Starting phenix.real_space_refine on Wed Mar 4 09:52:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e0g_47355/03_2026/9e0g_47355.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e0g_47355/03_2026/9e0g_47355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e0g_47355/03_2026/9e0g_47355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e0g_47355/03_2026/9e0g_47355.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e0g_47355/03_2026/9e0g_47355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e0g_47355/03_2026/9e0g_47355.map" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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 110 5.16 5 C 7739 2.51 5 N 2144 2.21 5 O 2157 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12159 Number of models: 1 Model: "" Number of chains: 7 Chain: "L" Number of atoms: 2777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2777 Classifications: {'peptide': 348} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 332} Chain breaks: 2 Chain: "X" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1495 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 10, 'TRANS': 173} Chain breaks: 4 Chain: "W" Number of atoms: 3400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3400 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 22, 'TRANS': 400} Chain breaks: 2 Chain: "K" Number of atoms: 4426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4426 Classifications: {'peptide': 552} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 520} Chain breaks: 3 Chain: "L" 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: "W" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "K" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 163 SG CYS L 415 75.666 74.662 50.985 1.00235.57 S ATOM 183 SG CYS L 418 75.109 73.340 54.576 1.00236.86 S ATOM 313 SG CYS L 435 74.720 71.102 52.110 1.00191.66 S ATOM 335 SG CYS L 438 72.068 72.985 52.065 1.00177.43 S ATOM 517 SG CYS L 458 66.313 80.988 46.908 1.00218.84 S ATOM 537 SG CYS L 461 67.448 79.703 50.279 1.00227.28 S ATOM 679 SG CYS L 480 66.620 83.309 49.775 1.00258.25 S ATOM 701 SG CYS L 483 69.668 82.697 49.004 1.00272.01 S ATOM 606 SG CYS L 470 60.920 85.965 36.339 1.00195.12 S ATOM 639 SG CYS L 475 62.020 82.108 35.207 1.00212.44 S ATOM 854 SG CYS L 504 64.194 84.467 36.619 1.00227.51 S ATOM 880 SG CYS L 507 63.549 84.716 33.082 1.00213.82 S ATOM 4439 SG CYS W 494 25.363 54.420 60.169 1.00279.92 S ATOM 4459 SG CYS W 497 26.842 58.189 59.166 1.00300.63 S ATOM 4581 SG CYS W 514 27.839 55.016 57.056 1.00264.58 S ATOM 4604 SG CYS W 517 29.003 55.655 59.806 1.00249.60 S ATOM 4772 SG CYS W 537 30.589 55.949 70.909 1.00256.13 S ATOM 4793 SG CYS W 540 30.208 57.907 67.471 1.00267.29 S ATOM 4930 SG CYS W 559 29.368 59.467 71.032 1.00286.84 S ATOM 4952 SG CYS W 562 27.215 57.786 69.387 1.00303.95 S ATOM 4856 SG CYS W 549 32.230 49.380 81.684 1.00233.89 S ATOM 4890 SG CYS W 554 33.628 46.999 79.279 1.00234.21 S ATOM 5099 SG CYS W 583 30.236 48.341 78.865 1.00283.69 S ATOM 5125 SG CYS W 586 30.806 45.335 80.550 1.00277.46 S ATOM 8886 SG CYS K 494 114.043 50.948 104.488 1.00236.79 S ATOM 8906 SG CYS K 497 112.943 54.930 105.420 1.00246.84 S ATOM 9028 SG CYS K 514 111.624 51.796 107.412 1.00225.95 S ATOM 9051 SG CYS K 517 110.596 52.666 104.658 1.00244.76 S ATOM 9219 SG CYS K 537 109.434 53.164 93.404 1.00235.07 S ATOM 9240 SG CYS K 540 109.980 54.953 96.953 1.00219.27 S ATOM 9377 SG CYS K 559 111.137 56.301 93.428 1.00254.05 S ATOM 9399 SG CYS K 562 113.081 54.432 95.146 1.00249.37 S ATOM 9303 SG CYS K 549 107.374 46.826 82.665 1.00270.90 S ATOM 9337 SG CYS K 554 105.610 44.578 85.080 1.00259.01 S ATOM 9550 SG CYS K 583 109.201 45.457 85.474 1.00273.79 S ATOM 9576 SG CYS K 586 108.231 42.663 83.886 1.00285.79 S Time building chain proxies: 2.65, per 1000 atoms: 0.22 Number of scatterers: 12159 At special positions: 0 Unit cell: (140.76, 106.812, 163.944, 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 110 16.00 O 2157 8.00 N 2144 7.00 C 7739 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 484.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K1001 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 494 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 517 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 497 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 514 " pdb=" ZN K1002 " pdb="ZN ZN K1002 " - pdb=" SG CYS K 537 " pdb="ZN ZN K1002 " - pdb=" SG CYS K 562 " pdb="ZN ZN K1002 " - pdb=" SG CYS K 559 " pdb="ZN ZN K1002 " - pdb=" SG CYS K 540 " pdb=" ZN K1003 " pdb="ZN ZN K1003 " - pdb=" SG CYS K 583 " pdb="ZN ZN K1003 " - pdb=" SG CYS K 554 " pdb="ZN ZN K1003 " - pdb=" SG CYS K 549 " pdb="ZN ZN K1003 " - pdb=" SG CYS K 586 " pdb=" ZN L1001 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 438 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 435 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 418 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 415 " pdb=" ZN L1002 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 461 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 480 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 483 " pdb="ZN ZN L1002 " - pdb=" SG CYS L 458 " pdb=" ZN L1003 " pdb="ZN ZN L1003 " - pdb=" SG CYS L 504 " pdb="ZN ZN L1003 " - pdb=" SG CYS L 470 " pdb="ZN ZN L1003 " - pdb=" SG CYS L 475 " pdb="ZN ZN L1003 " - pdb=" SG CYS L 507 " pdb=" ZN W1001 " pdb="ZN ZN W1001 " - pdb=" SG CYS W 517 " pdb="ZN ZN W1001 " - pdb=" SG CYS W 494 " pdb="ZN ZN W1001 " - pdb=" SG CYS W 497 " pdb="ZN ZN W1001 " - pdb=" SG CYS W 514 " pdb=" ZN W1002 " pdb="ZN ZN W1002 " - pdb=" SG CYS W 562 " pdb="ZN ZN W1002 " - pdb=" SG CYS W 537 " pdb="ZN ZN W1002 " - pdb=" SG CYS W 540 " pdb="ZN ZN W1002 " - pdb=" SG CYS W 559 " pdb=" ZN W1003 " pdb="ZN ZN W1003 " - pdb=" SG CYS W 583 " pdb="ZN ZN W1003 " - pdb=" SG CYS W 554 " pdb="ZN ZN W1003 " - pdb=" SG CYS W 549 " pdb="ZN ZN W1003 " - pdb=" SG CYS W 586 " Number of angles added : 54 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2774 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 17 sheets defined 40.3% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'L' and resid 396 through 407 removed outlier: 4.241A pdb=" N ALA L 405 " --> pdb=" O ALA L 401 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN L 406 " --> pdb=" O SER L 402 " (cutoff:3.500A) Processing helix chain 'L' and resid 435 through 445 removed outlier: 3.558A pdb=" N GLU L 444 " --> pdb=" O ASP L 440 " (cutoff:3.500A) Processing helix chain 'L' and resid 481 through 488 removed outlier: 3.554A pdb=" N VAL L 488 " --> pdb=" O LEU L 484 " (cutoff:3.500A) Processing helix chain 'L' and resid 491 through 499 removed outlier: 3.871A pdb=" N LEU L 498 " --> pdb=" O ALA L 494 " (cutoff:3.500A) Processing helix chain 'L' and resid 521 through 532 removed outlier: 3.713A pdb=" N PHE L 530 " --> pdb=" O LEU L 526 " (cutoff:3.500A) Processing helix chain 'L' and resid 565 through 575 removed outlier: 3.515A pdb=" N LEU L 569 " --> pdb=" O ALA L 565 " (cutoff:3.500A) Processing helix chain 'L' and resid 588 through 599 removed outlier: 3.779A pdb=" N ALA L 592 " --> pdb=" O GLU L 588 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL L 596 " --> pdb=" O ALA L 592 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LYS L 597 " --> pdb=" O VAL L 593 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N HIS L 598 " --> pdb=" O GLY L 594 " (cutoff:3.500A) Processing helix chain 'L' and resid 607 through 611 removed outlier: 3.657A pdb=" N ILE L 611 " --> pdb=" O VAL L 608 " (cutoff:3.500A) Processing helix chain 'L' and resid 613 through 619 removed outlier: 4.380A pdb=" N GLU L 617 " --> pdb=" O LYS L 613 " (cutoff:3.500A) Processing helix chain 'L' and resid 643 through 663 Processing helix chain 'L' and resid 683 through 695 Processing helix chain 'L' and resid 741 through 748 removed outlier: 3.522A pdb=" N LYS L 745 " --> pdb=" O GLY L 741 " (cutoff:3.500A) Processing helix chain 'L' and resid 751 through 761 removed outlier: 3.810A pdb=" N VAL L 755 " --> pdb=" O TRP L 751 " (cutoff:3.500A) Processing helix chain 'L' and resid 762 through 764 No H-bonds generated for 'chain 'L' and resid 762 through 764' Processing helix chain 'X' and resid 565 through 575 removed outlier: 3.560A pdb=" N LEU X 569 " --> pdb=" O ALA X 565 " (cutoff:3.500A) Processing helix chain 'X' and resid 587 through 598 removed outlier: 3.720A pdb=" N ILE X 591 " --> pdb=" O CYS X 587 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA X 592 " --> pdb=" O GLU X 588 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS X 597 " --> pdb=" O VAL X 593 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N HIS X 598 " --> pdb=" O GLY X 594 " (cutoff:3.500A) Processing helix chain 'X' and resid 607 through 611 removed outlier: 3.575A pdb=" N ASN X 610 " --> pdb=" O ASP X 607 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE X 611 " --> pdb=" O VAL X 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 607 through 611' Processing helix chain 'X' and resid 612 through 620 removed outlier: 3.660A pdb=" N TRP X 619 " --> pdb=" O ASN X 615 " (cutoff:3.500A) Processing helix chain 'X' and resid 641 through 662 removed outlier: 3.778A pdb=" N PHE X 652 " --> pdb=" O THR X 648 " (cutoff:3.500A) Processing helix chain 'X' and resid 683 through 694 Processing helix chain 'X' and resid 752 through 760 removed outlier: 3.594A pdb=" N ILE X 756 " --> pdb=" O SER X 752 " (cutoff:3.500A) Processing helix chain 'X' and resid 760 through 767 Processing helix chain 'W' and resid 477 through 485 removed outlier: 3.759A pdb=" N TYR W 481 " --> pdb=" O GLU W 477 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU W 482 " --> pdb=" O ARG W 478 " (cutoff:3.500A) Processing helix chain 'W' and resid 489 through 493 removed outlier: 3.529A pdb=" N ILE W 493 " --> pdb=" O ILE W 490 " (cutoff:3.500A) Processing helix chain 'W' and resid 514 through 525 Processing helix chain 'W' and resid 560 through 567 removed outlier: 3.542A pdb=" N ASP W 564 " --> pdb=" O VAL W 560 " (cutoff:3.500A) Processing helix chain 'W' and resid 570 through 578 Processing helix chain 'W' and resid 600 through 613 removed outlier: 3.863A pdb=" N PHE W 609 " --> pdb=" O LEU W 605 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA W 610 " --> pdb=" O GLN W 606 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N HIS W 613 " --> pdb=" O PHE W 609 " (cutoff:3.500A) Processing helix chain 'W' and resid 627 through 631 removed outlier: 3.673A pdb=" N ARG W 631 " --> pdb=" O ALA W 628 " (cutoff:3.500A) Processing helix chain 'W' and resid 644 through 654 Processing helix chain 'W' and resid 666 through 677 Processing helix chain 'W' and resid 691 through 698 Processing helix chain 'W' and resid 725 through 728 Processing helix chain 'W' and resid 729 through 742 Processing helix chain 'W' and resid 762 through 774 Processing helix chain 'W' and resid 814 through 819 removed outlier: 3.766A pdb=" N CYS W 818 " --> pdb=" O GLU W 814 " (cutoff:3.500A) Processing helix chain 'W' and resid 860 through 868 Processing helix chain 'W' and resid 881 through 892 Processing helix chain 'W' and resid 894 through 903 Processing helix chain 'W' and resid 904 through 908 Processing helix chain 'K' and resid 82 through 88 Processing helix chain 'K' and resid 88 through 107 removed outlier: 3.647A pdb=" N ARG K 92 " --> pdb=" O GLN K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 125 through 138 Proline residue: K 131 - end of helix removed outlier: 3.570A pdb=" N GLY K 138 " --> pdb=" O GLU K 134 " (cutoff:3.500A) Processing helix chain 'K' and resid 143 through 148 removed outlier: 3.907A pdb=" N LYS K 146 " --> pdb=" O SER K 143 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY K 147 " --> pdb=" O GLY K 144 " (cutoff:3.500A) Processing helix chain 'K' and resid 477 through 485 removed outlier: 3.830A pdb=" N TYR K 481 " --> pdb=" O GLU K 477 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU K 482 " --> pdb=" O ARG K 478 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL K 483 " --> pdb=" O LEU K 479 " (cutoff:3.500A) Processing helix chain 'K' and resid 489 through 493 Processing helix chain 'K' and resid 514 through 525 Processing helix chain 'K' and resid 560 through 566 Processing helix chain 'K' and resid 570 through 578 Processing helix chain 'K' and resid 600 through 613 removed outlier: 3.728A pdb=" N ALA K 610 " --> pdb=" O GLN K 606 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N HIS K 613 " --> pdb=" O PHE K 609 " (cutoff:3.500A) Processing helix chain 'K' and resid 627 through 631 Processing helix chain 'K' and resid 644 through 654 removed outlier: 3.630A pdb=" N LEU K 648 " --> pdb=" O ALA K 644 " (cutoff:3.500A) Processing helix chain 'K' and resid 666 through 677 Processing helix chain 'K' and resid 686 through 690 Processing helix chain 'K' and resid 691 through 698 Processing helix chain 'K' and resid 729 through 742 removed outlier: 3.525A pdb=" N GLU K 733 " --> pdb=" O ARG K 729 " (cutoff:3.500A) Processing helix chain 'K' and resid 762 through 774 Processing helix chain 'K' and resid 814 through 819 removed outlier: 3.719A pdb=" N CYS K 818 " --> pdb=" O GLU K 814 " (cutoff:3.500A) Processing helix chain 'K' and resid 860 through 868 Processing helix chain 'K' and resid 881 through 892 removed outlier: 3.505A pdb=" N SER K 892 " --> pdb=" O LEU K 888 " (cutoff:3.500A) Processing helix chain 'K' and resid 894 through 903 Processing helix chain 'K' and resid 904 through 906 No H-bonds generated for 'chain 'K' and resid 904 through 906' Processing sheet with id=AA1, first strand: chain 'L' and resid 467 through 469 Processing sheet with id=AA2, first strand: chain 'L' and resid 512 through 513 removed outlier: 3.578A pdb=" N LEU L 516 " --> pdb=" O HIS L 513 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 604 through 605 removed outlier: 7.649A pdb=" N ALA L 583 " --> pdb=" O VAL L 605 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL L 582 " --> pdb=" O VAL L 557 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER L 559 " --> pdb=" O VAL L 582 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER L 584 " --> pdb=" O SER L 559 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL L 625 " --> pdb=" O MET L 675 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 678 through 679 Processing sheet with id=AA5, first strand: chain 'X' and resid 578 through 584 removed outlier: 7.223A pdb=" N ILE X 555 " --> pdb=" O GLY X 579 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N TYR X 581 " --> pdb=" O ILE X 555 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VAL X 557 " --> pdb=" O TYR X 581 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ALA X 583 " --> pdb=" O VAL X 557 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N SER X 559 " --> pdb=" O ALA X 583 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ARG X 556 " --> pdb=" O LEU X 624 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ILE X 626 " --> pdb=" O ARG X 556 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LEU X 558 " --> pdb=" O ILE X 626 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU X 677 " --> pdb=" O GLY X 627 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'W' and resid 504 through 505 Processing sheet with id=AA7, first strand: chain 'W' and resid 546 through 548 Processing sheet with id=AA8, first strand: chain 'W' and resid 591 through 592 Processing sheet with id=AA9, first strand: chain 'W' and resid 682 through 684 removed outlier: 8.974A pdb=" N MET W 682 " --> pdb=" O ASP W 658 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TYR W 660 " --> pdb=" O MET W 682 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N VAL W 684 " --> pdb=" O TYR W 660 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ALA W 662 " --> pdb=" O VAL W 684 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ILE W 634 " --> pdb=" O ASP W 658 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N TYR W 660 " --> pdb=" O ILE W 634 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL W 636 " --> pdb=" O TYR W 660 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ALA W 662 " --> pdb=" O VAL W 636 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N SER W 638 " --> pdb=" O ALA W 662 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL W 704 " --> pdb=" O LEU W 754 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N GLU W 756 " --> pdb=" O VAL W 704 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N GLY W 706 " --> pdb=" O GLU W 756 " (cutoff:3.500A) removed outlier: 9.761A