Starting phenix.real_space_refine on Sat Oct 24 09:20:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11oh_75885/10_2026/11oh_75885.cif Found real_map, /net/cci-nas-00/data/ceres_data/11oh_75885/10_2026/11oh_75885.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11oh_75885/10_2026/11oh_75885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11oh_75885/10_2026/11oh_75885.map" model { file = "/net/cci-nas-00/data/ceres_data/11oh_75885/10_2026/11oh_75885.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11oh_75885/10_2026/11oh_75885.cif" } resolution = 3.58 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= 0.004 sd= 0.026 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 116 5.16 5 C 8046 2.51 5 N 2233 2.21 5 O 2254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12658 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1217 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 143} Chain breaks: 4 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'PHE:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3464 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 415} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "D" Number of atoms: 4525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4525 Classifications: {'peptide': 571} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 541} Chain breaks: 2 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 3365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3365 Classifications: {'peptide': 424} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 402} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "C" 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: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1389 SG CYS C 494 44.224 80.277 125.904 1.00237.49 S ATOM 1409 SG CYS C 497 40.582 79.299 126.576 1.00245.29 S ATOM 1531 SG CYS C 514 43.280 76.912 127.616 1.00227.57 S ATOM 1550 SG CYS C 517 42.580 77.465 123.968 1.00220.67 S ATOM 1718 SG CYS C 537 43.743 81.380 113.722 1.00217.82 S ATOM 1739 SG CYS C 540 40.737 80.110 115.721 1.00220.06 S ATOM 1876 SG CYS C 559 40.201 82.884 113.333 1.00234.72 S ATOM 1898 SG CYS C 562 42.122 83.641 116.395 1.00240.24 S ATOM 1802 SG CYS C 549 51.162 83.664 104.178 1.00235.38 S ATOM 1836 SG CYS C 554 53.623 81.126 105.661 1.00219.67 S ATOM 2049 SG CYS C 583 52.547 84.206 107.779 1.00237.51 S ATOM 2075 SG CYS C 586 54.892 84.516 105.127 1.00240.15 S ATOM 5890 SG CYS D 494 58.713 27.712 42.706 1.00189.87 S ATOM 5910 SG CYS D 497 55.172 28.288 41.571 1.00196.35 S ATOM 6032 SG CYS D 514 57.678 31.030 40.891 1.00189.15 S ATOM 6055 SG CYS D 517 56.275 30.207 44.359 1.00186.93 S ATOM 6223 SG CYS D 537 53.522 26.251 54.392 1.00192.72 S ATOM 6244 SG CYS D 540 51.431 27.692 51.514 1.00193.66 S ATOM 6381 SG CYS D 559 50.193 24.760 53.237 1.00205.04 S ATOM 6403 SG CYS D 562 52.939 24.103 51.119 1.00201.34 S ATOM 6307 SG CYS D 549 58.109 24.594 66.069 1.00194.64 S ATOM 6341 SG CYS D 554 60.655 27.147 64.731 1.00191.73 S ATOM 6554 SG CYS D 583 59.705 23.822 62.874 1.00197.84 S ATOM 6580 SG CYS D 586 61.987 24.017 65.915 1.00196.36 S ATOM 9378 SG CYS B 494 31.363 76.487 58.586 1.00384.85 S ATOM 9398 SG CYS B 497 31.500 73.495 60.913 1.00389.22 S ATOM 9520 SG CYS B 514 34.780 75.016 59.661 1.00375.08 S ATOM 9539 SG CYS B 517 32.603 73.075 57.354 1.00369.47 S ATOM 9707 SG CYS B 537 24.889 71.605 49.635 1.00388.99 S ATOM 9728 SG CYS B 540 26.060 69.846 52.801 1.00391.26 S ATOM 9865 SG CYS B 559 22.442 69.555 51.796 1.00410.19 S ATOM 9887 SG CYS B 562 23.683 72.788 53.112 1.00411.47 S ATOM 9791 SG CYS B 549 20.790 74.145 38.144 1.00395.88 S ATOM 9825 SG CYS B 554 24.282 75.537 37.325 1.00387.28 S ATOM 10038 SG CYS B 583 22.327 76.919 40.340 1.00406.94 S ATOM 10064 SG CYS B 586 21.398 77.811 36.946 1.00410.05 S Time building chain proxies: 2.94, per 1000 atoms: 0.23 Number of scatterers: 12658 At special positions: 0 Unit cell: (102.953, 109.469, 162.