Starting phenix.real_space_refine on Sat Mar 16 02:43:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eik_28159/03_2024/8eik_28159_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eik_28159/03_2024/8eik_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eik_28159/03_2024/8eik_28159.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eik_28159/03_2024/8eik_28159.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eik_28159/03_2024/8eik_28159_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eik_28159/03_2024/8eik_28159_updated.pdb" } 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 Residue "A GLU 609": "OE1" <-> "OE2" Residue "B GLU 502": "OE1" <-> "OE2" Residue "B GLU 715": "OE1" <-> "OE2" Residue "B GLU 853": "OE1" <-> "OE2" Residue "C GLU 464": "OE1" <-> "OE2" Residue "E GLU 797": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13487 Number of models: 1 Model: "" Number of chains: 13 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: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "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: 7.31, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 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: 4.71 Conformation dependent library (CDL) restraints added in 2.5 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... running ksdssp... Secondary structure from input PDB file: 72 helices and 13 sheets defined 31.0% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.74 Creating SS restraints... Processing helix chain 'A' and resid 417 through 426 Processing helix chain 'A' and resid 456 through 465 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) Processing helix chain 'A' and resid 501 through 505 removed outlier: 4.264A pdb=" N GLU A 505 " --> pdb=" O VAL A 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 501 through 505' Processing helix chain 'A' and resid 512 through 518 removed outlier: 3.517A pdb=" N LEU A 518 " --> pdb=" O ALA A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 551 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) Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 586 through 594 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 608 through 618 removed outlier: 3.870A pdb=" N VAL A 613 " --> pdb=" O GLU A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 638 Processing helix chain 'A' and resid 667 through 682 removed outlier: 3.614A pdb=" N ARG A 670 " --> pdb=" O GLY A 667 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU A 671 " --> pdb=" O THR A 668 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 672 " --> pdb=" O GLY A 669 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A 682 " --> pdb=" O LEU A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 714 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 723 through 725 No H-bonds generated for 'chain 'A' and resid 723 through 725' Processing helix chain 'A' and resid 756 through 759 Processing helix chain 'A' and resid 802 through 809 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 823 through 826 No H-bonds generated for 'chain 'A' and resid 823 through 826' Processing helix chain 'A' and resid 836 through 847 removed outlier: 3.716A pdb=" N ALA A 844 " --> pdb=" O ARG A 840 " (cutoff:3.500A) Proline residue: A 845 - end of helix Processing helix chain 'B' and resid 417 through 425 Processing helix chain 'B' and resid 431 through 433 No H-bonds generated for 'chain 'B' and resid 431 through 433' Processing helix chain 'B' and resid 456 through 465 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) Processing helix chain 'B' and resid 501 through 505 removed outlier: 3.861A pdb=" N GLU B 505 " --> pdb=" O VAL B 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 501 through 505' Processing helix chain 'B' and resid 512 through 518 Processing helix chain 'B' and resid 542 through 551 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) Processing helix chain 'B' and resid 586 through 593 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) Processing helix chain 'B' and resid 608 through 616 removed outlier: 3.739A pdb=" N GLY B 614 " --> pdb=" O SER B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 638 removed outlier: 3.742A pdb=" N GLU B 637 " --> pdb=" O LYS B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 682 removed outlier: 3.677A pdb=" N LEU B 678 " --> pdb=" O PHE B 675 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 679 " --> pdb=" O TYR B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 714 Processing helix chain 'B' and resid 757 through 759 No H-bonds generated for 'chain 'B' and resid 757 through 759' Processing helix chain 'B' and resid 804 through 808 Processing helix chain 'B' and resid 823 through 831 removed outlier: 3.540A pdb=" N LEU B 830 " --> pdb=" O ARG B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 848 Proline residue: