix chain 'A' and resid 570 through 578 Processing helix chain 'A' and resid 600 through 609 Processing helix chain 'A' and resid 644 through 653 Processing helix chain 'A' and resid 666 through 677 Processing helix chain 'A' and resid 691 through 699 Processing helix chain 'A' and resid 725 through 742 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 894 through 903 Processing helix chain 'A' and resid 904 through 909 removed outlier: 4.326A pdb=" N TYR A 908 " --> pdb=" O PRO A 904 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE A 909 " --> pdb=" O LEU A 905 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 904 through 909' Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.608A pdb=" N GLY B 317 " --> pdb=" O TRP B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 362 through 381 Processing helix chain 'B' and resid 396 through 412 Proline residue: B 405 - end of helix Processing helix chain 'B' and resid 418 through 423 removed outlier: 3.898A pdb=" N GLU B 423 " --> pdb=" O LYS B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 485 Processing helix chain 'B' and resid 489 through 493 Processing helix chain 'B' and resid 514 through 524 Processing helix chain 'B' and resid 560 through 567 Processing helix chain 'B' and resid 570 through 578 removed outlier: 3.686A pdb=" N GLU B 578 " --> pdb=" O ALA B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 611 Processing helix chain 'B' and resid 627 through 631 removed outlier: 3.645A pdb=" N ARG B 631 " --> pdb=" O ALA B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 653 Processing helix chain 'B' and resid 666 through 677 Processing helix chain 'B' and resid 691 through 698 Processing helix chain 'B' and resid 725 through 727 No H-bonds generated for 'chain 'B' and resid 725 through 727' Processing helix chain 'B' and resid 728 through 742 removed outlier: 4.124A pdb=" N PHE B 732 " --> pdb=" O GLY B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 774 Processing helix chain 'B' and resid 783 through 785 No H-bonds generated for 'chain 'B' and resid 783 through 785' Processing helix chain 'B' and resid 814 through 819 removed outlier: 4.041A pdb=" N CYS B 818 " --> pdb=" O GLU B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 868 Processing helix chain 'B' and resid 881 through 890 Processing helix chain 'B' and resid 894 through 903 Processing helix chain 'B' and resid 904 through 909 removed outlier: 3.903A pdb=" N PHE B 909 " --> pdb=" O LYS B 906 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 336 through 339 removed outlier: 3.715A pdb=" N SER C 337 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N TRP C 297 " --> pdb=" O MET C 345 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET C 345 " --> pdb=" O TRP C 297 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AA3, first strand: chain 'C' and resid 824 through 825 Processing sheet with id=AA4, first strand: chain 'E' and resid 657 through 663 removed outlier: 6.021A pdb=" N ILE E 634 " --> pdb=" O VAL E 657 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG E 659 " --> pdb=" O ILE E 634 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ARG E 635 " --> pdb=" O LEU E 703 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE E 705 " --> pdb=" O ARG E 635 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N LEU E 637 " --> pdb=" O ILE E 705 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLY E 706 " --> pdb=" O LEU E 754 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU E 756 " --> pdb=" O GLY E 706 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE E 755 " --> pdb=" O TRP E 795 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 824 through 825 removed outlier: 4.416A pdb=" N VAL E 850 " --> pdb=" O ASP E 857 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 657 through 663 removed outlier: 7.438A pdb=" N ILE F 634 " --> pdb=" O ASP F 658 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N TYR F 660 " --> pdb=" O ILE F 634 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL F 636 " --> pdb=" O TYR F 660 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ALA F 662 " --> pdb=" O VAL F 636 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N SER F 638 " --> pdb=" O ALA F 662 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ARG F 635 " --> pdb=" O LEU F 703 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILE F 705 " --> pdb=" O ARG F 635 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU F 637 " --> pdb=" O ILE F 705 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL F 704 " --> pdb=" O LEU F 754 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N GLU F 756 " --> pdb=" O VAL F 704 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLY F 706 " --> pdb=" O GLU F 756 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N VAL F 758 " --> pdb=" O GLY F 706 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 681 through 683 removed outlier: 6.768A pdb=" N TYR D 660 " --> pdb=" O MET D 682 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU D 703 " --> pdb=" O ARG D 635 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL D 704 " --> pdb=" O LEU D 754 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N GLU D 756 " --> pdb=" O VAL D 704 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 824 through 825 Processing sheet with id=AA9, first strand: chain 'A' and resid 681 through 683 removed outlier: 6.872A pdb=" N TYR A 660 " --> pdb=" O MET A 682 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 295 through 298 removed outlier: 3.587A pdb=" N ARG B 309 " --> pdb=" O MET B 329 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET B 329 " --> pdb=" O ARG B 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 546 through 548 removed outlier: 3.510A pdb=" N PHE B 558 " --> pdb=" O LEU B 547 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 634 through 635 removed outlier: 7.406A pdb=" N ILE B 634 " --> pdb=" O ASP B 658 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 754 through 758 removed outlier: 4.046A pdb=" N PHE B 755 " --> pdb=" O TRP B 795 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 824 through 825 removed outlier: 3.621A pdb=" N VAL B 850 " --> pdb=" O ASP B 857 " (cutoff:3.500A) 602 hydrogen bonds defined for protein. 1680 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: 2.65 Time building geometry restraints manager: 2.14 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: 5896 1.34 - 1.46: 4006 1.46 - 1.58: 7787 1.58 - 1.70: 0 1.70 - 1.82: 205 Bond restraints: 17894 Sorted by residual: bond pdb=" CA PRO A 619 " pdb=" C PRO A 619 " ideal model delta sigma weight residual 1.514 1.499 0.015 5.50e-03 3.31e+04 7.74e+00 bond pdb=" C PHE B 827 " pdb=" N SER B 828 " ideal model delta sigma weight residual 1.332 1.295 0.037 1.40e-02 5.10e+03 7.05e+00 bond pdb=" C LEU C 798 " pdb=" N PRO C 799 " ideal model delta sigma weight residual 1.333 1.307 0.026 1.01e-02 9.80e+03 6.86e+00 bond pdb=" N GLN C 615 " pdb=" CA GLN C 615 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.25e-02 6.40e+03 5.94e+00 bond pdb=" N ASP C 614 " pdb=" CA ASP C 614 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.18e-02 7.18e+03 5.82e+00 ... (remaining 17889 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 23778 2.00 - 4.01: 425 4.01 - 6.01: 45 6.01 - 8.01: 7 8.01 - 10.02: 4 Bond angle restraints: 24259 Sorted by residual: angle pdb=" C GLN C 615 " pdb=" CA GLN C 615 " pdb=" CB GLN C 615 " ideal model delta sigma weight residual 111.09 102.22 8.87 2.27e+00 1.94e-01 1.53e+01 angle pdb=" N ILE F 643 " pdb=" CA ILE F 643 " pdb=" C ILE F 643 " ideal model delta sigma weight residual 112.29 109.44 2.85 9.40e-01 1.13e+00 9.20e+00 angle pdb=" C CYS A 540 " pdb=" N CYS A 541 " pdb=" CA CYS A 541 " ideal model delta sigma weight residual 122.78 127.21 -4.43 1.52e+00 4.33e-01 8.48e+00 angle pdb=" CA LEU C 730 " pdb=" CB LEU C 730 " pdb=" CG LEU C 730 " ideal model