Starting phenix.real_space_refine on Thu Jul 31 17:07:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eik_28159/07_2025/8eik_28159.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eik_28159/07_2025/8eik_28159.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eik_28159/07_2025/8eik_28159.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eik_28159/07_2025/8eik_28159.map" model { file = "/net/cci-nas-00/data/ceres_data/8eik_28159/07_2025/8eik_28159.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eik_28159/07_2025/8eik_28159.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.028 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 120 5.16 5 C 8561 2.51 5 N 2354 2.21 5 O 2440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13487 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3343 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 52 Chain: "B" Number of atoms: 3394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3394 Classifications: {'peptide': 438} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 417} Chain breaks: 1 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 61 Chain: "D" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 785 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 120} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 286 Unresolved non-hydrogen angles: 366 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 156 Chain: "C" Number of atoms: 2922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 2922 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 387} Chain breaks: 2 Unresolved non-hydrogen bonds: 340 Unresolved non-hydrogen angles: 415 Unresolved non-hydrogen dihedrals: 278 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 8, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 17, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 229 Chain: "E" Number of atoms: 2814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2814 Classifications: {'peptide': 378} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 360} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 235 Unresolved non-hydrogen angles: 289 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'TYR:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 141 Chain: "F" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 139 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 23} Chain breaks: 1 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 52 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} 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: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 158 SG CYS A 435 26.807 29.745 167.457 1.00179.18 S ATOM 178 SG CYS A 438 27.679 25.861 166.403 1.00183.01 S ATOM 308 SG CYS A 455 30.077 27.864 168.268 1.00174.33 S ATOM 330 SG CYS A 458 29.322 28.835 164.782 1.00175.55 S ATOM 509 SG CYS A 478 26.389 33.085 155.363 1.00168.82 S ATOM 529 SG CYS A 481 26.987 30.168 157.729 1.00165.99 S ATOM 658 SG CYS A 500 25.060 29.608 154.390 1.00191.85 S ATOM 680 SG CYS A 503 23.494 31.416 157.280 1.00193.07 S ATOM 585 SG CYS A 490 24.081 43.664 147.424 1.00176.66 S ATOM 618 SG CYS A 495 26.932 45.151 149.458 1.00171.98 S ATOM 830 SG CYS A 524 23.752 43.668 151.181 1.00185.84 S ATOM 856 SG CYS A 527 23.636 46.946 149.470 1.00189.13 S ATOM 3522 SG CYS B 435 87.700 53.021 91.446 1.00103.31 S ATOM 3542 SG CYS B 438 86.309 49.767 89.490 1.00118.13 S ATOM 3672 SG CYS B 455 84.339 52.833 89.594 1.00105.17 S ATOM 3694 SG CYS B 458 84.887 50.841 92.772 1.00108.40 S ATOM 3876 SG CYS B 478 88.009 47.967 103.036 1.00119.04 S ATOM 3896 SG CYS B 481 86.970 47.313 99.482 1.00112.16 S ATOM 4038 SG CYS B 500 88.948 44.514 101.410 1.00116.85 S ATOM 4060 SG CYS B 503 90.556 47.664 100.179 1.00114.95 S ATOM 3965 SG CYS B 490 90.823 51.011 115.883 1.00112.96 S ATOM 3998 SG CYS B 495 88.306 53.446 114.359 1.00121.60 S ATOM 4209 SG CYS B 524 91.561 52.702 112.555 1.00120.33 S ATOM 4235 SG CYS B 527 91.654 54.709 115.747 1.00120.30 S ATOM 7640 SG CYS C 435 31.337 32.060 99.028 1.00180.00 S ATOM 7657 SG CYS C 438 34.352 30.910 101.533 1.00204.27 S ATOM 7775 SG CYS C 455 33.600 34.476 100.922 1.00182.14 S ATOM 7793 SG CYS C 458 35.026 32.366 98.173 1.00179.63 S ATOM 7952 SG CYS C 478 35.149 26.565 89.192 1.00189.81 S ATOM 7972 SG CYS C 481 35.570 27.322 92.832 1.00202.58 S ATOM 8088 SG CYS C 500 36.660 23.834 91.161 1.00193.88 S ATOM 8110 SG CYS C 503 33.020 24.751 91.806 1.00184.90 S ATOM 8022 SG CYS C 490 32.576 23.815 76.192 1.00186.62 S ATOM 8049 SG CYS C 495 32.216 27.564 76.553 1.00186.79 S ATOM 8238 SG CYS C 524 30.235 25.269 78.803 1.00197.74 S ATOM 8257 SG CYS C 527 29.298 25.567 75.122 1.00202.50 S ATOM 10822 SG CYS E 478 94.284 48.658 34.584 1.00170.89 S ATOM 10931 SG CYS E 495 85.858 56.157 38.779 1.00193.89 S Time building chain proxies: 8.96, per 1000 atoms: 0.66 Number of scatterers: 13487 At special positions: 0 Unit cell: (115.5, 100.1, 204.6, 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 120 16.00 O 2440 8.00 N 2354 7.00 C 8561 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.99 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 455 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 458 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 438 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 435 " pdb=" ZN A 903 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 503 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 481 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 478 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 500 " pdb=" ZN A 904 " pdb="ZN ZN A 904 " - pdb=" SG CYS A 527 " pdb="ZN ZN A 904 " - pdb=" SG CYS A 524 " pdb="ZN ZN A 904 " - pdb=" SG CYS A 490 " pdb="ZN ZN A 904 " - pdb=" SG CYS A 495 " pdb=" ZN B 902 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 455 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 458 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 438 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 435 " pdb=" ZN B 903 " pdb="ZN ZN B 903 " - pdb=" SG CYS B 503 " pdb="ZN ZN B 903 " - pdb=" SG CYS B 481 " pdb="ZN ZN B 903 " - pdb=" SG CYS B 478 " pdb="ZN ZN B 903 " - pdb=" SG CYS B 500 " pdb=" ZN B 904 " pdb="ZN ZN B 904 " - pdb=" SG CYS B 524 " pdb="ZN ZN B 904 " - pdb=" SG CYS B 490 " pdb="ZN ZN B 904 " - pdb=" SG CYS B 527 " pdb="ZN ZN B 904 " - pdb=" SG CYS B 495 " pdb=" ZN C 902 " pdb="ZN ZN C 902 " - pdb=" SG CYS C 455 " pdb="ZN ZN C 902 " - pdb=" SG CYS C 458 " pdb="ZN ZN C 902 " - pdb=" SG CYS C 438 " pdb="ZN ZN C 902 " - pdb=" SG CYS C 435 " pdb=" ZN C 903 " pdb="ZN ZN C 903 " - pdb=" SG CYS C 478 " pdb="ZN ZN C 903 " - pdb=" SG CYS C 503 " pdb="ZN ZN C 903 " - pdb=" SG CYS C 481 " pdb="ZN ZN C 903 " - pdb=" SG CYS C 500 " pdb=" ZN C 904 " pdb="ZN ZN C 904 " - pdb=" SG CYS C 524 " pdb="ZN ZN C 904 " - pdb=" SG CYS C 495 " pdb="ZN ZN C 904 " - pdb=" SG CYS C 490 " pdb="ZN ZN C 904 " - pdb=" SG CYS C 527 " pdb=" ZN E 902 " pdb="ZN ZN E 902 " - pdb=" SG CYS E 478 " pdb=" ZN E 903 " pdb="ZN ZN E 903 " - pdb=" SG CYS E 495 " Number of angles added : 54 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3348 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 18 sheets defined 38.4% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 416 through 426 removed outlier: 4.174A pdb=" N MET A 420 " --> pdb=" O SER A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 466 removed outlier: 4.172A pdb=" N GLU A 464 " --> pdb=" O ASP A 460 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU A 465 " --> pdb=" O ARG A 461 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE A 466 " --> pdb=" O PHE A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 506 removed outlier: 4.264A pdb=" N GLU A 505 " --> pdb=" O VAL A 501 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL A 506 " --> pdb=" O GLU A 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 501 through 506' Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.533A pdb=" N GLU A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 518 " --> pdb=" O ALA A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 552 removed outlier: 4.840A pdb=" N GLN A 547 " --> pdb=" O ASN A 543 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ALA A 548 " --> pdb=" O VAL A 544 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE A 549 " --> pdb=" O ARG A 545 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE A 550 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER A 552 " --> pdb=" O ALA A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 572 removed outlier: 3.951A pdb=" N ARG A 572 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 595 removed outlier: 3.773A pdb=" N LYS A 592 " --> pdb=" O TYR A 588 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 619 removed outlier: 3.870A pdb=" N VAL A 613 " --> pdb=" O GLU A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 639 removed outlier: 3.518A pdb=" N ILE A 636 " --> pdb=" O THR A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 669 Processing helix chain 'A' and resid 670 through 683 removed outlier: 3.741A pdb=" N GLU A 674 " --> pdb=" O ARG A 670 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE A 675 " --> pdb=" O LEU A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 715 removed outlier: 3.685A pdb=" N ASP A 709 " --> pdb=" O GLY A 705 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER A 711 " --> pdb=" O