Starting phenix.real_space_refine on Fri Aug 22 21:13:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eij_28158/08_2025/8eij_28158.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eij_28158/08_2025/8eij_28158.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8eij_28158/08_2025/8eij_28158.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eij_28158/08_2025/8eij_28158.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8eij_28158/08_2025/8eij_28158.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eij_28158/08_2025/8eij_28158.map" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 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 6 6.06 5 S 67 5.16 5 C 4981 2.51 5 N 1358 2.21 5 O 1401 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7813 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3290 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 3, 'ASP:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 83 Chain: "B" Number of atoms: 3374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3374 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 413} Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 9, 'ASN:plan1': 1, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 58 Chain: "D" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1091 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 141} Chain breaks: 4 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 5, 'ASP:plan': 3, 'GLU:plan': 5, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 79 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 135 SG CYS A 435 26.424 27.415 32.413 1.00178.98 S ATOM 155 SG CYS A 438 25.215 31.209 31.853 1.00187.35 S ATOM 285 SG CYS A 455 28.546 30.007 30.785 1.00177.92 S ATOM 307 SG CYS A 458 27.548 30.039 34.660 1.00170.71 S ATOM 486 SG CYS A 478 22.876 28.790 44.559 1.00175.25 S ATOM 506 SG CYS A 481 22.882 30.984 41.410 1.00178.78 S ATOM 634 SG CYS A 500 20.007 31.376 43.847 1.00186.48 S ATOM 656 SG CYS A 503 20.370 28.301 41.694 1.00188.66 S ATOM 562 SG CYS A 490 22.405 22.242 56.090 1.00184.01 S ATOM 594 SG CYS A 495 26.004 21.481 55.050 1.00179.16 S ATOM 802 SG CYS A 524 23.099 20.593 52.676 1.00185.18 S ATOM 828 SG CYS A 527 23.780 18.623 55.673 1.00186.73 S ATOM 3452 SG CYS B 435 62.529 63.225 118.249 1.00149.11 S ATOM 3472 SG CYS B 438 60.666 66.486 118.207 1.00153.62 S ATOM 3599 SG CYS B 455 58.974 63.401 119.750 1.00139.43 S ATOM 3621 SG CYS B 458 59.431 63.631 116.053 1.00135.76 S ATOM 3803 SG CYS B 478 63.011 64.741 105.525 1.00146.43 S ATOM 3823 SG CYS B 481 61.056 66.889 107.659 1.00161.00 S ATOM 3961 SG CYS B 500 63.713 68.585 105.341 1.00161.15 S ATOM 3983 SG CYS B 503 64.726 66.837 108.382 1.00155.41 S ATOM 3888 SG CYS B 490 71.769 59.476 96.562 1.00153.98 S ATOM 3921 SG CYS B 495 70.391 56.345 98.327 1.00159.43 S ATOM 4122 SG CYS B 524 72.350 58.893 100.342 1.00153.71 S ATOM 4148 SG CYS B 527 74.107 56.682 98.006 1.00159.17 S Time building chain proxies: 1.69, per 1000 atoms: 0.22 Number of scatterers: 7813 At special positions: 0 Unit cell: (91.3, 84.7, 135.3, 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 6 29.99 S 67 16.00 O 1401 8.00 N 1358 7.00 C 4981 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 388.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 435 " 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 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 500 " pdb="ZN ZN A 903 " - pdb=" SG CYS A 478 " pdb=" ZN A 904 " pdb="ZN ZN A 904 " - pdb=" SG CYS A 527 " pdb="ZN ZN A 904 " - pdb=" SG CYS A 495 " pdb="ZN ZN A 904 " - pdb=" SG CYS A 524 " pdb="ZN ZN A 904 " - pdb=" SG CYS A 490 " pdb=" ZN B 902 " 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 455 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 435 " pdb=" ZN B 903 " pdb="ZN ZN B 903 " - pdb=" SG CYS B 481 " pdb="ZN ZN B 903 " - pdb=" SG CYS B 503 " 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 527 " pdb="ZN ZN B 904 " - pdb=" SG CYS B 495 " pdb="ZN ZN B 904 " - pdb=" SG CYS B 490 " Number of angles added : 36 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1882 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 7 sheets defined 38.6% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 416 through 425 removed outlier: 3.807A pdb=" N MET A 420 " --> pdb=" O SER A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 434 removed outlier: 3.854A pdb=" N ASP A 433 " --> pdb=" O SER A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 466 removed outlier: 3.619A pdb=" N ASP A 460 " --> pdb=" O GLN A 456 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ARG A 461 " --> pdb=" O THR A 457 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE A 462 " --> pdb=" O CYS A 458 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE A 466 " --> pdb=" O PHE A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 508 removed outlier: 4.486A pdb=" N GLU A 505 " --> pdb=" O VAL A 501 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 506 " --> pdb=" O GLU A 502 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 507 " --> pdb=" O CYS A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 519 removed outlier: 3.667A pdb=" N ALA A 516 " --> pdb=" O THR A 512 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS A 517 " --> pdb=" O ALA A 513 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU A 518 " --> pdb=" O ALA A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 552 removed outlier: 4.375A pdb=" N GLN A 547 " --> pdb=" O ASN A 543 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA A 548 " --> pdb=" O VAL A 544 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE A 550 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 595 Processing helix chain 'A' and resid 607 through 617 removed outlier: 3.514A pdb=" N ILE A 611 " --> pdb=" O CYS A 607 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A 612 " --> pdb=" O GLU A 608 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS A 617 " --> pdb=" O VAL A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 631 removed outlier: 3.506A pdb=" N ASN A 630 " --> pdb=" O ASP A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 640 removed outlier: 4.135A pdb=" N ILE A 636 " --> pdb=" O THR A 632 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU A 637 " --> pdb=" O LYS A 633 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A 638 " --> pdb=" O LYS A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 669 No H-bonds generated for 'chain 'A' and resid 667 through 669' Processing helix chain 'A' and resid 670 through 683 removed outlier: 3.817A pdb=" N GLU A 674 " --> pdb=" O ARG A 670 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR A 681 " --> pdb=" O HIS A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 708 removed outlier: 3.943A pdb=" N LYS A 707 " --> pdb=" O LYS A 703 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ARG A 708 " --> pdb=" O VAL A 704 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 703 through 708' Processing helix chain 'A' and resid 708 through 714 Processing helix chain 'A' and resid 724 through 726 No H-bonds generated for 'chain 'A' and resid 724 through 726' Processing helix chain 'A' and resid 755 through 759 Processing helix chain 'A' and resid 801 through 809 removed outlier: 3.523A pdb=" N LEU A 805 " --> pdb=" O TRP A 801 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU A 806 " --> pdb=" O CYS A 802 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ARG A 807 " --> pdb=" O THR A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 829 removed outlier: 3.738A pdb=" N LYS A 828 " --> pdb=" O GLY A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 843 removed outlier: 3.540A pdb=" N HIS A 841 " --> pdb=" O PRO A 837 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 842 " --> pdb=" O VAL A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 849 removed outlier: 3.659A pdb=" N LYS A 847 " --> pdb=" O ALA A 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 426 removed outlier: 4.316A pdb=" N MET B 420 " --> pdb=" O SER B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 434 removed outlier: 3.891A pdb=" N GLY B 434 " --> pdb=" O LEU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 460 removed outlier: 3.526A pdb=" N ARG B 459 " --> pdb=" O CYS B 455 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP B 460 " --> pdb=" O GLN B 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 455 through 460' Processing helix chain 'B' and resid 461 through 466 removed outlier: 3.746A pdb=" N LEU B 465 " --> pdb=" O ARG B 461 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE B 466 " --> pdb=" O PHE B 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 461 through 466' Processing helix chain 'B' and resid 500 through 509 removed outlier: 4.577A pdb=" N LEU B 507 " --> pdb=" O CYS B 503 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 508 " --> pdb=" O LEU B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 519 removed outlier: 4.087A pdb=" N GLU B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 550 removed outlier: 3.599A pdb=" N ARG B 545 " --> pdb=" O ASP B 541 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA B 548 " --> pdb=" O VAL B 544 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE B 550 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 595 Processing helix chain 'B' and resid 607 through 618 removed outlier: 3.887A pdb=" N HIS B 618 " --> pdb=" O GLY B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 631 Processing helix chain 'B' and resid 632 through 640 removed outlier: 3.658A pdb=" N ILE B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 669 Processing helix chain 'B' and resid 670 through 683 removed outlier: 3.501A pdb=" N GLU B 674 " --> pdb=" O ARG B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 715 Processing helix chain 'B' and resid 724 through 726 No H-bonds generated for 'chain 'B' and resid 724 through 726' Processing helix chain 'B' and resid 755 through 760 removed outlier: 3.951A pdb=" N LEU B 760 " --> pdb=" O GLN B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 809 removed outlier: 3.588A pdb=" N ARG B 807 " --> pdb=" O THR B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 832 removed outlier: 3.566A pdb=" N ARG B 826 " --> pdb=" O GLY B 822 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG B 832 " --> pdb=" O LYS B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 844 Processing helix chain 'B' and resid 845 through 849 removed outlier: 3.538A pdb=" N TYR B 849 " --> pdb=" O LEU B 846 " (cutoff:3.500A) Processing helix chain 'D' and resid 585 through 594 removed outlier: 3.652A pdb=" N LEU D 589 " --> pdb=" O ALA D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 640 Processing helix chain 'D' and resid 667 through 683 removed outlier: 4.299A pdb=" N LEU D 671 " --> pdb=" O GLY D 667 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU D 674 " --> pdb=" O ARG