delta sigma weight residual 116.30 106.28 10.02 3.50e+00 8.16e-02 8.19e+00 angle pdb=" C PHE B 851 " pdb=" N MET B 852 " pdb=" CA MET B 852 " ideal model delta sigma weight residual 122.42 118.06 4.36 1.55e+00 4.16e-01 7.89e+00 ... (remaining 24254 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 9478 17.45 - 34.90: 839 34.90 - 52.35: 203 52.35 - 69.79: 49 69.79 - 87.24: 12 Dihedral angle restraints: 10581 sinusoidal: 3957 harmonic: 6624 Sorted by residual: dihedral pdb=" CA ASP C 702 " pdb=" C ASP C 702 " pdb=" N LEU C 703 " pdb=" CA LEU C 703 " ideal model delta harmonic sigma weight residual 180.00 160.81 19.19 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA PHE B 640 " pdb=" C PHE B 640 " pdb=" N ASP B 641 " pdb=" CA ASP B 641 " ideal model delta harmonic sigma weight residual -180.00 -161.05 -18.95 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA GLU C 523 " pdb=" C GLU C 523 " pdb=" N CYS C 524 " pdb=" CA CYS C 524 " ideal model delta harmonic sigma weight residual 180.00 -161.65 -18.35 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 10578 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1738 0.040 - 0.080: 677 0.080 - 0.119: 190 0.119 - 0.159: 19 0.159 - 0.199: 2 Chirality restraints: 2626 Sorted by residual: chirality pdb=" CA GLN C 615 " pdb=" N GLN C 615 " pdb=" C GLN C 615 " pdb=" CB GLN C 615 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.90e-01 chirality pdb=" CA TRP C 601 " pdb=" N TRP C 601 " pdb=" C TRP C 601 " pdb=" CB TRP C 601 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CA ASN C 553 " pdb=" N ASN C 553 " pdb=" C ASN C 553 " pdb=" CB ASN C 553 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.55e-01 ... (remaining 2623 not shown) Planarity restraints: 3186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 732 " -0.015 2.00e-02 2.50e+03 1.69e-02 4.99e+00 pdb=" CG PHE B 732 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE B 732 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE B 732 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 732 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 732 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 732 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 793 " -0.018 2.00e-02 2.50e+03 1.20e-02 2.86e+00 pdb=" CG TYR B 793 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR B 793 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR B 793 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 793 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 793 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 793 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 793 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 731 " -0.012 2.00e-02 2.50e+03 1.25e-02 2.73e+00 pdb=" CG PHE A 731 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE A 731 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 731 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 731 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 731 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 731 " -0.001 2.00e-02 2.50e+03 ... (remaining 3183 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 8956 2.97 - 3.46: 18549 3.46 - 3.94: 27276 3.94 - 4.42: 32396 4.42 - 4.90: 49252 Nonbonded interactions: 136429 Sorted by model distance: nonbonded pdb=" O MET D 852 " pdb=" OD1 ASN D 853 " model vdw 2.493 3.040 nonbonded pdb=" OE1 GLN C 615 " pdb=" NH2 ARG C 771 " model vdw 2.499 3.120 nonbonded pdb=" OE1 GLU C 814 " pdb=" O SER C 828 " model vdw 2.540 3.040 nonbonded pdb=" O THR C 875 " pdb=" OG1 THR C 875 " model vdw 2.551 3.040 nonbonded pdb=" N THR C 808 " pdb=" OG1 THR C 808 " model vdw 2.554 2.496 ... (remaining 136424 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' selection = (chain 'C' and (resid 289 or (resid 290 and (name N or name CA or name C or name \ O or name CB )) or resid 291 or (resid 292 and (name N or name CA or name C or \ name O or name CB )) or resid 293 or (resid 294 through 297 and (name N or name \ CA or name C or name O or name CB )) or resid 298 or (resid 299 through 301 and \ (name N or name CA or name C or name O or name CB )) or resid 302 or (resid 303 \ through 307 and (name N or name CA or name C or name O or name CB )) or (resid 3 \ 08 through 316 and (name N or name CA or name C or name O or name CB )) or resid \ 317 or (resid 318 through 323 and (name N or name CA or name C or name O or nam \ e CB )) or resid 324 or (resid 325 through 331 and (name N or name CA or name C \ or name O or name CB )) or resid 332 or (resid 333 and (name N or name CA or nam \ e C or name O or name CB )) or resid 334 or (resid 335 through 380 and (name N o \ r name CA or name C or name O or name CB )) or resid 381 or (resid 382 through 4 \ 11 and (name N or name CA or name C or name O or name CB )) or resid 412 through \ 413 or (resid 414 through 417 and (name N or name CA or name C or name O or nam \ e CB )) or resid 418 or (resid 419 through 420 and (name N or name CA or name C \ or name O or name CB )) or resid 421 or (resid 422 through 470 and (name N or na \ me CA or name C or name O or name CB )) or resid 471 through 1004)) } 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: 2.100 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.420 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 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:1.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 22.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 17942 Z= 0.276 Angle : 0.740 15.247 24331 Z= 0.354 Chirality : 0.044 0.199 2626 Planarity : 0.005 0.053 3186 Dihedral : 14.555 87.242 6317 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 1.18 % Allowed : 9.35 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % 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 (0.18), residues: 2274 helix: 0.32 (0.19), residues: 779 sheet: -1.44 (0.36), residues: 221 loop : -0.49 (0.18), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 688 TYR 0.028 0.002 TYR B 793 PHE 0.039 0.003 PHE B 732 TRP 0.026 0.002 TRP D 795 HIS 0.006 0.002 HIS C 588 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.28 (17894) covalent geometry : angle 0.65803 / 0.35 (24259) hydrogen bonds : bond 0.14560 / 9.49 ( 602) hydrogen bonds : angle 6.55892 / 4.64 ( 1680) metal coordination : bond 0.01305 / 0.87 ( 48) metal coordination : angle 6.24750 / 4.19 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 336 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 329 MET cc_start: 0.8640 (tpp) cc_final: 0.8250 (tmm) REVERT: C 548 MET cc_start: 0.8293 (mmp) cc_final: 0.8003 (mmp) REVERT: C 614 ASP cc_start: 0.8987 (OUTLIER) cc_final: 0.8509 (p0) REVERT: C 720 ARG cc_start: 0.7406 (ttt-90) cc_final: 0.7108 (mtp85) REVERT: C 761 MET cc_start: 0.8789 (ppp) cc_final: 0.8497 (ptt) REVERT: C 834 THR cc_start: 0.8788 (m) cc_final: 0.8459 (p) REVERT: E 781 ASP cc_start: 0.6093 (t0) cc_final: 0.5552 (t0) REVERT: E 848 PHE cc_start: 0.8380 (m-80) cc_final: 0.7900 (m-80) REVERT: E 849 PRO cc_start: 0.9161 (Cg_endo) cc_final: 0.8635 (Cg_exo) REVERT: D 548 MET cc_start: 0.2680 (mmt) cc_final: 0.0287 (pmm) REVERT: D 682 MET cc_start: 0.7545 (ttt) cc_final: 0.6484 (mpp) REVERT: D 739 HIS cc_start: 0.8187 (t-90) cc_final: 0.7868 (t-90) REVERT: D 793 TYR cc_start: 0.8512 (m-10) cc_final: 0.8102 (m-80) REVERT: D 833 ILE cc_start: 0.3504 (OUTLIER) cc_final: 0.2809 (tp) REVERT: D 851 PHE cc_start: 0.7552 (OUTLIER) cc_final: 0.6745 (t80) REVERT: D 859 LEU cc_start: 0.9200 (mt) cc_final: 0.8741 (mt) REVERT: D 880 MET cc_start: 0.5971 (mtm) cc_final: 0.5359 (ttm) REVERT: A 650 LEU cc_start: 0.7528 (mt) cc_final: 0.7239 (mt) REVERT: A 683 TYR cc_start: 0.4023 (m-80) cc_final: 0.2858 (m-80) REVERT: A 731 PHE cc_start: 0.9234 (t80) cc_final: 0.8946 (t80) REVERT: A 744 LYS cc_start: 0.7917 (mmtm) cc_final: 0.7661 (tptt) REVERT: A 757 ASN cc_start: 0.9069 (t0) cc_final: 0.8799 (t0) REVERT: B 489 ASN cc_start: 0.8916 (m-40) cc_final: 