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 9 29.99 S 116 16.00 O 2254 8.00 N 2233 7.00 C 8046 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: 1.05 Conformation dependent library (CDL) restraints added in 441.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1002 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 517 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 497 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 514 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 494 " pdb=" ZN B1003 " pdb="ZN ZN B1003 " - pdb=" SG CYS B 540 " pdb="ZN ZN B1003 " - pdb=" SG CYS B 559 " pdb="ZN ZN B1003 " - pdb=" SG CYS B 562 " pdb="ZN ZN B1003 " - pdb=" SG CYS B 537 " pdb=" ZN B1004 " pdb="ZN ZN B1004 " - pdb=" SG CYS B 586 " pdb="ZN ZN B1004 " - pdb=" SG CYS B 583 " pdb="ZN ZN B1004 " - pdb=" SG CYS B 554 " pdb="ZN ZN B1004 " - pdb=" SG CYS B 549 " pdb=" ZN C1002 " pdb="ZN ZN C1002 " - pdb=" SG CYS C 517 " pdb="ZN ZN C1002 " - pdb=" SG CYS C 497 " pdb="ZN ZN C1002 " - pdb=" SG CYS C 514 " pdb="ZN ZN C1002 " - pdb=" SG CYS C 494 " pdb=" ZN C1003 " pdb="ZN ZN C1003 " - pdb=" SG CYS C 559 " pdb="ZN ZN C1003 " - pdb=" SG CYS C 540 " pdb="ZN ZN C1003 " - pdb=" SG CYS C 562 " pdb="ZN ZN C1003 " - pdb=" SG CYS C 537 " pdb=" ZN C1004 " pdb="ZN ZN C1004 " - pdb=" SG CYS C 586 " pdb="ZN ZN C1004 " - pdb=" SG CYS C 583 " pdb="ZN ZN C1004 " - pdb=" SG CYS C 554 " pdb="ZN ZN C1004 " - pdb=" SG CYS C 549 " pdb=" ZN D1002 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 497 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 517 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 494 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 514 " pdb=" ZN D1003 " pdb="ZN ZN D1003 " - pdb=" SG CYS D 559 " pdb="ZN ZN D1003 " - pdb=" SG CYS D 540 " pdb="ZN ZN D1003 " - pdb=" SG CYS D 562 " pdb="ZN ZN D1003 " - pdb=" SG CYS D 537 " pdb=" ZN D1004 " pdb="ZN ZN D1004 " - pdb=" SG CYS D 583 " pdb="ZN ZN D1004 " - pdb=" SG CYS D 586 " pdb="ZN ZN D1004 " - pdb=" SG CYS D 549 " pdb="ZN ZN D1004 " - pdb=" SG CYS D 554 " Number of angles added : 54 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2932 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 11 sheets defined 39.5% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 644 through 654 Processing helix chain 'A' and resid 691 through 698 Processing helix chain 'A' and resid 724 through 742 removed outlier: 6.227A pdb=" N ARG A 729 " --> pdb=" O GLU A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 774 Processing helix chain 'A' and resid 894 through 903 Processing helix chain 'A' and resid 904 through 909 removed outlier: 3.904A pdb=" N TYR A 908 " --> pdb=" O PRO A 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 485 Processing helix chain 'C' and resid 489 through 493 Processing helix chain 'C' and resid 514 through 524 Processing helix chain 'C' and resid 559 through 567 Processing helix chain 'C' and resid 570 through 578 Processing helix chain 'C' and resid 600 through 609 Processing helix chain 'C' and resid 644 through 653 Processing helix chain 'C' and resid 666 through 677 Processing helix chain 'C' and resid 686 through 690 Processing helix chain 'C' and resid 691 through 699 Processing helix chain 'C' and resid 728 through 740 removed outlier: 4.006A pdb=" N PHE C 732 " --> pdb=" O GLY C 728 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 774 Processing helix chain 'C' and resid 783 through 785 No H-bonds generated for 'chain 'C' and resid 783 through 785' Processing helix chain 'C' and resid 814 through 819 removed outlier: 3.715A pdb=" N CYS C 818 " --> pdb=" O GLU