Starting phenix.real_space_refine on Wed Feb 14 22:49:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eii_28157/02_2024/8eii_28157_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eii_28157/02_2024/8eii_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eii_28157/02_2024/8eii_28157.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eii_28157/02_2024/8eii_28157.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eii_28157/02_2024/8eii_28157_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eii_28157/02_2024/8eii_28157_updated.pdb" } 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 Residue "A GLU 557": "OE1" <-> "OE2" Residue "A GLU 608": "OE1" <-> "OE2" Residue "A GLU 609": "OE1" <-> "OE2" Residue "B GLU 483": "OE1" <-> "OE2" Residue "B GLU 608": "OE1" <-> "OE2" Residue "C GLU 483": "OE1" <-> "OE2" Residue "D GLU 638": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 5.71, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.98 Conformation dependent library (CDL) restraints added in 1.9 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... running ksdssp... Secondary structure from input PDB file: 51 helices and 8 sheets defined 28.6% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 417 through 426 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 431 through 433 No H-bonds generated for 'chain 'A' and resid 431 through 433' Processing helix chain 'A' and resid 456 through 465 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) Processing helix chain 'A' and resid 512 through 515 No H-bonds generated for 'chain 'A' and resid 512 through 515' Processing helix chain 'A' and resid 542 through 551 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 586 through 594 Processing helix chain 'A' and resid 608 through 617 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 628 through 630 No H-bonds generated for 'chain 'A' and resid 628 through 630' Processing helix chain 'A' and resid 633 through 639 removed outlier: 4.465A pdb=" N GLU A 637 " --> pdb=" O LYS A 633 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU A 638 " --> pdb=" O LYS A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 671 removed outlier: 3.513A pdb=" N ARG A 670 " --> pdb=" O GLY A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 682 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 704 through 714 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 723 through 725 No H-bonds generated for 'chain 'A' and resid 723 through 725' Processing helix chain 'A' and resid 756 through 759 Processing helix chain 'A' and resid 805 through 808 No H-bonds generated for 'chain 'A' and resid 805 through 808' Processing helix chain 'A' and resid 823 through 826 No H-bonds generated for 'chain 'A' and resid 823 through 826' Processing helix chain 'A' and resid 830 through 832 No H-bonds generated for 'chain 'A' and resid 830 through 832' Processing helix chain 'A' and resid 836 through 842 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 846 No H-bonds generated for 'chain 'A' and resid 844 through 846' Processing helix chain 'B' and resid 417 through 425 Processing helix chain 'B' and resid 456 through 462 removed outlier: 3.867A pdb=" N ARG B 461 " --> pdb=" O THR B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 507 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) No H-bonds generated for 'chain 'B' and resid 501 through 507' Processing helix chain 'B' and resid 512 through 518 removed outlier: 3.648A pdb=" N LEU B 518 " --> pdb=" O ALA B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 551 removed outlier: 3.833A pdb=" N PHE B 550 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N THR B 551 " --> pdb=" O GLN B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 594 Processing helix chain 'B' and resid 608 through 616 removed outlier: 3.633A pdb=" N ALA B 612 " --> pdb=" O GLU B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 630 No H-bonds generated for 'chain 'B' and resid 628 through 630' Processing helix chain 'B' and resid 633 through 639 Processing helix chain 'B' and resid 667 through 681 removed outlier: 3.593A pdb=" N PHE B 672 " --> pdb=" O GLY B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 714 Processing helix chain 'B' and resid 757 through 759 No H-bonds generated for 'chain 'B' and resid 757 through 759' Processing helix chain 'B' and resid 802 through 808 Processing helix chain 'B' and resid 823 through 831 Processing helix chain 'B' and resid 836 through 848 Proline residue: B 845 - end of helix removed outlier: 5.189A pdb=" N ASP B 848 " --> pdb=" O ALA B 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 425 Processing helix chain 'C' and resid 456 through 464 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 502 through 505 No H-bonds generated for 'chain 'C' and resid 502 through 505' Processing helix chain 'C' and resid 512 through 516 Processing helix chain 'C' and resid 542 through 550 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 589 through 593 Processing helix chain 'C' and resid 628 through 630 No