0.8687 (t0) REVERT: B 607 MET cc_start: 0.9115 (ttm) cc_final: 0.8741 (tpp) REVERT: B 886 GLN cc_start: 0.8545 (tt0) cc_final: 0.8176 (tm-30) outliers start: 20 outliers final: 10 residues processed: 356 average time/residue: 0.1370 time to fit residues: 71.4912 Evaluate side-chains 238 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 225 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 615 GLN Chi-restraints excluded: chain C residue 808 THR Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 840 ILE Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain E residue 808 THR Chi-restraints excluded: chain D residue 727 THR Chi-restraints excluded: chain D residue 833 ILE Chi-restraints excluded: chain D residue 840 ILE Chi-restraints excluded: chain D residue 851 PHE Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 808 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: [216, 98, 194, 227, 107, 10, 66, 130, 124, 103, 200] chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.3980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 615 GLN ** C 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 900 HIS A 615 GLN B 516 ASN ** B 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 900 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.183664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.141337 restraints weight = 61465.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.135686 restraints weight = 41259.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.137064 restraints weight = 33429.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.136902 restraints weight = 27330.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.137238 restraints weight = 24526.388| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17942 Z= 0.140 Angle : 0.665 13.328 24331 Z= 0.314 Chirality : 0.042 0.172 2626 Planarity : 0.004 0.075 3186 Dihedral : 4.878 57.778 2543 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.78 % Allowed : 13.55 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % 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 (0.18), residues: 2274 helix: 0.68 (0.19), residues: 785 sheet: -1.23 (0.37), residues: 219 loop : -0.50 (0.18), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 771 TYR 0.020 0.002 TYR A 793 PHE 0.031 0.002 PHE C 732 TRP 0.017 0.001 TRP D 860 HIS 0.012 0.001 HIS D 873 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (17894) covalent geometry : angle 0.60416 / 0.31 (24259) hydrogen bonds : bond 0.03767 / 2.44 ( 602) hydrogen bonds : angle 5.20140 / 3.73 ( 1680) metal coordination : bond 0.00738 / 0.51 ( 48) metal coordination : angle 5.16100 / 3.43 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 247 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 329 MET cc_start: 0.8674 (tpp) cc_final: 0.8330 (tmm) REVERT: C 548 MET cc_start: 0.8423 (mmp) cc_final: 0.8055 (mmp) REVERT: C 715 ILE cc_start: 0.9357 (tt) cc_final: 0.8795 (pt) REVERT: C 739 HIS cc_start: 0.7614 (OUTLIER) cc_final: 0.6449 (t-90) REVERT: C 761 MET cc_start: 0.8949 (ppp) cc_final: 0.8414 (ptt) REVERT: C 882 ARG cc_start: 0.8371 (ttp-110) cc_final: 0.8159 (ttp80) REVERT: E 621 LYS cc_start: 0.1210 (pttt) cc_final: 0.0797 (pttm) REVERT: E 780 ILE cc_start: 0.7606 (mp) cc_final: 0.7270 (mp) REVERT: E 781 ASP cc_start: 0.5849 (t0) cc_final: 0.5161 (t70) REVERT: E 814 GLU cc_start: 0.4366 (mp0) cc_final: 0.3765 (pm20) REVERT: E 844 LYS cc_start: 0.4839 (tptp) cc_final: 0.4134 (mmtt) REVERT: E 876 ASP cc_start: 0.7942 (p0) cc_final: 0.7661 (p0) REVERT: E 897 VAL cc_start: 0.7242 (t) cc_final: 0.7003 (t) REVERT: D 548 MET cc_start: 0.3963 (mmt) cc_final: 0.0356 (pmm) REVERT: D 682 MET cc_start: 0.7488 (ttt) cc_final: 0.6565 (mpp) REVERT: D 739 HIS cc_start: 0.7920 (t-90) cc_final: 0.6090 (t-90) REVERT: D 793 TYR cc_start: 0.8309 (m-10) cc_final: 0.8070 (m-80) REVERT: D 851 PHE cc_start: 0.7554 (OUTLIER) cc_final: 0.6735 (t80) REVERT: D 880 MET cc_start: 0.5814 (mtm) cc_final: 0.5505 (ttm) REVERT: A 600 ASP cc_start: 0.3109 (OUTLIER) cc_final: 0.2883 (m-30) REVERT: A 674 MET cc_start: -0.3788 (mtt) cc_final: -0.4100 (mtm) REVERT: A 703 LEU cc_start: 0.9280 (tp) cc_final: 0.9044 (mm) REVERT: A 739 HIS cc_start: 0.8448 (t-90) cc_final: 0.8050 (t-90) REVERT: A 744 LYS cc_start: 0.7963 (mmtm) cc_final: 0.7717 (tptt) REVERT: A 757 ASN cc_start: 0.9096 (t0) cc_final: 0.8772 (t0) REVERT: B 489 ASN cc_start: 0.8834 (m-40) cc_final: 0.8545 (t0) REVERT: B 513 MET cc_start: 0.7357 (tpp) cc_final: 0.7076 (tpp) REVERT: B 523 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7722 (mm-30) REVERT: B 607 MET cc_start: 0.9067 (ttm) cc_final: 0.8760 (tpp) REVERT: B 701 PHE cc_start: 0.7652 (m-80) cc_final: 0.7273 (m-80) REVERT: B 723 LEU cc_start: 0.8358 (tt) cc_final: 0.7931 (tp) outliers start: 47 outliers final: 27 residues processed: 281 average time/residue: 0.1288 time to fit residues: 54.3137 Evaluate side-chains 230 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 808 THR Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain E residue 695 ILE Chi-restraints excluded: chain E residue 769 ILE Chi-restraints excluded: chain E residue 858 ILE Chi-restraints excluded: chain E residue 877 VAL Chi-restraints excluded: chain D residue 613 HIS Chi-restraints excluded: chain D residue 640 PHE Chi-restraints excluded: chain D residue 727 THR Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 833 ILE Chi-restraints excluded: chain D residue 840 ILE Chi-restraints excluded: chain D residue 851 PHE Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 557 CYS Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 786 SER Chi-restraints excluded: chain B residue 808 THR Chi-restraints excluded: chain B residue 818 CYS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 894 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: [218, 200, 174, 227, 190, 146, 152, 95, 215, 133, 13] chunk 218 optimal weight: 0.0870 chunk 200 optimal weight: 0.0470 chunk 174 optimal weight: 40.0000 chunk 227 optimal weight: 1.9990 chunk 190 optimal weight: 0.0670 chunk 146 optimal weight: 10.0000 chunk 152 optimal weight: 30.0000 chunk 95 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 757 ASN D 551 ASN ** D 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 776 ASN B 711 ASN ** B 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.180706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.132500 restraints weight = 56575.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.135206 restraints weight = 31949.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.135209 restraints weight = 18012.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.135822 restraints weight = 17567.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.135965 restraints weight = 15615.983| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17942 Z= 0.130 Angle : 0.618 11.457 24331 Z= 0.291 Chirality : 0.041 0.158 2626 Planarity : 0.004 0.076 3186 Dihedral : 4.428 57.773 2535 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.14 % Allowed : 15.80 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.18), residues: 2274 helix: 0.79 (0.19), residues: 799 sheet: -1.45 (0.35), residues: 233 loop : -0.49 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 771 TYR 0.023 0.001 TYR A 724 PHE 0.020 0.002 PHE C 732 TRP 0.016 0.001 TRP A 795 HIS 0.008 0.001 HIS D 789 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (17894) covalent geometry : angle 0.56644 / 0.29 (24259) hydrogen bonds : bond 0.03164 / 2.04 ( 602) hydrogen bonds : angle 4.87298 / 3.51 ( 1680) metal coordination : bond 0.00600 / 0.41 ( 48) metal coordination : angle 4.57218 / 3.03 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 225 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 329 MET cc_start: 0.8648 (tpp) cc_final: 0.8331 (mmp) REVERT: C 523 GLU cc_start: 0.8642 (mt-10) cc_final: 0.7985 (mt-10) REVERT: C 548 MET cc_start: 0.8382 (mmp) cc_final: 0.8096 (mmp) REVERT: C 555 CYS cc_start: 0.7799 (m) cc_final: 0.6901 (m) REVERT: C 666 CYS cc_start: 0.8390 (t) cc_final: 0.7692 (t) REVERT: C 739 HIS cc_start: 0.7703 (OUTLIER) cc_final: 0.6449 (t-90) REVERT: C 761 MET cc_start: 0.8903 (ppp) cc_final: 0.8515 (ptt) REVERT: E 621 LYS cc_start: 0.1243 (pttt) cc_final: 0.0731 (pttm) REVERT: E 812 LYS cc_start: 0.5417 (ttmm) cc_final: 0.4963 (ttpt) REVERT: E 817 GLU cc_start: 0.2895 (OUTLIER) cc_final: 0.2154 (pt0) REVERT: E 829 LYS cc_start: 0.6020 (tttt) cc_final: 0.5678 (tptt) REVERT: D 548 MET cc_start: 0.3895 (mmt) cc_final: 0.0094 (pmm) REVERT: D 682 MET cc_start: 0.7332 (ttt) cc_final: 0.6335 (mpp) REVERT: D 739 HIS cc_start: 0.8087 (t-90) cc_final: 0.6355 (t-90) REVERT: D 779 MET cc_start: 0.7426 (tmm) cc_final: 0.7147 (tmm) REVERT: D 793 TYR cc_start: 0.8377 (m-10) cc_final: 0.8084 (m-80) REVERT: D 851 PHE cc_start: 0.7503 (OUTLIER) cc_final: 0.6653 (t80) REVERT: D 880 MET cc_start: 0.6694 (mtm) cc_final: 0.6384 (ttm) REVERT: A 600 ASP cc_start: 0.2746 (OUTLIER) cc_final: 0.2517 (m-30) REVERT: A 739 HIS cc_start: 0.8395 (t-90) cc_final: 0.8007 (t-90) REVERT: A 757 ASN cc_start: 0.9088 (t0) cc_final: 0.8803 (t0) REVERT: A 795 TRP cc_start: 0.8444 (m-90) cc_final: 0.7759 (m-90) REVERT: B 489 ASN cc_start: 0.8833 (m-40) cc_final: 0.8558 (t0) REVERT: B 513 MET cc_start: 0.7312 (tpp) cc_final: 0.7010 (tpp) REVERT: B 607 MET cc_start: 0.9063 (ttm) cc_final: 0.8757 (tpp) REVERT: B 885 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7848 (ttt180) REVERT: B 886 GLN cc_start: 0.8516 (tt0) cc_final: 0.8016 (pp30) outliers start: 53 outliers final: 34 residues processed: 261 average time/residue: 0.1302 time to fit residues: 51.0592 Evaluate side-chains 244 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 205 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 808 THR Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain E residue 808 THR Chi-restraints excluded: chain E residue 817 GLU Chi-restraints excluded: chain E residue 819 LEU Chi-restraints excluded: chain E residue 848 PHE Chi-restraints excluded: chain E residue 858 ILE Chi-restraints excluded: chain E residue 877 VAL Chi-restraints excluded: chain D residue 551 ASN Chi-restraints excluded: chain D residue 613 HIS Chi-restraints excluded: chain D residue 615 GLN Chi-restraints excluded: chain D residue 640 PHE Chi-restraints excluded: chain D residue 727 THR Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 829 LYS Chi-restraints excluded: chain D residue 833 ILE Chi-restraints excluded: chain D residue 840 ILE Chi-restraints excluded: chain D residue 851 PHE Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 541 CYS Chi-restraints excluded: chain B residue 557 CYS Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 669 SER Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 786 SER Chi-restraints excluded: chain B residue 818 CYS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 885 ARG Chi-restraints excluded: chain B residue 894 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: [21, 187, 176, 119, 6, 219, 111, 118, 82, 144, 128] chunk 21 optimal weight: 0.8980 chunk 187 optimal weight: 7.9990 chunk 176 optimal weight: 20.0000 chunk 119 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 219 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 118 optimal weight: 0.2980 chunk 82 optimal weight: 2.9990 chunk 144 optimal weight: 9.9990 chunk 128 optimal weight: 0.0000 overall best weight: 1.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 HIS D 739 HIS ** D 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 GLN ** B 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.180196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.132619 restraints weight = 56256.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.134264 restraints weight = 30502.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.134669 restraints weight = 19823.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.135026 restraints weight = 18273.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.135140 restraints weight = 16099.685| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17942 Z= 0.137 Angle : 0.604 10.735 24331 Z= 0.288 Chirality : 0.041 0.168 2626 Planarity : 0.004 0.062 3186 Dihedral : 4.350 59.770 2534 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.84 % Allowed : 16.69 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.18), residues: 2274 helix: 0.94 (0.19), residues: 797 sheet: -1.40 (0.35), residues: 229 loop : -0.47 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 771 TYR 0.013 0.001 TYR C 793 PHE 0.019 0.001 PHE C 732 TRP 0.034 0.001 TRP D 860 HIS 0.005 0.001 HIS D 873 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (17894) covalent geometry : angle 0.55558 / 0.29 (24259) hydrogen bonds : bond 0.02898 / 1.90 ( 602) hydrogen bonds : angle 4.69039 / 3.37 ( 1680) metal coordination : bond 0.00602 / 0.41 ( 48) metal coordination : angle 4.37406 / 2.93 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 215 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 329 MET cc_start: 0.8535 (tpp) cc_final: 0.8242 (mmp) REVERT: C 523 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8067 (mt-10) REVERT: C 548 MET cc_start: 0.8356 (mmp) cc_final: 0.8152 (mmm) REVERT: C 555 CYS cc_start: 0.7778 (m) cc_final: 0.6908 (m) REVERT: C 666 CYS cc_start: 0.8340 (t) cc_final: 0.7698 (t) REVERT: C 761 MET cc_start: 0.8902 (ppp) cc_final: 0.8516 (ptt) REVERT: C 882 ARG cc_start: 0.8424 (ttp-110) cc_final: 0.8166 (ttp80) REVERT: E 621 LYS cc_start: 0.1156 (pttt) cc_final: 0.0638 (pttm) REVERT: E 814 GLU cc_start: 0.5903 (mp0) cc_final: 0.5673 (pm20) REVERT: E 885 ARG cc_start: 0.8797 (ttm-80) cc_final: 0.8481 (ppt170) REVERT: D 548 MET cc_start: 0.3877 (mmt) cc_final: -0.0157 (pmm) REVERT: D 618 ASP cc_start: 0.9000 (OUTLIER) cc_final: 0.8529 (p0) REVERT: D 682 MET cc_start: 0.7769 (ttt) cc_final: 0.6605 (mpp) REVERT: D 739 HIS cc_start: 0.7949 (OUTLIER) cc_final: 0.7691 (t-170) REVERT: D 779 MET cc_start: 0.7469 (tmm) cc_final: 0.7176 (tmm) REVERT: D 793 TYR cc_start: 0.8339 (m-10) cc_final: 0.8077 (m-80) REVERT: D 851 PHE cc_start: 0.7470 (OUTLIER) cc_final: 0.6544 (t80) REVERT: D 858 ILE cc_start: 0.9502 (tp) cc_final: 0.9138 (mm) REVERT: D 880 MET cc_start: 0.6724 (mtm) cc_final: 0.6277 (ttm) REVERT: A 739 HIS cc_start: 0.8293 (OUTLIER) cc_final: 0.7964 (t-90) REVERT: A 757 ASN cc_start: 0.9066 (t0) cc_final: 0.8752 (t0) REVERT: A 795 TRP cc_start: 0.8443 (m-90) cc_final: 0.7588 (m-90) REVERT: B 489 ASN cc_start: 0.8835 (m-40) cc_final: 0.8567 (t0) REVERT: B 513 MET cc_start: 0.7190 (tpp) cc_final: 0.6866 (tpp) REVERT: B 607 MET cc_start: 0.9062 (ttm) cc_final: 0.8760 (tpp) REVERT: B 701 PHE cc_start: 0.7678 (m-80) cc_final: 0.7224 (m-80) REVERT: B 885 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7930 (ttt180) REVERT: B 886 GLN cc_start: 0.8570 (tt0) cc_final: 0.8136 (tm-30) outliers start: 48 outliers final: 34 residues processed: 246 average time/residue: 0.1251 time to fit residues: 46.7023 Evaluate side-chains 243 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 204 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 808 THR Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain E residue 808 THR Chi-restraints excluded: chain E residue 812 LYS Chi-restraints excluded: chain E residue 858 ILE Chi-restraints excluded: chain E residue 877 VAL Chi-restraints excluded: chain D residue 518 LYS Chi-restraints excluded: chain D residue 536 TYR Chi-restraints excluded: chain D residue 615 GLN Chi-restraints excluded: chain D residue 618 ASP Chi-restraints excluded: chain D residue 640 PHE Chi-restraints excluded: chain D residue 727 THR Chi-restraints excluded: chain D residue 739 HIS Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 829 LYS Chi-restraints excluded: chain D residue 833 ILE Chi-restraints excluded: chain D residue 840 ILE Chi-restraints excluded: chain D residue 851 PHE Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 541 CYS Chi-restraints excluded: chain B residue 557 CYS Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 786 SER Chi-restraints excluded: chain B residue 818 CYS Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 885 ARG Chi-restraints excluded: chain B residue 894 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: [149, 138, 211, 10, 166, 117, 19, 48, 106, 202, 227] chunk 149 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 211 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 166 optimal weight: 0.3980 chunk 117 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 106 optimal weight: 20.0000 chunk 202 optimal weight: 0.9990 chunk 227 optimal weight: 0.6980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 582 ASN D 739 HIS ** D 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 873 HIS ** B 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 842 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.176787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.127215 restraints weight = 58596.