pdb=" N VAL W 758 " --> pdb=" O GLY W 706 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'W' and resid 788 through 789 Processing sheet with id=AB2, first strand: chain 'W' and resid 823 through 825 removed outlier: 4.359A pdb=" N VAL W 850 " --> pdb=" O ASP W 857 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 61 through 66 removed outlier: 3.602A pdb=" N LYS K 61 " --> pdb=" O TRP K 56 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N SER K 30 " --> pdb=" O LEU K 26 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LEU K 26 " --> pdb=" O SER K 30 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 504 through 505 Processing sheet with id=AB5, first strand: chain 'K' and resid 546 through 548 Processing sheet with id=AB6, first strand: chain 'K' and resid 591 through 592 Processing sheet with id=AB7, first strand: chain 'K' and resid 682 through 684 removed outlier: 7.395A pdb=" N ILE K 634 " --> pdb=" O ASP K 658 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N TYR K 660 " --> pdb=" O ILE K 634 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N VAL K 636 " --> pdb=" O TYR K 660 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ALA K 662 " --> pdb=" O VAL K 636 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N SER K 638 " --> pdb=" O ALA K 662 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ARG K 635 " --> pdb=" O LEU K 703 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ILE K 705 " --> pdb=" O ARG K 635 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU K 637 " --> pdb=" O ILE K 705 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N GLY K 707 " --> pdb=" O LEU K 637 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N LEU K 639 " --> pdb=" O GLY K 707 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL K 704 " --> pdb=" O LEU K 754 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N GLU K 756 " --> pdb=" O VAL K 704 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLY K 706 " --> pdb=" O GLU K 756 " (cutoff:3.500A) removed outlier: 9.827A pdb=" N VAL K 758 " --> pdb=" O GLY K 706 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 823 through 825 removed outlier: 4.350A pdb=" N VAL K 850 " --> pdb=" O ASP K 857 " (cutoff:3.500A) 392 hydrogen bonds defined for protein. 1107 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: 1.71 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3173 1.34 - 1.46: 2309 1.46 - 1.58: 6822 1.58 - 1.70: 0 1.70 - 1.82: 151 Bond restraints: 12455 Sorted by residual: bond pdb=" N VAL K 665 " pdb=" CA VAL K 665 " ideal model delta sigma weight residual 1.456 1.494 -0.037 9.50e-03 1.11e+04 1.54e+01 bond pdb=" N VAL W 665 " pdb=" CA VAL W 665 " ideal model delta sigma weight residual 1.456 1.492 -0.036 9.50e-03 1.11e+04 1.40e+01 bond pdb=" N ASN L 422 " pdb=" CA ASN L 422 " ideal model delta sigma weight residual 1.457 1.490 -0.034 9.10e-03 1.21e+04 1.39e+01 bond pdb=" N VAL W 785 " pdb=" CA VAL W 785 " ideal model delta sigma weight residual 1.452 1.494 -0.042 1.18e-02 7.18e+03 1.26e+01 bond pdb=" N VAL K 684 " pdb=" CA VAL K 684 " ideal model delta sigma weight residual 1.456 1.495 -0.038 1.14e-02 7.69e+03 1.13e+01 ... (remaining 12450 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 12059 1.55 - 3.11: 4277 3.11 - 4.66: 464 4.66 - 6.21: 12 6.21 - 7.77: 4 Bond angle restraints: 16816 Sorted by residual: angle pdb=" C LYS X 642 " pdb=" N GLY X 643 " pdb=" CA GLY X 643 " ideal model delta sigma weight residual 119.98 124.62 -4.64 1.11e+00 8.12e-01 1.75e+01 angle pdb=" C TYR W 623 " pdb=" N PRO W 624 " pdb=" CA PRO W 624 " ideal model delta sigma weight residual 119.66 122.60 -2.94 7.20e-01 1.93e+00 1.66e+01 angle pdb=" C GLY X 649 " pdb=" N ARG X 650 " pdb=" CA ARG X 650 " ideal model delta sigma weight residual 120.28 125.67 -5.39 1.34e+00 5.57e-01 1.62e+01 angle pdb=" C THR K 645 " pdb=" N GLY K 646 " pdb=" CA GLY K 646 " ideal model delta sigma weight residual 119.98 124.44 -4.46 1.11e+00 8.12e-01 1.61e+01 angle pdb=" C THR W 645 " pdb=" N GLY W 646 " pdb=" CA GLY W 646 " ideal model delta sigma weight residual 120.03 124.52 -4.49 1.12e+00 7.97e-01 1.61e+01 ... (remaining 16811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.73: 7058 14.73 - 29.45: 275 29.45 - 44.18: 51 44.18 - 58.90: 5 58.90 - 73.63: 2 Dihedral angle restraints: 7391 sinusoidal: 3067 harmonic: 4324 Sorted by residual: dihedral pdb=" CA GLU W 523 " pdb=" C GLU W 523 " pdb=" N CYS W 524 " pdb=" CA CYS W 524 " ideal model delta harmonic sigma weight residual -180.00 -156.30 -23.70 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA TRP X 751 " pdb=" C TRP X 751 " pdb=" N SER X 752 " pdb=" CA SER X 752 " ideal model delta harmonic sigma weight residual 180.00 -160.99 -19.01 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA LEU K 504 " pdb=" C LEU K 504 " pdb=" N GLU K 505 " pdb=" CA GLU K 505 " ideal model delta harmonic sigma weight residual 180.00 161.81 18.19 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 7388 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 728 0.045 - 0.091: 603 0.091 - 0.136: 317 0.136 - 0.181: 97 0.181 - 0.227: 4 Chirality restraints: 1749 Sorted by residual: chirality pdb=" CG LEU W 566 " pdb=" CB LEU W 566 " pdb=" CD1 LEU W 566 " pdb=" CD2 LEU W 566 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA VAL W 684 " pdb=" N VAL W 684 " pdb=" C VAL W 684 " pdb=" CB VAL W 684 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ILE W 858 " pdb=" N ILE W 858 " pdb=" C ILE W 858 " pdb=" CB ILE W 858 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.66e-01 ... (remaining 1746 not shown) Planarity restraints: 2179 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN L 510 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.37e+00 pdb=" C GLN L 510 " 0.053 2.00e-02 2.50e+03 pdb=" O GLN L 510 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG L 511 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU L 539 " 0.013 2.00e-02 2.50e+03 2.79e-02 7.79e+00 pdb=" C GLU L 539 " -0.048 2.00e-02 2.50e+03 pdb=" O GLU L 539 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA L 540 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE X 652 " 0.016 2.00e-02 2.50e+03 1.21e-02 2.58e+00 pdb=" CG PHE X 652 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE X 652 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE X 652 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE X 652 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE X 652 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE X 652 " 0.004 2.00e-02 2.50e+03 ... (remaining 2176 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 2676 2.85 - 3.36: 11236 3.36 - 3.87: 18660 3.87 - 4.39: 21291 4.39 - 4.90: 36113 Nonbonded interactions: 89976 Sorted by model distance: nonbonded pdb=" O CYS L 415 " pdb=" CA GLY L 419 " model vdw 2.333 3.440 nonbonded pdb=" OH TYR L 661 " pdb=" OE2 GLU W 774 " model vdw 2.336 3.040 nonbonded pdb=" OD2 ASP L 533 " pdb=" O PRO L 698 " model vdw 2.356 3.040 nonbonded pdb=" O ILE W 643 " pdb=" OH TYR W 874 " model vdw 2.380 3.040 nonbonded pdb=" O ARG K 635 " pdb=" N ASP K 702 " model vdw 2.404 3.120 ... (remaining 89971 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 7.