B 845 - end of helix removed outlier: 5.351A pdb=" N ASP B 848 " --> pdb=" O ALA B 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 593 Processing helix chain 'D' and resid 628 through 630 No H-bonds generated for 'chain 'D' and resid 628 through 630' Processing helix chain 'D' and resid 633 through 639 Processing helix chain 'D' and resid 668 through 682 removed outlier: 3.624A pdb=" N GLU D 674 " --> pdb=" O ARG D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 704 through 713 Processing helix chain 'D' and resid 836 through 842 Processing helix chain 'C' and resid 417 through 425 removed outlier: 3.502A pdb=" N ALA C 421 " --> pdb=" O ARG C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 433 No H-bonds generated for 'chain 'C' and resid 431 through 433' Processing helix chain 'C' and resid 456 through 465 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 505 removed outlier: 3.990A pdb=" N GLU C 505 " --> pdb=" O VAL C 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 501 through 505' Processing helix chain 'C' and resid 512 through 518 Processing helix chain 'C' and resid 542 through 545 No H-bonds generated for 'chain 'C' and resid 542 through 545' Processing helix chain 'C' and resid 547 through 550 No H-bonds generated for 'chain 'C' and resid 547 through 550' Processing helix chain 'C' and resid 569 through 571 No H-bonds generated for 'chain 'C' and resid 569 through 571' Processing helix chain 'C' and resid 586 through 593 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 608 through 616 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 628 through 630 No H-bonds generated for 'chain 'C' and resid 628 through 630' Processing helix chain 'C' and resid 633 through 638 Processing helix chain 'C' and resid 670 through 682 removed outlier: 4.013A pdb=" N GLU C 674 " --> pdb=" O ARG C 670 " (cutoff:3.500A) 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 704 through 714 Processing helix chain 'C' and resid 723 through 725 No H-bonds generated for 'chain 'C' and resid 723 through 725' Processing helix chain 'C' and resid 756 through 759 Processing helix chain 'C' and resid 804 through 809 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) No H-bonds generated for 'chain 'C' and resid 804 through 809' Processing helix chain 'C' and resid 823 through 831 removed outlier: 3.775A pdb=" N LEU C 830 " --> pdb=" O ARG C 826 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 848 Proline residue: C 845 - end of helix removed outlier: 5.462A pdb=" N ASP C 848 " --> pdb=" O ALA C 844 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 464 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 502 through 507 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) No H-bonds generated for 'chain 'E' and resid 502 through 507' Processing helix chain 'E' and resid 546 through 551 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) No H-bonds generated for 'chain 'E' and resid 546 through 551' Processing helix chain 'E' and resid 586 through 594 Processing helix chain 'E' and resid 608 through 618 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 628 through 630 No H-bonds generated for 'chain 'E' and resid 628 through 630' Processing helix chain 'E' and resid 633 through 639 Processing helix chain 'E' and resid 667 through 680 removed outlier: 3.502A pdb=" N ARG E 670 " --> pdb=" O GLY E 667 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU E 671 " --> pdb=" O THR E 668 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE E 672 " --> pdb=" O GLY E 669 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE E 673 " --> pdb=" O ARG E 670 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE E 675 " --> pdb=" O PHE E 672 " (cutoff:3.500A) Processing helix chain 'E' and resid 704 through 714 Processing helix chain 'E' and resid 723 through 725 No H-bonds generated for 'chain 'E' and resid 723 through 725' Processing helix chain 'E' and resid 802 through 809 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) No H-bonds generated for 'chain 'E' and resid 802 through 809' Processing helix chain 'E' and resid 823 through 832 removed outlier: 4.124A pdb=" N ARG E 832 " --> pdb=" O LYS E 828 " (cutoff:3.500A) Processing helix chain 'E' and resid 836 through 842 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 848 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) No H-bonds generated for 'chain 'E' and resid 844 through 848' Processing helix chain 'F' and resid 668 through 678 Processing helix chain 'F' and resid 706 through 713 Processing sheet with id= A, 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= B, first strand: chain 'A' and resid 719 through 722 removed outlier: 3.704A pdb=" N VAL A 719 " --> pdb=" O PHE A 735 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE A 721 " --> pdb=" O ARG A 733 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ARG