Starting phenix.real_space_refine on Fri Jan 17 09:11:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eii_28157/01_2025/8eii_28157.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eii_28157/01_2025/8eii_28157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eii_28157/01_2025/8eii_28157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eii_28157/01_2025/8eii_28157.map" model { file = "/net/cci-nas-00/data/ceres_data/8eii_28157/01_2025/8eii_28157.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eii_28157/01_2025/8eii_28157.cif" } resolution = 3.12 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= 0.029 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 9 6.06 5 S 90 5.16 5 C 6633 2.51 5 N 1825 2.21 5 O 1894 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 10451 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3332 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 410} Chain breaks: 1 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3432 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 418} Chain breaks: 2 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "C" Number of atoms: 2499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2499 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 322} Chain breaks: 2 Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 265 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 12, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 138 Chain: "D" Number of atoms: 1127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1127 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 144} Chain breaks: 4 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 79 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: 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 151 SG CYS A 435 34.161 22.021 118.519 1.00133.83 S ATOM 171 SG CYS A 438 37.587 19.955 118.643 1.00140.11 S ATOM 297 SG CYS A 455 37.157 23.250 120.415 1.00124.64 S ATOM 319 SG CYS A 458 37.229 23.256 116.702 1.00127.31 S ATOM 498 SG CYS A 478 33.149 23.101 105.912 1.00129.04 S ATOM 518 SG CYS A 481 36.041 21.707 107.810 1.00138.63 S ATOM 647 SG CYS A 500 34.991 20.074 104.496 1.00137.71 S ATOM 669 SG CYS A 503 32.886 19.656 107.652 1.00143.33 S ATOM 574 SG CYS A 490 24.961 27.838 96.912 1.00144.25 S ATOM 607 SG CYS A 495 24.856 30.924 99.234 1.00138.86 S ATOM 819 SG CYS A 524 23.835 27.558 100.641 1.00142.88 S ATOM 845 SG CYS A 527 21.665 29.346 98.239 1.00152.31 S ATOM 3514 SG CYS B 435 62.985 82.936 45.557 1.00 77.40 S ATOM 3534 SG CYS B 438 65.558 80.476 44.393 1.00 74.64 S ATOM 3664 SG CYS B 455 62.005 80.264 43.089 1.00 64.69 S ATOM 3686 SG CYS B 458 62.594 79.370 46.714 1.00 52.27 S ATOM 3868 SG CYS B 478 65.679 81.499 57.154 1.00 74.89 S ATOM 3888 SG CYS B 481 66.214 79.628 53.948 1.00 73.93 S ATOM 4030 SG CYS B 500 69.217 80.332 56.274 1.00 79.43 S ATOM 4052 SG CYS B 503 67.830 83.031 54.243 1.00 82.95 S ATOM 3957 SG CYS B 490 63.089 84.702 69.616 1.00 88.19 S ATOM 3990 SG CYS B 495 59.266 85.342 68.828 1.00 92.73 S ATOM 4205 SG CYS B 524 62.135 86.590 66.499 1.00 83.47 S ATOM 4231 SG CYS B 527 61.177 88.158 69.722 1.00 89.76 S ATOM 6912 SG CYS C 435 47.144 26.157 51.580 1.00112.09 S ATOM 6932 SG CYS C 438 49.562 26.263 54.433 1.00123.02 S ATOM 7049 SG CYS C 455 46.686 28.753 54.300 1.00120.36 S ATOM 7071 SG CYS C 458 49.578 29.159 51.926 1.00120.81 S ATOM 7233 SG CYS C 478 56.557 25.662 42.067 1.00117.56 S ATOM 7251 SG CYS C 481 57.090 27.565 45.335 1.00122.55 S ATOM 7386 SG CYS C 500 59.373 24.599 44.493 1.00124.51 S ATOM 7408 SG CYS C 503 56.017 23.965 45.556 1.00118.30 S ATOM 7320 SG CYS C 490 57.472 22.237 30.001 1.00126.61 S ATOM 7352 SG CYS C 495 54.862 24.912 29.830 1.00119.54 S ATOM 7531 SG CYS C 524 54.393 21.867 32.175 1.00115.16 S ATOM 7547 SG CYS C 527 53.985 21.502 28.457 1.00119.26 S Time building chain proxies: 7.28, per 1000 atoms: 0.70 Number of scatterers: 10451 At special positions: 0 Unit cell: (88, 110, 163.9, 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 9 29.99 S 90 16.00 O 1894 8.00 N 1825 7.00 C 6633 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 1.6 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 435 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 438 " pdb=" ZN A 903 " 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 503 " 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 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 435 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 455 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 438 " pdb="ZN ZN B 902 " - pdb=" SG CYS B 458 " pdb=" ZN B 903 " pdb="ZN ZN B 903 " - pdb=" SG CYS B 500 " 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 B 904 " pdb="ZN ZN B 904 " - pdb=" SG CYS B 527 " pdb="ZN ZN B 904 " - pdb=" SG CYS B 524 " pdb="ZN ZN B 904 " - pdb=" SG CYS B 495 " pdb="ZN ZN B 904 " - pdb=" SG CYS B 490 " pdb=" ZN C 901 " pdb="ZN ZN C 901 " - pdb=" SG CYS C 455 " pdb="ZN ZN C 901 " - pdb=" SG CYS C 438 " pdb="ZN ZN C 901 " - pdb=" SG CYS C 435 " pdb="ZN ZN C 901 " - pdb=" SG CYS C 458 " pdb=" ZN C 902 " pdb="ZN ZN C 902 " - pdb=" SG CYS C 503 " pdb="ZN ZN C 902 " - pdb=" SG CYS C 500 " pdb="ZN ZN C 902 " - pdb=" SG CYS C 481 " pdb="ZN ZN C 902 " - pdb=" SG CYS C 478 " pdb=" ZN C 903 " pdb="ZN ZN C 903 " - pdb=" SG CYS C 495 " pdb="ZN ZN C 903 " - pdb=" SG CYS C 490 " pdb="ZN ZN C 903 " - pdb=" SG CYS C 524 " pdb="ZN ZN C 903 " - pdb=" SG CYS C 527 " Number of angles added : 54 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2528 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 15 sheets defined 35.7% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 416 through 426 removed outlier: 4.579A pdb=" N MET A 420 " --> pdb=" O SER A 416 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN A 426 " --> pdb=" O SER A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 434 removed outlier: 4.108A pdb=" N ASP A 433 " --> pdb=" O SER A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 466 removed outlier: 3.627A pdb=" N ARG A 461 " --> pdb=" O THR A 457 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU A 464 " --> pdb=" O ASP A 460 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A 466 " --> pdb=" O PHE A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 516 removed outlier: 3.779A pdb=" N GLU A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A 516 " --> pdb=" O THR A 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 511 through 516' Processing helix chain 'A' and resid 541 through 552 removed outlier: 3.884A pdb=" N GLN A 547 " --> pdb=" O ASN A 543 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N PHE A 550 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR A 551 " --> pdb=" O GLN A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 595 removed outlier: 3.549A pdb=" N LEU A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 618 removed outlier: 3.857A pdb=" N VAL A 613 " --> pdb=" O GLU A 609 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 616 " --> pdb=" O ALA A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 631 Processing helix chain 'A' and resid 632 through 633 No H-bonds generated for 'chain 'A' and resid 632 through 633' Processing helix chain 'A' and resid 634 through 640 removed outlier: 3.611A pdb=" N GLU A 638 " --> pdb=" O LYS A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 671 removed outlier: 3.501A pdb=" N GLY A 669 " --> pdb=" O GLU A 666 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 670 " --> pdb=" O GLY A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 683 removed outlier: 3.871A pdb=" N LEU A 678 " --> pdb=" O GLU A 674 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR A 681 " --> pdb=" O HIS A 677 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER A 682 " --> pdb=" O LEU A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 715 removed outlier: 3.974A pdb=" N ARG A 708 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ASP A 709 " --> pdb=" O GLY A 705 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 710 " --> pdb=" O ASP A 706 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER A 711 " --> pdb=" O LYS A 707 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 712 " --> pdb=" O ARG A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 726 No H-bonds generated for 'chain 'A' and resid 724 through 726' Processing helix chain 'A' and resid 755 through 760 removed outlier: 4.039A pdb=" N LEU A 760 " --> pdb=" O GLN A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 809 removed outlier: 3.534A pdb=" N ILE A 808 " --> pdb=" O GLU A 804 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 804 through 809' Processing helix chain 'A' and resid 822 through 827 removed outlier: 3.526A pdb=" N GLN A 827 " --> pdb=" O ARG A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 833 removed outlier: 3.666A pdb=" N ARG A 832 " --> pdb=" O LEU A 829 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER A 833 " --> pdb=" O LEU A 830 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 829 through 833' Processing helix chain 'A' and resid 835 through 843 removed outlier: 3.663A pdb=" N LEU A 842 " --> pdb=" O VAL A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 847 Processing helix chain 'B' and resid 416 through 426 removed outlier: 3.690A pdb=" N MET B 420 " --> pdb=" O SER B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 463 removed outlier: 3.867A