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.820 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3770 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 : 0.011 0.083 12491 Z= 0.863 Angle : 1.632 34.362 16870 Z= 1.063 Chirality : 0.074 0.227 1749 Planarity : 0.003 0.035 2179 Dihedral : 8.470 73.628 4617 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.77 (0.17), residues: 1477 helix: -1.89 (0.18), residues: 513 sheet: -1.17 (0.40), residues: 126 loop : -1.93 (0.17), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG W 476 TYR 0.023 0.002 TYR K 584 PHE 0.027 0.002 PHE X 652 TRP 0.018 0.002 TRP K 32 HIS 0.006 0.001 HIS X 657 Details of bonding type rmsd covalent geometry : bond 0.01140 (12455) covalent geometry : angle 1.40577 (16816) hydrogen bonds : bond 0.18267 ( 392) hydrogen bonds : angle 7.77552 ( 1107) metal coordination : bond 0.02608 ( 36) metal coordination : angle 14.71180 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 508 LEU cc_start: 0.7384 (mt) cc_final: 0.7175 (mt) REVERT: L 584 SER cc_start: 0.5808 (p) cc_final: 0.5394 (t) REVERT: L 656 TYR cc_start: 0.5854 (t80) cc_final: 0.5569 (t80) REVERT: L 659 LEU cc_start: 0.7162 (tp) cc_final: 0.6946 (tp) REVERT: L 688 ARG cc_start: 0.7524 (mtt180) cc_final: 0.7287 (mtt180) REVERT: L 693 PHE cc_start: 0.6567 (m-80) cc_final: 0.5773 (m-80) REVERT: L 694 LEU cc_start: 0.6284 (tp) cc_final: 0.5650 (tp) REVERT: L 714 TYR cc_start: 0.4461 (p90) cc_final: 0.4248 (p90) REVERT: X 653 PHE cc_start: 0.7549 (m-80) cc_final: 0.7299 (m-10) REVERT: X 676 PHE cc_start: 0.6962 (t80) cc_final: 0.6300 (t80) REVERT: W 637 LEU cc_start: 0.7514 (tp) cc_final: 0.7277 (tp) REVERT: W 648 LEU cc_start: 0.8278 (tp) cc_final: 0.8072 (tp) REVERT: W 667 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6981 (mm-30) REVERT: W 733 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7250 (mm-30) REVERT: W 737 LEU cc_start: 0.7888 (mt) cc_final: 0.7326 (mt) REVERT: W 740 ASP cc_start: 0.6929 (m-30) cc_final: 0.6645 (t0) REVERT: W 761 MET cc_start: 0.4268 (ptm) cc_final: 0.3933 (ptm) REVERT: W 864 MET cc_start: 0.7987 (ttm) cc_final: 0.7381 (ttm) REVERT: W 875 THR cc_start: 0.6581 (m) cc_final: 0.6248 (m) REVERT: W 886 GLN cc_start: 0.8303 (mt0) cc_final: 0.7862 (mp10) REVERT: W 899 ARG cc_start: 0.7650 (ttt90) cc_final: 0.7336 (ttt90) REVERT: K 41 MET cc_start: -0.4166 (mmm) cc_final: -0.4675 (mmm) REVERT: K 637 LEU cc_start: 0.8516 (tp) cc_final: 0.7998 (tp) REVERT: K 674 MET cc_start: 0.7143 (mtp) cc_final: 0.6674 (ptp) REVERT: K 713 LEU cc_start: 0.6918 (mt) cc_final: 0.6222 (mt) REVERT: K 755 PHE cc_start: 0.5155 (t80) cc_final: 0.3815 (t80) REVERT: K 761 MET cc_start: -0.0387 (ptm) cc_final: -0.0997 (ptm) REVERT: K 797 ASN cc_start: 0.6207 (p0) cc_final: 0.5790 (p0) REVERT: K 870 PHE cc_start: 0.6455 (m-80) cc_final: 0.6212 (m-80) REVERT: K 882 ARG cc_start: 0.8259 (ptt90) cc_final: 0.7525 (ttp80) REVERT: K 901 LEU cc_start: 0.8467 (mt) cc_final: 0.8179 (mt) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.1335 time to fit residues: 45.3771 Evaluate side-chains 228 residues out of total 1303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.0770 chunk 91 optimal weight: 0.2980 chunk 55 optimal weight: 30.0000 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 710 HIS W 900 HIS ** K 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 900 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5278 r_free = 0.5278 target = 0.291262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.5046 r_free = 0.5046 target = 0.257370 restraints weight = 27136.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.5084 r_free = 0.5084 target = 0.262573 restraints weight = 18787.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.5116 r_free = 0.5116 target = 0.266947 restraints weight = 13985.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.5141 r_free = 0.5141 target = 0.270550 restraints weight = 10657.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5152 r_free = 0.5152 target = 0.272163 restraints weight = 8319.939| |-----------------------------------------------------------------------------| r_work (final): 0.5146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3717 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12491 Z= 0.126 Angle : 0.642 10.151 16870 Z= 0.301 Chirality : 0.041 0.158 1749 Planarity : 0.004 0.045 2179 Dihedral : 4.082 17.221 1669 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.77 % Allowed : 5.22 % Favored : 94.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.19), residues: 1477 helix: -0.02 (0.21), residues: 522 sheet: -0.76 (0.43), residues: 121 loop : -1.28 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG W 823 TYR 0.013 0.001 TYR L 447 PHE 0.033 0.001 PHE W 772 TRP 0.022 0.001 TRP W 753 HIS 0.007 0.001 HIS L 657 Details of bonding type rmsd covalent geometry : bond 0.00261 (12455) covalent geometry : angle 0.58060 (16816) hydrogen bonds : bond 0.03947 ( 392) hydrogen bonds : angle 5.24080 ( 1107) metal coordination : bond 0.00634 ( 36) metal coordination : angle 4.88044 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 230 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 584 SER cc_start: 0.5718 (p) cc_final: 0.5406 (t) REVERT: L 656 TYR cc_start: 0.6071 (t80) cc_final: 0.5760 (t80) REVERT: L 694 LEU cc_start: 0.6365 (tp) cc_final: 0.5819 (tp) REVERT: X 676 PHE cc_start: 0.6457 (t80) cc_final: 0.5323 (t80) REVERT: W 648 LEU cc_start: 0.8115 (tp) cc_final: 0.7820 (tp) REVERT: W 667 GLU cc_start: 0.6934 (mm-30) cc_final: 0.6734 (mm-30) REVERT: W 681 ILE cc_start: 0.6166 (mm) cc_final: 0.5350 (mm) REVERT: W 683 TYR cc_start: 0.5484 (m-80) cc_final: 0.5019 (m-80) REVERT: W 737 LEU cc_start: 0.7734 (mt) cc_final: 0.7449 (mt) REVERT: W 740 ASP cc_start: 0.6915 (m-30) cc_final: 0.6686 (t0) REVERT: W 772 PHE cc_start: 0.6261 (m-80) cc_final: 0.5769 (m-80) REVERT: W 864 MET cc_start: 0.7993 (ttm) cc_final: 0.7509 (ttm) REVERT: W 899 ARG cc_start: 0.7605 (ttt90) cc_final: 0.7389 (ttt180) REVERT: K 41 MET cc_start: -0.4152 (mmm) cc_final: -0.4650 (mmm) REVERT: K 637 LEU cc_start: 0.8467 (tp) cc_final: 0.8121 (tp) REVERT: K 639 LEU cc_start: 0.8137 (mt) cc_final: 0.7925 (mt) REVERT: K 674 MET cc_start: 0.6792 (mtp) cc_final: 0.6437 (mtp) REVERT: K 713 LEU cc_start: 0.6720 (mt) cc_final: 0.6371 (mt) REVERT: K 755 PHE cc_start: 0.4526 (t80) cc_final: 0.3869 (t80) REVERT: K 761 MET cc_start: -0.1086 (ptm) cc_final: -0.1922 (ptm) REVERT: K 797 ASN cc_start: 0.5978 (p0) cc_final: 0.5497 (p0) REVERT: K 882 ARG cc_start: 0.7729 (ptt90) cc_final: 0.7043 (ttp80) REVERT: K 901 LEU cc_start: 0.8406 (mt) cc_final: 0.8121 (mt) outliers start: 10 outliers final: 6 residues processed: 232 average time/residue: 0.1342 time to fit residues: 41.7368 Evaluate side-chains 228 residues out of total 1303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 222 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 558 LEU Chi-restraints excluded: chain W residue 754 LEU Chi-restraints excluded: chain W residue 875 THR Chi-restraints excluded: chain K residue 684 VAL Chi-restraints excluded: chain K residue 877 VAL Chi-restraints excluded: chain K residue 883 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 140 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 132 optimal weight: 0.4980 chunk 126 optimal weight: 1.9990 chunk 1 optimal weight: 0.0050 chunk 129 optimal weight: 0.1980 chunk 7 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 117 optimal weight: 0.1980 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 513 HIS K 129 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5282 r_free = 0.5282 target = 0.291979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.5029 r_free = 0.5029 target = 0.256559 restraints weight = 28002.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.5066 r_free = 0.5066 target = 0.261396 restraints weight = 19916.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.5100 r_free = 0.5100 target = 0.265856 restraints weight = 15224.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.5128 r_free = 0.5128 target = 0.269682 restraints weight = 11812.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.5146 r_free = 0.5146 target = 0.272171 restraints weight = 9441.185| |-----------------------------------------------------------------------------| r_work (final): 0.5133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3768 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12491 Z= 0.116 Angle : 0.601 8.227 16870 Z= 0.288 Chirality : 0.040 0.140 1749 Planarity : 0.004 0.036 2179 Dihedral : 3.935 16.498 1669 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.00 % Allowed : 7.75 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.20), residues: 1477 helix: 0.44 (0.22), residues: 527 sheet: -0.47 (0.45), residues: 117 loop : -1.10 (0.19), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG W 767 TYR 0.012 0.001 TYR X 656 PHE 0.041 0.001 PHE L 693 TRP 0.023 0.001 TRP W 795 HIS 0.008 0.001 HIS X 657 Details of bonding type rmsd covalent geometry : bond 0.00247 (12455) covalent geometry : angle 0.55132 (16816) hydrogen bonds : bond 0.03602 ( 392) hydrogen bonds : angle 4.91766 ( 1107) metal coordination : bond 0.00529 ( 36) metal coordination : angle 4.28015 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 225 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 400 MET