C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 835 through 839 Processing helix chain 'C' and resid 860 through 868 removed outlier: 3.721A pdb=" N PHE C 868 " --> pdb=" O MET C 864 " (cutoff:3.500A) Processing helix chain 'C' and resid 881 through 890 Processing helix chain 'C' and resid 894 through 903 Processing helix chain 'C' and resid 904 through 909 removed outlier: 4.307A pdb=" N TYR C 908 " --> pdb=" O PRO C 904 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE C 909 " --> pdb=" O LEU C 905 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 904 through 909' Processing helix chain 'D' and resid 313 through 317 Processing helix chain 'D' and resid 340 through 344 Processing helix chain 'D' and resid 356 through 362 Processing helix chain 'D' and resid 362 through 381 Processing helix chain 'D' and resid 395 through 412 Proline residue: D 405 - end of helix Processing helix chain 'D' and resid 418 through 423 removed outlier: 3.826A pdb=" N GLU D 423 " --> pdb=" O LYS D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 485 Processing helix chain 'D' and resid 489 through 493 removed outlier: 3.564A pdb=" N ILE D 493 " --> pdb=" O ILE D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 524 removed outlier: 3.672A pdb=" N CYS D 524 " --> pdb=" O CYS D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 567 removed outlier: 3.500A pdb=" N VAL D 563 " --> pdb=" O CYS D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 578 removed outlier: 3.582A pdb=" N GLU D 578 " --> pdb=" O ALA D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 611 Processing helix chain 'D' and resid 627 through 631 removed outlier: 3.600A pdb=" N ARG D 631 " --> pdb=" O ALA D 628 " (cutoff:3.500A) Processing helix chain 'D' and resid 644 through 653 Processing helix chain 'D' and resid 666 through 677 Processing helix chain 'D' and resid 691 through 698 Processing helix chain 'D' and resid 725 through 728 Processing helix chain 'D' and resid 729 through 742 Processing helix chain 'D' and resid 762 through 774 Processing helix chain 'D' and resid 783 through 785 No H-bonds generated for 'chain 'D' and resid 783 through 785' Processing helix chain 'D' and resid 814 through 819 removed outlier: 4.092A pdb=" N CYS D 818 " --> pdb=" O GLU D 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 860 through 868 Processing helix chain 'D' and resid 881 through 890 Processing helix chain 'D' and resid 894 through 903 Processing helix chain 'D' and resid 904 through 909 Processing helix chain 'B' and resid 476 through 485 Processing helix chain 'B' and resid 489 through 493 Processing helix chain 'B' and resid 514 through 524 Processing helix chain 'B' and resid 559 through 567 Processing helix chain 'B' and resid 570 through 578 Processing helix chain 'B' and resid 600 through 609 Processing helix chain 'B' and resid 644 through 653 Processing helix chain 'B' and resid 666 through 677 Processing helix chain 'B' and resid 691 through 699 Processing helix chain 'B' and resid 725 through 742 removed outlier: 3.587A pdb=" N LEU B 730 " --> pdb=" O GLY B 726 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU B 733 " --> pdb=" O ARG B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 774 Processing helix chain 'B' and resid 783 through 785 No H-bonds generated for 'chain 'B' and resid 783 through 785' Processing helix chain 'B' and resid 814 through 819 removed outlier: 3.611A pdb=" N CYS B 818 " --> pdb=" O GLU B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 839 Processing helix chain 'B' and resid 860 through 868 removed outlier: 3.699A pdb=" N PHE B 868 " --> pdb=" O MET B 864 " (cutoff:3.500A) Processing helix chain 'B' and resid 881 through 890 Processing helix chain 'B' and resid 894 through 903 Processing helix