D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 703 through 715 Processing helix chain 'D' and resid 836 through 843 Processing helix chain 'D' and resid 844 through 848 removed outlier: 3.860A pdb=" N LYS D 847 " --> pdb=" O ALA D 844 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP D 848 " --> pdb=" O PRO D 845 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 844 through 848' Processing sheet with id=AA1, first strand: chain 'A' and resid 487 through 489 Processing sheet with id=AA2, first strand: chain 'A' and resid 600 through 601 removed outlier: 6.140A pdb=" N LYS A 600 " --> pdb=" O VAL A 577 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU A 644 " --> pdb=" O ARG A 576 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL A 645 " --> pdb=" O MET A 695 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N GLU A 697 " --> pdb=" O VAL A 645 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE A 696 " --> pdb=" O TRP A 736 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG A 733 " --> pdb=" O ILE A 721 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 721 " --> pdb=" O ARG A 733 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A 719 " --> pdb=" O PHE A 735 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 764 through 766 removed outlier: 3.813A pdb=" N VAL A 791 " --> pdb=" O ASP A 798 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 623 through 625 removed outlier: 8.945A pdb=" N LYS B 623 " --> pdb=" O GLY B 599 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TYR B 601 " --> pdb=" O LYS B 623 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL B 625 " --> pdb=" O TYR B 601 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ALA B 603 " --> pdb=" O VAL B 625 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ILE B 575 " --> pdb=" O LYS B 600 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL B 602 " --> pdb=" O ILE B 575 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL B 577 " --> pdb=" O VAL B 602 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N SER B 604 " --> pdb=" O VAL B 577 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N SER B 579 " --> pdb=" O SER B 604 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ARG B 576 " --> pdb=" O LEU B 644 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N ILE B 646 " --> pdb=" O ARG B 576 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU B 578 " --> pdb=" O ILE B 646 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 695 through 699 removed outlier: 4.073A pdb=" N PHE B 696 " --> pdb=" O TRP B 736 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN B 698 " --> pdb=" O TYR B 734 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 765 through 766 removed outlier: 4.073A pdb=" N ILE B 765 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL B 792 " --> pdb=" O ILE B 765 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL B 791 " --> pdb=" O ASP B 798 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 697 through 699 removed outlier: 3.697A pdb=" N ILE D 721 " --> pdb=" O ARG D 733 " (cutoff:3.500A) 189 hydrogen bonds defined for protein. 513 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: 0.77 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2554 1.34 - 1.46: 1868 1.46 - 1.58: 3484 1.58 - 1.70: 0 1.70 - 1.82: 89 Bond restraints: 7995 Sorted by residual: bond pdb=" C2 SAH A 901 " pdb=" N3 SAH A 901 " ideal model delta sigma weight residual 1.322 1.381 -0.059 2.00e-02 2.50e+03 8.62e+00 bond pdb=" C2 SAH B 901 " pdb=" N3 SAH B 901 " ideal model delta sigma weight residual 1.322 1.380 -0.058 2.00e-02 2.50e+03 8.34e+00 bond pdb=" CA HIS D 677 " pdb=" C HIS D 677 " ideal model delta sigma weight residual 1.524 1.489 0.034 1.27e-02 6.20e+03 7.30e+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 7.18e+00 bond pdb=" C8 SAH B 901 " pdb=" N7 SAH B 901 " ideal model delta sigma weight residual 1.299 1.352 -0.053 2.00e-02 2.50e+03 7.14e+00 ... (remaining 7990 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 10668 2.39 - 4.78: 151 4.78 - 7.17: 22 7.17 - 9.55: 8 9.55 - 11.94: 3 Bond angle restraints: 10852 Sorted by residual: angle pdb=" CA GLU B 715 " pdb=" CB GLU B 715 " pdb=" CG GLU B 715 " ideal model delta sigma weight residual 114.10 124.02 -9.92 2.00e+00 2.50e-01 2.46e+01 angle pdb=" N ASP D 706 " pdb=" CA ASP D 706 " pdb=" C ASP D 706 " ideal model delta sigma weight residual 111.07 105.97 5.10 1.07e+00 8.73e-01 2.28e+01 angle pdb=" C ASN B 442 " pdb=" N PRO B 443 " pdb=" CA PRO B 443 " ideal model delta sigma weight residual 119.84 125.15 -5.31 1.25e+00 6.40e-01 1.80e+01 angle pdb=" CG SAH B 901 " pdb=" SD SAH B 901 " pdb=" C5' SAH B 901 " ideal model delta sigma weight residual 101.77 89.83 11.94 3.00e+00 1.11e-01 1.58e+01 angle pdb=" C GLU B 715 " pdb=" CA GLU B 715 " pdb=" CB GLU B 715 " ideal model delta sigma weight residual 112.27 119.13 -6.86 1.75e+00 3.27e-01 1.54e+01 ... (remaining 10847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4104 17.94 - 35.87: 486 35.87 - 53.80: 95 53.80 - 71.74: 9 71.74 - 89.67: 4 Dihedral angle restraints: 4698 sinusoidal: 1771 harmonic: 2927 Sorted by residual: dihedral pdb=" CA ASN D 626 " pdb=" C ASN D 626 " pdb=" N ASP D 627 " pdb=" CA ASP D 627 " ideal model delta harmonic sigma weight residual 180.00 160.12 19.88 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" C GLU B 715 " pdb=" N GLU B 715 " pdb=" CA GLU B 715 " pdb=" CB GLU B 715 " ideal model delta