cc_start: 0.6771 (ptp) cc_final: 0.6110 (tpt) REVERT: L 584 SER cc_start: 0.5815 (p) cc_final: 0.5483 (t) REVERT: L 689 ASP cc_start: 0.6524 (m-30) cc_final: 0.6293 (m-30) REVERT: L 692 ARG cc_start: 0.7334 (mmt180) cc_final: 0.6840 (mmt180) REVERT: W 648 LEU cc_start: 0.8125 (tp) cc_final: 0.7834 (tp) REVERT: W 667 GLU cc_start: 0.7027 (mm-30) cc_final: 0.6744 (mm-30) REVERT: W 683 TYR cc_start: 0.5343 (m-80) cc_final: 0.5015 (m-80) REVERT: W 737 LEU cc_start: 0.7726 (mt) cc_final: 0.7491 (mt) REVERT: W 771 ARG cc_start: 0.7364 (mtm110) cc_final: 0.7116 (mtm-85) REVERT: W 864 MET cc_start: 0.7916 (ttm) cc_final: 0.7549 (ttm) REVERT: W 893 TRP cc_start: 0.5791 (m-10) cc_final: 0.5559 (m-10) REVERT: K 41 MET cc_start: -0.4199 (mmm) cc_final: -0.4688 (mmm) REVERT: K 639 LEU cc_start: 0.8174 (mt) cc_final: 0.7890 (mt) REVERT: K 674 MET cc_start: 0.6931 (mtp) cc_final: 0.6545 (mtp) REVERT: K 713 LEU cc_start: 0.6861 (mt) cc_final: 0.6482 (mt) REVERT: K 755 PHE cc_start: 0.4655 (t80) cc_final: 0.4053 (t80) REVERT: K 761 MET cc_start: -0.0830 (ptm) cc_final: -0.1712 (ptm) REVERT: K 795 TRP cc_start: 0.4080 (m-90) cc_final: 0.3673 (m-90) REVERT: K 882 ARG cc_start: 0.7946 (ptt90) cc_final: 0.7156 (ttp80) REVERT: K 901 LEU cc_start: 0.8435 (mt) cc_final: 0.8159 (mt) outliers start: 13 outliers final: 9 residues processed: 228 average time/residue: 0.1382 time to fit residues: 42.3099 Evaluate side-chains 229 residues out of total 1303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 220 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 659 LEU Chi-restraints excluded: chain X residue 700 MET Chi-restraints excluded: chain W residue 639 LEU Chi-restraints excluded: chain W residue 684 VAL Chi-restraints excluded: chain W residue 754 LEU Chi-restraints excluded: chain W residue 875 THR Chi-restraints excluded: chain K residue 513 MET Chi-restraints excluded: chain K residue 684 VAL Chi-restraints excluded: chain K residue 877 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 44 optimal weight: 0.5980 chunk 141 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 128 optimal weight: 0.0040 chunk 48 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 137 optimal weight: 0.4980 chunk 105 optimal weight: 50.0000 chunk 58 optimal weight: 9.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 515 GLN K 847 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5265 r_free = 0.5265 target = 0.291100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4988 r_free = 0.4988 target = 0.253670 restraints weight = 28018.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.5032 r_free = 0.5032 target = 0.259114 restraints weight = 19454.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.5067 r_free = 0.5067 target = 0.263557 restraints weight = 14411.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.5092 r_free = 0.5092 target = 0.266951 restraints weight = 11165.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.5103 r_free = 0.5103 target = 0.268265 restraints weight = 9011.524| |-----------------------------------------------------------------------------| r_work (final): 0.5090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3988 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12491 Z= 0.131 Angle : 0.613 9.758 16870 Z= 0.298 Chirality : 0.041 0.153 1749 Planarity : 0.004 0.067 2179 Dihedral : 3.974 18.949 1669 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.23 % Allowed : 8.21 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.20), residues: 1477 helix: 0.58 (0.22), residues: 528 sheet: -0.47 (0.46), residues: 116 loop : -0.96 (0.19), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 670 TYR 0.022 0.001 TYR L 714 PHE 0.054 0.002 PHE W 772 TRP 0.032 0.001 TRP W 795 HIS 0.007 0.001 HIS L 657 Details of bonding type rmsd covalent geometry : bond 0.00274 (12455) covalent geometry : angle 0.57149 (16816) hydrogen bonds : bond 0.03499 ( 392) hydrogen bonds : angle 4.95393 ( 1107) metal coordination : bond 0.00466 ( 36) metal coordination : angle 3.95342 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 228 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 400 MET cc_start: 0.6743 (ptp) cc_final: 0.6118 (tpt) REVERT: L 440 ASP cc_start: 0.8216 (m-30) cc_final: 0.7643 (m-30) REVERT: L 584 SER cc_start: 0.5883 (p) cc_final: 0.5516 (t) REVERT: L 674 TRP cc_start: 0.6281 (p90) cc_final: 0.6049 (p90) REVERT: L 686 ASP cc_start: 0.6624 (t0) cc_final: 0.6374 (t0) REVERT: L 692 ARG cc_start: 0.7295 (mmt180) cc_final: 0.6714 (mmt180) REVERT: L 740 ARG cc_start: 0.7112 (ttp-110) cc_final: 0.6875 (ttp-110) REVERT: W 667 GLU cc_start: 0.6920 (mm-30) cc_final: 0.6624 (mm-30) REVERT: W 730 LEU cc_start: 0.7664 (mt) cc_final: 0.7396 (mt) REVERT: W 864 MET cc_start: 0.7703 (ttm) cc_final: 0.7133 (ttm) REVERT: K 41 MET cc_start: -0.4179 (mmm) cc_final: -0.4668 (mmm) REVERT: K 639 LEU cc_start: 0.8048 (mt) cc_final: 0.7822 (mt) REVERT: K 682 MET cc_start: 0.3821 (tmm) cc_final: 0.3453 (tmm) REVERT: K 729 ARG cc_start: 0.4482 (pmt-80) cc_final: 0.3625 (pmt-80) REVERT: K 755 PHE cc_start: 0.4930 (t80) cc_final: 0.3122 (t80) REVERT: K 761 MET cc_start: -0.0894 (ptm) cc_final: -0.1849 (ptm) REVERT: K 795 TRP cc_start: 0.4120 (m-90) cc_final: 0.3356 (m-90) REVERT: K 882 ARG cc_start: 0.7657 (ptt90) cc_final: 0.6942 (ttp80) REVERT: K 901 LEU cc_start: 0.8378 (mt) cc_final: 0.8118 (mt) outliers start: 16 outliers final: 8 residues processed: 233 average time/residue: 0.1296 time to fit residues: 40.7833 Evaluate side-chains 231 residues out of total 1303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 223 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 659 LEU Chi-restraints excluded: chain X residue 700 MET Chi-restraints excluded: chain W residue 639 LEU Chi-restraints excluded: chain W residue 693 LYS Chi-restraints excluded: chain K residue 513 MET Chi-restraints excluded: chain K residue 684 VAL Chi-restraints excluded: chain K residue 767 ARG Chi-restraints excluded: chain K residue 877 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 23 optimal weight: 0.9980 chunk 105 optimal weight: 50.0000 chunk 55 optimal weight: 2.9990 chunk 56 optimal weight: 30.0000 chunk 127 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 116 optimal weight: 0.0030 chunk 66 optimal weight: 0.0470 chunk 140 optimal weight: 0.0570 chunk 96 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 overall best weight: 0.8208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 739 HIS K 757 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5243 r_free = 0.5243 target = 0.289596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4912 r_free = 0.4912 target = 0.245630 restraints weight = 28542.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4958 r_free = 0.4958 target = 0.251067 restraints weight = 19771.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4997 r_free = 0.4997 target = 0.255796 restraints weight = 15173.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.5025 r_free = 0.5025 target = 0.259184 restraints weight = 12096.