A 733 " --> pdb=" O ILE A 721 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 487 through 489 Processing sheet with id= D, first strand: chain 'B' and resid 644 through 647 removed outlier: 7.457A pdb=" N VAL B 577 " --> pdb=" O GLY B 599 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYR B 601 " --> pdb=" O VAL B 577 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N SER B 579 " --> pdb=" O TYR B 601 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ALA B 603 " --> pdb=" O SER B 579 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 695 through 699 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= F, 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= G, first strand: chain 'D' and resid 577 through 579 removed outlier: 3.616A pdb=" N VAL D 602 " --> pdb=" O VAL D 577 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER D 579 " --> pdb=" O VAL D 602 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 487 through 489 Processing sheet with id= I, first strand: chain 'C' and resid 644 through 647 removed outlier: 7.243A pdb=" N VAL C 577 " --> pdb=" O GLY C 599 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N TYR C 601 " --> pdb=" O VAL C 577 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N SER C 579 " --> pdb=" O TYR C 601 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 719 through 722 removed outlier: 3.844A pdb=" N VAL C 719 " --> pdb=" O PHE C 735 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE C 721 " --> pdb=" O ARG C 733 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG C 733 " --> pdb=" O ILE C 721 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 644 through 647 removed outlier: 7.751A pdb=" N VAL E 577 " --> pdb=" O GLY E 599 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TYR E 601 " --> pdb=" O VAL E 577 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N SER E 579 " --> pdb=" O TYR E 601 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 695 through 699 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= M, first strand: chain 'E' and resid 791 through 793 removed outlier: 3.804A pdb=" N VAL E 791 " --> pdb=" O ASP E 798 " (cutoff:3.500A) 241 hydrogen bonds defined for protein. 618 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.15 Time building geometry restraints manager: 5.17 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: 90.87 - 99.50: 5 99.50 - 108.12: 567 108.12 - 116.74: 8824 116.74 - 125.36: 9081 125.36 - 133.98: 240 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: 332 2.69 - 3.24: 13039 3.24 - 3.79: 19498 3.79 - 4.35: 25891 4.35 - 4.90: 41411 Nonbonded interactions: 100171 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 2.440 nonbonded pdb=" OG1 THR A 632 " pdb=" OD1 ASN A 635 " model vdw 2.212 2.440 ... (remaining 100166 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 2.230 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: 10.940 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 38.100 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.940 ------------------------------------------------------------------------------- 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 13775 Z= 0.205 Angle : 0.691 10.895 18717 Z= 0.360 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 *********************** 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 fitting. rotamer outliers: 5 poor density : 149 time to evaluate : 1.504 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: 0.2290 time to fit residues: 52.6220 Evaluate side-chains 145 residues out of total 1577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 142 time to evaluate : 1.215 ------------------------------------------------------------------------------- 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: 6.9990 chunk 134 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 45 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 chunk 71 optimal weight: 0.6980 chunk 138 optimal weight: 0.0030 chunk 53 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN C 827 GLN E 635 ASN E 751 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.0732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13775 Z= 0.184 Angle : 0.537 6.124 18717 Z= 0.278 Chirality : 0.040 0.171 2083 Planarity : 0.004 0.060 2433 Dihedral : 4.882 51.915 1953 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.94 % Allowed : 18.78 % Favored : 78.28 % 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: -1.46 (0.20), residues: 1766 helix: -0.35 (0.24), residues: 475 sheet: -3.52 (0.39), residues: 111 loop : -0.97 (0.19), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 542 HIS 0.003 0.001 HIS B 814 PHE 0.013 0.001 PHE E 672 TYR 0.008 0.001 TYR B 734 ARG 0.008 0.000 ARG B 497 *********************** 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 185 residues out of total 