pdb=" N ARG B 461 " --> pdb=" O THR B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 508 removed outlier: 3.566A pdb=" N LEU B 504 " --> pdb=" O CYS B 500 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU B 505 " --> pdb=" O VAL B 501 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VAL B 506 " --> pdb=" O GLU B 502 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU B 507 " --> pdb=" O CYS B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 519 removed outlier: 3.636A pdb=" N GLU B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 518 " --> pdb=" O ALA B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 550 removed outlier: 3.833A 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: 3.633A pdb=" N ALA B 612 " --> pdb=" O GLU B 608 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N HIS B 618 " --> pdb=" O GLY B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 631 removed outlier: 3.865A pdb=" N ILE B 631 " --> pdb=" O VAL B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 640 removed outlier: 3.877A pdb=" N ILE B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 670 Processing helix chain 'B' and resid 671 through 682 removed outlier: 3.607A pdb=" N PHE B 675 " --> pdb=" O LEU B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 715 Processing helix chain 'B' and resid 756 through 760 removed outlier: 3.927A pdb=" N LEU B 760 " --> pdb=" O GLN B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 809 Processing helix chain 'B' and resid 822 through 832 removed outlier: 3.725A 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 Processing helix chain 'C' and resid 416 through 426 Processing helix chain 'C' and resid 455 through 465 removed outlier: 4.721A pdb=" N ARG C 461 " --> pdb=" O THR C 457 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE C 462 " --> pdb=" O CYS C 458 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU C 463 " --> pdb=" O ARG C 459 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU C 464 " --> pdb=" O ASP C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 506 Processing helix chain 'C' and resid 511 through 517 Processing helix chain 'C' and resid 541 through 551 removed outlier: 3.590A pdb=" N ARG C 545 " --> pdb=" O ASP C 541 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN C 547 " --> pdb=" O ASN C 543 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE C 550 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 594 removed outlier: 3.566A pdb=" N LEU C 594 " --> pdb=" O VAL C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 631 Processing helix chain 'C' and resid 632 through 640 Processing helix chain 'C' and resid 668 through 683 removed outlier: 3.614A pdb=" N PHE C 672 " --> pdb=" O THR C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 715 Processing helix chain 'C' and resid 836 through 844 Processing helix chain 'C' and resid 845 through 849 Processing helix chain 'D' and resid 585 through 594 removed outlier: 4.389A pdb=" N LEU D 589 " --> pdb=" O ALA D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 631 removed outlier: 3.697A pdb=" N ASN D 630 " --> pdb=" O ASP D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 640 removed outlier: 3.539A pdb=" N ILE D 636 " --> pdb=" O THR D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 682 removed outlier: 4.248A pdb=" N LEU D 671 " --> pdb=" O GLY D 667 " (cutoff:3.500A) Processing helix chain 'D' and resid 703 through 715 Processing helix chain 'D' and resid 835 through 844 removed outlier: 4.246A pdb=" N ILE D 839 " --> pdb=" O SER D 835 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 850 removed outlier: 3.608A pdb=" N PHE D 850 " --> pdb=" O LYS D 847 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 445 through 446 Processing sheet with id=AA2, first strand: chain 'A' and resid 598 through 604 removed outlier: 6.877A pdb=" N ILE A 575 " --> pdb=" O GLY A 599 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N TYR A 601 " --> pdb=" O ILE A 575 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL A 577 " --> pdb=" O TYR A 601 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ALA A 603 " --> pdb=" O VAL A 577 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N SER A 579 " --> pdb=" O ALA A 603 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU A 644 " --> pdb=" O ARG A 576 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 580 " --> pdb=" O ILE A 646 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 697 through 699 removed outlier: 3.787A pdb=" N ARG A 733 " --> pdb=" O ILE A 721 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE A 721 " --> pdb=" O ARG A 733 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 765 