harmonic sigma weight residual -122.60 -131.92 9.32 0 2.50e+00 1.60e-01 1.39e+01 dihedral pdb=" CA GLU A 464 " pdb=" C GLU A 464 " pdb=" N LEU A 465 " pdb=" CA LEU A 465 " ideal model delta harmonic sigma weight residual 180.00 -161.87 -18.13 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 4695 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1041 0.063 - 0.126: 137 0.126 - 0.188: 3 0.188 - 0.251: 1 0.251 - 0.314: 1 Chirality restraints: 1183 Sorted by residual: chirality pdb=" CA ASN B 442 " pdb=" N ASN B 442 " pdb=" C ASN B 442 " pdb=" CB ASN B 442 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.47e+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 2.32 0.19 2.00e-01 2.50e+01 9.23e-01 chirality pdb=" CA ASP D 706 " pdb=" N ASP D 706 " pdb=" C ASP D 706 " pdb=" CB ASP D 706 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.12e-01 ... (remaining 1180 not shown) Planarity restraints: 1407 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 441 " 0.014 2.00e-02 2.50e+03 2.83e-02 8.03e+00 pdb=" C LYS B 441 " -0.049 2.00e-02 2.50e+03 pdb=" O LYS B 441 " 0.018 2.00e-02 2.50e+03 pdb=" N ASN B 442 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY D 640 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO D 641 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 641 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 641 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 705 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C GLY D 705 " -0.029 2.00e-02 2.50e+03 pdb=" O GLY D 705 " 0.011 2.00e-02 2.50e+03 pdb=" N ASP D 706 " 0.010 2.00e-02 2.50e+03 ... (remaining 1404 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 331 2.72 - 3.26: 7711 3.26 - 3.81: 11605 3.81 - 4.35: 14144 4.35 - 4.90: 23743 Nonbonded interactions: 57534 Sorted by model distance: nonbonded pdb=" O ASN B 738 " pdb=" ND2 ASN B 738 " model vdw 2.172 3.120 nonbonded pdb=" OG SER B 491 " pdb=" O TRP B 522 " model vdw 2.227 3.040 nonbonded pdb=" OD1 ASP A 709 " pdb=" NH2 ARG A 712 " model vdw 2.260 3.120 nonbonded pdb=" O SER D 649 " pdb=" OG SER D 649 " model vdw 2.297 3.040 nonbonded pdb=" OE2 GLU B 605 " pdb=" O2' SAH B 901 " model vdw 2.300 3.040 ... (remaining 57529 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 415 through 441 or (resid 442 and (name N or name CA or na \ me C or name O or name CB )) or resid 443 through 504 or (resid 505 and (name N \ or name CA or name C or name O or name CB )) or resid 506 through 509 or (resid \ 510 and (name N or name CA or name C or name O or name CB )) or resid 511 throug \ h 518 or (resid 519 and (name N or name CA or name C or name O or name CB )) or \ resid 520 through 556 or (resid 557 and (name N or name CA or name C or name O o \ r name CB )) or resid 558 or (resid 559 through 560 and (name N or name CA or na \ me C or name O or name CB )) or resid 561 through 633 or (resid 634 and (name N \ or name CA or name C or name O or name CB )) or resid 635 through 724 or (resid \ 725 and (name N or name CA or name C or name O or name CB )) or resid 726 throug \ h 773 or resid 777 or resid 788 through 796 or (resid 797 and (name N or name CA \ or name C or name O or name CB )) or resid 798 through 904)) selection = (chain 'B' and ((resid 415 and (name N or name CA or name C or name O or name CB \ )) or resid 416 through 426 or (resid 427 through 430 and (name N or name CA or \ name C or name O or name CB )) or resid 431 through 432 or (resid 433 and (name \ N or name CA or name C or name O or name CB )) or resid 434 through 471 or (res \ id 472 and (name N or name CA or name C or name O or name CB )) or resid 473 thr \ ough 484 or (resid 485 through 487 and (name N or name CA or name C or name O or \ name CB )) or resid 488 through 493 or (resid 494 and (name N or name CA or nam \ e C or name O or name CB )) or resid 495 through 517 or (resid 518 through 519 a \ nd (name N or name CA or name C or name O or name CB )) or resid 520 through 529 \ or (resid 530 through 531 and (name N or name CA or name C or name O or name CB \ )) or resid 532 through 536 or (resid 537 through 538 and (name N or name CA or \ name C or name O or name CB )) or resid 539 or (resid 540 through 541 and (name \ N or name CA or name C or name O or name CB )) or resid 542 through 572 or (res \ id 573 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name NE )) or resid 574 through 651 or (resid 652 and (name N or name CA o \ r name C or name O or name CB )) or resid 653 through 656 or (resid 657 through \ 658 and (name N or name CA or name C or name O or name CB )) or resid 659 throug \ h 660 or (resid 661 through 662 and (name N or name CA or name C or name O or na \ me CB )) or resid 663 through 665 or (resid 666 and (name N or name CA or name C \ or name O or name CB )) or resid 667 through 702 or (resid 703 and (name N or n \ ame CA or name C or name O or name CB )) or resid 704 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 )) o \ r resid 768 through 773 or resid 785 or resid 788 through 795 or (resid 796 thro \ ugh 797 and (name N or name CA or name C or name O or name CB )) or resid 798 th \ rough 852 or (resid 853 and (name N or name CA or name C or name O or name CB )) \ or resid 901 through 904)) } 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: 3.150 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.310 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 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 0.062 