1577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 147 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 674 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7533 (mm-30) REVERT: D 635 ASN cc_start: 0.8432 (m-40) cc_final: 0.8215 (t0) REVERT: C 528 LEU cc_start: 0.4579 (OUTLIER) cc_final: 0.4233 (mp) REVERT: C 698 ASN cc_start: 0.7792 (t0) cc_final: 0.7553 (t0) REVERT: E 695 MET cc_start: 0.3996 (ttm) cc_final: 0.3567 (mtt) REVERT: E 742 MET cc_start: 0.4641 (mtp) cc_final: 0.4397 (mtm) outliers start: 38 outliers final: 22 residues processed: 171 average time/residue: 0.2405 time to fit residues: 60.4670 Evaluate side-chains 163 residues out of total 1577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 139 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 GLN Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 668 THR 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 554 THR Chi-restraints excluded: chain B residue 674 GLU 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 632 THR Chi-restraints excluded: chain D residue 739 LEU 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 719 VAL Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 635 ASN Chi-restraints excluded: chain E residue 717 ASN Chi-restraints excluded: chain E residue 803 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 20.0000 chunk 49 optimal weight: 0.4980 chunk 133 optimal weight: 0.9990 chunk 109 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 chunk 173 optimal weight: 9.9990 chunk 143 optimal weight: 8.9990 chunk 159 optimal weight: 0.0470 chunk 54 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 overall best weight: 1.7084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 751 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13775 Z= 0.287 Angle : 0.580 7.771 18717 Z= 0.299 Chirality : 0.041 0.170 2083 Planarity : 0.004 0.053 2433 Dihedral : 5.052 57.567 1947 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 4.02 % Allowed : 19.55 % Favored : 76.43 % 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: -1.55 (0.20), residues: 1766 helix: -0.40 (0.24), residues: 482 sheet: -3.49 (0.38), residues: 127 loop : -1.02 (0.19), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 694 HIS 0.007 0.001 HIS B 814 PHE 0.014 0.002 PHE C 811 TYR 0.018 0.001 TYR E 734 ARG 0.008 0.001 ARG A 545 *********************** 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 fitting. rotamer outliers: 52 poor density : 137 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 674 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7548 (mm-30) REVERT: C 528 LEU cc_start: 0.4274 (OUTLIER) cc_final: 0.3885 (mp) REVERT: C 698 ASN cc_start: 0.7813 (t0) cc_final: 0.7560 (t0) REVERT: C 720 MET cc_start: 0.8101 (tmm) cc_final: 0.7753 (tmm) REVERT: E 695 MET cc_start: 0.4089 (ttm) cc_final: 0.3792 (mtt) REVERT: E 733 ARG cc_start: 0.6284 (mpt180) cc_final: 0.5458 (mtt90) outliers start: 52 outliers final: 36 residues processed: 174 average time/residue: 0.2191 time to fit residues: 58.6412 Evaluate side-chains 171 residues out of total 1577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 133 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 526 MET 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 668 THR Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 816 THR 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 674 GLU Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 704 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 739 LEU Chi-restraints excluded: chain C residue 500 CYS 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 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 806 GLU Chi-restraints excluded: chain C residue 828 LYS 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 717 ASN Chi-restraints excluded: chain E residue 775 THR 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 159 optimal weight: 4.9990 chunk 121 optimal weight: 0.0980 chunk 83 optimal weight: 0.0870 chunk 17 optimal weight: 0.3980 chunk 76 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 161 optimal weight: 6.9990 chunk 171 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 153 optimal weight: 0.9980 chunk 46 optimal weight: 0.0670 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 827 GLN E 635 ASN E 680 ASN E 751 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13775 Z= 0.131 Angle : 0.495 6.100 18717 Z= 0.254 Chirality : 0.038 0.161 2083 Planarity : 0.004 0.051 2433 Dihedral : 4.550 56.961 1947 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.94 % Allowed : 20.94 % Favored : 76.12 % 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: -1.21 (0.20), residues: 1766 helix: -0.05 (0.25), residues: 478 sheet: -3.07 (0.42), residues: 111 loop : -0.89 (0.19), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 639 HIS 0.002 0.000 HIS B 730 PHE 0.019 