through 766 removed outlier: 3.642A pdb=" N ILE A 765 " --> pdb=" O VAL A 792 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 445 through 446 removed outlier: 3.627A pdb=" N SER B 445 " --> pdb=" O LEU B 454 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 454 " --> pdb=" O SER B 445 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 488 through 489 removed outlier: 3.548A pdb=" N LEU B 488 " --> pdb=" O PHE B 499 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 532 through 533 removed outlier: 3.628A pdb=" N HIS B 533 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 536 " --> pdb=" O HIS B 533 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 623 through 625 removed outlier: 6.356A pdb=" N ILE B 575 " --> pdb=" O LYS B 600 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N VAL B 602 " --> pdb=" O ILE B 575 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL B 577 " --> pdb=" O VAL B 602 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N SER B 604 " --> pdb=" O VAL B 577 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N SER B 579 " --> pdb=" O SER B 604 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ARG B 576 " --> pdb=" O LEU B 644 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ILE B 646 " --> pdb=" O ARG B 576 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU B 578 " --> pdb=" O ILE B 646 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU B 697 " --> pdb=" O GLY B 647 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG B 733 " --> pdb=" O ILE B 721 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE B 721 " --> pdb=" O ARG B 733 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 765 through 766 removed outlier: 3.688A pdb=" N VAL B 791 " --> pdb=" O ASP B 798 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 445 through 446 Processing sheet with id=AB2, first strand: chain 'C' and resid 488 through 489 Processing sheet with id=AB3, first strand: chain 'C' and resid 598 through 601 removed outlier: 7.261A pdb=" N ILE C 575 " --> pdb=" O GLY C 599 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N TYR C 601 " --> pdb=" O ILE C 575 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL C 577 " --> pdb=" O TYR C 601 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU C 644 " --> pdb=" O ARG C 576 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 697 through 698 removed outlier: 3.664A pdb=" N ASN C 698 " --> pdb=" O TYR C 734 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ARG C 733 " --> pdb=" O ILE C 721 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE C 721 " --> pdb=" O ARG C 733 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL C 719 " --> pdb=" O PHE C 735 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 598 through 603 removed outlier: 6.966A pdb=" N ILE D 575 " --> pdb=" O GLY D 599 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N TYR D 601 " --> pdb=" O ILE D 575 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL D 577 " --> pdb=" O TYR D 601 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ALA D 603 " --> pdb=" O VAL D 577 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N SER D 579 " --> pdb=" O ALA D 603 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N ILE D 646 " --> pdb=" O ARG D 576 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LEU D 578 " --> pdb=" O ILE D 646 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 719 through 720 removed outlier: 3.554A pdb=" N VAL D 719 " --> pdb=" O PHE D 735 " (cutoff:3.500A) 254 hydrogen bonds defined for protein. 675 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.30 Time building geometry restraints manager: 2.86 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: 3432 1.34 - 1.46: 1975 1.46 - 1.58: 5158 1.58 - 1.70: 1 1.70 - 1.82: 117 Bond restraints: 10683 Sorted by residual: 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 8.27e+00 bond pdb=" C2 SAH A 901 " pdb=" N3 SAH A 901 " ideal model delta sigma weight residual 1.322 1.379 -0.057 2.00e-02 2.50e+03 8.10e+00 bond pdb=" C8 SAH A 901 " pdb=" N7 SAH A 901 " ideal model delta sigma weight residual 1.299 1.352 -0.053 2.00e-02 2.50e+03 7.07e+00 bond pdb=" C8 SAH B 901 " pdb=" N7 SAH B 901 " ideal model delta sigma weight residual 1.299 1.351 -0.052 2.00e-02 2.50e+03 6.85e+00 bond pdb=" C2 SAH B 901 " pdb=" N1 SAH B 901 " ideal model delta sigma weight residual 1.330 1.379 -0.049 2.00e-02 2.50e+03 5.92e+00 ... (remaining 10678 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 14181 2.05 - 4.10: 266 4.10 - 6.15: 36 6.15 - 8.19: 9 8.19 - 10.24: 7 Bond angle restraints: 14499 Sorted by residual: angle pdb=" C HIS C 447 " pdb=" N PRO C 448 " pdb=" CA PRO C 448 " ideal model