LYS A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 726 No H-bonds generated for 'chain 'A' and resid 724 through 726' Processing helix chain 'A' and resid 755 through 760 removed outlier: 4.065A pdb=" N LEU A 760 " --> pdb=" O GLN A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 810 removed outlier: 4.177A pdb=" N ARG A 807 " --> pdb=" O THR A 803 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 808 " --> pdb=" O GLU A 804 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N PHE A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 827 removed outlier: 3.913A pdb=" N GLN A 827 " --> pdb=" O ARG A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 832 removed outlier: 3.663A pdb=" N ARG A 832 " --> pdb=" O LYS A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 843 Processing helix chain 'A' and resid 844 through 848 Processing helix chain 'B' and resid 416 through 426 removed outlier: 3.766A pdb=" N MET B 420 " --> pdb=" O SER B 416 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN B 426 " --> pdb=" O SER B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 434 removed outlier: 3.779A pdb=" N ASP B 433 " --> pdb=" O SER B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 466 removed outlier: 4.306A pdb=" N ARG B 461 " --> pdb=" O THR B 457 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLU B 464 " --> pdb=" O ASP B 460 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 465 " --> pdb=" O ARG B 461 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE B 466 " --> pdb=" O PHE B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 506 removed outlier: 3.861A pdb=" N GLU B 505 " --> pdb=" O VAL B 501 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL B 506 " --> pdb=" O GLU B 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 501 through 506' Processing helix chain 'B' and resid 511 through 519 removed outlier: 3.702A pdb=" N GLU B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 552 removed outlier: 4.469A pdb=" N GLN B 547 " --> pdb=" O ASN B 543 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA B 548 " --> pdb=" O VAL B 544 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE B 549 " --> pdb=" O ARG B 545 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N PHE B 550 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER B 552 " --> pdb=" O ALA B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 594 removed outlier: 3.655A pdb=" N LYS B 592 " --> pdb=" O TYR B 588 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU B 593 " --> pdb=" O LEU B 589 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 594 " --> pdb=" O VAL B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 618 removed outlier: 3.739A pdb=" N GLY B 614 " --> pdb=" O SER B 610 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS B 618 " --> pdb=" O GLY B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 639 Processing helix chain 'B' and resid 666 through 669 removed outlier: 4.152A pdb=" N GLY B 669 " --> pdb=" O GLU B 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 666 through 669' Processing helix chain 'B' and resid 670 through 683 removed outlier: 4.014A pdb=" N GLU B 674 " --> pdb=" O ARG B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 715 Processing helix chain 'B' and resid 756 through 760 removed outlier: 3.625A pdb=" N LEU B 760 " --> pdb=" O GLN B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 809 removed outlier: 3.766A pdb=" N PHE B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 832 removed outlier: 3.540A pdb=" N LEU B 830 " --> pdb=" O ARG B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 844 Processing helix chain 'B' and resid 845 through 849 removed outlier: 3.520A pdb=" N ASP B 848 " --> pdb=" O PRO B 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 585 through 594 Processing helix chain 'D' and resid 627 through 631 removed outlier: 3.860A pdb=" N ILE D 631 " --> pdb=" O VAL D 628 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 640 Processing helix chain 'D' and resid 667 through 683 removed outlier: 3.781A pdb=" N LEU D 671 " --> pdb=" O GLY D 667 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU D 674 " --> pdb=" O ARG D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 703 through 714 removed outlier: 3.739A pdb=" N LEU D 714 " --> pdb=" O ILE D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 843 Processing helix chain 'C' and resid 417 through 426 removed outlier: 3.502A pdb=" N ALA C 421 " --> pdb=" O ARG C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 434 removed outlier: 3.623A pdb=" N ASP C 433 " --> pdb=" O SER C 430 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY C 434 " --> pdb=" O LEU C 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 430 through 434' Processing helix chain 'C' and resid 455 through 466 removed outlier: 3.853A pdb=" N ARG C 461 " --> pdb=" O THR C 457 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE C 462 " --> pdb=" O CYS C 458 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU C 463 " --> pdb=" O ARG C 459 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLU C 464 " --> pdb=" O ASP C 460 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU C 465 " --> pdb=" O ARG C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 506 removed outlier: 3.990A pdb=" N GLU C 505 " --> pdb=" O VAL C 501 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL C 506 " --> pdb=" O GLU C 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 501 through 506' Processing helix chain 'C' and resid 511 through 519 Processing helix chain 'C' and resid 541 through 546 removed outlier: 3.535A pdb=" N ARG C 545 " --> pdb=" O ASP C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 551 Processing helix chain 'C' and resid 568 through 572 removed outlier: 3.642A pdb=" N ARG C 572 " --> pdb=" O ALA C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 594 removed outlier: 3.510A pdb=" N VAL C 590 " --> pdb=" O THR C 586 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS C 592 " --> pdb=" O TYR C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 617 removed outlier: 3.534A pdb=" N ALA C 612 " --> pdb=" O GLU C 608 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL C 613 " --> pdb=" O GLU C 609 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY C 614 " --> pdb=" O SER C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 631 Processing helix chain 'C' and resid 632 through 639 removed outlier: 3.588A pdb=" N ILE C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 683 removed outlier: 3.571A pdb=" N ASN C 680 " --> pdb=" O TYR C 676 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR C 681 " --> pdb=" O HIS C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 715 Processing helix chain 'C' and resid 724 through 726 No H-bonds generated for 'chain 'C' and resid 724 through 726' Processing helix chain 'C' and resid 755 through 760 removed outlier: 3.924A pdb=" N LEU C 760 " --> pdb=" O GLN C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 803 through 810 removed outlier: 3.858A pdb=" N ARG C 807 " --> pdb=" O THR C 803 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE C 808 " --> pdb=" O GLU C 804 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE C 809 " --> pdb=" O LEU C 805 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY C 810 " --> pdb=" O GLU C 806 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 803 through 810' Processing helix chain 'C' and resid 822 through 832 removed outlier: 3.775A pdb=" N LEU C 830 " --> pdb=" O ARG C 826 " (cutoff:3.500A) Processing helix chain 'C' and resid 835 through 844 Processing helix chain 'C' and resid 845 through 849 removed outlier: 3.626A pdb=" N ASP C 848 " --> pdb=" O PRO C 845 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 465 removed outlier: 3.566A pdb=" N ASP E 460 " --> pdb=" O GLN E 456 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG E 461 " --> pdb=" O THR E 457 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU E 464 " --> pdb=" O ASP E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 501 through 508 removed outlier: 4.358A pdb=" N GLU E 505 " --> pdb=" O VAL E 501 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL E 506 " --> pdb=" O GLU E 502 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU E 507 " --> pdb=" O CYS E 503 " (cutoff:3.500A) Processing helix chain 'E' and resid 545 through 552 removed outlier: 3.541A pdb=" N PHE E 549 " --> pdb=" O ARG E 545 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE E 550 " --> pdb=" O LEU E 546 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR E 551 " --> pdb=" O GLN E 547 " (cutoff:3.500A) Processing helix chain 'E' and resid 585 through 595 removed outlier: 3.618A pdb=" N GLY E 595 " --> pdb=" O LEU E 591 " (cutoff:3.500A) Processing helix chain 'E' and resid 607 through 619 removed outlier: 3.737A pdb=" N ALA E 612 " --> pdb=" O GLU E 608 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL E 613 " --> pdb=" O GLU E 609 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY E 614 " --> pdb=" O SER E 610 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 631 Processing helix chain 'E' and resid 632 through 640 Processing helix chain 'E' and resid 666 through 670 removed outlier: 3.577A pdb=" N GLY E 669 " --> pdb=" O GLU E 666 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG E 670 " --> pdb=" O GLY E 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 666 through 670' Processing helix chain 'E' and resid 671 through 681 removed outlier: 3.803A pdb=" N PHE E 675 " --> pdb=" O LEU E 671 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR E 676 " --> pdb=" O PHE E 672 " (cutoff:3.500A) Processing helix chain 'E' and resid 703 through 715 Processing helix chain 'E' and resid 724 through 726 No H-bonds generated for 'chain 'E' and resid 724 through 726' Processing helix chain 'E' and resid 801 through 810 removed outlier: 3.747A pdb=" N GLU E 806 " --> pdb=" O CYS E 802 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ARG E 807 " --> pdb=" O THR E 803 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE E 808 " --> pdb=" O GLU E 804 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE E 809 " --> pdb=" O LEU E 805 " (cutoff:3.500A) Processing helix chain 'E' and resid 822 through 833 removed outlier: 4.124A pdb=" N ARG E 832 " --> pdb=" O LYS E 828 " (cutoff:3.500A) Processing helix chain 'E' and resid 835 through 843 removed outlier: 3.672A pdb=" N LEU E 842 " --> pdb=" O VAL E 838 " (cutoff:3.500A) Processing helix chain 'E' and resid 844 through 849 removed outlier: 3.511A pdb=" N LYS E 847 " --> pdb=" O ALA E 844 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP E 848 " --> pdb=" O PRO E 845 " (cutoff:3.500A) Processing helix chain 'F' and resid 667 through 679 removed outlier: 4.045A pdb=" N LEU F 671 " --> pdb=" O GLY F 667 " (cutoff:3.500A) Processing helix chain 'F' and resid 706 through 714 Processing sheet with id=AA1, first strand: chain 'A' and resid 445 through 446 Processing sheet with id=AA2, first strand: chain 'A' and resid 487 through 489 removed outlier: 3.593A pdb=" N LEU A 488 " --> pdb=" O PHE A 499 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 598 through 600 removed outlier: 7.207A pdb=" N ILE A 575 " --> pdb=" O GLY A 599 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU A 644 " --> pdb=" O ARG A 576 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 698 through 699 removed outlier: 4.522A pdb=" N ARG A 733 " --> pdb=" O ILE A 721 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE A 721 " --> pdb=" O ARG A 733 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A 719 " --> pdb=" O PHE A 735 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 765 through 766 removed outlier: 4.007A pdb=" N VAL A 791 " --> pdb=" O ASP A 798 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 487 through 489 Processing sheet with id=AA7, first strand: chain 'B' and resid 598 through 604 removed outlier: 5.989A pdb=" N ILE B 575 " --> pdb=" O LYS B 600 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N VAL B 602 " --> pdb=" O ILE B 575 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL B 577 " --> pdb=" O VAL B 602 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N SER B 604 " --> pdb=" O VAL B 577 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N SER B 579 " --> pdb=" O SER B 604 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET B 695 " --> pdb=" O VAL B 645 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU B 697 " --> pdb=" O GLY B 647 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG B 733 " --> pdb=" O ILE B 721 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE B 721 " --> pdb=" O ARG B 733 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 791 through 793 removed outlier: 4.068A pdb=" N VAL B 791 " --> pdb=" O ASP B 798 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 577 through 578 removed outlier: 6.847A pdb=" N VAL D 577 " --> pdb=" O VAL D 602 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 698 through 699 Processing sheet with id=AB2, first strand: chain 'C' and resid 445 through 446 Processing sheet with id=AB3, first strand: chain 'C' and resid 487 through 489 Processing sheet with id=AB4, first strand: chain 'C' and resid 598 through 601 removed outlier: 7.192A pdb=" N ILE C 575 " --> pdb=" O GLY C 599 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N TYR C 601 " --> pdb=" O ILE C 575 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL C 577 " --> pdb=" O TYR C 601 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 698 through 699 removed outlier: 3.702A pdb=" N ARG C 733 " --> pdb=" O ILE C 721 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE C 721 " --> pdb=" O ARG C 733 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 765 through 766 removed outlier: 3.985A pdb=" N ILE C 765 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL C 791 " --> pdb=" O ASP C 798 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 445 through 446 Processing sheet with id=AB8, first strand: chain 'E' and resid 623 through 624 removed outlier: 8.861A pdb=" N LYS E 623 " --> pdb=" O GLY E 599 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N TYR E 601 " --> pdb=" O LYS E 623 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N ILE E 575 " --> pdb=" O GLY E 599 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N TYR E 601 " --> pdb=" O ILE E 575 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL E 577 " --> pdb=" O TYR E 601 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA E 603 " --> pdb=" O VAL E 577 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N SER E 579 " --> pdb=" O ALA E 603 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N VAL E 645 " --> pdb=" O MET E 695 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N GLU E 697 " --> pdb=" O VAL E 645 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLY E 647 " --> pdb=" O GLU E 697 " (cutoff:3.500A) removed outlier: 10.008A pdb=" N VAL E 699 " --> pdb=" O GLY E 647 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE E 696 " --> pdb=" O TRP E 736 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE E 721 " --> pdb=" O ARG E 733 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 765 through 766 removed outlier: 4.192A pdb=" N ILE E 765 " --> pdb=" O VAL E 792 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL E 791 " --> pdb=" O ASP E 798 " (cutoff:3.500A) 340 hydrogen bonds defined for protein. 924 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: 3.62 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3032 1.33 - 1.45: 3160 1.45 - 1.58: 7427 1.58 - 1.70: 0 1.70 - 1.82: 156 Bond restraints: 13775 Sorted by residual: bond pdb=" C ILE A 747 " pdb=" O ILE A 747 " ideal model delta sigma weight residual 1.236 1.207 0.029 9.90e-03 1.02e+04 8.76e+00 bond pdb=" C2 SAH C 901 " pdb=" N3 SAH C 901 " ideal model delta sigma weight residual 1.322 1.381 -0.059 2.00e-02 2.50e+03 8.59e+00 bond pdb=" C2 SAH B 901 " pdb=" N3 SAH B 901 " ideal model delta sigma weight residual 1.322 1.378 -0.056 2.00e-02 2.50e+03 7.89e+00 bond pdb=" C2 SAH A 901 " pdb=" N3 SAH A 901 " ideal model delta sigma weight residual 1.322 1.378 -0.056 2.00e-02 2.50e+03 7.88e+00 bond pdb=" C8 SAH A 901 " pdb=" N7 SAH A 901 " ideal model delta sigma weight residual 1.299 1.353 -0.054 2.00e-02 2.50e+03 7.23e+00 ... (remaining 13770 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 18386 2.18 - 4.36: 259 4.36 - 6.54: 53 6.54 - 8.72: 10 8.72 - 10.90: 9 Bond angle restraints: 18717 Sorted by residual: angle pdb=" N LEU B 556 " pdb=" CA LEU B 556 " pdb=" C LEU B 556 " ideal model delta sigma weight residual 113.16 121.85 -8.69 1.24e+00 6.50e-01 4.91e+01 angle pdb=" N VAL A 657 " pdb=" CA VAL A 657 " pdb=" C VAL A 657 " ideal model delta sigma weight residual 113.53 107.32 6.21 9.80e-01 1.04e+00 4.01e+01 angle pdb=" C ASN A 658 " pdb=" N PRO A 659 " pdb=" CA PRO A 659 " ideal model delta sigma weight residual 119.05 124.82 -5.77 1.11e+00 8.12e-01 2.71e+01 angle pdb=" CA VAL A 657 " pdb=" C VAL A 657 " pdb=" N ASN A 658 " ideal model delta sigma weight residual 119.31 113.64 5.67 1.15e+00 7.56e-01 2.43e+01 angle pdb=" N TYR B 558 " pdb=" CA TYR B 558 " pdb=" C TYR B 558 " ideal model delta sigma weight residual 110.43 116.72 -6.29 1.31e+00 5.83e-01 2.30e+01 ... (remaining 18712 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 7087 17.71 - 35.41: 788 35.41 - 53.11: 167 53.11 - 70.82: 24 70.82 - 88.52: 9 Dihedral angle restraints: 8075 sinusoidal: 2884 harmonic: 5191 Sorted by residual: dihedral pdb=" CA CYS A 482 " pdb=" C CYS A 482 " pdb=" N GLU A 483 " pdb=" CA GLU A 483 " ideal model delta harmonic sigma weight residual -180.00 -150.64 -29.36 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" C LEU B 556 " pdb=" N LEU B 556 " pdb=" CA LEU B 556 " pdb=" CB LEU B 556 " ideal model delta harmonic sigma weight residual -122.60 -136.98 14.38 0 2.50e+00 1.60e-01 3.31e+01 dihedral pdb=" CA CYS B 482 " pdb=" C CYS B 482 " pdb=" N GLU B 483 " pdb=" CA GLU B 483 " ideal model delta harmonic sigma weight residual -180.00 -151.91 -28.09 0 5.00e+00 4.00e-02 3.16e+01 ... (remaining 8072 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.135: 2073 0.135 - 0.269: 6 0.269 - 0.404: 2 0.404 - 0.538: 1 0.538 - 0.673: 1 Chirality restraints: 2083 Sorted by residual: chirality pdb=" CA LEU B 556 " pdb=" N LEU B 556 " pdb=" C LEU B 556 " pdb=" CB LEU B 556 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" CA ARG A 744 " pdb=" N ARG A 744 " pdb=" C ARG A 744 " pdb=" CB ARG A 744 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.56e+00 chirality pdb=" CA GLU B 715 " pdb=" N GLU B 715 " pdb=" C GLU B 715 " pdb=" CB GLU B 