8019 Z= 0.171 Angle : 0.770 11.942 10888 Z= 0.387 Chirality : 0.042 0.314 1183 Planarity : 0.004 0.043 1407 Dihedral : 15.166 89.671 2816 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.38 % Allowed : 13.17 % Favored : 86.45 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.92 (0.27), residues: 997 helix: -0.43 (0.34), residues: 253 sheet: -2.92 (0.52), residues: 88 loop : -1.42 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 440 TYR 0.008 0.001 TYR B 588 PHE 0.018 0.001 PHE D 672 TRP 0.018 0.001 TRP D 639 HIS 0.003 0.001 HIS D 677 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 7995) covalent geometry : angle 0.73059 (10852) hydrogen bonds : bond 0.25089 ( 189) hydrogen bonds : angle 8.09826 ( 513) metal coordination : bond 0.00710 ( 24) metal coordination : angle 4.29317 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 94 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 497 ARG cc_start: 0.7028 (mtt90) cc_final: 0.6314 (mtm-85) REVERT: B 754 LEU cc_start: 0.7510 (tp) cc_final: 0.6982 (mp) REVERT: B 772 GLN cc_start: 0.7067 (OUTLIER) cc_final: 0.6817 (pp30) REVERT: D 842 LEU cc_start: 0.8504 (mm) cc_final: 0.8139 (mm) outliers start: 3 outliers final: 1 residues processed: 94 average time/residue: 0.0796 time to fit residues: 10.0602 Evaluate side-chains 85 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain B residue 772 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.0370 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.0670 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.0050 overall best weight: 0.3410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 738 ASN B 772 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.195817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.146269 restraints weight = 10078.848| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 3.05 r_work: 0.3791 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8019 Z= 0.105 Angle : 0.591 9.066 10888 Z= 0.285 Chirality : 0.040 0.133 1183 Planarity : 0.004 0.044 1407 Dihedral : 5.386 56.771 1117 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.41 % Allowed : 16.11 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.28), residues: 997 helix: 0.00 (0.32), residues: 276 sheet: -2.54 (0.55), residues: 88 loop : -1.25 (0.26), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 690 TYR 0.008 0.001 TYR D 849 PHE 0.016 0.001 PHE D 675 TRP 0.011 0.001 TRP D 639 HIS 0.003 0.001 HIS D 677 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 7995) covalent geometry : angle 0.54878 (10852) hydrogen bonds : bond 0.03588 ( 189) hydrogen bonds : angle 5.16842 ( 513) metal coordination : bond 0.00606 ( 24) metal coordination : angle 3.83900 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 496 CYS cc_start: 0.7579 (m) cc_final: 0.7193 (m) REVERT: B 497 ARG cc_start: 0.6939 (mtt90) cc_final: 0.6724 (mtm110) REVERT: B 531 ARG cc_start: 0.6009 (OUTLIER) cc_final: 0.5651 (mmp80) REVERT: B 754 LEU cc_start: 0.7527 (tp) cc_final: 0.6912 (mp) REVERT: D 842 LEU cc_start: 0.8541 (mm) cc_final: 0.8058 (mm) outliers start: 11 outliers final: 4 residues processed: 98 average time/residue: 0.1074 time to fit residues: 13.8012 Evaluate side-chains 88 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain B residue 531 ARG Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain D residue 668 THR Chi-restraints excluded: chain D residue 848 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 79 optimal weight: 0.0020 chunk 91 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 6 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 0.0020 chunk 76 optimal weight: 0.3980 chunk 92 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 HIS A 820 ASN D 635 ASN D 680 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.193539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.158448 restraints weight = 10073.074| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 3.90 r_work: 0.3866 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8019 Z= 0.105 Angle : 0.557 8.864 10888 Z= 0.269 Chirality : 0.040 0.147 1183 Planarity : 0.004 0.036 1407 Dihedral : 4.845 54.218 1110 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.43 % Allowed : 17.52 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.28), residues: 997 helix: 0.21 (0.33), residues: 281 sheet: -2.85 (0.50), residues: 99 loop : -1.16 (0.27), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 629 TYR 0.007 0.001 TYR B 624 PHE 0.014 0.001 PHE D 672 TRP 0.010 0.001 TRP D 694 HIS 0.002 0.001 HIS A 677 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 7995) covalent geometry : angle 0.51948 (10852) hydrogen bonds : bond 0.03180 ( 189) hydrogen bonds : angle 4.65709 ( 513) metal coordination : bond 0.00557 ( 24) metal coordination : angle 3.53834 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 CYS cc_start: 0.7480 (m) cc_final: 0.7230 (m) REVERT: A 702 MET cc_start: 0.7281 (ptt) cc_final: 0.7049 (ptt) REVERT: B 531 ARG cc_start: 0.5854 (OUTLIER) cc_final: 0.5533 (mmp80) REVERT: B 754 LEU cc_start: 0.7620 (tp) cc_final: 0.7120 (mp) REVERT: B 827 GLN cc_start: 0.6694 (pp30) cc_final: 0.6372 (pp30) REVERT: D 702 MET cc_start: 0.2872 (OUTLIER) cc_final: 0.1632 (ppp) REVERT: D 842 LEU cc_start: 0.8606 (mm) cc_final: 0.8117 (mm) outliers start: 19 outliers final: 10 residues processed: 98 average time/residue: 0.0882 time to fit residues: 11.6715 Evaluate side-chains 92 