delta sigma weight residual 118.85 126.95 -8.10 1.09e+00 8.42e-01 5.52e+01 angle pdb=" CA PRO A 448 " pdb=" N PRO A 448 " pdb=" CD PRO A 448 " ideal model delta sigma weight residual 112.00 105.08 6.92 1.40e+00 5.10e-01 2.44e+01 angle pdb=" C PRO C 448 " pdb=" N LEU C 449 " pdb=" CA LEU C 449 " ideal model delta sigma weight residual 120.88 114.92 5.96 1.62e+00 3.81e-01 1.35e+01 angle pdb=" N ILE A 584 " pdb=" CA ILE A 584 " pdb=" C ILE A 584 " ideal model delta sigma weight residual 111.77 108.06 3.71 1.04e+00 9.25e-01 1.28e+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 91.53 10.24 3.00e+00 1.11e-01 1.17e+01 ... (remaining 14494 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 5574 17.96 - 35.91: 590 35.91 - 53.87: 125 53.87 - 71.83: 10 71.83 - 89.79: 8 Dihedral angle restraints: 6307 sinusoidal: 2377 harmonic: 3930 Sorted by residual: dihedral pdb=" CA VAL C 606 " pdb=" C VAL C 606 " pdb=" N CYS C 607 " pdb=" CA CYS C 607 " ideal model delta harmonic sigma weight residual 180.00 -158.81 -21.19 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA TYR A 467 " pdb=" C TYR A 467 " pdb=" N MET A 468 " pdb=" CA MET A 468 " ideal model delta harmonic sigma weight residual 180.00 160.79 19.21 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA ASP C 582 " pdb=" C ASP C 582 " pdb=" N GLY C 583 " pdb=" CA GLY C 583 " ideal model delta harmonic sigma weight residual 180.00 162.10 17.90 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 6304 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 921 0.031 - 0.061: 441 0.061 - 0.092: 155 0.092 - 0.123: 59 0.123 - 0.153: 8 Chirality restraints: 1584 Sorted by residual: chirality pdb=" CA ASN B 820 " pdb=" N ASN B 820 " pdb=" C ASN B 820 " pdb=" CB ASN B 820 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.86e-01 chirality pdb=" CA ILE A 646 " pdb=" N ILE A 646 " pdb=" C ILE A 646 " pdb=" CB ILE A 646 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.36e-01 chirality pdb=" CA VAL B 625 " pdb=" N VAL B 625 " pdb=" C VAL B 625 " pdb=" CB VAL B 625 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.90e-01 ... (remaining 1581 not shown) Planarity restraints: 1890 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 573 " 0.059 5.00e-02 4.00e+02 8.98e-02 1.29e+01 pdb=" N PRO D 574 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO D 574 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO D 574 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 744 " -0.049 5.00e-02 4.00e+02 7.20e-02 8.30e+00 pdb=" N PRO C 745 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO C 745 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 745 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 447 " -0.050 5.00e-02 4.00e+02 7.18e-02 8.24e+00 pdb=" N PRO A 448 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 448 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 448 " -0.039 5.00e-02 4.00e+02 ... (remaining 1887 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 968 2.74 - 3.28: 10181 3.28 - 3.82: 15819 3.82 - 4.36: 18791 4.36 - 4.90: 32553 Nonbonded interactions: 78312 Sorted by model distance: nonbonded pdb=" OE2 GLU B 605 " pdb=" O2' SAH B 901 " model vdw 2.205 3.040 nonbonded pdb=" NE ARG A 576 " pdb=" O PRO A 641 " model vdw 2.230 3.120 nonbonded pdb=" OD1 ASP C 709 " pdb=" NH2 ARG C 712 " model vdw 2.252 3.120 nonbonded pdb=" O SER A 819 " pdb=" OG SER A 819 " model vdw 2.261 3.040 nonbonded pdb=" NH2 ARG B 764 " pdb=" OD2 ASP B 798 " model vdw 2.272 3.120 ... (remaining 78307 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 414 through 556 or (resid 557 and (name N or name CA or na \ me C or name O or name CB )) or resid 558 or (resid 559 through 560 and (name N \ or name CA or name 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 throug \ h 724 or (resid 725 and (name N or name CA or name C or name O or name CB )) or \ resid 726 through 773 or (resid 774 and (name N or name CA or name C or name O o \ r name CB )) or resid 775 or resid 777 or resid 788 through 796 or (resid 797 an \ d (name N or name CA or name C or name O or name CB )) or resid 798 through 853 \ or resid 901 or resid 902 through 904)) selection = (chain 'B' and (resid 414 through 417 or (resid 418 and (name N or name CA or na \ me C or name O or name CB )) or resid 419 through 425 or (resid 426 and (name N \ or name CA or name C or name O or name CB )) or resid 427 through 428 or (resid \ 429 and (name N or name CA or name C or name O or name CB )) or resid 430 throug \ h 440 or (resid 441 and (name N or name CA or name C or name O or name CB )) or \ resid 442 through 471 or (resid 472 and (name N or name CA or name C or name O o \ r name CB )) or resid 473 through 484 or (resid 485 through 487 and (name N or n \ ame CA or name C or name O or name CB )) or resid 488 through 517 or (resid 518 \ and (name N or name CA or name C or name O or name CB )) or resid 519 through 53 \ 0 or (resid 531 and (name N or name CA or name C or name O or name CB )) or resi \ d 532 through 536 or (resid 537 and (name N or name CA or name C or name O or na \ me CB )) or resid 538 through 539 or (resid 540 and (name N or name CA or name C \ or name O or name CB )) or resid 541 through 572 or (resid 573 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name NE )) or res \ id 574 through 660 or (resid 661 through 662 and (name N or name CA or name C or \ name O or name CB )) or resid 663 through 702 or (resid 703 and (name N or name \ 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 )) or r \ esid 768 through 776 or resid 782 or resid 788 through 795 or (resid 796 through \ 797 and (name N or name CA or name C or name O or name CB )) or resid 798 throu \ gh 852 or (resid 853 and (name N or name CA or name C or name O or name CB )) or \ resid 901 or resid 902 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: 2.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 28.210 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 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 : 0.004 0.096 10683 Z= 0.270 Angle : 0.718 10.243 14499 Z= 0.397 Chirality : 0.042 0.153 1584 Planarity : 0.005 0.090 1890 Dihedral : 15.071 89.787 3779 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.10 % Allowed : 12.68 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % 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: -2.07 (0.23), residues: 1338 helix: -0.77 (0.28), residues: 365 sheet: -3.17 (0.41), residues: 121 loop : -1.39 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 736 HIS 0.011 0.002 HIS A 533 PHE 0.021 0.002 PHE A 549 TYR 0.022 0.001 TYR B 624 ARG 0.006 0.000 ARG A 497 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 526 MET cc_start: 0.5552 (mtt) cc_final: 0.5348 (mtt) REVERT: A 549 PHE cc_start: 0.6205 (t80) cc_final: 0.5992 (t80) outliers start: 1 outliers final: 1 residues processed: 110 average time/residue: 0.2630 time to fit residues: 40.1597 Evaluate side-chains 110 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 754 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 64 optimal weight: 0.0030 chunk 78 optimal weight: 2.9990 chunk 122 optimal weight: 20.0000 overall best weight: 0.6992 ------------------------------------------------------------------------------- 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 519 GLN C 492 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.198446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.142335 restraints weight = 12934.772| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 3.44 r_work: 0.3499 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.0811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10683 Z= 0.206 Angle : 0.561 8.532 14499 Z= 0.291 Chirality : 0.041 0.155 1584 Planarity : 0.005 0.066 1890 Dihedral : 4.573 32.131 1495 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.72 % Allowed : 12.96 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % 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: -1.87 (0.23), residues: 1338 helix: -0.57 (0.27), residues: 386 sheet: -3.14 (0.44), residues: 109 loop : -1.31 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 736 HIS 0.011 0.001 HIS A 677 PHE 0.016 0.001 PHE D 675 TYR 0.014 0.001 TYR B 624 ARG 0.005 0.000 ARG D 708 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 609 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7138 (mt-10) REVERT: A 702 MET cc_start: 0.6546 (ptt) cc_final: 0.5865 (ptt) REVERT: A 708 ARG cc_start: 0.7111 (mtt-85) cc_final: 0.6559 (mmt180) REVERT: B 541 ASP cc_start: 0.7555 (p0) cc_final: 0.7306 (p0) REVERT: B 751 ASN cc_start: 0.8029 (t0) cc_final: 0.7757 (t0) REVERT: B 799 VAL cc_start: 0.7796 (OUTLIER) cc_final: 0.7557 (m) outliers start: 18 outliers final: 10 residues processed: 125 average time/residue: 0.2841 time to fit residues: 49.0300 Evaluate side-chains 116 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 799 VAL Chi-restraints excluded: chain B residue 853 GLU Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 628 VAL Chi-restraints excluded: chain D residue 700 VAL Chi-restraints excluded: chain D residue 836 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 76 optimal weight: 0.5980 chunk 9 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 82 optimal weight: 0.0270 chunk 16 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 chunk 124 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 