chain 'B' and resid 904 through 909 removed outlier: 3.963A pdb=" N TYR B 908 " --> pdb=" O PRO B 904 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 682 through 684 removed outlier: 8.823A pdb=" N MET A 682 " --> pdb=" O ASP A 658 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TYR A 660 " --> pdb=" O MET A 682 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N VAL A 684 " --> pdb=" O TYR A 660 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ALA A 662 " --> pdb=" O VAL A 684 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ILE A 634 " --> pdb=" O ASP A 658 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N TYR A 660 " --> pdb=" O ILE A 634 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL A 636 " --> pdb=" O TYR A 660 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ALA A 662 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N SER A 638 " --> pdb=" O ALA A 662 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL A 704 " --> pdb=" O LEU A 754 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N GLU A 756 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N GLY A 706 " --> pdb=" O GLU A 756 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 504 through 505 Processing sheet with id=AA3, first strand: chain 'C' and resid 591 through 592 removed outlier: 4.264A pdb=" N LEU C 595 " --> pdb=" O TYR C 592 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 681 through 683 removed outlier: 8.905A pdb=" N MET C 682 " --> pdb=" O ASP C 658 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N TYR C 660 " --> pdb=" O MET C 682 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ILE C 634 " --> pdb=" O VAL C 657 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU C 703 " --> pdb=" O ARG C 635 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE C 705 " --> pdb=" O LEU C 637 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL C 704 " --> pdb=" O LEU C 754 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N GLU C 756 " --> pdb=" O VAL C 704 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 823 through 825 Processing sheet with id=AA6, first strand: chain 'D' and resid 296 through 298 removed outlier: 3.821A pdb=" N SER D 337 " --> pdb=" O VAL D 328 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 657 through 660 removed outlier: 7.531A pdb=" N ILE D 634 " --> pdb=" O ASP D 658 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N TYR D 660 " --> pdb=" O ILE D 634 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL D 636 " --> pdb=" O TYR D 660 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE D 705 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 754 through 758 removed outlier: 3.949A pdb=" N PHE D 755 " --> pdb=" O TRP D 795 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 824 through 825 removed outlier: 3.768A pdb=" N VAL D 850 " --> pdb=" O ASP D 857 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 681 through 683 removed outlier: 7.068A pdb=" N TYR B 660 " --> pdb=" O MET B 682 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE B 705 " --> pdb=" O LEU B 637 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL B 704 " --> pdb=" O LEU B 754 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N GLU B 756 " --> pdb=" O VAL B 704 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY B 706 " --> pdb=" O GLU B 756 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N VAL B 758 " --> pdb=" O GLY B 706 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 823 through 825 424 hydrogen bonds defined for protein. 