715 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.39 2.00e-01 2.50e+01 3.71e+00 ... (remaining 2080 not shown) Planarity restraints: 2433 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 567 " -0.035 5.00e-02 4.00e+02 5.26e-02 4.43e+00 pdb=" N PRO E 568 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO E 568 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 568 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN E 717 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.32e+00 pdb=" C ASN E 717 " 0.032 2.00e-02 2.50e+03 pdb=" O ASN E 717 " -0.012 2.00e-02 2.50e+03 pdb=" N PRO E 718 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE E 789 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.32e+00 pdb=" N PRO E 790 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO E 790 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 790 " 0.025 5.00e-02 4.00e+02 ... (remaining 2430 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 319 2.69 - 3.24: 12985 3.24 - 3.79: 19397 3.79 - 4.35: 25720 4.35 - 4.90: 41354 Nonbonded interactions: 99775 Sorted by model distance: nonbonded pdb=" O CYS E 455 " pdb="ZN ZN E 901 " model vdw 2.133 2.230 nonbonded pdb=" N CYS E 455 " pdb="ZN ZN E 901 " model vdw 2.168 2.310 nonbonded pdb=" N CYS E 481 " pdb="ZN ZN E 902 " model vdw 2.202 2.310 nonbonded pdb=" OG SER A 604 " pdb=" O ASN A 626 " model vdw 2.207 3.040 nonbonded pdb=" OG1 THR A 632 " pdb=" OD1 ASN A 635 " model vdw 2.212 3.040 ... (remaining 99770 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 432 or (resid 433 and (name N or name CA or name C or name \ O or name CB )) or resid 434 through 435 or (resid 436 and (name N or name CA o \ r name C or name O or name CB )) or resid 437 through 440 or (resid 441 through \ 442 and (name N or name CA or name C or name O or name CB )) or resid 443 throug \ h 444 or (resid 445 and (name N or name CA or name C or name O or name CB )) or \ resid 446 through 450 or (resid 451 and (name N or name CA or name C or name O o \ r name CB )) or resid 452 through 455 or (resid 456 and (name N or name CA or na \ me C or name O or name CB )) or resid 457 through 460 or (resid 461 and (name N \ or name CA or name C or name O or name CB )) or resid 462 through 469 or (resid \ 470 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 or (resid 474 and (name N or name CA or name C or name O or name CB )) or \ resid 475 or (resid 476 and (name N or name CA or name C or name O or name CB )) \ or resid 477 through 487 or (resid 488 through 489 and (name N or name CA or na \ me C or name O or name CB )) or resid 490 or (resid 491 through 493 and (name N \ or name CA or name C or name O or name CB )) or resid 494 through 495 or (resid \ 496 and (name N or name CA or name C or name O or name CB )) or resid 497 throug \ h 506 or (resid 507 and (name N or name CA or name C or name O or name CB )) or \ resid 508 through 509 or resid 530 through 531 or (resid 532 through 533 and (na \ me N or name CA or name C or name O or name CB )) or resid 534 through 535 or (r \ esid 536 through 537 and (name N or name CA or name C or name O or name CB )) or \ resid 538 through 542 or (resid 543 and (name N or name CA or name C or name O \ or name CB )) or resid 544 through 552 or (resid 553 and (name N or name CA or n \ ame C or name O or name CB )) or (resid 558 through 567 and (name N or name CA o \ r name C or name O or name CB )) or resid 568 through 571 or (resid 572 through \ 573 and (name N or name CA or name C or name O or name CB )) or resid 574 throug \ h 580 or (resid 581 and (name N or name CA or name C or name O or name CB )) or \ resid 582 through 596 or (resid 597 and (name N or name CA or name C or name O o \ r name CB )) or resid 598 through 599 or (resid 600 and (name N or name CA or na \ me C or name O or name CB )) or resid 601 through 606 or (resid 607 through 609 \ and (name N or name CA or name C or name O or name CB )) or resid 610 through 61 \ 8 or (resid 619 and (name N or name CA or name C or name O or name CB )) or resi \ d 620 through 625 or (resid 626 and (name N or name CA or name C or name O or na \ me CB )) or resid 627 or (resid 628 and (name N or name CA or name C or name O o \ r name CB )) or (resid 629 and (name N or name CA or name C or name O or name CB \ or name CG or name CD )) or (resid 630 through 631 and (name N or name CA or na \ me C or name O or name CB )) or resid 632 or (resid 633 through 634 and (name N \ or name CA or name C or name O or name CB )) or resid 635 or (resid 636 through \ 638 and (name N or name CA or name C or name O or name CB )) or resid 639 throug \ h 651 or resid 669 or (resid 670 and (name N or name CA or name C or name O or n \ ame CB )) or resid 671 through 672 or (resid 673 through 674 and (name N or name \ CA or name C or name O or name CB )) or resid 675 or (resid 676 and (name N or \ name CA or name C or name O or name CB )) or resid 677 or (resid 678 and (name N \ or name CA or name C or name O or name CB )) or resid 679 through 680 or (resid \ 681 and (name N or name CA or name C or name O or name CB )) or resid 682 throu \ gh 688 or (resid 689 and (name N or name CA or name C or name O or name CB )) or \ resid 690 through 701 or (resid 702 through 704 and (name N or name CA or name \ C or name O or name CB )) or resid 705 or (resid 706 through 709 and (name N or \ name CA or name C or name O or name CB )) or resid 710 through 714 or (resid 715 \ and (name N or name CA or name C or name O or name CB )) or resid 716 through 7 \ 24 or (resid 725 and (name N or name CA or name C or name O or name CB )) or res \ id 726 through 737 or (resid 738 and (name N or name CA or name C or name O or n \ ame CB )) or resid 739 through 751 or (resid 752 and (name N or name CA or name \ C or name O or name CB )) or resid 753 through 754 or (resid 755 and (name N or \ name CA or name C or name O or name CB )) or resid 756 or (resid 757 and (name N \ or name CA or name C or name O or name CB )) or resid 758 through 760 or (resid \ 761 through 762 and (name N or name CA or name C or name O or name CB )) or res \ id 763 through 768 or (resid 769 and (name N or name CA or name C or name O or n \ ame CB )) or resid 770 through 771 or (resid 772 and (name N or name CA or name \ C or name O or name CB )) or resid 773 or resid 789 through 793 or (resid 794 an \ d (name N or name CA or name C or name O or name CB )) or (resid 795 through 798 \ and (name N or name CA or name C or name O or name CB )) or resid 799 through 8 \ 22 or (resid 823 and (name N or name CA or name C or name O or name CB )) or res \ id 824 through 846 or (resid 847 through 848 and (name N or name CA or name C or \ name O or name CB )) or resid 849 or (resid 850 through 851 and (name N or name \ CA or name C or name O or name CB )) or resid 852 through 853 or resid 902 thro \ ugh 903)) selection = (chain 'B' and (resid 432 or (resid 433 and (name N or name CA or name C or name \ O or name CB )) or resid 434 through 435 or (resid 436 and (name N or name CA o \ r name C or name O or name CB )) or resid 437 through 440 or (resid 441 through \ 442 and (name N or name CA or name C or name O or name CB )) or resid 443 throug \ h 444 or (resid 445 and (name N or name CA or name C or name O or name CB )) or \ resid 446 through 450 or (resid 451 and (name N or name CA or name C or name O o \ r name CB )) or resid 452 through 455 or (resid 456 and (name N or name CA or na \ me C or name O or name CB )) or resid 457 through 460 or (resid 461 and (name N \ or name CA or name C or name O or name CB )) or resid 462 through 469 or (resid \ 470 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 or (resid 474 and (name N or name CA or name C or name O or name CB )) or \ resid 475 or (resid 476 and (name N or name CA or name C or name O or name CB )) \ or resid 477 through 484 or (resid 485 through 489 and (name N or name CA or na \ me C or name O or name CB )) or resid 490 or (resid 491 through 493 and (name N \ or name CA or name C or name O or name CB )) or resid 494 through 495 or (resid \ 496 and (name N or name CA or name C or name O or name CB )) or resid 497 throug \ h 506 or (resid 507 and (name N or name CA or name C or name O or name CB )) or \ resid 508 through 509 or resid 530 through 531 or (resid 532 through 533 and (na \ me N or name CA or name C or name O or name CB )) or resid 534 through 535 or (r \ esid 536 through 537 and (name N or name CA or name C or name O or name CB )) or \ resid 538 through 542 or (resid 543 and (name N or name CA or name C or name O \ or name CB )) or resid 544 through 552 or (resid 553 and (name N or name CA or n \ ame C or name O or name CB )) or (resid 558 through 567 and (name N or name CA o \ r name C or name O or name CB )) or resid 568 through 572 or (resid 573 and (nam \ e N or name CA or name C or name O or name CB )) or resid 574 through 580 or (re \ sid 581 and (name N or name CA or name C or name O or name CB )) or resid 582 th \ rough 596 or (resid 597 and (name N or name CA or name C or name O or name CB )) \ or resid 598 through 599 or (resid 600 and (name N or name CA or name C or name \ O or name CB )) or resid 601 through 606 or (resid 607 through 609 and (name N \ or name CA or name C or name O or name CB )) or resid 610 through 618 or (resid \ 619 and (name N or name CA or name C or name O or name CB )) or resid 620 