overall best weight: 0.8440 ------------------------------------------------------------------------------- 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 519 GLN ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.197520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.139904 restraints weight = 13150.271| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 3.03 r_work: 0.3524 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10683 Z= 0.216 Angle : 0.561 8.926 14499 Z= 0.288 Chirality : 0.041 0.158 1584 Planarity : 0.004 0.057 1890 Dihedral : 4.381 19.760 1493 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.76 % Allowed : 13.92 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % 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: -1.79 (0.23), residues: 1338 helix: -0.47 (0.27), residues: 395 sheet: -2.88 (0.44), residues: 115 loop : -1.30 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 736 HIS 0.009 0.001 HIS A 677 PHE 0.012 0.001 PHE D 675 TYR 0.018 0.001 TYR B 624 ARG 0.003 0.000 ARG A 497 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 526 MET cc_start: 0.6733 (mtt) cc_final: 0.6242 (mtm) REVERT: A 528 LEU cc_start: 0.6480 (OUTLIER) cc_final: 0.6107 (mt) REVERT: A 702 MET cc_start: 0.7111 (ptt) cc_final: 0.6629 (ptt) REVERT: A 708 ARG cc_start: 0.7209 (mtt-85) cc_final: 0.6645 (mmt180) REVERT: B 519 GLN cc_start: 0.5414 (OUTLIER) cc_final: 0.5008 (pp30) REVERT: B 541 ASP cc_start: 0.7816 (p0) cc_final: 0.7516 (p0) REVERT: B 594 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.6868 (mm) REVERT: B 751 ASN cc_start: 0.8115 (t0) cc_final: 0.7895 (t0) REVERT: B 823 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.6900 (tpt170) outliers start: 29 outliers final: 17 residues processed: 127 average time/residue: 0.2809 time to fit residues: 49.6018 Evaluate side-chains 125 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain B residue 519 GLN Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 683 ARG Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 823 ARG Chi-restraints excluded: chain B residue 853 GLU Chi-restraints excluded: chain C residue 508 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 D residue 577 VAL Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 836 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 4 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 101 optimal weight: 0.0040 chunk 25 optimal weight: 0.0060 chunk 37 optimal weight: 0.0030 chunk 108 optimal weight: 1.9990 overall best weight: 0.3018 ------------------------------------------------------------------------------- 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 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 680 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.199885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.143019 restraints weight = 13023.030| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 3.37 r_work: 0.3507 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10683 Z= 0.147 Angle : 0.515 9.389 14499 Z= 0.264 Chirality : 0.040 0.145 1584 Planarity : 0.004 0.053 1890 Dihedral : 4.127 18.430 1493 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.81 % Allowed : 15.92 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % 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: -1.58 (0.23), residues: 1338 helix: -0.27 (0.27), residues: 398 sheet: -2.75 (0.44), residues: 115 loop : -1.19 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 736 HIS 0.007 0.001 HIS A 677 PHE 0.017 0.001 PHE B 466 TYR 0.014 0.001 TYR B 624 ARG 0.002 0.000 ARG A 497 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 1.218 Fit side-chains revert: symmetry clash REVERT: A 526 MET cc_start: 0.6734 (mtt) cc_final: 0.5691 (mtm) REVERT: A 528 LEU cc_start: 0.6519 (OUTLIER) cc_final: 0.6134 (mt) REVERT: A 702 MET cc_start: 0.7261 (ptt) cc_final: 0.6807 (ptt) REVERT: A 708 ARG cc_start: 0.7082 (mtt-85) cc_final: 0.6560 (mmt180) REVERT: B 541 ASP cc_start: 0.7630 (p0) cc_final: 0.7285 (p0) REVERT: B 594 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.6768 (mm) REVERT: B 799 VAL cc_start: 0.7852 (OUTLIER) cc_final: 0.7627 (m) REVERT: B 823 ARG cc_start: 0.7237 (OUTLIER) cc_final: 0.6822 (tpt170) outliers start: 19 outliers final: 11 residues processed: 119 average time/residue: 0.2656 time to fit residues: 44.1419 Evaluate side-chains 117 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 704 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 799 VAL Chi-restraints excluded: chain B residue 823 ARG Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 726 VAL Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 700 VAL Chi-restraints excluded: chain D