H-bonds generated for 'chain 'C' and resid 628 through 630' Processing helix chain 'C' and resid 633 through 639 Processing helix chain 'C' and resid 669 through 682 Processing helix chain 'C' and resid 704 through 714 Processing helix chain 'C' and resid 837 through 848 Proline residue: C 845 - end of helix removed outlier: 5.145A pdb=" N ASP C 848 " --> pdb=" O ALA C 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 593 Processing helix chain 'D' and resid 628 through 630 No H-bonds generated for 'chain 'D' and resid 628 through 630' Processing helix chain 'D' and resid 633 through 639 Processing helix chain 'D' and resid 668 through 681 Processing helix chain 'D' and resid 704 through 714 Processing helix chain 'D' and resid 836 through 849 Proline residue: D 845 - end of helix removed outlier: 6.311A pdb=" N ASP D 848 " --> pdb=" O ALA D 844 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N TYR D 849 " --> pdb=" O PRO D 845 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 644 through 647 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) removed outlier: 7.086A pdb=" N VAL A 577 " --> pdb=" O GLY A 599 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TYR A 601 " --> pdb=" O VAL A 577 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N SER A 579 " --> pdb=" O TYR A 601 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ALA A 603 " --> pdb=" O SER A 579 " (cutoff:3.500A) Processing sheet with id= B, 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= C, first strand: chain 'A' and resid 791 through 793 Processing sheet with id= D, first strand: chain 'B' and resid 719 through 722 removed outlier: 3.644A pdb=" N ILE B 721 " --> pdb=" O ARG B 733 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG B 733 " --> pdb=" O ILE B 721 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU B 697 " --> pdb=" O GLY B 647 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY B 648 " --> pdb=" O LEU B 580 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N VAL B 577 " --> pdb=" O GLY B 599 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TYR B 601 " --> pdb=" O VAL B 577 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N SER B 579 " --> pdb=" O TYR B 601 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ALA B 603 " --> pdb=" O SER B 579 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LYS B 623 " --> pdb=" O ALA B 603 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 719 through 721 removed outlier: 3.594A pdb=" N VAL C 719 " --> pdb=" O PHE C 735 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE C 721 " --> pdb=" O ARG C 733 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ARG C 733 " --> pdb=" O ILE C 721 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 575 through 577 removed outlier: 7.627A pdb=" N VAL C 577 " --> pdb=" O GLY C 599 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TYR C 601 " --> pdb=" O VAL C 577 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 696 through 698 removed outlier: 4.131A pdb=" N PHE D 696 " --> pdb=" O TRP D 736 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ASN D 698 " --> pdb=" O TYR D 734 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TYR D 734 " --> pdb=" O ASN D 698 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL D 719 " --> pdb=" O PHE D 735 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 575 through 579 removed outlier: 7.624A pdb=" N VAL D 577 " --> pdb=" O GLY D 599 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N TYR D 601 " --> pdb=" O VAL D 577 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N SER D 579 " --> pdb=" O TYR D 601 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ALA D 603 " --> pdb=" O SER D 579 " (cutoff:3.500A) 182 hydrogen bonds defined for protein. 489 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.52 Time building geometry restraints manager: 4.30 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: 91.53 - 100.03: 3 100.03 - 108.53: 551 108.53 - 117.03: 6801 117.03 - 125.53: 6960 125.53 - 134.03: 184 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: 972 2.74 - 3.28: 10236 3.28 - 3.82: 15881 3.82 - 4.36: 18932 4.36 - 4.90: 32579 Nonbonded interactions: 78600 Sorted by model distance: nonbonded pdb=" OE2 GLU B 605 " pdb=" O2' SAH B 901 " model vdw 2.205 2.440 nonbonded pdb=" NE ARG A 576 " pdb=" O PRO A 641 " model vdw 2.230 2.520 nonbonded pdb=" OD1 ASP C 709 " pdb=" NH2 ARG C 712 " model vdw 2.252 2.520 nonbonded pdb=" O SER A 819 " pdb=" OG SER A 819 " model vdw 2.261 2.440 nonbonded pdb=" NH2 ARG B 764 " pdb=" OD2 ASP B 798 " model vdw 2.272 2.520 ... (remaining 78595 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 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: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.800 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 31.310 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.830 ------------------------------------------------------------------------------- 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= 0.264 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 fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 1.301 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: 0.2604 time to fit residues: 39.8566 Evaluate side-chains 110 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 1.228 ------------------------------------------------------------------------------- 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: 1.9990 chunk 102 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 122 optimal weight: 20.