throug \ h 625 or (resid 626 and (name N or name CA or name C or name O or name CB )) or \ resid 627 or (resid 628 and (name N or name CA or name C or name O or name CB )) \ or (resid 629 and (name N or name CA or name C or name O or name CB or name CG \ or name CD )) or (resid 630 through 631 and (name N or name CA or name C or name \ O or name CB )) or resid 632 or (resid 633 through 634 and (name N or name CA o \ r name C or name O or name CB )) or resid 635 or (resid 636 through 638 and (nam \ e N or name CA or name C or name O or name CB )) or resid 639 through 651 or res \ id 669 or (resid 670 and (name N or name CA or name C or name O or name CB )) or \ resid 671 through 672 or (resid 673 through 674 and (name N or name CA or name \ C or name O or name CB )) or resid 675 or (resid 676 and (name N or name CA or n \ ame C or name O or name CB )) or resid 677 or (resid 678 and (name N or name CA \ or name C or name O or name CB )) or resid 679 through 688 or (resid 689 and (na \ me N or name CA or name C or name O or name CB )) or resid 690 through 701 or (r \ esid 702 through 704 and (name N or name CA or name C or name O or name CB )) or \ resid 705 or (resid 706 through 709 and (name N or name CA or name C or name O \ or name CB )) or resid 710 through 714 or (resid 715 and (name N or name CA or n \ ame C or name O or name CB )) or resid 716 through 737 or (resid 738 and (name N \ or name CA or name C or name O or name CB )) or resid 739 through 751 or (resid \ 752 and (name N or name CA or name C or name O or name CB )) or resid 753 throu \ gh 754 or (resid 755 and (name N or name CA or name C or name O or name CB )) or \ resid 756 or (resid 757 and (name N or name CA or name C or name O or name CB ) \ ) or resid 758 through 760 or (resid 761 through 762 and (name N or name CA or n \ ame C or name O or name CB )) or resid 763 through 766 or (resid 767 and (name N \ or name CA or name C or name O or name CB or name CG or name CD )) or resid 768 \ or (resid 769 and (name N or name CA or name C or name O or name CB )) or resid \ 770 through 771 or (resid 772 and (name N or name CA or name C or name O or nam \ e CB )) or resid 773 or resid 789 through 793 or (resid 794 and (name N or name \ CA or name C or name O or name CB )) or resid 795 or (resid 796 through 798 and \ (name N or name CA or name C or name O or name CB )) or resid 799 through 822 or \ (resid 823 and (name N or name CA or name C or name O or name CB )) or resid 82 \ 4 through 846 or (resid 847 through 848 and (name N or name CA or name C or name \ O or name CB )) or resid 849 or (resid 850 through 851 and (name N or name CA o \ r name C or name O or name CB )) or resid 852 or (resid 853 and (name N or name \ CA or name C or name O or name CB )) or resid 902 through 903)) selection = (chain 'C' and (resid 432 through 509 or resid 530 through 553 or (resid 558 thr \ ough 567 and (name N or name CA or name C or name O or name CB )) or resid 568 t \ hrough 580 or (resid 581 and (name N or name CA or name C or name O or name CB ) \ ) or resid 582 through 606 or (resid 607 through 609 and (name N or name CA or n \ ame C or name O or name CB )) or resid 610 through 625 or (resid 626 and (name N \ or name CA or name C or name O or name CB )) or resid 627 or (resid 628 and (na \ me N or name CA or name C or name O or name CB )) or (resid 629 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD )) or (resid 630 thr \ ough 631 and (name N or name CA or name C or name O or name CB )) or resid 632 o \ r (resid 633 through 634 and (name N or name CA or name C or name O or name CB ) \ ) or resid 635 or (resid 636 through 638 and (name N or name CA or name C or nam \ e O or name CB )) or resid 639 through 651 or resid 669 through 672 or (resid 67 \ 3 through 674 and (name N or name CA or name C or name O or name CB )) or resid \ 675 or (resid 676 and (name N or name CA or name C or name O or name CB )) or re \ sid 677 or (resid 678 and (name N or name CA or name C or name O or name CB )) o \ r resid 679 through 680 or (resid 681 and (name N or name CA or name C or name O \ or name CB )) or resid 682 through 701 or (resid 702 through 704 and (name N or \ name CA or name C or name O or name CB )) or resid 705 or (resid 706 through 70 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 710 through \ 714 or (resid 715 and (name N or name CA or name C or name O or name CB )) or re \ sid 716 through 724 or (resid 725 and (name N or name CA or name C or name O or \ name CB )) or resid 726 through 766 or (resid 767 and (name N or name CA or name \ C or name O or name CB or name CG or name CD )) or resid 768 through 853 or res \ id 902 through 903)) selection = (chain 'E' and (resid 432 or (resid 433 and (name N or name CA or name C or name \ O or name CB )) or resid 434 through 435 or (resid 436 and (name N or name CA o \ r name C or name O or name CB )) or resid 437 through 440 or (resid 441 through \ 442 and (name N or name CA or name C or name O or name CB )) or resid 443 throug \ h 444 or (resid 445 and (name N or name CA or name C or name O or name CB )) or \ resid 446 through 450 or (resid 451 and (name N or name CA or name C or name O o \ r name CB )) or resid 452 through 455 or (resid 456 and (name N or name CA or na \ me C or name O or name CB )) or resid 457 through 460 or (resid 461 and (name N \ or name CA or name C or name O or name CB )) or resid 462 through 469 or (resid \ 470 through 472 and (name N or name CA or name C or name O or name CB )) or resi \ d 473 or (resid 474 and (name N or name CA or name C or name O or name CB )) or \ resid 475 or (resid 476 and (name N or name CA or name C or name O or name CB )) \ or resid 477 through 487 or (resid 488 through 489 and (name N or name CA or na \ me C or name O or name CB )) or resid 490 or (resid 491 through 493 and (name N \ or name CA or name C or name O or name CB )) or resid 494 through 495 or (resid \ 496 and (name N or name CA or name C or name O or name CB )) or resid 497 throug \ h 506 or (resid 507 and (name N or name CA or name C or name O or name CB )) or \ resid 508 through 531 or (resid 532 through 533 and (name N or name CA or name C \ or name O or name CB )) or resid 534 through 535 or (resid 536 through 537 and \ (name N or name CA or name C or name O or name CB )) or resid 538 through 542 or \ (resid 543 and (name N or name CA or name C or name O or name CB )) or resid 54 \ 4 through 552 or (resid 553 through 567 and (name N or name CA or name C or name \ O or name CB )) or resid 568 through 596 or (resid 597 and (name N or name CA o \ r name C or name O or name CB )) or resid 598 through 599 or (resid 600 and (nam \ e N or name CA or name C or name O or name CB )) or resid 601 through 618 or (re \ sid 619 and (name N or name CA or name C or name O or name CB )) or resid 620 th \ rough 633 or (resid 634 and (name N or name CA or name C or name O or name CB )) \ or resid 635 through 651 or resid 669 or (resid 670 and (name N or name CA or n \ ame C or name O or name CB )) or resid 671 through 688 or (resid 689 and (name N \ or name CA or name C or name O or name CB )) or resid 690 through 708 or (resid \ 709 and (name N or name CA or name C or name O or name CB )) or resid 710 throu \ gh 724 or (resid 725 and (name N or name CA or name C or name O or name CB )) or \ resid 726 through 737 or (resid 738 and (name N or name CA or name C or name O \ or name CB )) or resid 739 through 751 or (resid 752 and (name N or name CA or n \ ame C or name O or name CB )) or resid 753 through 754 or (resid 755 and (name N \ or name CA or name C or name O or name CB )) or resid 756 or (resid 757 and (na \ me N or name CA or name C or name O or name CB )) or resid 758 through 760 or (r \ esid 761 through 762 and (name N or name CA or name C or name O or name CB )) or \ resid 763 through 768 or (resid 769 and (name N or name CA or name C or name O \ or name CB )) or resid 770 through 771 or (resid 772 and (name N or name CA or n \ ame C or name O or name CB )) or resid 773 or resid 789 through 793 or (resid 79 \ 4 and (name N or name CA or name C or name O or name CB )) or (resid 795 through \ 798 and (name N or name CA or name C or name O or name CB )) or resid 799 throu \ gh 822 or (resid 823 and (name N or name CA or name C or name O or name CB )) or \ resid 824 through 846 or (resid 847 through 848 and (name N or name CA or name \ C or name O or name CB )) or resid 849 or (resid 850 through 851 and (name N or \ name CA or name C or name O or name CB )) or resid 852 through 853 or resid 902 \ through 903)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.660 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 34.390 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 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 : 0.003 0.059 13813 Z= 0.165 Angle : 0.724 12.846 18771 Z= 0.362 Chirality : 0.046 0.673 2083 Planarity : 0.004 0.053 2433 Dihedral : 15.512 88.525 4727 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.39 % Allowed : 19.94 % Favored : 79.68 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.20), residues: 1766 helix: -0.61 (0.24), residues: 476 sheet: -3.84 (0.36), residues: 112 loop : -0.98 (0.19), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 736 HIS 0.003 0.001 HIS B 730 PHE 0.031 0.001 PHE E 672 TYR 0.016 0.001 TYR E 734 ARG 0.009 0.000 ARG B 497 Details of bonding type rmsd hydrogen bonds : bond 0.29509 ( 340) hydrogen bonds : angle 7.75395 ( 924) metal coordination : bond 0.00836 ( 38) metal coordination : angle 4.07238 ( 54) covalent geometry : bond 0.00323 (13775) covalent geometry : angle 0.69099 (18717) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 149 time to evaluate : 1.402 Fit side-chains revert: symmetry clash REVERT: A 601 TYR cc_start: 0.7522 (t80) cc_final: 0.7160 (t80) REVERT: B 558 TYR cc_start: 0.7705 (OUTLIER) cc_final: 0.7116 (m-80) REVERT: D 702 MET cc_start: 0.3594 (ppp) cc_final: 0.2534 (mmm) REVERT: E 695 MET cc_start: 0.4311 (ttm) cc_final: 0.4020 (mtt) REVERT: E 793 MET cc_start: 0.4400 (tpt) cc_final: 0.4145 (tpt) outliers start: 5 outliers final: 2 residues processed: 153 average time/residue: 0.2300 time to fit residues: 52.9456 Evaluate side-chains 145 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 142 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 744 ARG Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain B residue 558 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 0.0060 chunk 134 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 45 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 138 optimal weight: 40.0000 chunk 53 optimal weight: 8.9990 chunk 84 optimal weight: 0.7980 chunk 103 optimal weight: 0.0980 chunk 160 optimal weight: 5.