residue 836 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 38 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 69 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 93 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 ASN B 519 GLN ** B 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.197948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.140178 restraints weight = 13043.049| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 3.48 r_work: 0.3472 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10683 Z= 0.211 Angle : 0.553 9.308 14499 Z= 0.283 Chirality : 0.041 0.172 1584 Planarity : 0.004 0.053 1890 Dihedral : 4.179 19.337 1493 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 2.19 % Allowed : 16.40 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % 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: -1.51 (0.23), residues: 1338 helix: -0.20 (0.27), residues: 393 sheet: -2.61 (0.43), residues: 124 loop : -1.14 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 736 HIS 0.007 0.001 HIS A 677 PHE 0.010 0.001 PHE C 673 TYR 0.018 0.001 TYR B 624 ARG 0.006 0.000 ARG A 497 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2676 Ramachandran restraints generated. 1338 Oldfield, 0 Emsley, 1338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 702 MET cc_start: 0.7444 (ptt) cc_final: 0.7119 (ptt) REVERT: B 519 GLN cc_start: 0.5723 (OUTLIER) cc_final: 0.5445 (pp30) REVERT: B 541 ASP cc_start: 0.7685 (p0) cc_final: 0.7336 (p0) REVERT: B 594 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.6862 (mm) REVERT: B 751 ASN cc_start: 0.7808 (t0) cc_final: 0.7515 (t0) REVERT: B 799 VAL cc_start: 0.7967 (OUTLIER) cc_final: 0.7747 (m) REVERT: B 823 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.6897 (tpt170) outliers start: 23 outliers final: 19 residues processed: 123 average time/residue: 0.2644 time to fit residues: 45.5563 Evaluate side-chains 126 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain B residue 519 GLN Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 683 ARG Chi-restraints excluded: chain B residue 704 VAL Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 799 VAL Chi-restraints excluded: chain B residue 823 ARG Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 463 LEU 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 D residue 577 VAL Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 700 VAL Chi-restraints excluded: chain D residue 836 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.2784 > 50: distance: 52 - 76: 16.245 distance: 56 - 84: 16.679 distance: 61 - 92: 35.325 distance: 68 - 76: 15.583 distance: 69 - 98: 36.783 distance: 76 - 77: 10.335 distance: 77 - 78: 4.904 distance: 77 - 80: 28.300 distance: 78 - 79: 25.866 distance: 78 - 84: 20.065 distance: 79 - 109: 25.503 distance: 80 - 81: 32.058 distance: 81 - 82: 15.526 distance: 81 - 83: 30.579 distance: 84 - 85: 6.450 distance: 85 - 86: 18.161 distance: 85 - 88: 24.760 distance: 86 - 87: 27.929 distance: 86 - 92: 16.220 distance: 87 - 120: 12.713 distance: 88 - 89: 21.591 distance: 88 - 90: 27.065 distance: 89 - 91: 12.440 distance: 92 - 93: 3.215 distance: 93 - 94: 11.232 distance: 94 - 95: 8.662 distance: 94 - 98: 29.016 distance: 95 - 128: 30.365 distance: 98 - 99: 13.412 distance: 99 - 100: 34.973 distance: 99 - 102: 27.777 distance: 100 - 101: 18.112 distance: 100 - 109: 15.870 distance: 104 - 105: 18.752 distance: 105 - 106: 18.584 distance: 106 - 107: 26.850 distance: 106 - 108: 22.134 distance: 109 - 110: 8.830 distance: 110 - 111: 7.610 distance: 111 - 112: 19.188 distance: 111 - 120: 7.548 distance: 114 - 115: 15.922 distance: 114 - 116: 9.278 distance: 115 - 117: 8.244 distance: 116 - 118: 13.515 distance: 117 - 119: 17.384 distance: 118 - 119: 13.333 distance: 120 - 121: 30.615 distance: 121 - 122: 11.904 distance: 121 - 124: 12.069 distance: 122 - 123: 6.898 distance: 122 - 128: 30.368 distance: 124 - 125: 49.560 distance: 125 - 126: 40.230 distance: 125 - 127: 12.971 distance: 128 - 129: 15.897 distance: 129 - 132: 29.985 distance: 132 - 133: 13.089 distance: 133 - 134: 25.705 distance: 134 - 135: 25.138 distance: 134 - 136: 11.691 distance: 138 - 141: 20.936 distance: 139 - 140: 7.855 distance: 139 - 143: 4.687 distance: 141 - 142: 22.348 distance: 143 - 144: 7.964 distance: 144 - 145: 6.267 distance: 144 - 147: 35.521 distance: 145 - 146: 10.720 distance: 145 - 151: 4.589 distance: 147 - 148: 39.327 distance: 148 - 149: 4.903 distance: 148 - 150: 12.722 distance: 151 - 152: 3.662 distance: 151 - 157: 16.307 distance: 152 - 153: 14.808 distance: 152 - 155: 14.648 distance: 153 - 154: 8.773 distance: 153 - 158: 26.445 distance: 155 - 156: 41.222 distance: 156 - 157: 7.189