0.001 PHE E 672 TYR 0.012 0.001 TYR B 734 ARG 0.004 0.000 ARG B 497 *********************** 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 188 residues out of total 1577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 150 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 823 ARG cc_start: 0.7418 (tpt90) cc_final: 0.7184 (tpt170) REVERT: B 446 PHE cc_start: 0.8112 (p90) cc_final: 0.7411 (p90) REVERT: C 528 LEU cc_start: 0.4428 (OUTLIER) cc_final: 0.4083 (mp) REVERT: C 698 ASN cc_start: 0.7754 (t0) cc_final: 0.7525 (t0) outliers start: 38 outliers final: 23 residues processed: 176 average time/residue: 0.2341 time to fit residues: 61.2303 Evaluate side-chains 165 residues out of total 1577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 141 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 816 THR 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 D residue 580 LEU Chi-restraints excluded: chain D residue 739 LEU Chi-restraints excluded: chain C residue 465 LEU 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 828 LYS Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 577 VAL Chi-restraints excluded: chain E residue 717 ASN 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 142 optimal weight: 20.0000 chunk 97 optimal weight: 20.0000 chunk 2 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 145 optimal weight: 8.9990 chunk 118 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 30.0000 chunk 153 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 C 827 GLN E 751 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 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 : 0.008 0.091 13775 Z= 0.551 Angle : 0.747 9.076 18717 Z= 0.387 Chirality : 0.048 0.210 2083 Planarity : 0.006 0.051 2433 Dihedral : 5.624 53.097 1947 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 5.18 % Allowed : 20.40 % Favored : 74.42 % 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: -1.92 (0.20), residues: 1766 helix: -0.76 (0.24), residues: 482 sheet: -3.59 (0.37), residues: 136 loop : -1.21 (0.19), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 694 HIS 0.008 0.002 HIS A 618 PHE 0.030 0.003 PHE A 735 TYR 0.029 0.002 TYR C 588 ARG 0.007 0.001 ARG A 826 *********************** 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 211 residues out of total 1577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 144 time to evaluate : 1.466 Fit side-chains REVERT: B 733 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.7432 (mmt90) REVERT: D 708 ARG cc_start: 0.6392 (OUTLIER) cc_final: 0.5283 (tmm-80) REVERT: C 746 VAL cc_start: 0.7303 (OUTLIER) cc_final: 0.7093 (p) REVERT: C 805 LEU cc_start: 0.7105 (mt) cc_final: 0.6890 (tt) REVERT: E 733 ARG cc_start: 0.6314 (mpt180) cc_final: 0.6096 (mtt90) outliers start: 67 outliers final: 47 residues processed: 192 average time/residue: 0.2311 time to fit residues: 65.9172 Evaluate side-chains 188 residues out of total 1577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 138 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 553 ASP Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 668 THR 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 B residue 444 VAL Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 704 VAL Chi-restraints excluded: chain B residue 711 SER 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 632 THR Chi-restraints excluded: chain D residue 708 ARG Chi-restraints excluded: chain D residue 739 LEU Chi-restraints excluded: chain C residue 446 PHE Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 544 VAL 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 746 VAL Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 806 GLU Chi-restraints excluded: chain C residue 828 LYS 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 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 775 THR Chi-restraints excluded: chain E residue 803 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 0.6980 chunk 154 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 100 optimal weight: 9.9990 chunk 42 optimal weight: 0.5980 chunk 171 optimal weight: 1.9990 chunk 142 optimal weight: 20.0000 chunk 79 optimal weight: 0.5980 chunk 14 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 89 optimal weight: 20.