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 HIS Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 651 CYS Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 481 CYS Chi-restraints excluded: chain B residue 531 ARG Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 635 ASN Chi-restraints excluded: chain D residue 668 THR Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 848 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 52 optimal weight: 0.6980 chunk 58 optimal weight: 0.0040 chunk 37 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 100 optimal weight: 0.0050 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 72 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.4606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 772 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.193308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.158092 restraints weight = 10197.892| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 4.08 r_work: 0.3858 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8019 Z= 0.103 Angle : 0.568 10.723 10888 Z= 0.266 Chirality : 0.040 0.178 1183 Planarity : 0.003 0.035 1407 Dihedral : 4.755 51.160 1110 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.81 % Allowed : 18.16 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.28), residues: 997 helix: 0.35 (0.33), residues: 281 sheet: -2.77 (0.52), residues: 97 loop : -1.08 (0.27), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 576 TYR 0.013 0.001 TYR D 676 PHE 0.009 0.001 PHE A 789 TRP 0.010 0.001 TRP D 694 HIS 0.003 0.001 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 7995) covalent geometry : angle 0.51460 (10852) hydrogen bonds : bond 0.02836 ( 189) hydrogen bonds : angle 4.43512 ( 513) metal coordination : bond 0.00896 ( 24) metal coordination : angle 4.22361 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 496 CYS cc_start: 0.7483 (m) cc_final: 0.7222 (m) REVERT: A 830 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.7118 (mt) REVERT: B 531 ARG cc_start: 0.5745 (OUTLIER) cc_final: 0.5452 (mmp80) REVERT: B 754 LEU cc_start: 0.7621 (tp) cc_final: 0.7128 (mp) REVERT: D 580 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.6726 (tt) REVERT: D 702 MET cc_start: 0.2752 (OUTLIER) cc_final: 0.1552 (ppp) REVERT: D 842 LEU cc_start: 0.8661 (mm) cc_final: 0.8158 (mm) outliers start: 22 outliers final: 9 residues processed: 95 average time/residue: 0.0943 time to fit residues: 12.0671 Evaluate side-chains 90 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 HIS Chi-restraints excluded: chain A residue 497 ARG Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 531 ARG Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 668 THR Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 848 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 17 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 90 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 70 optimal weight: 0.2980 chunk 61 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 730 HIS B 820 ASN D 635 ASN D 680 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.190659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.155437 restraints weight = 10191.730| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 3.97 r_work: 0.3820 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8019 Z= 0.153 Angle : 0.627 9.358 10888 Z= 0.296 Chirality : 0.042 0.165 1183 Planarity : 0.004 0.037 1407 Dihedral : 5.034 50.543 1110 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.20 % Allowed : 19.31 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.28), residues: 997 helix: 0.21 (0.33), residues: 281 sheet: -2.90 (0.52), residues: 95 loop : -1.20 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 576 TYR 0.009 0.001 TYR A 676 PHE 0.012 0.001 PHE D 672 TRP 0.009 0.001 TRP D 694 HIS 0.003 0.001 HIS A 677 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 7995) covalent geometry : angle 0.57351 (10852) hydrogen bonds : bond 0.03276 ( 189) hydrogen bonds : angle 4.55061 ( 513) metal coordination : bond 0.00673 ( 24) metal coordination : angle 4.45841 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 531 ARG cc_start: 0.6024 (OUTLIER) cc_final: 0.5661 (mmp80) REVERT: D 702 MET cc_start: 0.2661 (OUTLIER) cc_final: 0.1478 (ppp) REVERT: D 842 LEU cc_start: 0.8734 (mm) cc_final: 0.8217 (mm) outliers start: 25 outliers final: 13 residues processed: 95 average time/residue: 0.0954 time to fit residues: 12.2418 Evaluate side-chains 89 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 651 CYS Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 481 CYS Chi-restraints excluded: chain B residue 531 ARG Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 668 THR Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 848 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 22 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 46 optimal weight: 0.2980 chunk 91 optimal weight: 0.4980 chunk 16 optimal weight: 0.6980 chunk 41 optimal weight: 0.0870 chunk 27 optimal weight: 0.0030 chunk 77 optimal weight: 1.9990 overall best weight: 0.3168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.193803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.158480 restraints weight = 10062.919| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 4.05 r_work: 0.3869 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8019 Z= 0.094 Angle : 0.563 8.638 10888 Z= 0.265 Chirality : 0.040 0.153 1183 Planarity : 