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 827 GLN E 635 ASN E 751 ASN E 757 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.221681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.161514 restraints weight = 18502.611| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 3.21 r_work: 0.3785 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work: 0.3656 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13813 Z= 0.114 Angle : 0.606 13.277 18771 Z= 0.297 Chirality : 0.040 0.179 2083 Planarity : 0.004 0.061 2433 Dihedral : 4.913 50.450 1953 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.40 % Allowed : 18.24 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.20), residues: 1766 helix: -0.33 (0.23), residues: 513 sheet: -3.31 (0.38), residues: 125 loop : -0.92 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 542 HIS 0.004 0.001 HIS E 677 PHE 0.014 0.001 PHE E 672 TYR 0.012 0.001 TYR B 676 ARG 0.007 0.000 ARG B 497 Details of bonding type rmsd hydrogen bonds : bond 0.04495 ( 340) hydrogen bonds : angle 5.22704 ( 924) metal coordination : bond 0.00802 ( 38) metal coordination : angle 4.26570 ( 54) covalent geometry : bond 0.00244 (13775) covalent geometry : angle 0.56193 (18717) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 519 GLN cc_start: 0.6488 (pt0) cc_final: 0.5442 (tm-30) REVERT: C 528 LEU cc_start: 0.5241 (OUTLIER) cc_final: 0.4894 (mp) REVERT: E 695 MET cc_start: 0.1652 (ttm) cc_final: 0.1366 (mtt) REVERT: E 733 ARG cc_start: 0.6486 (mpt180) cc_final: 0.6205 (mpt180) REVERT: E 742 MET cc_start: 0.5557 (mtp) cc_final: 0.5160 (mtm) outliers start: 31 outliers final: 16 residues processed: 176 average time/residue: 0.2331 time to fit residues: 61.0723 Evaluate side-chains 159 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 704 VAL Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 739 LEU Chi-restraints excluded: chain C residue 446 PHE Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain E residue 717 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 42 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 163 optimal weight: 20.0000 chunk 63 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 chunk 122 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 94 optimal weight: 30.0000 chunk 9 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 677 HIS E 751 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4808 r_free = 0.4808 target = 0.221098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.162585 restraints weight = 18747.257| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 4.22 r_work: 0.3733 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13813 Z= 0.118 Angle : 0.586 12.302 18771 Z= 0.283 Chirality : 0.040 0.176 2083 Planarity : 0.004 0.049 2433 Dihedral : 4.733 52.736 1947 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.25 % Allowed : 19.32 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.20), residues: 1766 helix: -0.13 (0.23), residues: 525 sheet: -3.10 (0.40), residues: 125 loop : -0.88 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 542 HIS 0.012 0.001 HIS E 677 PHE 0.015 0.001 PHE C 549 TYR 0.021 0.001 TYR E 734 ARG 0.009 0.000 ARG B 670 Details of bonding type rmsd hydrogen bonds : bond 0.03974 ( 340) hydrogen bonds : angle 4.86628 ( 924) metal coordination : bond 0.00737 ( 38) metal coordination : angle 4.10952 ( 54) covalent geometry : bond 0.00267 (13775) covalent geometry : angle 0.54383 (18717) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 147 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 519 GLN cc_start: 0.6336 (pt0) cc_final: 0.5375 (tm-30) REVERT: A 681 TYR cc_start: 0.7405 (OUTLIER) cc_final: 0.6899 (m-10) REVERT: B 436 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6618 (mp) REVERT: B 832 ARG cc_start: 0.8353 (ptt180) cc_final: 0.8143 (ptt180) REVERT: E 594 LEU cc_start: 0.7271 (mm) cc_final: 0.6968 (mm) REVERT: E 742 MET cc_start: 0.6050 (mtp) cc_final: 0.5537 (mtm) outliers start: 42 outliers final: 29 residues processed: 177 average time/residue: 0.2465 time to fit residues: 64.5558 Evaluate side-chains 167 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 681 TYR Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 739 LEU Chi-restraints excluded: chain C residue 446 PHE Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 550 PHE Chi-restraints excluded: chain C residue 596 ILE Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 833 SER Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 577 VAL Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 717 ASN Chi-restraints excluded: chain E residue 803 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 91 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 141 optimal weight: 0.5980 chunk 109 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 chunk 164 optimal weight: 5.9990 chunk 156 optimal weight: 0.4980 chunk 113 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 652 ASN ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 635 ASN D 698 ASN E 677 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.213662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.154212 restraints weight = 18456.932| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 3.27 r_work: 0.3652 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.092 13813 Z= 0.314 Angle : 0.775 14.165 18771 Z= 0.381 Chirality : 0.047 0.204 2083 Planarity : 0.006 0.072 2433 Dihedral : 5.667 55.949 1947 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 5.26 % Allowed : 19.24 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.20), residues: 1766 helix: -0.73 (0.23), residues: 521 sheet: -3.68 (0.36), residues: 135 loop : -1.12 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 542 HIS 0.009 0.002 HIS E 677 PHE 0.026 0.003 PHE A 735 TYR 0.024 0.002 TYR C 588 ARG 0.006 0.001 ARG A 545 Details of bonding type rmsd hydrogen bonds : bond 0.05062 ( 340) hydrogen bonds : angle 5.62381 ( 924) metal coordination : bond 0.00888 ( 38) metal coordination : angle 4.82099 ( 54) covalent geometry : bond 0.00751 (13775) covalent geometry : angle 0.73160 (18717) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 133 time to evaluate : 1.611 Fit side-chains revert: symmetry clash REVERT: A 519 GLN cc_start: 0.6286 (pt0) cc_final: 0.5261 (tm-30) REVERT: A 681 TYR cc_start: 0.7622 (OUTLIER) cc_final: 0.7136 (m-10) REVERT: A 842 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7164 (tt) REVERT: B 733 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.7503 (mmt90) REVERT: C 805 LEU cc_start: 0.7218 (mt) cc_final: 0.6993 (tt) REVERT: E 734 TYR cc_start: 0.4730 (t80) cc_final: 0.4440 (t80) outliers start: 68 outliers final: 44 residues processed: 188 average time/residue: 0.2220 time to fit residues: 63.8460 Evaluate side-chains 173 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 126 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 681 TYR Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 704 VAL Chi-restraints excluded: chain B residue 719 VAL Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 733 ARG Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 799 VAL Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 739 LEU Chi-restraints excluded: chain C residue 446 PHE Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 550 PHE Chi-restraints excluded: chain C residue 596 ILE Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 704 VAL Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 726 VAL Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 806 GLU Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 833 SER Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 577 VAL Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 700 VAL Chi-restraints excluded: chain E residue 717 ASN Chi-restraints excluded: chain E residue 760 LEU Chi-restraints excluded: chain E residue 803 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 88 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 