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 772 GLN B 543 ASN ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 635 ASN C 827 GLN E 751 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6713 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13775 Z= 0.182 Angle : 0.542 6.539 18717 Z= 0.280 Chirality : 0.040 0.165 2083 Planarity : 0.004 0.050 2433 Dihedral : 4.962 49.191 1947 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.25 % Allowed : 22.10 % Favored : 74.65 % 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: -1.46 (0.20), residues: 1766 helix: -0.33 (0.24), residues: 480 sheet: -3.20 (0.41), residues: 117 loop : -1.00 (0.19), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP E 736 HIS 0.004 0.001 HIS B 730 PHE 0.022 0.001 PHE E 672 TYR 0.015 0.001 TYR A 588 ARG 0.005 0.000 ARG E 712 *********************** 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 188 residues out of total 1577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 146 time to evaluate : 1.801 Fit side-chains REVERT: A 592 LYS cc_start: 0.7448 (mttm) cc_final: 0.7203 (mttp) REVERT: A 695 MET cc_start: 0.7645 (tmm) cc_final: 0.7240 (ttp) REVERT: B 446 PHE cc_start: 0.8170 (p90) cc_final: 0.7329 (p90) REVERT: B 611 ILE cc_start: 0.7576 (mt) cc_final: 0.7175 (mt) REVERT: C 420 MET cc_start: 0.3395 (OUTLIER) cc_final: 0.2472 (ptp) REVERT: C 482 CYS cc_start: 0.5445 (OUTLIER) cc_final: 0.4616 (t) REVERT: C 528 LEU cc_start: 0.3997 (OUTLIER) cc_final: 0.3689 (mp) REVERT: C 698 ASN cc_start: 0.7843 (t0) cc_final: 0.7594 (t0) REVERT: C 720 MET cc_start: 0.8158 (tmm) cc_final: 0.7816 (tmm) REVERT: E 677 HIS cc_start: 0.7241 (t-90) cc_final: 0.6184 (m170) outliers start: 42 outliers final: 30 residues processed: 176 average time/residue: 0.2259 time to fit residues: 60.4733 Evaluate side-chains 170 residues out of total 1577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 137 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 852 CYS 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 711 SER 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 420 MET Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 482 CYS Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 596 ILE Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 828 LYS Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 508 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 696 PHE Chi-restraints excluded: chain E residue 700 VAL Chi-restraints excluded: chain E residue 717 ASN 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 165 optimal weight: 0.2980 chunk 19 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 125 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 chunk 144 optimal weight: 20.0000 chunk 95 optimal weight: 1.9990 chunk 170 optimal weight: 7.9990 chunk 106 optimal weight: 7.9990 chunk 104 optimal weight: 0.9980 chunk 78 optimal weight: 0.4980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 635 ASN C 763 ASN C 827 GLN E 751 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13775 Z= 0.167 Angle : 0.524 7.255 18717 Z= 0.269 Chirality : 0.039 0.158 2083 Planarity : 0.004 0.050 2433 Dihedral : 4.662 45.719 1947 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.32 % Allowed : 22.18 % Favored : 74.50 % 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: -1.19 (0.20), residues: 1766 helix: -0.02 (0.25), residues: 480 sheet: -2.93 (0.42), residues: 112 loop : -0.90 (0.19), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 542 HIS 0.003 0.001 HIS B 814 PHE 0.023 0.001 PHE C 549 TYR 0.011 0.001 TYR B 734 ARG 0.009 0.000 ARG A 545 *********************** 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 191 residues out of total 1577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 148 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 545 ARG cc_start: 0.6460 (tpt-90) cc_final: 0.6187 (tpt-90) REVERT: A 695 MET cc_start: 0.7539 (tmm) cc_final: 0.7230 (ttp) REVERT: A 823 ARG cc_start: 0.7368 (tpt90) cc_final: 0.7090 (tpt170) REVERT: B 446 PHE cc_start: 0.8140 (p90) cc_final: 0.7336 (p90) REVERT: B 611 ILE cc_start: 0.7563 (mt) cc_final: 0.7224 (mt) REVERT: C 420 MET cc_start: 0.3366 (OUTLIER) cc_final: 0.2456 (ptp) REVERT: C 482 CYS cc_start: 0.5418 (OUTLIER) cc_final: 0.4596 (t) REVERT: C 528 LEU cc_start: 0.3961 (OUTLIER) cc_final: 0.3661 (mp) REVERT: C 698 ASN cc_start: 0.7815 (t0) cc_final: 0.7550 (t0) REVERT: C 720 MET cc_start: 0.8028 (tmm) cc_final: 0.7717 (tmm) REVERT: E 677 HIS cc_start: 0.7271 (t-90) cc_final: 0.6234 (m170) REVERT: E 720 MET cc_start: 0.5932 (mmm) cc_final: 0.5677 (tpt) outliers start: 43 outliers final: 30 residues processed: 178 average time/residue: 0.2308 time to fit residues: 61.6841 Evaluate side-chains 175 residues out of total 1577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 142 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 668 THR 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 852 CYS 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 711 SER Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 635 ASN Chi-restraints excluded: chain D residue 739 LEU Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 482 CYS Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 544 VAL 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 806 GLU Chi-restraints excluded: chain C residue 828 LYS 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 696 PHE Chi-restraints excluded: chain E residue 717 ASN 