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.5047 r_free = 0.5047 target = 0.262150 restraints weight = 10014.148| |-----------------------------------------------------------------------------| r_work (final): 0.5034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4270 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 12491 Z= 0.166 Angle : 0.668 11.237 16870 Z= 0.331 Chirality : 0.042 0.176 1749 Planarity : 0.005 0.070 2179 Dihedral : 4.325 23.709 1669 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.46 % Allowed : 8.90 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.21), residues: 1477 helix: 0.49 (0.22), residues: 526 sheet: -0.90 (0.47), residues: 108 loop : -0.78 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG W 885 TYR 0.027 0.001 TYR L 714 PHE 0.053 0.002 PHE L 653 TRP 0.027 0.002 TRP W 795 HIS 0.007 0.001 HIS L 657 Details of bonding type rmsd covalent geometry : bond 0.00337 (12455) covalent geometry : angle 0.62835 (16816) hydrogen bonds : bond 0.03935 ( 392) hydrogen bonds : angle 5.26946 ( 1107) metal coordination : bond 0.00529 ( 36) metal coordination : angle 4.08115 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 225 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 400 MET cc_start: 0.6675 (ptp) cc_final: 0.6139 (tpt) REVERT: L 436 GLN cc_start: 0.8377 (tm-30) cc_final: 0.7951 (pm20) REVERT: L 480 CYS cc_start: 0.5672 (OUTLIER) cc_final: 0.5451 (p) REVERT: L 584 SER cc_start: 0.6003 (p) cc_final: 0.5600 (t) REVERT: L 692 ARG cc_start: 0.7573 (mmt180) cc_final: 0.7146 (mmt180) REVERT: L 693 PHE cc_start: 0.6137 (m-80) cc_final: 0.5888 (m-80) REVERT: L 740 ARG cc_start: 0.7366 (ttp-110) cc_final: 0.7108 (ttp-110) REVERT: X 676 PHE cc_start: 0.6797 (t80) cc_final: 0.6520 (t80) REVERT: W 667 GLU cc_start: 0.7047 (mm-30) cc_final: 0.6741 (mm-30) REVERT: W 766 LYS cc_start: 0.6759 (ptpt) cc_final: 0.6468 (ptpt) REVERT: W 899 ARG cc_start: 0.7746 (tpt170) cc_final: 0.7285 (ttt90) REVERT: K 41 MET cc_start: -0.4199 (mmm) cc_final: -0.4652 (mmm) REVERT: K 729 ARG cc_start: 0.4732 (pmt-80) cc_final: 0.3628 (pmt-80) REVERT: K 761 MET cc_start: -0.1359 (ptm) cc_final: -0.2232 (ptm) REVERT: K 864 MET cc_start: 0.8028 (mtm) cc_final: 0.7761 (mtm) REVERT: K 882 ARG cc_start: 0.7570 (ptt90) cc_final: 0.6866 (ttp80) REVERT: K 901 LEU cc_start: 0.8449 (mt) cc_final: 0.8215 (mt) outliers start: 19 outliers final: 12 residues processed: 231 average time/residue: 0.1296 time to fit residues: 40.6948 Evaluate side-chains 232 residues out of total 1303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 219 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 480 CYS Chi-restraints excluded: chain L residue 504 CYS Chi-restraints excluded: chain L residue 659 LEU Chi-restraints excluded: chain L residue 675 MET Chi-restraints excluded: chain L residue 676 PHE Chi-restraints excluded: chain X residue 558 LEU Chi-restraints excluded: chain X residue 700 MET Chi-restraints excluded: chain W residue 639 LEU Chi-restraints excluded: chain W residue 693 LYS Chi-restraints excluded: chain W residue 739 HIS Chi-restraints excluded: chain K residue 513 MET Chi-restraints excluded: chain K residue 684 VAL Chi-restraints excluded: chain K residue 754 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 128 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 88 optimal weight: 0.0870 chunk 49 optimal weight: 4.9990 chunk 86 optimal weight: 0.0000 chunk 133 optimal weight: 0.9990 chunk 127 optimal weight: 0.7980 chunk 144 optimal weight: 0.8980 overall best weight: 0.5162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5251 r_free = 0.5251 target = 0.290814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4937 r_free = 0.4937 target = 0.248245 restraints weight = 28019.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4984 r_free = 0.4984 target = 0.253904 restraints weight = 19480.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.5019 r_free = 0.5019 target = 0.258318 restraints weight = 14710.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.5046 r_free = 0.5046 target = 0.261606 restraints weight = 11799.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.5067 r_free = 0.5067 target = 0.264447 restraints weight = 9804.612| |-----------------------------------------------------------------------------| r_work (final): 0.5053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4188 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12491 Z= 0.122 Angle : 0.620 10.846 16870 Z= 0.304 Chirality : 0.041 0.153 1749 Planarity : 0.004 0.085 2179 Dihedral : 4.242 28.956 1669 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.00 % Allowed : 10.82 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.21), residues: 1477 helix: 0.60 (0.23), residues: 528 sheet: -0.73 (0.47), residues: 116 loop : -0.68 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG L 663 TYR 0.025 0.001 TYR L 714 PHE 0.047 0.002 PHE L 653 TRP 0.046 0.002 TRP K 860 HIS 0.007 0.001 HIS W 739 Details of bonding type rmsd covalent geometry : bond 0.00256 (12455) covalent geometry : angle 0.58470 (16816) hydrogen bonds : bond 0.03479 ( 392) hydrogen bonds : angle 5.02191 ( 1107) metal coordination : bond 0.00425 ( 36) metal coordination : angle 3.67896 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 225 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 400 MET cc_start: 0.6489 (ptp) cc_final: 0.6128 (tpt) REVERT: L 584 SER cc_start: 0.5965 (p) cc_final: 0.5563 (t) REVERT: L 689 ASP cc_start: 0.6641 (m-30) cc_final: 0.6339 (m-30) REVERT: L 692 ARG cc_start: 0.7496 (mmt180) cc_final: 0.7190 (mmt180) REVERT: L 740 ARG cc_start: 0.7270 (ttp-110) cc_final: 0.7028 (ttp-110) REVERT: X 676 PHE cc_start: 0.6745 (t80) cc_final: 0.6410 (t80) REVERT: W 667 GLU cc_start: 0.6961 (mm-30) cc_final: 0.6659 (mm-30) REVERT: W 730 LEU cc_start: 0.7798 (mt) cc_final: 0.7571 (mt) REVERT: W 766 LYS cc_start: 0.6613 (ptpt) cc_final: 0.6284 (ptpt) REVERT: W 887 ARG cc_start: 0.7547 (ptt180) cc_final: 0.7204 (ptt180) REVERT: W 899 ARG cc_start: 0.7632 (tpt170) cc_final: 0.7181 (ttt90) REVERT: K 41 MET cc_start: -0.4150 (mmm) cc_final: -0.4614 (mmm) REVERT: K 682 MET cc_start: 0.3855 (tmm) cc_final: 0.3244 (tmm) REVERT: K 729 ARG cc_start: 0.4805 (pmt-80) cc_final: 0.3552 (pmt-80) REVERT: K 761 MET cc_start: -0.0968 (ptm) cc_final: -0.1965 (ptm) REVERT: K 860 TRP cc_start: 0.7090 (m-10) cc_final: 0.6882 (m-10) REVERT: K 882 ARG cc_start: 0.7482 (ptt90) cc_final: 0.6802 (ttp80) REVERT: K 901 LEU cc_start: 0.8440 (mt) cc_final: 0.8203 (mt) outliers start: 13 outliers final: 8 residues processed: 228 average time/residue: 0.1313 time to fit residues: 40.7873 Evaluate side-chains 229 residues out of total 1303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 221 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 659 LEU Chi-restraints excluded: chain X residue 558 LEU Chi-restraints excluded: chain W residue 639 LEU Chi-restraints excluded: chain W residue 684 VAL Chi-restraints excluded: chain W residue 739 HIS Chi-restraints excluded: chain K residue 513 MET Chi-restraints excluded: chain K residue 667 GLU Chi-restraints excluded: chain K residue 684 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 43 optimal weight: 0.7980 chunk 120 optimal weight: 7.9990 chunk 58 optimal weight: 50.0000 chunk 25 optimal weight: 0.6980 chunk 118 optimal weight: 0.8980 chunk 119 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 111 optimal weight: 30.0000 chunk 12 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 739 HIS ** W 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 86 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5237 r_free = 0.5237 target = 0.289749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4924 r_free = 0.4924 target = 0.247184 restraints weight = 26645.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4973 r_free = 0.4973 target = 0.253115 restraints weight = 18153.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.5008 r_free = 0.5008 target = 0.257366 restraints weight = 13539.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.5035 r_free = 0.5035 target = 0.260613 restraints weight = 10742.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.5052 r_free = 0.5052 target = 0.262928 restraints weight = 8914.585| |-----------------------------------------------------------------------------| r_work (final): 0.5034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4241 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12491 Z= 0.152 Angle : 0.643 9.819 16870 Z= 0.319 Chirality : 0.042 0.167 1749 Planarity : 0.005 0.077 2179 Dihedral : 4.495 48.196 1669 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.15 % Allowed : 10.74 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.21), residues: 1477 helix: 0.50 (0.23), residues: 534 sheet: -0.93 (0.46), residues: 117 loop : -0.61 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 517 TYR 0.024 0.001 TYR L 714 PHE 0.046 0.002 PHE L 653 TRP 0.039 0.002 TRP W 753 HIS 0.007 0.001 HIS X 657 Details of bonding type rmsd covalent geometry : bond 0.00310 (12455) covalent geometry : angle 0.60530 (16816) hydrogen bonds : bond 0.03737 ( 392) hydrogen bonds : angle 5.22460 ( 1107) metal coordination : bond 0.00806 ( 36) metal coordination : angle 3.90671 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 225 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 584 SER cc_start: 0.5918 (p) cc_final: 0.5526 (t) REVERT: L 614 LYS cc_start: 0.8196 (mttp) cc_final: 0.7817 (mmmt) REVERT: L 693 PHE cc_start: 0.5943 (m-80) cc_final: 0.5701 (m-80) REVERT: L 740 ARG cc_start: 0.7351 (ttp-110) cc_final: 0.7128 (ttp-110) REVERT: W 649 VAL cc_start: 0.7812 (t) cc_final: 0.7594 (p) REVERT: W 667 GLU cc_start: 0.6989 (mm-30) cc_final: 0.6668 (mm-30) REVERT: W 730 LEU cc_start: 0.7911 (mt) cc_final: 0.7681 (mt) REVERT: W 766 LYS cc_start: 0.6687 (ptpt) cc_final: 0.6340 (ptpt) REVERT: W 864 MET cc_start: 0.7573 (ttm) cc_final: 0.7220 (ttm) REVERT: W 887 ARG cc_start: 0.7632 (ptt180) cc_final: 0.7344 (ptt180) REVERT: W 899 ARG cc_start: 0.7664 (ttt180) cc_final: 0.7335 (ttt180) REVERT: K 41 MET cc_start: -0.4104 (mmm) cc_final: -0.4572 (mmm) REVERT: K 682 MET cc_start: 0.4220 (tmm) cc_final: 0.3694 (tmm) REVERT: K 729 ARG cc_start: 0.4764 (pmt-80) cc_final: 0.3316 (pmt-80) REVERT: K 761 MET cc_start: -0.1669 (ptm) cc_final: -0.2517 (ptm) REVERT: K 768 ASP cc_start: 0.7427 (m-30) cc_final: 0.6455 (m-30) REVERT: K 772 PHE cc_start: 0.6462 (m-80) cc_final: 0.6109 (m-80) REVERT: K 882 ARG cc_start: 0.7510 (ptt90) cc_final: 0.6835 (ttp80) REVERT: K 901 LEU cc_start: 0.8504 (mt) cc_final: 0.8290 (mt) outliers start: 15 outliers final: 11 residues processed: 230 average time/residue: 0.1254 time to fit residues: 39.5379 Evaluate side-chains 232 residues out of total 1303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 221 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 504 CYS Chi-restraints excluded: chain L residue 659 LEU Chi-restraints excluded: chain X residue 558 LEU Chi-restraints excluded: chain X residue 582 VAL Chi-restraints excluded: chain X residue 700 MET Chi-restraints excluded: chain W residue 485 GLN Chi-restraints excluded: chain W residue 639 LEU Chi-restraints excluded: chain W residue 684 VAL Chi-restraints excluded: chain W residue 739 HIS Chi-restraints excluded: chain K residue 513 MET Chi-restraints excluded: chain K residue 684 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 40 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 104 optimal weight: 8.9990 chunk 128 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 94 optimal weight: 50.0000 chunk 96 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 757 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5240 r_free = 0.5240 target = 0.289996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4923 r_free = 0.4923 target = 0.247372 restraints weight = 26648.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4971 r_free = 0.4971 target = 0.252978 restraints weight = 18179.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.5008 r_free = 0.5008 target = 0.257534 restraints weight = 13671.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.5035 r_free = 0.5035 target = 0.260784 restraints weight = 10828.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.5054 r_free = 0.5054 target = 0.263371 restraints weight = 8936.236| |-----------------------------------------------------------------------------| r_work (final): 0.5033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4250 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12491 Z= 0.146 Angle : 0.649 9.365 16870 Z= 0.319 Chirality : 0.042 0.181 1749 Planarity : 0.005 0.098 2179 Dihedral : 4.574 55.139 1669 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.23 % Allowed : 11.74 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.21), residues: 1477 helix: 0.47 (0.23), residues: 532 sheet: -0.85 (0.46), residues: 119 loop : -0.59 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG L 517 TYR 0.023 0.001 TYR L 714 PHE 0.050 0.002 PHE L 653 TRP 0.068 0.002 TRP K 860 HIS 0.014 0.001 HIS W 739 Details of bonding type rmsd covalent geometry : bond 0.00303 (12455) covalent geometry : angle 0.61032 (16816) hydrogen bonds : bond 0.03688 ( 392) hydrogen bonds : angle 5.26922 ( 1107) metal coordination : bond 0.00648 ( 36) metal coordination : angle 3.96005 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 221 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 584 SER cc_start: 0.5893 (p) cc_final: 0.5474 (t) REVERT: L 614 LYS cc_start: 0.8146 (mttp) cc_final: 0.7800 (mmmt) REVERT: W 667 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6795 (mm-30) REVERT: W 709 PRO cc_start: 0.8050 (Cg_exo) cc_final: 0.7830 (Cg_endo) REVERT: W 730 LEU cc_start: 0.7984 (mt) cc_final: 0.7748 (mt) REVERT: W 766 LYS cc_start: 0.6721 (ptpt) cc_final: 0.6379 (ptpt) REVERT: W 887 ARG cc_start: 0.7652 (ptt180) cc_final: 0.7347 (ptt180) REVERT: W 899 ARG cc_start: 0.7629 (ttt180) cc_final: 0.7300 (ttt90) REVERT: K 41 MET cc_start: -0.4072 (mmm) cc_final: -0.4543 (mmm) REVERT: K 564 ASP cc_start: 0.7282 (m-30) cc_final: 0.6687 (p0) REVERT: K 682 MET cc_start: 0.4217 (tmm) cc_final: 0.3827 (tmm) REVERT: K 729 ARG cc_start: 0.4910 (pmt-80) cc_final: 0.3363 (pmt-80) REVERT: K 761 MET cc_start: -0.1865 (ptm) cc_final: -0.2697 (ptm) REVERT: K 768 ASP cc_start: 0.7422 (m-30) cc_final: 0.6460 (m-30) REVERT: K 772 PHE cc_start: 0.6498 (m-80) cc_final: 0.6203 (m-80) REVERT: K 882 ARG cc_start: 0.7526 (ptt90) cc_final: 0.6833 (ttp80) REVERT: K 901 LEU cc_start: 0.8514 (mt) cc_final: 0.8304 (mt) outliers start: 16 outliers final: 13 residues processed: 225 average time/residue: 0.1301 time to fit residues: 39.9726 Evaluate side-chains 228 residues out of total 1303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 215 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 504 CYS Chi-restraints excluded: chain L residue 659 LEU Chi-restraints excluded: chain L residue 663 ARG Chi-restraints excluded: chain X residue 582 VAL Chi-restraints excluded: chain X residue 700 MET Chi-restraints excluded: chain W residue 485 GLN Chi-restraints excluded: chain W residue 639 LEU Chi-restraints excluded: chain W residue 739 HIS Chi-restraints excluded: chain W residue 753 TRP Chi-restraints excluded: chain W residue 757 ASN Chi-restraints excluded: chain K residue 513 MET Chi-restraints excluded: chain K residue 684 VAL Chi-restraints excluded: chain K residue 779 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 98 optimal weight: 0.9980 chunk 94 optimal weight: 0.0270 chunk 37 optimal weight: 6.9990 chunk 119 optimal weight: 0.1980 chunk 36 optimal weight: 0.8980 chunk 105 optimal weight: 10.0000 chunk 135 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 113 optimal weight: 0.0070 chunk 27 optimal weight: 2.9990 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 739 HIS W 757 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5246 r_free = 0.5246 target = 0.291106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4939 r_free = 0.4939 target = 0.249759 restraints weight = 26845.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4986 r_free = 0.4986 target = 0.255519 restraints weight = 18636.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.5020 r_free = 0.5020 target = 0.259591 restraints weight = 13897.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.5045 r_free = 0.5045 target = 0.262803 restraints weight = 11045.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.5063 r_free = 0.5063 target = 0.265026 restraints weight = 9128.638| |-----------------------------------------------------------------------------| r_work (final): 0.5043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4191 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12491 Z= 0.119 Angle : 0.633 8.687 16870 Z= 0.312 Chirality : 0.042 0.188 1749 Planarity : 0.004 0.067 2179 Dihedral : 4.474 53.808 1669 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.92 % Allowed : 12.74 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.21), residues: 1477 helix: 0.58 (0.23), residues: 532 sheet: -0.77 (0.49), residues: 108 loop : -0.55 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 609 TYR 0.029 0.001 TYR L 714 PHE 0.064 0.002 PHE W 772 TRP 0.051 0.001 TRP K 860 HIS 0.004 0.001 HIS X 657 Details of bonding type rmsd covalent geometry : bond 0.00254 (12455) covalent geometry : angle 0.59579 (16816) hydrogen bonds : bond 0.03512 ( 392) hydrogen bonds : angle 5.13202 ( 1107) metal coordination : bond 0.00540 ( 36) metal coordination : angle 3.80951 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 218 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 397 ARG cc_start: 0.8453 (ttp-170) cc_final: 0.8148 (ttp-170) REVERT: L 