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.130827 restraints weight = 30336.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.131151 restraints weight = 16426.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.131549 restraints weight = 14919.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.131870 restraints weight = 13816.701| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17942 Z= 0.163 Angle : 0.616 11.136 24331 Z= 0.292 Chirality : 0.042 0.173 2626 Planarity : 0.004 0.055 3186 Dihedral : 4.377 59.488 2534 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.43 % Allowed : 16.98 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.18), residues: 2274 helix: 0.99 (0.19), residues: 792 sheet: -1.45 (0.35), residues: 232 loop : -0.43 (0.18), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 771 TYR 0.022 0.001 TYR A 724 PHE 0.020 0.002 PHE C 732 TRP 0.018 0.001 TRP D 860 HIS 0.005 0.001 HIS D 847 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (17894) covalent geometry : angle 0.56297 / 0.29 (24259) hydrogen bonds : bond 0.02864 / 1.89 ( 602) hydrogen bonds : angle 4.64211 / 3.35 ( 1680) metal coordination : bond 0.00653 / 0.45 ( 48) metal coordination : angle 4.63582 / 3.13 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 207 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 523 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8059 (mt-10) REVERT: C 548 MET cc_start: 0.8419 (mmp) cc_final: 0.8112 (mmp) REVERT: C 555 CYS cc_start: 0.7759 (m) cc_final: 0.6959 (m) REVERT: C 585 MET cc_start: 0.7788 (tpt) cc_final: 0.7576 (tpt) REVERT: C 666 CYS cc_start: 0.8289 (t) cc_final: 0.7687 (t) REVERT: C 761 MET cc_start: 0.8946 (ppp) cc_final: 0.8602 (ptt) REVERT: C 882 ARG cc_start: 0.8435 (ttp-110) cc_final: 0.8160 (ttp80) REVERT: E 621 LYS cc_start: 0.1281 (pttt) cc_final: 0.0852 (pttm) REVERT: E 801 MET cc_start: 0.3186 (mtt) cc_final: 0.2165 (mmt) REVERT: E 814 GLU cc_start: 0.5893 (mp0) cc_final: 0.4673 (pp20) REVERT: E 819 LEU cc_start: 0.3976 (mt) cc_final: 0.3603 (tp) REVERT: E 868 PHE cc_start: 0.3198 (m-10) cc_final: 0.2689 (m-10) REVERT: D 548 MET cc_start: 0.4203 (mmt) cc_final: 0.0190 (pmm) REVERT: D 618 ASP cc_start: 0.8944 (OUTLIER) cc_final: 0.8501 (p0) REVERT: D 682 MET cc_start: 0.7884 (ttt) cc_final: 0.6711 (mpp) REVERT: D 779 MET cc_start: 0.7456 (tmm) cc_final: 0.7123 (tmm) REVERT: D 851 PHE cc_start: 0.7520 (OUTLIER) cc_final: 0.6560 (t80) REVERT: D 880 MET cc_start: 0.6722 (mtm) cc_final: 0.6226 (ttm) REVERT: A 585 MET cc_start: -0.1284 (mpp) cc_final: -0.3146 (tpt) REVERT: A 600 ASP cc_start: 0.2794 (OUTLIER) cc_final: 0.2560 (m-30) REVERT: A 739 HIS cc_start: 0.8331 (OUTLIER) cc_final: 0.8055 (t-90) REVERT: A 757 ASN cc_start: 0.9070 (t0) cc_final: 0.8782 (t0) REVERT: A 795 TRP cc_start: 0.8501 (m-90) cc_final: 0.7514 (m-90) REVERT: B 489 ASN cc_start: 0.8853 (m-40) cc_final: 0.8594 (t0) REVERT: B 513 MET cc_start: 0.7231 (tpp) cc_final: 0.6892 (tpp) REVERT: B 607 MET cc_start: 0.8980 (ttm) cc_final: 0.8690 (tpp) REVERT: B 701 PHE cc_start: 0.7779 (m-80) cc_final: 0.7344 (m-80) REVERT: B 885 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.8047 (ttt180) REVERT: B 886 GLN cc_start: 0.8632 (tt0) cc_final: 0.8134 (tm-30) outliers start: 58 outliers final: 38 residues processed: 252 average time/residue: 0.1229 time to fit residues: 46.9466 Evaluate side-chains 241 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 198 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 513 MET Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 612 ASN Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 808 THR Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain E residue 808 THR Chi-restraints excluded: chain E residue 858 ILE Chi-restraints excluded: chain E residue 877 VAL Chi-restraints excluded: chain D residue 518 LYS Chi-restraints excluded: chain D residue 536 TYR Chi-restraints excluded: chain D residue 615 GLN Chi-restraints excluded: chain D residue 618 ASP Chi-restraints excluded: chain D residue 640 PHE Chi-restraints excluded: chain D residue 727 THR Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 783 LYS Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 829 LYS Chi-restraints excluded: chain D residue 833 ILE Chi-restraints excluded: chain D residue 840 ILE Chi-restraints excluded: chain D residue 851 PHE Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 541 CYS Chi-restraints excluded: chain B residue 557 CYS Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 786 SER Chi-restraints excluded: chain B residue 818 CYS Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 885 ARG Chi-restraints excluded: chain B residue 894 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: [127, 180, 11, 13, 12, 1, 105, 156, 46, 17, 185] chunk 127 optimal weight: 3.9990 chunk 180 optimal weight: 30.0000 chunk 11 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 900 HIS D 551 ASN ** D 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 GLN B 842 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.173282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.123105 restraints weight = 58680.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.126219 restraints weight = 30421.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.126213 restraints weight = 17458.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.126445 restraints weight = 15412.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.126636 restraints weight = 14755.103| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 17942 Z= 0.286 Angle : 0.749 14.563 24331 Z= 0.357 Chirality : 0.044 0.242 2626 Planarity : 0.005 0.052 3186 Dihedral : 4.804 59.627 2534 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.73 % Allowed : 17.51 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % 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 (0.18), residues: 2274 helix: 0.74 (0.19), residues: 790 sheet: -1.76 (0.37), residues: 195 loop : -0.61 (0.17), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 729 TYR 0.029 0.002 TYR C 481 PHE 0.029 0.003 PHE C 732 TRP 0.016 0.002 TRP D 860 HIS 0.013 0.002 HIS D 739 Details of bonding type rmsd/Z covalent geometry : bond 0.00635 / 0.29 (17894) covalent geometry : angle 0.68269 / 0.35 (24259) hydrogen bonds : bond 0.03493 / 2.30 ( 602) hydrogen bonds : angle 4.92621 / 3.53 ( 1680) metal coordination : bond 0.01090 / 0.73 ( 48) metal coordination : angle 5.69399 / 3.83 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 208 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 523 GLU cc_start: 0.8612 (mt-10) cc_final: 0.7812 (mt-10) REVERT: C 555 CYS cc_start: 0.8168 (m) cc_final: 0.7441 (m) REVERT: C 666 CYS cc_start: 0.8395 (t) cc_final: 0.7758 (t) REVERT: C 739 HIS cc_start: 0.8026 (OUTLIER) cc_final: 0.7730 (t-170) REVERT: C 761 MET cc_start: 0.9055 (ppp) cc_final: 0.8734 (ptt) REVERT: C 882 ARG cc_start: 0.8587 (ttp-110) cc_final: 0.8263 (ttp80) REVERT: E 621 LYS cc_start: 0.1149 (pttt) cc_final: 0.0927 (pttm) REVERT: E 801 MET cc_start: 0.3848 (mtt) cc_final: 0.2722 (mmt) REVERT: E 814 GLU cc_start: 0.5194 (mp0) cc_final: 0.4827 (pm20) REVERT: E 819 LEU cc_start: 0.4029 (mt) cc_final: 0.3565 (tp) REVERT: E 827 PHE cc_start: 0.2554 (m-80) cc_final: 0.2277 (m-80) REVERT: D 548 MET cc_start: 0.4027 (mmt) cc_final: 0.0341 (pmm) REVERT: D 682 MET cc_start: 0.8094 (ttt) cc_final: 0.6900 (mpp) REVERT: D 793 TYR cc_start: 0.8581 (m-80) cc_final: 0.8352 (m-80) REVERT: D 851 PHE cc_start: 0.7299 (OUTLIER) cc_final: 0.6384 (t80) REVERT: D 880 MET cc_start: 0.6596 (mtm) cc_final: 0.6266 (ttm) REVERT: A 585 MET cc_start: -0.1256 (mpp) cc_final: -0.3085 (tpt) REVERT: A 600 ASP cc_start: 0.2904 (OUTLIER) cc_final: 0.2676 (m-30) REVERT: A 757 ASN cc_start: 0.9090 (t0) cc_final: 0.8833 (t0) REVERT: A 795 TRP cc_start: 0.8803 (m-90) cc_final: 0.7920 (m-90) REVERT: B 607 MET cc_start: 0.9055 (ttm) cc_final: 0.8695 (tmm) REVERT: B 701 PHE cc_start: 0.7926 (m-80) cc_final: 0.7489 (m-80) REVERT: B 886 GLN cc_start: 0.8660 (tt0) cc_final: 0.8209 (tm-30) outliers start: 63 outliers final: 38 residues processed: 259 average time/residue: 0.1224 time to fit residues: 48.3195 Evaluate side-chains 229 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 188 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 513 MET Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 612 ASN Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 808 THR Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain E residue 780 ILE Chi-restraints excluded: chain E residue 808 THR Chi-restraints excluded: chain E residue 848 PHE Chi-restraints excluded: chain E residue 858 ILE Chi-restraints excluded: chain E residue 877 VAL Chi-restraints excluded: chain D residue 536 TYR Chi-restraints excluded: chain D residue 640 PHE Chi-restraints excluded: chain D residue 727 THR Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 783 LYS Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 833 ILE Chi-restraints excluded: chain D residue 840 ILE Chi-restraints excluded: chain D residue 851 PHE Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 522 LEU Chi-restraints excluded: chain B residue 557 CYS Chi-restraints excluded: chain B residue 609 PHE Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 786 SER Chi-restraints excluded: chain B residue 818 CYS Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 894 SER Chi-restraints excluded: chain B residue 897 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: [177, 38, 189, 86, 92, 14, 131, 184, 46, 29, 61] chunk 177 optimal weight: 50.0000 chunk 38 optimal weight: 0.7980 chunk 189 optimal weight: 0.9980 chunk 86 optimal weight: 50.0000 chunk 92 optimal weight: 30.0000 chunk 14 optimal weight: 0.2980 chunk 131 optimal weight: 20.0000 chunk 184 optimal weight: 9.9990 chunk 46 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 61 optimal weight: 30.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 402 GLN ** C 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 GLN ** D 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.177527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.129516 restraints weight = 56295.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.131664 restraints weight = 33416.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.132069 restraints weight = 18708.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.132505 restraints weight = 18366.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.132888 restraints weight = 15430.484| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17942 Z= 0.123 Angle : 0.657 14.873 24331 Z= 0.304 Chirality : 0.042 0.220 2626 Planarity : 0.004 0.053 3186 Dihedral : 4.512 59.390 2533 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.90 % Allowed : 18.99 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.18), residues: 2274 helix: 0.94 (0.19), residues: 796 sheet: -1.54 (0.37), residues: 195 loop : -0.55 (0.18), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 688 TYR 0.026 0.001 TYR A 724 PHE 0.024 0.002 PHE E 701 TRP 0.012 0.001 TRP D 795 HIS 0.004 0.001 HIS B 900 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (17894) covalent geometry : angle 0.59644 / 0.30 (24259) hydrogen bonds : bond 0.02816 / 1.87 ( 602) hydrogen bonds : angle 4.57497 / 3.29 ( 1680) metal coordination : bond 0.00670 / 0.52 ( 48) metal coordination : angle 5.11554 / 3.51 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 196 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 548 MET cc_start: 0.8218 (mmp) cc_final: 0.7731 (mmp) REVERT: C 666 CYS cc_start: 0.8415 (t) cc_final: 0.7701 (t) REVERT: C 817 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8071 (mp0) REVERT: C 882 ARG cc_start: 0.8571 (ttp-110) cc_final: 0.8212 (ttp80) REVERT: E 621 LYS cc_start: 0.1373 (pttt) cc_final: 0.1024 (pttm) REVERT: E 801 MET cc_start: 0.3442 (mtt) cc_final: 0.2551 (mmt) REVERT: E 819 LEU cc_start: 0.4229 (mt) cc_final: 0.4011 (tp) REVERT: D 548 MET cc_start: 0.4038 (mmt) cc_final: 0.0274 (pmm) REVERT: D 682 MET cc_start: 0.7903 (ttt) cc_final: 0.6755 (mpp) REVERT: D 793 TYR cc_start: 0.8282 (m-80) cc_final: 0.7775 (m-80) REVERT: D 851 PHE cc_start: 0.7228 (OUTLIER) cc_final: 0.6384 (t80) REVERT: D 880 MET cc_start: 0.6664 (mtm) cc_final: 0.6331 (ttm) REVERT: A 600 ASP cc_start: 0.2782 (OUTLIER) cc_final: 0.2546 (m-30) REVERT: A 739 HIS cc_start: 0.8388 (OUTLIER) cc_final: 0.8094 (t-90) REVERT: A 757 ASN cc_start: 0.9071 (t0) cc_final: 0.8661 (t0) REVERT: A 795 TRP cc_start: 0.8633 (m-90) cc_final: 0.7549 (m-90) REVERT: B 474 ARG cc_start: 0.9132 (ttt180) cc_final: 0.8774 (ptm160) REVERT: B 513 MET cc_start: 0.6483 (tpp) cc_final: 0.6259 (tpp) REVERT: B 607 MET cc_start: 0.9004 (ttm) cc_final: 0.8677 (tpp) REVERT: B 701 PHE cc_start: 0.7854 (m-80) cc_final: 0.7417 (m-80) REVERT: B 886 GLN cc_start: 0.8705 (tt0) cc_final: 0.8083 (tm-30) outliers start: 49 outliers final: 31 residues processed: 236 average time/residue: 0.1230 time to fit residues: 44.7026 Evaluate side-chains 226 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 191 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 513 MET Chi-restraints excluded: chain C residue 808 THR Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain E residue 808 THR Chi-restraints excluded: chain E residue 858 ILE Chi-restraints excluded: chain E residue 877 VAL Chi-restraints excluded: chain D residue 536 TYR Chi-restraints excluded: chain D residue 640 PHE Chi-restraints excluded: chain D residue 727 THR Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 763 VAL Chi-restraints excluded: chain D residue 783 LYS Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 833 ILE Chi-restraints excluded: chain D residue 840 ILE Chi-restraints excluded: chain D residue 851 PHE Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 557 CYS Chi-restraints excluded: chain B residue 609 PHE Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 786 SER Chi-restraints excluded: chain B residue 818 CYS Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 894 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: [22, 191, 195, 17, 212, 79, 106, 35, 179, 15, 94] chunk 22 optimal weight: 1.9990 chunk 191 optimal weight: 0.9990 chunk 195 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 212 optimal weight: 0.0980 chunk 79 optimal weight: 4.9990 chunk 106 optimal weight: 30.0000 chunk 35 optimal weight: 0.0980 chunk 179 optimal weight: 20.0000 chunk 15 optimal weight: 0.9990 chunk 94 optimal weight: 50.0000 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 GLN ** B 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.178414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.130423 restraints weight = 56874.