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 105 optimal weight: 30.0000 chunk 68 optimal weight: 0.5980 chunk 101 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 134 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 635 ASN C 763 ASN C 827 GLN E 751 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13775 Z= 0.203 Angle : 0.538 7.946 18717 Z= 0.276 Chirality : 0.040 0.155 2083 Planarity : 0.004 0.051 2433 Dihedral : 4.643 48.374 1947 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.32 % Allowed : 22.18 % Favored : 74.50 % 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: -1.15 (0.21), residues: 1766 helix: 0.05 (0.25), residues: 481 sheet: -2.96 (0.42), residues: 117 loop : -0.87 (0.19), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 542 HIS 0.005 0.001 HIS B 814 PHE 0.024 0.001 PHE E 642 TYR 0.015 0.001 TYR E 734 ARG 0.008 0.000 ARG A 545 *********************** 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 182 residues out of total 1577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 139 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 695 MET cc_start: 0.7610 (tmm) cc_final: 0.7285 (ttp) REVERT: A 823 ARG cc_start: 0.7374 (tpt90) cc_final: 0.7072 (tpt170) REVERT: B 446 PHE cc_start: 0.8193 (p90) cc_final: 0.7426 (p90) REVERT: B 544 VAL cc_start: 0.8281 (OUTLIER) cc_final: 0.8072 (p) REVERT: B 611 ILE cc_start: 0.7637 (mt) cc_final: 0.7304 (mt) REVERT: B 733 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.7473 (mmt90) REVERT: C 482 CYS cc_start: 0.5583 (OUTLIER) cc_final: 0.4771 (t) REVERT: C 698 ASN cc_start: 0.7798 (t0) cc_final: 0.7554 (t0) REVERT: C 720 MET cc_start: 0.8050 (tmm) cc_final: 0.7751 (tmm) REVERT: E 593 GLU cc_start: 0.6152 (tm-30) cc_final: 0.5870 (tm-30) REVERT: E 677 HIS cc_start: 0.7275 (t-90) cc_final: 0.6265 (m170) outliers start: 43 outliers final: 31 residues processed: 171 average time/residue: 0.2275 time to fit residues: 59.8749 Evaluate side-chains 171 residues out of total 1577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 137 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 668 THR 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 852 CYS 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 711 SER Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 733 ARG Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 739 LEU Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 482 CYS Chi-restraints excluded: chain C residue 544 VAL 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 726 VAL Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 806 GLU Chi-restraints excluded: chain C residue 828 LYS Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 696 PHE Chi-restraints excluded: chain E residue 717 ASN 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 163 optimal weight: 0.0870 chunk 149 optimal weight: 0.0040 chunk 158 optimal weight: 10.0000 chunk 95 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 143 optimal weight: 0.0040 chunk 150 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 168 optimal weight: 6.9990 overall best weight: 0.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 635 ASN C 763 ASN C 827 GLN E 751 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13775 Z= 0.135 Angle : 0.505 8.026 18717 Z= 0.256 Chirality : 0.039 0.154 2083 Planarity : 0.004 0.052 2433 Dihedral : 4.264 42.619 1947 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.01 % Allowed : 22.64 % Favored : 74.34 % 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: -0.90 (0.21), residues: 1766 helix: 0.24 (0.25), residues: 475 sheet: -2.67 (0.43), residues: 112 loop : -0.72 (0.19), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 542 HIS 0.002 0.001 HIS C 677 PHE 0.021 0.001 PHE E 642 TYR 0.011 0.001 TYR B 734 ARG 0.004 0.000 ARG E 733 *********************** 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 189 residues out of total 1577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 150 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 695 MET cc_start: 0.7537 (tmm) cc_final: 0.7172 (ttp) REVERT: A 823 ARG cc_start: 0.7432 (tpt90) cc_final: 0.7134 (ttt180) REVERT: B 446 PHE cc_start: 0.8205 (p90) cc_final: 0.7454 (p90) REVERT: B 611 ILE cc_start: 0.7033 (mt) cc_final: 0.6740 (mt) REVERT: C 420 MET cc_start: 0.3421 (OUTLIER) cc_final: 0.2639 (ptp) REVERT: C 482 CYS cc_start: 0.5526 (OUTLIER) cc_final: 0.4700 (t) REVERT: C 698 ASN cc_start: 0.7769 (t0) cc_final: 0.7535 (t0) REVERT: E 677 HIS cc_start: 0.7314 (t-90) cc_final: 0.6384 (m170) outliers start: 39 outliers final: 28 residues processed: 177 average time/residue: 0.2123 time to fit residues: 58.4897 Evaluate side-chains 172 residues out of total 1577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 142 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 668 THR Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 