1158 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: 1.72 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4178 1.34 - 1.46: 3029 1.46 - 1.58: 5601 1.58 - 1.70: 0 1.70 - 1.82: 161 Bond restraints: 12969 Sorted by residual: bond pdb=" CA GLU B 725 " pdb=" CB GLU B 725 " ideal model delta sigma weight residual 1.518 1.545 -0.028 2.08e-02 2.31e+03 1.77e+00 bond pdb=" C TYR D 592 " pdb=" N GLY D 593 " ideal model delta sigma weight residual 1.331 1.316 0.014 1.46e-02 4.69e+03 9.22e-01 bond pdb=" CA ILE D 643 " pdb=" C ILE D 643 " ideal model delta sigma weight residual 1.530 1.520 0.010 1.12e-02 7.97e+03 8.68e-01 bond pdb=" CA ASN B 853 " pdb=" CB ASN B 853 " ideal model delta sigma weight residual 1.527 1.543 -0.016 1.70e-02 3.46e+03 8.36e-01 bond pdb=" C TYR B 724 " pdb=" N GLU B 725 " ideal model delta sigma weight residual 1.325 1.335 -0.010 1.14e-02 7.69e+03 8.18e-01 ... (remaining 12964 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 17251 1.55 - 3.10: 258 3.10 - 4.66: 31 4.66 - 6.21: 10 6.21 - 7.76: 2 Bond angle restraints: 17552 Sorted by residual: angle pdb=" CA TYR D 724 " pdb=" CB TYR D 724 " pdb=" CG TYR D 724 " ideal model delta sigma weight residual 113.90 119.49 -5.59 1.80e+00 3.09e-01 9.66e+00 angle pdb=" N LYS C 841 " pdb=" CA LYS C 841 " pdb=" C LYS C 841 " ideal model delta sigma weight residual 114.62 111.23 3.39 1.14e+00 7.69e-01 8.86e+00 angle pdb=" N GLU D 733 " pdb=" CA GLU D 733 " pdb=" C GLU D 733 " ideal model delta sigma weight residual 111.28 108.20 3.08 1.09e+00 8.42e-01 7.99e+00 angle pdb=" CA GLU B 725 " pdb=" CB GLU B 725 " pdb=" CG GLU B 725 " ideal model delta sigma weight residual 114.10 119.44 -5.34 2.00e+00 2.50e-01 7.12e+00 angle pdb=" CB MET D 364 " pdb=" CG MET D 364 " pdb=" SD MET D 364 " ideal model delta sigma weight residual 112.70 120.46 -7.76 3.00e+00 1.11e-01 6.69e+00 ... (remaining 17547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 6884 17.40 - 34.80: 598 34.80 - 52.20: 146 52.20 - 69.60: 29 69.60 - 87.00: 12 Dihedral angle restraints: 7669 sinusoidal: 3109 harmonic: 4560 Sorted by residual: dihedral pdb=" CB GLU B 814 " pdb=" CG GLU B 814 " pdb=" CD GLU B 814 " pdb=" OE1 GLU B 814 " ideal model delta sinusoidal sigma weight residual 0.00 87.00 -87.00 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CB GLU C 814 " pdb=" CG GLU C 814 " pdb=" CD GLU C 814 " pdb=" OE1 GLU C 814 " ideal model delta sinusoidal sigma weight residual 0.00 86.83 -86.83 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CA PHE C 794 " pdb=" C PHE C 794 " pdb=" N TRP C 795 " pdb=" CA TRP C 795 " ideal model delta harmonic sigma weight residual 180.00 164.19 15.81 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 7666 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1091 0.029 - 0.058: 512 0.058 - 0.086: 171 0.086 - 0.115: 68 0.115 - 0.144: 11 Chirality restraints: 1853 Sorted by residual: chirality pdb=" CA ASN C 853 " pdb=" N ASN C 853 " pdb=" C ASN C 853 " pdb=" CB ASN C 853 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" CA ASN D 553 " pdb=" N ASN D 553 " pdb=" C ASN D 553 " pdb=" CB ASN D 553 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA ASN B 853 " pdb=" N ASN B 853 " pdb=" C ASN B 853 " pdb=" CB ASN B 853 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.98e-01 ... (remaining 1850 not shown) Planarity restraints: 2281 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 724 " -0.022 2.00e-02 2.50e+03 1.84e-02 6.76e+00 pdb=" CG TYR D 724 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR D 724 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR D 724 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR D 724 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR D 724 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR D 724 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 724 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 404 " 0.035 5.00e-02 4.00e+02 5.34e-02 4.56e+00 pdb=" N PRO D 405 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO D 405 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 405 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 729 " 0.008 2.00e-02 2.50e+03 1.54e-02 2.38e+00 pdb=" C ARG B 729 " -0.027 2.00e-02 2.50e+03 pdb=" O ARG B 729 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU B 730 " 0.009 2.00e-02 2.50e+03 ... (remaining 2278 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 5642 2.95 - 3.44: 13307 3.44 - 3.93: 20323 3.93 - 4.41: 23441 4.41 - 4.90: 36708 Nonbonded interactions: 99421 Sorted by model distance: nonbonded pdb=" O MET C 852 " pdb=" OD1 ASN C 853 " model vdw 2.464 3.040 nonbonded pdb=" O MET B 852 " pdb=" OD1 ASN B 853 " model vdw 2.497 3.040 nonbonded pdb=" N THR D 808 " pdb=" OG1 THR D 808 " model vdw 2.548 2.496 nonbonded pdb=" N SAH D1001 " pdb=" OXT SAH D1001 " model vdw 2.567 2.496 nonbonded pdb=" N THR C 875 " pdb=" OG1 THR C 875 " model vdw 2.575 2.496 ... (remaining 99416 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = (chain 'C' and (resid 475 through 709 or resid 724 through 1004)) } 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: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 12.830 Find NCS groups from input model: 0.140 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13005 Z= 0.146 Angle : 0.561 10.286 17606 Z= 0.277 Chirality : 0.039 0.144 1853 Planarity : 0.004 0.053 2281 Dihedral : 14.291 86.997 4737 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.20 % Allowed : 8.41 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: -0.02 (0.22), residues: 1563 helix: 0.59 (0.24), residues: 521 sheet: -0.96 (0.49), residues: 126 loop : -0.14 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 836 TYR 0.046 0.001 TYR D 724 PHE 0.018 0.002 PHE C 909 TRP 0.016 0.001 TRP B 795 HIS 0.005 0.001 HIS B 900 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (12969) covalent geometry : angle 0.51092 / 0.27 (17552) hydrogen bonds : bond 0.15356 / 10.01 ( 424) hydrogen bonds : angle 6.78836 / 4.82 ( 1158) metal coordination : bond 0.00664 / 0.45 ( 36) metal coordination : angle 4.19494 / 3.00 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 267 time to evaluate : 0.300 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: A 702 ASP cc_start: 0.8728 (m-30) cc_final: 0.8509 (m-30) REVERT: A 793 TYR cc_start: 0.7869 (m-80) cc_final: 0.7398 (m-80) REVERT: A 794 PHE cc_start: 0.8971 (m-80) cc_final: 0.8588 (m-80) REVERT: C 513 MET cc_start: 0.9030 (ttp) cc_final: 0.8736 (tmm) REVERT: C 557 CYS cc_start: 0.7042 (m) cc_final: 0.6515 (p) REVERT: C 668 ASP cc_start: 0.8763 (m-30) cc_final: 0.8413 (m-30) REVERT: C 875 THR cc_start: 0.8935 (OUTLIER) cc_final: 0.8636 (p) REVERT: D 329 MET cc_start: 0.8694 (tpp) cc_final: 0.8375 (tmm) REVERT: D 606 GLN cc_start: 0.9225 (mm110) cc_final: 0.8382 (tm-30) REVERT: D 732 PHE cc_start: 0.7987 (m-80) cc_final: 0.7467 (m-80) REVERT: D 882 ARG cc_start: 0.8595 (ptm-80) cc_final: 0.8255 (ptm-80) REVERT: B 513 MET cc_start: 0.7966 (ttp) cc_final: 0.7363 (tpp) REVERT: B 548 MET cc_start: 0.4145 (mmt) cc_final: 0.3474 (mtm) REVERT: B 653 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8534 (mm) REVERT: B 669 SER cc_start: 0.8650 (m) cc_final: 0.8350 (p) REVERT: B 682 MET cc_start: 0.7360 (ttt) cc_final: 0.7056 (mpp) REVERT: B 880 MET cc_start: 0.1122 (mtm) cc_final: -0.0602 (ttm) REVERT: B 901 LEU cc_start: 0.9603 (mt) cc_final: 0.9392 (mt) outliers start: 16 outliers final: 3 residues processed: 282 average time/residue: 0.1228 time to fit residues: 48.4035 Evaluate side-chains 172 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 167 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 834 THR Chi-restraints excluded: chain C residue 875 THR Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain B residue 653 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 40.0000 overall best weight: 2.