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.132324 restraints weight = 31315.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.132541 restraints weight = 18273.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.133116 restraints weight = 17533.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.133473 restraints weight = 15653.585| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17942 Z= 0.127 Angle : 0.657 17.106 24331 Z= 0.301 Chirality : 0.042 0.256 2626 Planarity : 0.004 0.061 3186 Dihedral : 4.411 58.914 2533 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.72 % Allowed : 19.47 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % 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: -0.12 (0.18), residues: 2274 helix: 1.04 (0.19), residues: 793 sheet: -1.53 (0.36), residues: 216 loop : -0.48 (0.18), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 688 TYR 0.026 0.001 TYR A 724 PHE 0.019 0.001 PHE E 909 TRP 0.012 0.001 TRP A 795 HIS 0.004 0.001 HIS B 900 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (17894) covalent geometry : angle 0.59267 / 0.30 (24259) hydrogen bonds : bond 0.02715 / 1.82 ( 602) hydrogen bonds : angle 4.51976 / 3.27 ( 1680) metal coordination : bond 0.00688 / 0.50 ( 48) metal coordination : angle 5.26643 / 3.59 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 199 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 523 GLU cc_start: 0.8682 (mt-10) cc_final: 0.7969 (mt-10) REVERT: C 548 MET cc_start: 0.8153 (mmp) cc_final: 0.7627 (mmp) REVERT: C 555 CYS cc_start: 0.7636 (m) cc_final: 0.6630 (m) REVERT: C 666 CYS cc_start: 0.8441 (t) cc_final: 0.7720 (t) REVERT: C 739 HIS cc_start: 0.7806 (OUTLIER) cc_final: 0.7515 (t-170) REVERT: C 882 ARG cc_start: 0.8540 (ttp-110) cc_final: 0.8176 (ttp80) REVERT: E 621 LYS cc_start: 0.1286 (pttt) cc_final: 0.1045 (pttm) REVERT: E 701 PHE cc_start: 0.5241 (m-10) cc_final: 0.4829 (m-10) REVERT: E 801 MET cc_start: 0.3353 (mtt) cc_final: 0.2472 (mmt) REVERT: E 814 GLU cc_start: 0.4647 (pm20) cc_final: 0.4335 (pm20) REVERT: E 819 LEU cc_start: 0.4275 (mt) cc_final: 0.4058 (tp) REVERT: E 829 LYS cc_start: 0.6909 (tppt) cc_final: 0.6695 (tppt) REVERT: E 856 GLU cc_start: 0.6164 (tp30) cc_final: 0.5878 (tp30) REVERT: D 548 MET cc_start: 0.4136 (mmt) cc_final: 0.0293 (pmm) REVERT: D 682 MET cc_start: 0.7872 (ttt) cc_final: 0.6755 (mpp) REVERT: D 793 TYR cc_start: 0.8219 (m-80) cc_final: 0.7159 (m-80) REVERT: D 851 PHE cc_start: 0.7256 (OUTLIER) cc_final: 0.6374 (t80) REVERT: A 585 MET cc_start: -0.1236 (mpp) cc_final: -0.3169 (tpt) REVERT: A 600 ASP cc_start: 0.2738 (OUTLIER) cc_final: 0.2499 (m-30) REVERT: A 739 HIS cc_start: 0.8330 (OUTLIER) cc_final: 0.8054 (t-90) REVERT: A 757 ASN cc_start: 0.9062 (t0) cc_final: 0.8714 (t0) REVERT: A 795 TRP cc_start: 0.8596 (m-90) cc_final: 0.7275 (m-90) REVERT: B 513 MET cc_start: 0.6446 (tpp) cc_final: 0.6222 (tpp) REVERT: B 607 MET cc_start: 0.8995 (ttm) cc_final: 0.8758 (tpp) REVERT: B 701 PHE cc_start: 0.7858 (m-80) cc_final: 0.7419 (m-80) REVERT: B 886 GLN cc_start: 0.8715 (tt0) cc_final: 0.8101 (tm-30) outliers start: 46 outliers final: 34 residues processed: 237 average time/residue: 0.1224 time to fit residues: 44.4322 Evaluate side-chains 234 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 196 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 513 MET Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 612 ASN Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 808 THR Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain E residue 808 THR Chi-restraints excluded: chain E residue 858 ILE Chi-restraints excluded: chain E residue 877 VAL Chi-restraints excluded: chain D residue 613 HIS Chi-restraints excluded: chain D residue 727 THR Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 783 LYS Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 833 ILE Chi-restraints excluded: chain D residue 840 ILE Chi-restraints excluded: chain D residue 851 PHE Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 557 CYS Chi-restraints excluded: chain B residue 609 PHE Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 786 SER Chi-restraints excluded: chain B residue 818 CYS Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 894 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: [119, 186, 97, 179, 40, 188, 64, 203, 107, 162, 79] chunk 119 optimal weight: 0.9980 chunk 186 optimal weight: 0.9990 chunk 97 optimal weight: 0.0020 chunk 179 optimal weight: 20.0000 chunk 40 optimal weight: 0.4980 chunk 188 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 203 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 162 optimal weight: 20.0000 chunk 79 optimal weight: 0.9980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 842 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.178314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.130472 restraints weight = 56686.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.132440 restraints weight = 29907.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.133133 restraints weight = 18116.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.133382 restraints weight = 16538.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.133596 restraints weight = 14954.302| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17942 Z= 0.116 Angle : 0.653 14.950 24331 Z= 0.298 Chirality : 0.041 0.220 2626 Planarity : 0.003 0.050 3186 Dihedral : 4.328 58.691 2533 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.43 % Allowed : 19.76 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % 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: -0.08 (0.18), residues: 2274 helix: 1.06 (0.19), residues: 793 sheet: -1.47 (0.36), residues: 213 loop : -0.47 (0.18), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 688 TYR 0.020 0.001 TYR D 536 PHE 0.020 0.001 PHE E 868 TRP 0.012 0.001 TRP A 795 HIS 0.004 0.001 HIS B 900 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (17894) covalent geometry : angle 0.59237 / 0.29 (24259) hydrogen bonds : bond 0.02598 / 1.72 ( 602) hydrogen bonds : angle 4.43033 / 3.21 ( 1680) metal coordination : bond 0.00585 / 0.40 ( 48) metal coordination : angle 5.08178 / 3.51 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 201 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 523 GLU cc_start: 0.8669 (mt-10) cc_final: 0.7947 (mt-10) REVERT: C 548 MET cc_start: 0.8117 (mmp) cc_final: 0.7584 (mmp) REVERT: C 555 CYS cc_start: 0.7610 (m) cc_final: 0.6570 (m) REVERT: C 666 CYS cc_start: 0.8381 (t) cc_final: 0.7711 (t) REVERT: C 739 HIS cc_start: 0.7720 (OUTLIER) cc_final: 0.7455 (t-170) REVERT: C 817 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8012 (mp0) REVERT: E 621 LYS cc_start: 0.1252 (pttt) cc_final: 0.1029 (pttm) REVERT: E 701 PHE cc_start: 0.5347 (m-10) cc_final: 0.4967 (m-10) REVERT: E 801 MET cc_start: 0.3169 (mtt) cc_final: 0.2468 (mmt) REVERT: E 814 GLU cc_start: 0.4131 (pm20) cc_final: 0.3637 (pm20) REVERT: E 829 LYS cc_start: 0.6732 (tppt) cc_final: 0.6490 (tppt) REVERT: D 548 MET cc_start: 0.4103 (mmt) cc_final: 0.0329 (pmm) REVERT: D 682 MET cc_start: 0.7680 (ttt) cc_final: 0.6549 (mpp) REVERT: D 793 TYR cc_start: 0.8234 (m-80) cc_final: 0.7219 (m-80) REVERT: D 851 PHE cc_start: 0.7276 (OUTLIER) cc_final: 0.6438 (t80) REVERT: A 585 MET cc_start: -0.1258 (mpp) cc_final: -0.3178 (tpt) REVERT: A 600 ASP cc_start: 0.2729 (OUTLIER) cc_final: 0.2487 (m-30) REVERT: A 739 HIS cc_start: 0.8292 (OUTLIER) cc_final: 0.8029 (t-90) REVERT: A 757 ASN cc_start: 0.9101 (t0) cc_final: 0.8553 (t0) REVERT: A 794 PHE cc_start: 0.8185 (m-80) cc_final: 0.7921 (m-80) REVERT: A 795 TRP cc_start: 0.8496 (m-90) cc_final: 0.7226 (m-90) REVERT: B 513 MET cc_start: 0.6433 (tpp) cc_final: 0.6208 (tpp) REVERT: B 607 MET cc_start: 0.8975 (ttm) cc_final: 0.8770 (tpp) REVERT: B 701 PHE cc_start: 0.7802 (m-80) cc_final: 0.7334 (m-80) REVERT: B 886 GLN cc_start: 0.8672 (tt0) cc_final: 0.8079 (tm-30) outliers start: 41 outliers final: 29 residues processed: 234 average time/residue: 0.1202 time to fit residues: 43.5000 Evaluate side-chains 230 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 196 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 513 MET Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 808 THR Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 835 THR Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain E residue 779 MET Chi-restraints excluded: chain E residue 858 ILE Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 783 LYS Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 833 ILE Chi-restraints excluded: chain D residue 840 ILE Chi-restraints excluded: chain D residue 851 PHE Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 557 CYS Chi-restraints excluded: chain B residue 609 PHE Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 786 SER Chi-restraints excluded: chain B residue 818 CYS Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 894 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: [30, 144, 57, 156, 90, 87, 129, 133, 21, 138, 202] chunk 30 optimal weight: 0.7980 chunk 144 optimal weight: 30.0000 chunk 57 optimal weight: 0.0970 chunk 156 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 129 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 138 optimal weight: 6.9990 chunk 202 optimal weight: 1.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.174573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.123961 restraints weight = 58609.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.127091 restraints weight = 33158.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.127581 restraints weight = 18019.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.127768 restraints weight = 15712.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.127934 restraints weight = 14211.853| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 17942 Z= 0.195 Angle : 0.703 15.296 24331 Z= 0.325 Chirality : 0.043 0.216 2626 Planarity : 0.004 0.050 3186 Dihedral : 4.492 59.316 2532 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.31 % Allowed : 20.00 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % 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: -0.13 (0.18), residues: 2274 helix: 1.03 (0.19), residues: 790 sheet: -1.53 (0.36), residues: 215 loop : -0.49 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 688 TYR 0.019 0.002 TYR B 481 PHE 0.061 0.002 PHE A 902 TRP 0.015 0.002 TRP B 860 HIS 0.004 0.001 HIS C 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.20 (17894) covalent geometry : angle 0.64192 / 0.32 (24259) hydrogen bonds : bond 0.02900 / 1.91 ( 602) hydrogen bonds : angle 4.55412 / 3.29 ( 1680) metal coordination : bond 0.00811 / 0.54 ( 48) metal coordination : angle 5.31866 / 3.58 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 202 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 523 GLU cc_start: 0.8664 (mt-10) cc_final: 0.7975 (mt-10) REVERT: C 548 MET cc_start: 0.8224 (mmp) cc_final: 0.7745 (mmp) REVERT: C 555 CYS cc_start: 0.7970 (m) cc_final: 0.6977 (m) REVERT: C 666 CYS cc_start: 0.8429 (t) cc_final: 0.7766 (t) REVERT: C 739 HIS cc_start: 0.7818 (OUTLIER) cc_final: 0.7565 (t-170) REVERT: C 817 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8029 (mp0) REVERT: C 882 ARG cc_start: 0.8547 (ttp-110) cc_final: 0.8299 (ttp80) REVERT: E 621 LYS cc_start: 0.1552 (pttt) cc_final: 0.1315 (pttm) REVERT: E 701 PHE cc_start: 0.4977 (m-10) cc_final: 0.4086 (m-80) REVERT: E 801 MET cc_start: 0.3930 (mtt) cc_final: 0.3089 (mmt) REVERT: E 814 GLU cc_start: 0.3951 (pm20) cc_final: 0.3279 (pm20) REVERT: E 829 LYS cc_start: 0.6816 (tppt) cc_final: 0.6577 (tppt) REVERT: D 548 MET cc_start: 0.4218 (mmt) cc_final: 0.0687 (pmm) REVERT: D 682 MET cc_start: 0.7895 (ttt) cc_final: 0.6760 (mpp) REVERT: D 793 TYR cc_start: 0.8293 (m-80) cc_final: 0.7297 (m-80) REVERT: D 851 PHE cc_start: 0.7280 (OUTLIER) cc_final: 0.6450 (t80) REVERT: A 585 MET cc_start: -0.1223 (mpp) cc_final: -0.3112 (tpt) REVERT: A 600 ASP cc_start: 0.2908 (OUTLIER) cc_final: 0.2670 (m-30) REVERT: A 757 ASN cc_start: 0.8990 (t0) cc_final: 0.8707 (t0) REVERT: B 474 ARG cc_start: 0.9154 (ttt180) cc_final: 0.8819 (ptm160) REVERT: B 513 MET cc_start: 0.6684 (tpp) cc_final: 0.6446 (tpp) REVERT: B 607 MET cc_start: 0.9005 (ttm) cc_final: 0.8782 (tpp) REVERT: B 701 PHE cc_start: 0.7892 (m-80) cc_final: 0.7463 (m-80) REVERT: B 886 GLN cc_start: 0.8766 (tt0) cc_final: 0.8119 (tm-30) outliers start: 39 outliers final: 31 residues processed: 232 average time/residue: 0.1269 time to fit residues: 44.8368 Evaluate side-chains 231 residues out of total 2005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 196 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 320 ARG Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 513 MET Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 612 ASN Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 808 THR Chi-restraints excluded: chain C residue 817 GLU Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain E residue 622 VAL Chi-restraints excluded: chain E residue 779 MET Chi-restraints excluded: chain E residue 848 PHE Chi-restraints excluded: chain E residue 858 ILE Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 783 LYS Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 833 ILE Chi-restraints excluded: chain D residue 840 ILE Chi-restraints excluded: chain D residue 851 PHE Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 557 CYS Chi-restraints excluded: chain B residue 609 PHE Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 670 ILE Chi-restraints excluded: chain B residue 786 SER Chi-restraints excluded: chain B residue 818 CYS Chi-restraints excluded: chain B residue 862 THR Chi-restraints excluded: chain B residue 894 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: [31, 225, 149, 158, 15, 210, 124, 160, 61, 8, 123] chunk 31 optimal weight: 0.4980 chunk 225 optimal weight: 0.5980 chunk 149 optimal weight: 3.9990 chunk 158 optimal weight: 30.0000 chunk 15 optimal weight: 0.0980 chunk 210 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 160 optimal weight: 0.1980 chunk 61 optimal weight: 50.0000 chunk 8 optimal weight: 0.9980 chunk 123 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 757 ASN ** B 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.176677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.129433 restraints weight = 58107.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.131195 restraints weight = 31637.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.131772 restraints weight = 17975.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.132398 restraints weight = 16234.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.132643 restraints weight = 14619.188| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17942 Z= 0.110 Angle : 0.657 13.041 24331 Z= 0.303 Chirality : 0.042 0.219 2626 Planarity : 0.003 0.049 3186 Dihedral : 4.326 59.159 2532 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.01 % Allowed : 20.53 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % 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: -0.07 (0.18), residues: 2274 helix: 1.10 (0.19), residues: 792 sheet: -1.49 (0.34), residues: 233 loop : -0.45 (0.18), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 688 TYR 0.013 0.001 TYR C 660 PHE 0.051 0.002 PHE A 902 TRP 0.011 0.001 TRP C 601 HIS 0.004 0.001 HIS B 900 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (17894) covalent geometry : angle 0.60200 / 0.30 (24259) hydrogen bonds : bond 0.02594 / 1.72 ( 602) hydrogen bonds : angle 4.38875 / 3.18 ( 1680) metal coordination : bond 0.00561 / 0.39 ( 48) metal coordination : angle 4.85898 / 3.36 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4057.47 seconds wall clock time: 70 minutes 2.07 seconds (4202.07 seconds total)