0.003 0.034 1407 Dihedral : 4.656 49.611 1110 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.69 % Allowed : 19.82 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.28), residues: 997 helix: 0.30 (0.33), residues: 281 sheet: -2.65 (0.54), residues: 95 loop : -1.09 (0.27), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 576 TYR 0.009 0.001 TYR B 624 PHE 0.016 0.001 PHE D 672 TRP 0.012 0.001 TRP D 694 HIS 0.003 0.001 HIS A 677 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 7995) covalent geometry : angle 0.51301 (10852) hydrogen bonds : bond 0.02629 ( 189) hydrogen bonds : angle 4.21910 ( 513) metal coordination : bond 0.00643 ( 24) metal coordination : angle 4.07720 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 496 CYS cc_start: 0.7399 (m) cc_final: 0.7130 (m) REVERT: B 531 ARG cc_start: 0.5782 (OUTLIER) cc_final: 0.5460 (mmp80) REVERT: B 754 LEU cc_start: 0.7616 (tp) cc_final: 0.7169 (mp) REVERT: D 695 MET cc_start: 0.8602 (tpt) cc_final: 0.8339 (tpt) REVERT: D 702 MET cc_start: 0.2622 (OUTLIER) cc_final: 0.1438 (ppp) REVERT: D 842 LEU cc_start: 0.8711 (mm) cc_final: 0.8182 (mm) outliers start: 21 outliers final: 12 residues processed: 98 average time/residue: 0.0987 time to fit residues: 12.9257 Evaluate side-chains 90 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 HIS Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 651 CYS Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 481 CYS Chi-restraints excluded: chain B residue 531 ARG Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 848 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 86 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 65 optimal weight: 0.0040 chunk 7 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 HIS B 738 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.190166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.142784 restraints weight = 10404.292| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.69 r_work: 0.3770 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8019 Z= 0.172 Angle : 0.645 11.409 10888 Z= 0.309 Chirality : 0.042 0.181 1183 Planarity : 0.004 0.038 1407 Dihedral : 4.973 51.556 1110 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.56 % Allowed : 21.10 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.28), residues: 997 helix: 0.08 (0.32), residues: 287 sheet: -2.88 (0.53), residues: 95 loop : -1.17 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 576 TYR 0.022 0.001 TYR B 624 PHE 0.019 0.001 PHE D 672 TRP 0.014 0.001 TRP A 694 HIS 0.008 0.001 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 7995) covalent geometry : angle 0.59498 (10852) hydrogen bonds : bond 0.03356 ( 189) hydrogen bonds : angle 4.58877 ( 513) metal coordination : bond 0.00724 ( 24) metal coordination : angle 4.37781 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.327 Fit side-chains REVERT: B 531 ARG cc_start: 0.5983 (OUTLIER) cc_final: 0.5622 (mmp80) REVERT: D 695 MET cc_start: 0.8627 (tpt) cc_final: 0.8278 (tpt) REVERT: D 702 MET cc_start: 0.2188 (OUTLIER) cc_final: 0.1222 (ppp) REVERT: D 842 LEU cc_start: 0.8652 (mm) cc_final: 0.8094 (mm) outliers start: 20 outliers final: 15 residues processed: 97 average time/residue: 0.1014 time to fit residues: 13.3510 Evaluate side-chains 94 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 HIS Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 651 CYS Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 481 CYS Chi-restraints excluded: chain B residue 531 ARG Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 632 THR Chi-restraints excluded: chain D residue 679 LEU Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 848 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 38 optimal weight: 0.0000 chunk 93 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 94 optimal weight: 0.1980 chunk 31 optimal weight: 0.9980 chunk 66 optimal weight: 0.0970 chunk 64 optimal weight: 0.2980 chunk 65 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 overall best weight: 0.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 HIS B 738 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.193779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.158412 restraints weight = 10149.998| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 3.91 r_work: 0.3868 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8019 Z= 0.101 Angle : 0.588 8.904 10888 Z= 0.281 Chirality : 0.041 0.172 1183 Planarity : 0.004 0.043 1407 Dihedral : 4.648 51.491 1110 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.30 % Allowed : 21.87 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.28), residues: 997 helix: 0.30 (0.33), residues: 288 sheet: -2.55 (0.56), residues: 95 loop : -1.06 (0.27), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 576 TYR 0.016 0.001 TYR B 624 PHE 0.029 0.001 PHE D 675 TRP 0.014 0.001 TRP D 694 HIS 0.007 0.001 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 7995) covalent geometry : angle 0.54387 (10852) hydrogen bonds : bond 0.02644 ( 189) hydrogen bonds : angle 4.21275 ( 513) metal coordination : bond 0.00754 ( 24) metal coordination : angle 3.91243 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.333 Fit side-chains REVERT: B 531 ARG cc_start: 0.5778 (OUTLIER) cc_final: 0.5449 (mmp80) REVERT: D 580 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.6705 (tt) REVERT: D 695 MET cc_start: 0.8573 (tpt) cc_final: 0.8314 (tpt) REVERT: D 702 MET cc_start: 