131 optimal weight: 0.8980 chunk 63 optimal weight: 0.0980 chunk 147 optimal weight: 0.8980 chunk 82 optimal weight: 0.0570 chunk 38 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 chunk 59 optimal weight: 0.0060 chunk 52 optimal weight: 4.9990 overall best weight: 0.3914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 772 GLN A 827 GLN ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 635 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.220092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.160959 restraints weight = 18758.328| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 4.52 r_work: 0.3728 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13813 Z= 0.099 Angle : 0.577 12.040 18771 Z= 0.278 Chirality : 0.040 0.176 2083 Planarity : 0.004 0.060 2433 Dihedral : 4.796 50.350 1947 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.86 % Allowed : 21.25 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.21), residues: 1766 helix: -0.12 (0.24), residues: 523 sheet: -3.18 (0.39), residues: 127 loop : -0.88 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP E 736 HIS 0.004 0.001 HIS B 730 PHE 0.014 0.001 PHE A 462 TYR 0.015 0.001 TYR B 734 ARG 0.006 0.000 ARG B 670 Details of bonding type rmsd hydrogen bonds : bond 0.03188 ( 340) hydrogen bonds : angle 4.62936 ( 924) metal coordination : bond 0.00758 ( 38) metal coordination : angle 4.10658 ( 54) covalent geometry : bond 0.00218 (13775) covalent geometry : angle 0.53398 (18717) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 146 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 519 GLN cc_start: 0.6301 (pt0) cc_final: 0.5383 (tm-30) REVERT: A 681 TYR cc_start: 0.7449 (OUTLIER) cc_final: 0.6987 (m-10) REVERT: A 798 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7536 (t70) REVERT: B 436 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.6599 (mp) REVERT: B 611 ILE cc_start: 0.7252 (mt) cc_final: 0.6934 (mt) REVERT: C 420 MET cc_start: 0.2261 (OUTLIER) cc_final: 0.1779 (ptp) REVERT: C 463 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6881 (mp) REVERT: E 733 ARG cc_start: 0.6064 (mpt180) cc_final: 0.5777 (mpt180) REVERT: E 770 LYS cc_start: 0.6287 (mmtm) cc_final: 0.5689 (mmtp) outliers start: 37 outliers final: 21 residues processed: 175 average time/residue: 0.2339 time to fit residues: 61.8594 Evaluate side-chains 163 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 681 TYR Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 798 ASP Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 739 LEU Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 446 PHE Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 550 PHE Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain E residue 577 VAL Chi-restraints excluded: chain E residue 596 ILE Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 717 ASN Chi-restraints excluded: chain E residue 760 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 86 optimal weight: 8.9990 chunk 74 optimal weight: 0.7980 chunk 158 optimal weight: 20.0000 chunk 96 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 156 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 143 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.216212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.158030 restraints weight = 18538.698| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 3.34 r_work: 0.3692 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13813 Z= 0.169 Angle : 0.620 12.074 18771 Z= 0.301 Chirality : 0.042 0.183 2083 Planarity : 0.004 0.072 2433 Dihedral : 4.967 49.837 1947 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 4.17 % Allowed : 20.32 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.20), residues: 1766 helix: -0.07 (0.24), residues: 521 sheet: -3.21 (0.40), residues: 127 loop : -0.95 (0.19), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 542 HIS 0.005 0.001 HIS B 814 PHE 0.020 0.002 PHE E 672 TYR 0.015 0.001 TYR A 588 ARG 0.006 0.000 ARG C 538 Details of bonding type rmsd hydrogen bonds : bond 0.03746 ( 340) hydrogen bonds : angle 4.82081 ( 924) metal coordination : bond 0.00702 ( 38) metal coordination : angle 4.09079 ( 54) covalent geometry : bond 0.00404 (13775) covalent geometry : angle 0.58098 (18717) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 135 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 519 GLN cc_start: 0.6536 (pt0) cc_final: 0.5461 (tm-30) REVERT: A 681 TYR cc_start: 0.7549 (OUTLIER) cc_final: 0.7101 (m-10) REVERT: B 436 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6947 (mp) REVERT: C 420 MET cc_start: 0.2399 (OUTLIER) cc_final: 0.1853 (ptp) REVERT: C 463 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6869 (mp) REVERT: E 593 GLU cc_start: 0.7332 (tm-30) cc_final: 0.6883 (tm-30) outliers start: 54 outliers final: 41 residues processed: 178 average time/residue: 0.2199 time to fit residues: 60.3365 Evaluate side-chains 177 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 132 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 681 TYR Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 632 THR Chi-restraints excluded: chain D residue 708 ARG Chi-restraints excluded: chain D residue 739 LEU Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 446 PHE Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 550 PHE Chi-restraints excluded: chain C residue 596 ILE Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 704 VAL Chi-restraints excluded: chain C residue 707 LYS Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 726 VAL Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 806 GLU Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 833 SER Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 577 VAL Chi-restraints excluded: chain E residue 596 ILE Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 717 ASN Chi-restraints excluded: chain E residue 760 LEU Chi-restraints excluded: chain E residue 803 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 128 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 97 optimal weight: 0.6980 chunk 0 optimal weight: 30.0000 chunk 34 optimal weight: 0.6980 chunk 98 optimal weight: 10.0000 chunk 144 optimal weight: 0.8980 chunk 109 optimal weight: 0.3980 chunk 90 optimal weight: 8.9990 chunk 48 optimal weight: 0.6980 chunk 156 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 635 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.218681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.151521 restraints weight = 18598.088| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 4.13 r_work: 0.3708 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13813 Z= 0.102 Angle : 0.566 11.211 18771 Z= 0.272 Chirality : 0.040 0.173 2083 Planarity : 0.004 0.074 2433 Dihedral : 4.609 45.617 1947 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.86 % Allowed : 21.72 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.21), residues: 1766 helix: 0.20 (0.24), residues: 525 sheet: -2.91 (0.41), residues: 127 loop : -0.81 (0.20), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP C 542 HIS 0.003 0.001 HIS B 677 PHE 0.014 0.001 PHE A 466 TYR 0.010 0.001 TYR B 734 ARG 0.004 0.000 ARG B 670 Details of bonding type rmsd hydrogen bonds : bond 0.03047 ( 340) hydrogen bonds : angle 4.44792 ( 924) metal coordination : bond 0.00692 ( 38) metal coordination : angle 3.92346 ( 54) covalent geometry : bond 0.00236 (13775) covalent geometry : angle 0.52606 (18717) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 519 GLN cc_start: 0.6403 (pt0) cc_final: 0.5411 (tm-30) REVERT: A 592 LYS cc_start: 0.7245 (mttm) cc_final: 0.7031 (mttp) REVERT: A 681 TYR cc_start: 0.7362 (OUTLIER) cc_final: 0.6887 (m-10) REVERT: B 436 LEU cc_start: 0.6905 (OUTLIER) cc_final: 0.6678 (mp) REVERT: B 811 PHE cc_start: 0.7390 (m-80) cc_final: 0.7113 (m-80) REVERT: C 420 MET cc_start: 0.2369 (OUTLIER) cc_final: 0.1857 (ptp) REVERT: C 463 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.7093 (mp) REVERT: E 770 LYS cc_start: 0.6579 (mmtm) cc_final: 0.5943 (mmtp) outliers start: 37 outliers final: 28 residues processed: 172 average time/residue: 0.2181 time to fit residues: 57.3668 Evaluate side-chains 170 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 681 TYR Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 793 MET Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 739 LEU Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 446 PHE Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 550 PHE Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 577 VAL Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 700 VAL Chi-restraints excluded: chain E residue 760 LEU Chi-restraints excluded: chain E residue 803 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 24 optimal weight: 0.0370 chunk 169 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 79 optimal weight: 0.0000 chunk 31 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 105 optimal weight: 20.0000 chunk 162 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 overall best weight: 0.