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 680 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.0557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10683 Z= 0.240 Angle : 0.558 7.553 14499 Z= 0.287 Chirality : 0.042 0.163 1584 Planarity : 0.005 0.064 1890 Dihedral : 4.596 32.590 1495 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.19 % Allowed : 13.16 % Favored : 84.65 % 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: -1.98 (0.23), residues: 1338 helix: -0.73 (0.28), residues: 362 sheet: -3.03 (0.41), residues: 122 loop : -1.32 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 736 HIS 0.009 0.001 HIS A 677 PHE 0.015 0.002 PHE D 675 TYR 0.019 0.001 TYR B 624 ARG 0.004 0.000 ARG A 497 *********************** 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 126 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 103 time to evaluate : 1.226 Fit side-chains revert: symmetry clash REVERT: A 702 MET cc_start: 0.6443 (ptt) cc_final: 0.5954 (ptt) REVERT: B 751 ASN cc_start: 0.7912 (t0) cc_final: 0.7669 (t0) REVERT: B 823 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.6683 (tpt170) outliers start: 23 outliers final: 12 residues processed: 116 average time/residue: 0.2735 time to fit residues: 45.7062 Evaluate side-chains 113 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 823 ARG 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 C residue 746 VAL Chi-restraints excluded: chain D residue 578 LEU 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 68 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 132 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 98 optimal weight: 20.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10683 Z= 0.298 Angle : 0.597 7.701 14499 Z= 0.307 Chirality : 0.043 0.173 1584 Planarity : 0.005 0.056 1890 Dihedral : 4.657 23.239 1493 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 2.19 % Allowed : 15.82 % Favored : 81.98 % 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: -2.03 (0.23), residues: 1338 helix: -0.77 (0.28), residues: 365 sheet: -3.01 (0.40), residues: 123 loop : -1.37 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 736 HIS 0.009 0.001 HIS A 677 PHE 0.016 0.002 PHE A 696 TYR 0.025 0.002 TYR B 624 ARG 0.006 0.000 ARG C 461 *********************** 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 123 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 100 time to evaluate : 1.492 Fit side-chains REVERT: A 702 MET cc_start: 0.7217 (ptt) cc_final: 0.6919 (ptt) REVERT: B 823 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.6787 (tpt170) outliers start: 23 outliers final: 18 residues processed: 112 average time/residue: 0.2501 time to fit residues: 39.1011 Evaluate side-chains 116 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 97 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 719 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 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 823 ARG Chi-restraints excluded: chain B residue 853 GLU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 123 optimal weight: 30.0000 chunk 130 optimal weight: 0.1980 chunk 64 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 820 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10683 Z= 0.180 Angle : 0.529 8.221 14499 Z= 0.270 Chirality : 0.041 0.174 1584 Planarity : 0.004 0.052 1890 Dihedral : 4.333 21.397 1493 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.67 % Allowed : 15.82 % Favored : 81.51 % 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: -1.83 (0.23), residues: 1338 helix: -0.51 (0.28), residues: 365 sheet: -2.77 (0.42), residues: 122 loop : -1.30 (0.22), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 736 HIS 0.008 0.001 HIS A 677 PHE 0.017 0.001 PHE D 675 TYR 0.019 0.001 TYR B 624 ARG 0.004 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 131 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 103 time to evaluate : 1.243 Fit side-chains REVERT: A 702 MET cc_start: 0.7263 (ptt) cc_final: 0.6989 (ptt) REVERT: B 594 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7534 (mm) REVERT: B 751 ASN cc_start: 0.7676 (t0) cc_final: 0.7377 (t0) REVERT: B 823 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.6690 (tpt170) outliers start: 28 outliers final: 18 residues processed: 119 average time/residue: 0.2751 time to fit residues: 45.6132 Evaluate side-chains 118 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 803 THR 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 420 MET Chi-restraints excluded: chain B residue 438 CYS 