0.2449 (OUTLIER) cc_final: 0.1303 (ppp) REVERT: D 842 LEU cc_start: 0.8597 (mm) cc_final: 0.8065 (mm) outliers start: 18 outliers final: 13 residues processed: 90 average time/residue: 0.0891 time to fit residues: 11.2038 Evaluate side-chains 90 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 HIS Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 651 CYS Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 481 CYS Chi-restraints excluded: chain B residue 531 ARG Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 632 THR Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 848 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 48 optimal weight: 0.1980 chunk 67 optimal weight: 0.5980 chunk 46 optimal weight: 0.0470 chunk 30 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 74 optimal weight: 0.4980 chunk 76 optimal weight: 4.9990 chunk 37 optimal weight: 0.0270 chunk 55 optimal weight: 0.9980 chunk 99 optimal weight: 7.9990 overall best weight: 0.2736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 HIS B 738 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.194624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.152247 restraints weight = 10148.586| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 2.76 r_work: 0.3938 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3805 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8019 Z= 0.100 Angle : 0.579 8.111 10888 Z= 0.278 Chirality : 0.040 0.166 1183 Planarity : 0.004 0.042 1407 Dihedral : 4.500 49.573 1110 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.81 % Allowed : 21.48 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.28), residues: 997 helix: 0.40 (0.33), residues: 288 sheet: -2.41 (0.56), residues: 95 loop : -0.99 (0.27), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 576 TYR 0.007 0.001 TYR B 624 PHE 0.026 0.001 PHE D 675 TRP 0.012 0.001 TRP D 694 HIS 0.009 0.001 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 7995) covalent geometry : angle 0.53941 (10852) hydrogen bonds : bond 0.02544 ( 189) hydrogen bonds : angle 4.09748 ( 513) metal coordination : bond 0.00701 ( 24) metal coordination : angle 3.70440 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.305 Fit side-chains REVERT: B 531 ARG cc_start: 0.5910 (OUTLIER) cc_final: 0.5580 (mmp80) REVERT: B 754 LEU cc_start: 0.7735 (tp) cc_final: 0.7278 (mp) REVERT: D 580 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.6808 (tt) REVERT: D 630 ASN cc_start: 0.7791 (m110) cc_final: 0.7542 (p0) REVERT: D 695 MET cc_start: 0.8562 (tpt) cc_final: 0.8314 (tpt) REVERT: D 702 MET cc_start: 0.2414 (OUTLIER) cc_final: 0.1278 (ppp) REVERT: D 842 LEU cc_start: 0.8597 (mm) cc_final: 0.8075 (mm) outliers start: 22 outliers final: 14 residues processed: 97 average time/residue: 0.0921 time to fit residues: 12.3267 Evaluate side-chains 93 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 HIS Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 651 CYS Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 481 CYS Chi-restraints excluded: chain B residue 531 ARG Chi-restraints excluded: chain B residue 593 GLU Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 632 THR Chi-restraints excluded: chain D residue 668 THR Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 848 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.7244 > 50: distance: 17 - 20: 20.800 distance: 20 - 21: 20.243 distance: 21 - 22: 9.769 distance: 21 - 24: 27.456 distance: 22 - 23: 18.276 distance: 22 - 25: 38.894 distance: 25 - 26: 29.845 distance: 26 - 27: 42.324 distance: 26 - 29: 13.076 distance: 27 - 28: 44.812 distance: 27 - 36: 59.724 distance: 29 - 30: 6.635 distance: 30 - 31: 22.336 distance: 31 - 32: 4.541 distance: 32 - 33: 21.736 distance: 33 - 34: 9.138 distance: 33 - 35: 8.916 distance: 36 - 37: 54.927 distance: 37 - 38: 24.730 distance: 37 - 40: 22.404 distance: 38 - 39: 43.975 distance: 38 - 47: 19.698 distance: 40 - 41: 13.787 distance: 41 - 42: 35.780 distance: 42 - 43: 18.697 distance: 43 - 44: 13.341 distance: 44 - 45: 14.373 distance: 44 - 46: 10.772 distance: 47 - 48: 10.876 distance: 47 - 53: 22.870 distance: 48 - 49: 21.936 distance: 48 - 51: 26.373 distance: 49 - 50: 19.786 distance: 49 - 54: 25.259 distance: 51 - 52: 21.381 distance: 52 - 53: 22.803 distance: 54 - 55: 26.903 distance: 55 - 56: 13.980 distance: 55 - 58: 3.647 distance: 56 - 57: 31.133 distance: 56 - 62: 9.734 distance: 58 - 59: 10.408 distance: 58 - 60: 13.530 distance: 59 - 61: 6.512 distance: 62 - 63: 15.054 distance: 63 - 64: 24.746 distance: 63 - 66: 12.533 distance: 64 - 65: 31.292 distance: 64 - 73: 12.932 distance: 66 - 67: 14.946 distance: 67 - 68: 13.003 distance: 69 - 70: 13.339 distance: 70 - 71: 11.632 distance: 70 - 72: 20.629 distance: 73 - 74: 37.533 distance: 74 - 75: 12.673 distance: 74 - 77: 26.740 distance: 75 - 76: 29.312 distance: 75 - 80: 23.029 distance: 77 - 78: 16.715 distance: 77 - 79: 31.064 distance: 80 - 81: 12.759 distance: 81 - 82: 27.720 distance: 81 - 84: 9.713 distance: 82 - 83: 44.726 distance: 82 - 88: 10.797 distance: 84 - 85: 14.569 distance: 85 - 86: 24.216 distance: 85 - 87: 22.480 distance: 88 - 89: 34.824 distance: 89 - 90: 17.382 distance: 89 - 92: 25.919 distance: 90 - 91: 30.051 distance: 92 - 93: 31.174 distance: 94 - 95: 20.737 distance: 95 - 96: 8.846 distance: 95 - 98: 8.948 distance: 96 - 97: 17.911 distance: 96 - 102: 21.548 distance: 98 - 99: 7.246 distance: 99 - 100: 12.961 distance: 99 - 101: 23.687