400 MET cc_start: 0.6469 (ptp) cc_final: 0.6193 (tpt) REVERT: L 584 SER cc_start: 0.5741 (p) cc_final: 0.5395 (t) REVERT: L 614 LYS cc_start: 0.8251 (mttp) cc_final: 0.7821 (mmmt) REVERT: W 667 GLU cc_start: 0.6991 (mm-30) cc_final: 0.6672 (mm-30) REVERT: W 730 LEU cc_start: 0.7889 (mt) cc_final: 0.7667 (mt) REVERT: W 766 LYS cc_start: 0.6596 (ptpt) cc_final: 0.6255 (ptpt) REVERT: W 887 ARG cc_start: 0.7628 (ptt180) cc_final: 0.7320 (ptt180) REVERT: W 899 ARG cc_start: 0.7660 (ttt180) cc_final: 0.7384 (ttt90) REVERT: K 41 MET cc_start: -0.4091 (mmm) cc_final: -0.4568 (mmm) REVERT: K 564 ASP cc_start: 0.7326 (m-30) cc_final: 0.6721 (p0) REVERT: K 682 MET cc_start: 0.4163 (tmm) cc_final: 0.3852 (tmm) REVERT: K 729 ARG cc_start: 0.4836 (pmt-80) cc_final: 0.3255 (pmt-80) REVERT: K 761 MET cc_start: -0.1717 (ptm) cc_final: -0.2545 (ptm) REVERT: K 768 ASP cc_start: 0.7400 (m-30) cc_final: 0.6408 (m-30) REVERT: K 772 PHE cc_start: 0.6370 (m-80) cc_final: 0.6131 (m-80) REVERT: K 882 ARG cc_start: 0.7475 (ptt90) cc_final: 0.6793 (ttp80) REVERT: K 901 LEU cc_start: 0.8488 (mt) cc_final: 0.8274 (mt) outliers start: 12 outliers final: 12 residues processed: 221 average time/residue: 0.1294 time to fit residues: 39.1196 Evaluate side-chains 230 residues out of total 1303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 218 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 504 CYS Chi-restraints excluded: chain L residue 659 LEU Chi-restraints excluded: chain L residue 663 ARG Chi-restraints excluded: chain X residue 582 VAL Chi-restraints excluded: chain X residue 700 MET Chi-restraints excluded: chain W residue 485 GLN Chi-restraints excluded: chain W residue 639 LEU Chi-restraints excluded: chain W residue 739 HIS Chi-restraints excluded: chain W residue 753 TRP Chi-restraints excluded: chain W residue 757 ASN Chi-restraints excluded: chain K residue 513 MET Chi-restraints excluded: chain K residue 684 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 12 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 chunk 32 optimal weight: 0.0770 chunk 122 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 47 optimal weight: 0.1980 chunk 48 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 739 HIS W 757 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5239 r_free = 0.5239 target = 0.290483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4915 r_free = 0.4915 target = 0.247306 restraints weight = 27007.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4966 r_free = 0.4966 target = 0.253377 restraints weight = 18399.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.5002 r_free = 0.5002 target = 0.257801 restraints weight = 13672.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.5029 r_free = 0.5029 target = 0.261095 restraints weight = 10742.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.5049 r_free = 0.5049 target = 0.263614 restraints weight = 8843.918| |-----------------------------------------------------------------------------| r_work (final): 0.5028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4254 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12491 Z= 0.136 Angle : 0.663 15.521 16870 Z= 0.324 Chirality : 0.042 0.190 1749 Planarity : 0.005 0.061 2179 Dihedral : 4.548 55.908 1669 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.07 % Allowed : 12.74 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.21), residues: 1477 helix: 0.54 (0.23), residues: 532 sheet: -0.81 (0.46), residues: 119 loop : -0.55 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 609 TYR 0.025 0.001 TYR L 714 PHE 0.059 0.002 PHE W 772 TRP 0.102 0.002 TRP K 860 HIS 0.014 0.001 HIS W 739 Details of bonding type rmsd covalent geometry : bond 0.00286 (12455) covalent geometry : angle 0.61309 (16816) hydrogen bonds : bond 0.03663 ( 392) hydrogen bonds : angle 5.22311 ( 1107) metal coordination : bond 0.00548 ( 36) metal coordination : angle 4.49677 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2954 Ramachandran restraints generated. 1477 Oldfield, 0 Emsley, 1477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 218 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 436 GLN cc_start: 0.8576 (tm-30) cc_final: 0.7708 (pm20) REVERT: L 440 ASP cc_start: 0.8320 (m-30) cc_final: 0.7807 (p0) REVERT: L 614 LYS cc_start: 0.8291 (mttp) cc_final: 0.7856 (mmmt) REVERT: W 667 GLU cc_start: 0.6981 (mm-30) cc_final: 0.6651 (mm-30) REVERT: W 730 LEU cc_start: 0.7918 (mt) cc_final: 0.7696 (mt) REVERT: W 766 LYS cc_start: 0.6662 (ptpt) cc_final: 0.6315 (ptpt) REVERT: W 887 ARG cc_start: 0.7732 (ptt180) cc_final: 0.7403 (ptt-90) REVERT: W 899 ARG cc_start: 0.7648 (ttt180) cc_final: 0.7185 (ttt90) REVERT: K 41 MET cc_start: -0.4058 (mmm) cc_final: -0.4533 (mmm) REVERT: K 682 MET cc_start: 0.4164 (tmm) cc_final: 0.3865 (tmm) REVERT: K 729 ARG cc_start: 0.4995 (pmt-80) cc_final: 0.3430 (pmt-80) REVERT: K 761 MET cc_start: -0.1909 (ptm) cc_final: -0.2705 (ptm) REVERT: K 768 ASP cc_start: 0.7411 (m-30) cc_final: 0.6435 (m-30) REVERT: K 772 PHE cc_start: 0.6438 (m-80) cc_final: 0.6225 (m-80) REVERT: K 901 LEU cc_start: 0.8522 (mt) cc_final: 0.8315 (mt) outliers start: 14 outliers final: 12 residues processed: 222 average time/residue: 0.1255 time to fit residues: 38.2560 Evaluate side-chains 226 residues out of total 1303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 214 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 659 LEU Chi-restraints excluded: chain L residue 663 ARG Chi-restraints excluded: chain X residue 582 VAL Chi-restraints excluded: chain X residue 700 MET Chi-restraints excluded: chain W residue 485 GLN Chi-restraints excluded: chain W residue 639 LEU Chi-restraints excluded: chain W residue 739 HIS Chi-restraints excluded: chain W residue 757 ASN Chi-restraints excluded: chain W residue 789 HIS Chi-restraints excluded: chain K residue 513 MET Chi-restraints excluded: chain K residue 684 VAL Chi-restraints excluded: chain K residue 779 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 92 optimal weight: 0.9980 chunk 113 optimal weight: 8.9990 chunk 29 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 65 optimal weight: 30.0000 chunk 42 optimal weight: 0.8980 chunk 148 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 147 optimal weight: 0.7980 chunk 84 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 739 HIS W 757 ASN ** W 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 847 HIS ** W 879 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5235 r_free = 0.5235 target = 0.289999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4912 r_free = 0.4912 target = 0.246844 restraints weight = 26903.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4962 r_free = 0.4962 target = 0.252906 restraints weight = 18434.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4997 r_free = 0.4997 target = 0.257239 restraints weight = 13754.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.5024 r_free = 0.5024 target = 0.260519 restraints weight = 10893.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.5043 r_free = 0.5043 target = 0.263042 restraints weight = 8975.438| |-----------------------------------------------------------------------------| r_work (final): 0.5024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4298 moved from start: 0.5122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12491 Z= 0.145 Angle : 0.674 12.136 16870 Z= 0.333 Chirality : 0.043 0.180 1749 Planarity : 0.005 0.055 2179 Dihedral : 4.590 56.372 1669 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.00 % Allowed : 13.05 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.21), residues: 1477 helix: 0.48 (0.23), residues: 531 sheet: -0.93 (0.46), residues: 121 loop : -0.54 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 882 TYR 0.025 0.001 TYR L 714 PHE 0.058 0.002 PHE W 772 TRP 0.076 0.002 TRP K 860 HIS 0.013 0.001 HIS W 739 Details of bonding type rmsd covalent geometry : bond 0.00303 (12455) covalent geometry : angle 0.63610 (16816) hydrogen bonds : bond 0.03799 ( 392) hydrogen bonds : angle 5.34765 ( 1107) metal coordination : bond 0.00559 ( 36) metal coordination : angle 4.00507 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2968.59 seconds wall clock time: 51 minutes 24.04 seconds (3084.04 seconds total)