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4805 r_free = 0.4805 target = 0.220687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.161979 restraints weight = 18911.176| |-----------------------------------------------------------------------------| r_work (start): 0.4138 rms_B_bonded: 4.18 r_work: 0.3742 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13813 Z= 0.097 Angle : 0.564 10.645 18771 Z= 0.271 Chirality : 0.039 0.163 2083 Planarity : 0.004 0.075 2433 Dihedral : 4.415 45.576 1947 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.55 % Allowed : 22.18 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.21), residues: 1766 helix: 0.38 (0.24), residues: 531 sheet: -2.74 (0.41), residues: 126 loop : -0.72 (0.20), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 542 HIS 0.002 0.001 HIS B 677 PHE 0.019 0.001 PHE E 672 TYR 0.016 0.001 TYR A 601 ARG 0.004 0.000 ARG C 538 Details of bonding type rmsd hydrogen bonds : bond 0.02869 ( 340) hydrogen bonds : angle 4.27886 ( 924) metal coordination : bond 0.00696 ( 38) metal coordination : angle 3.83756 ( 54) covalent geometry : bond 0.00217 (13775) covalent geometry : angle 0.52549 (18717) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 146 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 GLN cc_start: 0.6522 (pt0) cc_final: 0.5716 (tt0) REVERT: A 592 LYS cc_start: 0.7162 (mttm) cc_final: 0.6872 (mttp) REVERT: A 681 TYR cc_start: 0.7439 (OUTLIER) cc_final: 0.6969 (m-10) REVERT: B 436 LEU cc_start: 0.6739 (OUTLIER) cc_final: 0.6523 (mp) REVERT: B 464 GLU cc_start: 0.6756 (mp0) cc_final: 0.6453 (mp0) REVERT: B 811 PHE cc_start: 0.7267 (m-80) cc_final: 0.7032 (m-80) REVERT: C 420 MET cc_start: 0.2421 (OUTLIER) cc_final: 0.1942 (ptp) REVERT: C 542 TRP cc_start: 0.7793 (p-90) cc_final: 0.7553 (p-90) REVERT: C 793 MET cc_start: 0.7019 (tpt) cc_final: 0.6509 (tpp) outliers start: 33 outliers final: 24 residues processed: 169 average time/residue: 0.2344 time to fit residues: 60.2623 Evaluate side-chains 166 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 681 TYR Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 793 MET Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 632 THR Chi-restraints excluded: chain D residue 708 ARG Chi-restraints excluded: chain D residue 739 LEU Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 446 PHE Chi-restraints excluded: chain C residue 550 PHE Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 577 VAL Chi-restraints excluded: chain E residue 596 ILE Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 803 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 111 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 143 optimal weight: 30.0000 chunk 34 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 70 optimal weight: 0.6980 chunk 106 optimal weight: 5.9990 chunk 79 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 656 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.218407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.152578 restraints weight = 18459.619| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 4.19 r_work: 0.3682 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13813 Z= 0.114 Angle : 0.582 10.521 18771 Z= 0.280 Chirality : 0.040 0.160 2083 Planarity : 0.004 0.073 2433 Dihedral : 4.424 49.481 1945 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.63 % Allowed : 22.33 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.21), residues: 1766 helix: 0.36 (0.24), residues: 531 sheet: -2.77 (0.41), residues: 126 loop : -0.71 (0.20), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 542 HIS 0.003 0.001 HIS B 814 PHE 0.026 0.001 PHE E 642 TYR 0.025 0.001 TYR E 734 ARG 0.014 0.000 ARG A 545 Details of bonding type rmsd hydrogen bonds : bond 0.03092 ( 340) hydrogen bonds : angle 4.38708 ( 924) metal coordination : bond 0.00668 ( 38) metal coordination : angle 3.75015 ( 54) covalent geometry : bond 0.00265 (13775) covalent geometry : angle 0.54643 (18717) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 519 GLN cc_start: 0.6462 (pt0) cc_final: 0.5652 (tt0) REVERT: A 681 TYR cc_start: 0.7271 (OUTLIER) cc_final: 0.6800 (m-10) REVERT: B 436 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6725 (mp) REVERT: C 420 MET cc_start: 0.2424 (OUTLIER) cc_final: 0.1946 (ptp) REVERT: C 542 TRP cc_start: 0.7693 (p-90) cc_final: 0.7426 (p-90) REVERT: C 793 MET cc_start: 0.7040 (tpt) cc_final: 0.6524 (tpp) REVERT: C 806 GLU cc_start: 0.7560 (tp30) cc_final: 0.7235 (tp30) REVERT: E 593 GLU cc_start: 0.7296 (tm-30) cc_final: 0.6826 (tm-30) REVERT: E 770 LYS cc_start: 0.6364 (mmtm) cc_final: 0.5693 (mmtp) outliers start: 34 outliers final: 24 residues processed: 166 average time/residue: 0.2290 time to fit residues: 58.2847 Evaluate side-chains 165 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 681 TYR Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 793 MET Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 632 THR Chi-restraints excluded: chain D residue 708 ARG Chi-restraints excluded: chain D residue 739 LEU Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 446 PHE Chi-restraints excluded: chain C residue 550 PHE Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 624 TYR Chi-restraints excluded: chain E residue 700 VAL Chi-restraints excluded: chain E residue 803 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 42 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.218204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.151015 restraints weight = 18425.584| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 4.09 r_work: 0.3706 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13813 Z= 0.124 Angle : 0.585 10.544 18771 Z= 0.282 Chirality : 0.040 0.151 2083 Planarity : 0.004 0.072 2433 Dihedral : 4.455 49.853 1945 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.16 % Allowed : 22.87 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.21), residues: 1766 helix: 0.32 (0.24), residues: 533 sheet: -2.65 (0.41), residues: 126 loop : -0.72 (0.20), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 542 HIS 0.003 0.001 HIS B 814 PHE 0.023 0.001 PHE E 642 TYR 0.023 0.001 TYR E 734 ARG 0.009 0.000 ARG A 545 Details of bonding type rmsd hydrogen bonds : bond 0.03181 ( 340) hydrogen bonds : angle 4.42327 ( 924) metal coordination : bond 0.00663 ( 38) metal coordination : angle 3.80915 ( 54) covalent geometry : bond 0.00292 (13775) covalent geometry : angle 0.54868 (18717) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3532 Ramachandran restraints generated. 1766 Oldfield, 0 Emsley, 1766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 1.402 Fit side-chains REVERT: A 519 GLN cc_start: 0.6497 (pt0) cc_final: 0.5658 (tt0) REVERT: A 681 TYR cc_start: 0.7270 (OUTLIER) cc_final: 0.6749 (m-10) REVERT: B 436 LEU cc_start: 0.6811 (OUTLIER) cc_final: 0.6610 (mp) REVERT: D 708 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7081 (mtm180) REVERT: C 420 MET cc_start: 0.2701 (OUTLIER) cc_final: 0.2082 (ptp) REVERT: C 526 MET cc_start: 0.6267 (ttt) cc_final: 0.5922 (ttt) REVERT: C 793 MET cc_start: 0.6994 (tpt) cc_final: 0.6466 (tpp) REVERT: C 806 GLU cc_start: 0.7670 (tp30) cc_final: 0.7313 (tp30) REVERT: E 593 GLU cc_start: 0.7343 (tm-30) cc_final: 0.6879 (tm-30) REVERT: E 697 GLU cc_start: 0.4198 (mp0) cc_final: 0.3615 (tm-30) REVERT: E 721 ILE cc_start: 0.6750 (mm) cc_final: 0.6414 (mt) REVERT: E 733 ARG cc_start: 0.6587 (mpt180) cc_final: 0.6145 (mpt180) REVERT: E 770 LYS cc_start: 0.6572 (mmtm) cc_final: 0.5923 (mmtp) outliers start: 28 outliers final: 23 residues processed: 161 average time/residue: 0.2180 time to fit residues: 53.9217 Evaluate side-chains 165 residues out of total 1577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 681 TYR Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 632 THR Chi-restraints excluded: chain D residue 708 ARG Chi-restraints excluded: chain D residue 739 LEU Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 446 PHE Chi-restraints excluded: chain C residue 550 PHE Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 624 TYR Chi-restraints excluded: chain E residue 700 VAL Chi-restraints excluded: chain E residue 803 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 99 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 167 optimal weight: 0.9990 chunk 147 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 105 optimal weight: 20.0000 chunk 71 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 827 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.217091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.150713 restraints weight = 18648.451| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 3.73 r_work: 0.3698 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13813 Z= 0.154 Angle : 0.614 10.824 18771 Z= 0.297 Chirality : 0.041 0.200 2083 Planarity : 0.004 0.072 2433 Dihedral : 4.634 52.526 1945 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.55 % Allowed : 22.64 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.21), residues: 1766 helix: 0.21 (0.24), residues: 527 sheet: -2.73 (0.41), residues: 126 loop : -0.75 (0.20), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 736 HIS 0.005 0.001 HIS B 814 PHE 0.023 0.002 PHE D 675 TYR 0.028 0.001 TYR E 734 ARG 0.009 0.000 ARG A 545 Details of bonding type rmsd hydrogen bonds : bond 0.03469 ( 340) hydrogen bonds : angle 4.61918 ( 924) metal coordination : bond 0.00669 ( 38) metal coordination : angle 3.92509 ( 54) covalent geometry : bond 0.00366 (13775) covalent geometry : angle 0.57779 (18717) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11380.11 seconds wall clock time: 193 minutes 28.20 seconds (11608.20 seconds total)