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 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 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 706 ASP 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 108 optimal weight: 0.0970 chunk 74 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 97 optimal weight: 0.0470 chunk 53 optimal weight: 0.0770 chunk 111 optimal weight: 0.9990 chunk 90 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 117 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 overall best weight: 0.3434 ------------------------------------------------------------------------------- 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 680 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10683 Z= 0.142 Angle : 0.495 8.328 14499 Z= 0.254 Chirality : 0.040 0.140 1584 Planarity : 0.004 0.051 1890 Dihedral : 3.982 18.234 1493 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.67 % Allowed : 16.49 % Favored : 80.84 % 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: -1.64 (0.23), residues: 1338 helix: -0.32 (0.28), residues: 372 sheet: -2.58 (0.43), residues: 123 loop : -1.22 (0.22), residues: 843 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 0.014 0.001 PHE A 549 TYR 0.014 0.001 TYR B 624 ARG 0.002 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 132 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 104 time to evaluate : 1.185 Fit side-chains REVERT: A 415 GLN cc_start: 0.5650 (OUTLIER) cc_final: 0.5258 (mt0) REVERT: A 468 MET cc_start: 0.6352 (mtm) cc_final: 0.6020 (mtm) REVERT: A 528 LEU cc_start: 0.6040 (OUTLIER) cc_final: 0.5674 (mm) REVERT: A 702 MET cc_start: 0.7334 (ptt) cc_final: 0.7093 (ptt) REVERT: B 594 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7575 (mm) REVERT: B 751 ASN cc_start: 0.7700 (t0) cc_final: 0.7349 (t0) REVERT: B 823 ARG cc_start: 0.7295 (OUTLIER) cc_final: 0.6622 (tpt170) outliers start: 28 outliers final: 17 residues processed: 121 average time/residue: 0.2399 time to fit residues: 41.1729 Evaluate side-chains 120 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 99 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 GLN 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 A residue 838 VAL Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 515 GLU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 656 ASN Chi-restraints excluded: chain B residue 704 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 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 ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 3.9990 chunk 117 optimal weight: 0.1980 chunk 25 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 130 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 68 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10683 Z= 0.291 Angle : 0.582 8.151 14499 Z= 0.298 Chirality : 0.043 0.169 1584 Planarity : 0.004 0.051 1890 Dihedral : 4.412 22.106 1493 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 3.05 % Allowed : 17.25 % Favored : 79.69 % 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: -1.75 (0.23), residues: 1338 helix: -0.52 (0.28), residues: 371 sheet: -2.59 (0.43), residues: 122 loop : -1.25 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 736 HIS 0.007 0.001 HIS A 677 PHE 0.014 0.002 PHE A 696 TYR 0.024 0.001 TYR B 624 ARG 0.004 0.000 ARG A 497 *********************** REFINEMENT MACRO_CYCLE 6 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 fitting. rotamer outliers: 32 poor density : 102 time to evaluate : 1.235 Fit side-chains REVERT: A 415 GLN cc_start: 0.5635 (OUTLIER) cc_final: 0.5213 (pt0) REVERT: A 468 MET cc_start: 0.6350 (mtm) cc_final: 0.5923 (mtm) REVERT: A 528 LEU cc_start: 0.5856 (OUTLIER) cc_final: 0.5567 (mm) REVERT: A 702 MET cc_start: 0.7480 (ptt) cc_final: 0.7111 (ptt) REVERT: A 708 ARG cc_start: 0.7348 (mpt-90) cc_final: 0.7135 (mpt180) REVERT: B 594 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7508 (mm) REVERT: B 751 ASN cc_start: 0.7843 (t0) cc_final: 0.7515 (t0) REVERT: B 823 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.6648 (tpt170) outliers start: 32 outliers final: 25 residues processed: 121 average time/residue: 0.2516 time to fit residues: 42.4842 Evaluate side-chains 129 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 100 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 GLN Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 803 THR 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 438 CYS Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 515 GLU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 656 ASN 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 823 ARG Chi-restraints excluded: chain B residue 853 GLU 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 681 TYR Chi-restraints excluded: chain D residue 700 VAL Chi-restraints excluded: chain D residue 706 ASP Chi-restraints excluded: chain D residue 836 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 chunk 73 optimal weight: 0.8980 chunk 109 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 130 