852 CYS 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 711 SER Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 635 ASN Chi-restraints excluded: chain D residue 739 LEU Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 482 CYS Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain E residue 508 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 696 PHE Chi-restraints excluded: chain E residue 717 ASN 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 102 optimal weight: 0.2980 chunk 79 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 chunk 162 optimal weight: 0.9980 chunk 140 optimal weight: 30.0000 chunk 14 optimal weight: 0.0770 chunk 108 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 149 optimal weight: 20.0000 overall best weight: 1.2540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 635 ASN C 763 ASN C 827 GLN E 751 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13775 Z= 0.230 Angle : 0.555 8.003 18717 Z= 0.281 Chirality : 0.041 0.153 2083 Planarity : 0.004 0.052 2433 Dihedral : 4.434 49.052 1945 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 2.40 % Allowed : 23.42 % Favored : 74.19 % 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: -1.03 (0.21), residues: 1766 helix: 0.12 (0.25), residues: 480 sheet: -2.73 (0.43), residues: 116 loop : -0.80 (0.19), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 542 HIS 0.006 0.001 HIS B 814 PHE 0.028 0.002 PHE E 642 TYR 0.019 0.001 TYR E 734 ARG 0.003 0.000 ARG E 733 ********************** 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 174 residues out of total 1577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 143 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 601 TYR cc_start: 0.7420 (t80) cc_final: 0.7068 (t80) REVERT: A 695 MET cc_start: 0.7650 (tmm) cc_final: 0.7292 (ttp) REVERT: A 823 ARG cc_start: 0.7308 (tpt90) cc_final: 0.7038 (tpt170) REVERT: B 446 PHE cc_start: 0.8213 (p90) cc_final: 0.7483 (p90) REVERT: B 611 ILE cc_start: 0.7751 (mt) cc_final: 0.7371 (mt) REVERT: B 733 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7478 (mmt90) REVERT: C 482 CYS cc_start: 0.5529 (OUTLIER) cc_final: 0.4734 (t) REVERT: C 698 ASN cc_start: 0.7824 (t0) cc_final: 0.7576 (t0) REVERT: C 720 MET cc_start: 0.8001 (tmm) cc_final: 0.7678 (tmm) REVERT: E 593 GLU cc_start: 0.6149 (tm-30) cc_final: 0.5858 (tm-30) REVERT: E 677 HIS cc_start: 0.7289 (t-90) cc_final: 0.6397 (m170) outliers start: 31 outliers final: 27 residues processed: 167 average time/residue: 0.2179 time to fit residues: 55.3481 Evaluate side-chains 170 residues out of total 1577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 141 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 526 MET 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 668 THR Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 852 CYS 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 711 SER Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 733 ARG Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 635 ASN Chi-restraints excluded: chain D residue 739 LEU Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 482 CYS Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 763 ASN Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 622 ILE Chi-restraints excluded: chain E residue 696 PHE 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 43 optimal weight: 10.0000 chunk 129 optimal weight: 0.6980 chunk 20 optimal weight: 0.4980 chunk 39 optimal weight: 0.6980 chunk 140 optimal weight: 30.0000 chunk 58 optimal weight: 0.6980 chunk 144 optimal weight: 40.0000 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 9.9990 chunk 123 optimal weight: 0.0470 chunk 8 optimal weight: 4.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 635 ASN C 763 ASN C 827 GLN E 751 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4767 r_free = 0.4767 target = 0.218647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.160110 restraints weight = 18575.742| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 3.26 r_work: 0.3735 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work: 0.3601 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13775 Z= 0.151 Angle : 0.522 8.231 18717 Z= 0.264 Chirality : 0.039 0.152 2083 Planarity : 0.004 0.052 2433 Dihedral : 4.277 46.560 1945 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.32 % Allowed : 23.88 % Favored : 73.80 % 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: -0.92 (0.21), residues: 1766 helix: 0.20 (0.25), residues: 482 sheet: -2.53 (0.44), residues: 112 loop : -0.75 (0.19), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 542 HIS 0.003 0.001 HIS B 730 PHE 0.020 0.001 PHE D 675 TYR 0.012 0.001 TYR E 762 ARG 0.003 0.000 ARG B 497 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3219.14 seconds wall clock time: 58 minutes 6.63 seconds (3486.63 seconds total)