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 79 optimal weight: 0.3980 chunk 60 optimal weight: 2.9990 chunk 80 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10683 Z= 0.166 Angle : 0.512 8.561 14499 Z= 0.263 Chirality : 0.040 0.146 1584 Planarity : 0.004 0.049 1890 Dihedral : 4.104 19.409 1493 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.67 % Allowed : 17.92 % Favored : 79.41 % 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: -1.61 (0.23), residues: 1338 helix: -0.38 (0.28), residues: 373 sheet: -2.50 (0.43), residues: 123 loop : -1.16 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 736 HIS 0.007 0.001 HIS A 533 PHE 0.015 0.001 PHE A 549 TYR 0.014 0.001 TYR B 624 ARG 0.005 0.000 ARG D 712 *********************** REFINEMENT MACRO_CYCLE 7 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 131 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 103 time to evaluate : 1.174 Fit side-chains REVERT: A 415 GLN cc_start: 0.5566 (OUTLIER) cc_final: 0.4655 (pt0) REVERT: A 528 LEU cc_start: 0.5785 (OUTLIER) cc_final: 0.5537 (mm) REVERT: A 702 MET cc_start: 0.7544 (ptt) cc_final: 0.7240 (ptt) REVERT: A 708 ARG cc_start: 0.7365 (mpt-90) cc_final: 0.7159 (mpt180) REVERT: B 594 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7606 (mm) REVERT: B 751 ASN cc_start: 0.7878 (t0) cc_final: 0.7622 (t0) REVERT: B 823 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6633 (tpt170) outliers start: 28 outliers final: 22 residues processed: 121 average time/residue: 0.2597 time to fit residues: 43.4274 Evaluate side-chains 128 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 102 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 GLN Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 515 GLU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 656 ASN 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 823 ARG Chi-restraints excluded: chain B residue 853 GLU Chi-restraints excluded: chain C residue 646 ILE 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 681 TYR Chi-restraints excluded: chain D residue 700 VAL Chi-restraints excluded: chain D residue 836 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 0.0980 chunk 77 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 25 optimal weight: 2.9990 chunk 82 optimal weight: 0.0470 chunk 88 optimal weight: 8.9990 chunk 64 optimal weight: 0.6980 chunk 12 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 118 optimal weight: 0.0020 chunk 124 optimal weight: 0.7980 overall best weight: 0.2686 ------------------------------------------------------------------------------- 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 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10683 Z= 0.135 Angle : 0.484 8.732 14499 Z= 0.248 Chirality : 0.039 0.141 1584 Planarity : 0.004 0.048 1890 Dihedral : 3.790 16.247 1493 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.57 % Allowed : 18.30 % Favored : 79.12 % 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: -1.43 (0.23), residues: 1338 helix: -0.14 (0.29), residues: 373 sheet: -2.34 (0.43), residues: 124 loop : -1.11 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 736 HIS 0.008 0.001 HIS A 533 PHE 0.020 0.001 PHE D 675 TYR 0.012 0.001 TYR A 849 ARG 0.005 0.000 ARG D 712 *********************** REFINEMENT MACRO_CYCLE 8 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 132 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 105 time to evaluate : 1.145 Fit side-chains REVERT: A 528 LEU cc_start: 0.6022 (OUTLIER) cc_final: 0.5707 (mm) REVERT: A 702 MET cc_start: 0.7491 (ptt) cc_final: 0.7228 (ptt) REVERT: B 594 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7544 (mm) REVERT: B 751 ASN cc_start: 0.7846 (t0) cc_final: 0.7632 (t0) REVERT: B 823 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.6619 (tpt170) outliers start: 27 outliers final: 21 residues processed: 122 average time/residue: 0.2475 time to fit residues: 42.9995 Evaluate side-chains 128 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 104 time to evaluate : 2.937 ------------------------------------------------------------------------------- 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 803 THR Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 697 GLU 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 823 ARG Chi-restraints excluded: chain B residue 853 GLU 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 681 TYR Chi-restraints excluded: chain D residue 700 VAL Chi-restraints excluded: chain D residue 836 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 2.9990 chunk 121 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 109 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 820 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 621 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.1421 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= 0.234 Angle : 0.545 8.545 14499 Z= 0.278 Chirality : 0.041 0.157 1584 Planarity : 0.004 0.048 1890 Dihedral : 4.124 19.339 1493 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.05 % Allowed : 18.02 % Favored : 78.93 % 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: -0.35 (0.28), residues: 377 sheet: -2.36 (0.43), residues: 123 loop : -1.17 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 736 HIS 0.011 0.001 HIS A 533 PHE 0.014 0.001 PHE A 549 TYR 0.021 0.001 TYR B 624 ARG 0.005 0.000 ARG C 461 *********************** REFINEMENT MACRO_CYCLE 9 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 135 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 103 time to evaluate : 1.191 Fit side-chains revert: symmetry clash REVERT: A 415 GLN cc_start: 0.5449 (OUTLIER) cc_final: 0.5100 (pt0) REVERT: A 702 MET cc_start: 0.7607 (ptt) cc_final: 0.7280 (ptt) REVERT: A 708 ARG cc_start: 0.7346 (mpt-90) cc_final: 0.7040 (mpt180) REVERT: B 594 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7596 (mm) REVERT: B 823 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.6630 (tpt170) outliers start: 32 outliers final: 25 residues processed: 124 average time/residue: 0.2482 time to fit residues: 42.9586 Evaluate side-chains 130 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 102 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 GLN Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 803 THR 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 438 CYS Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 515 GLU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 697 GLU 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 823 ARG Chi-restraints excluded: chain B residue 853 GLU Chi-restraints excluded: chain C residue 646 ILE 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 681 TYR Chi-restraints excluded: chain D residue 700 VAL Chi-restraints excluded: chain D residue 836 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 89 optimal weight: 0.2980 chunk 134 optimal weight: 1.9990 chunk 123 optimal weight: 30.0000 chunk 107 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.1465 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= 0.194 Angle : 0.547 15.783 14499 Z= 0.274 Chirality : 0.040 0.156 1584 Planarity : 0.004 0.050 1890 Dihedral : 4.085 19.245 1493 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.67 % Allowed : 18.59 % Favored : 78.74 % 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: -1.57 (0.23), residues: 1338 helix: -0.34 (0.28), residues: 379 sheet: -2.33 (0.43), residues: 123 loop : -1.18 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 694 HIS 0.011 0.001 HIS A 533 PHE 0.013 0.001 PHE D 675 TYR 0.017 0.001 TYR B 624 ARG 0.005 0.000 ARG C 461 ********************** REFINEMENT MACRO_CYCLE 10 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 129 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 101 time to evaluate : 1.126 Fit side-chains revert: symmetry clash REVERT: A 415 GLN cc_start: 0.5461 (OUTLIER) cc_final: 0.5097 (pt0) REVERT: A 549 PHE cc_start: 0.6332 (t80) cc_final: 0.6119 (t80) REVERT: A 702 MET cc_start: 0.7596 (ptt) cc_final: 0.7267 (ptt) REVERT: A 708 ARG cc_start: 0.7311 (mpt-90) cc_final: 0.7020 (mpt180) REVERT: B 594 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7635 (mm) REVERT: B 823 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.6628 (tpt170) outliers start: 28 outliers final: 24 residues processed: 118 average time/residue: 0.2583 time to fit residues: 42.3151 Evaluate side-chains 128 residues out of total 1185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 101 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 GLN Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 803 THR 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 438 CYS Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 515 GLU 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 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 646 ILE 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 681 TYR Chi-restraints excluded: chain D residue 700 VAL Chi-restraints excluded: chain D residue 836 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 98 optimal weight: 20.0000 chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 0.1980 chunk 94 optimal weight: 30.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.197405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.138893 restraints weight = 13091.884| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 3.31 r_work: 0.3523 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10683 Z= 0.183 Angle : 0.536 13.527 14499 Z= 0.269 Chirality : 0.040 0.153 1584 Planarity : 0.004 0.049 1890 Dihedral : 4.024 20.653 1493 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 2.86 % Allowed : 18.49 % Favored : 78.65 % 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: -1.49 (0.23), residues: 1338 helix: -0.23 (0.28), residues: 373 sheet: -2.23 (0.43), residues: 123 loop : -1.16 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 736 HIS 0.011 0.001 HIS A 533 PHE 0.013 0.001 PHE D 675 TYR 0.015 0.001 TYR B 624 ARG 0.005 0.000 ARG C 461 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2623.39 seconds wall clock time: 48 minutes 2.92 seconds (2882.92 seconds total)