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 501 ASN C 534 GLN ** C 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 588 HIS D 615 GLN D 886 GLN B 739 HIS B 789 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.131976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.087837 restraints weight = 38899.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.090498 restraints weight = 19912.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.092105 restraints weight = 13761.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.093148 restraints weight = 11147.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.093696 restraints weight = 9894.775| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13005 Z= 0.197 Angle : 0.674 12.344 17606 Z= 0.325 Chirality : 0.042 0.198 1853 Planarity : 0.004 0.061 2281 Dihedral : 4.485 41.370 1760 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.10 % Allowed : 14.58 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: -0.23 (0.22), residues: 1563 helix: 0.45 (0.23), residues: 527 sheet: -0.99 (0.48), residues: 125 loop : -0.31 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 771 TYR 0.013 0.002 TYR D 793 PHE 0.021 0.002 PHE C 701 TRP 0.026 0.002 TRP D 860 HIS 0.005 0.001 HIS D 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.20 (12969) covalent geometry : angle 0.63044 / 0.32 (17552) hydrogen bonds : bond 0.03928 / 2.62 ( 424) hydrogen bonds : angle 5.55828 / 3.96 ( 1158) metal coordination : bond 0.00750 / 0.53 ( 36) metal coordination : angle 4.35377 / 3.24 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 0.410 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: A 683 TYR cc_start: 0.8202 (OUTLIER) cc_final: 0.7319 (t80) REVERT: A 754 LEU cc_start: 0.9263 (tt) cc_final: 0.8541 (mp) REVERT: C 548 MET cc_start: 0.7931 (mmp) cc_final: 0.7612 (mmp) REVERT: C 557 CYS cc_start: 0.6942 (m) cc_final: 0.6574 (m) REVERT: C 667 GLU cc_start: 0.8168 (pm20) cc_final: 0.7851 (pm20) REVERT: C 668 ASP cc_start: 0.8579 (m-30) cc_final: 0.8058 (m-30) REVERT: C 771 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7513 (mtm-85) REVERT: D 306 TRP cc_start: 0.7497 (m100) cc_final: 0.6684 (m100) REVERT: D 329 MET cc_start: 0.8627 (tpp) cc_final: 0.8401 (tmm) REVERT: D 513 MET cc_start: 0.8983 (mtp) cc_final: 0.8690 (mmm) REVERT: D 606 GLN cc_start: 0.9218 (mm110) cc_final: 0.8382 (tm-30) REVERT: D 715 ILE cc_start: 0.9513 (tp) cc_final: 0.9186 (mm) REVERT: D 882 ARG cc_start: 0.8597 (ptm-80) cc_final: 0.8214 (ptm-80) REVERT: B 513 MET cc_start: 0.7869 (ttp) cc_final: 0.7310 (tpp) REVERT: B 548 MET cc_start: 0.4166 (mmt) cc_final: 0.3560 (mtm) REVERT: B 669 SER cc_start: 0.8575 (m) cc_final: 0.8359 (p) REVERT: B 724 TYR cc_start: 0.3891 (m-80) cc_final: 0.3518 (m-80) REVERT: B 739 HIS cc_start: 0.7982 (OUTLIER) cc_final: 0.7534 (t70) REVERT: B 793 TYR cc_start: 0.8487 (m-80) cc_final: 0.8174 (m-80) REVERT: B 864 MET cc_start: 0.6914 (mmm) cc_final: 0.6479 (mmm) REVERT: B 880 MET cc_start: 0.1008 (mtm) cc_final: -0.1057 (ttm) outliers start: 28 outliers final: 15 residues processed: 198 average time/residue: 0.1175 time to fit residues: 33.3102 Evaluate side-chains 176 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 759 VAL Chi-restraints excluded: chain C residue 771 ARG Chi-restraints excluded: chain C residue 834 THR Chi-restraints excluded: chain C residue 851 PHE Chi-restraints excluded: chain C residue 861 CYS Chi-restraints excluded: chain C residue 875 THR Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain D residue 789 HIS Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 834 THR Chi-restraints excluded: chain B residue 536 TYR Chi-restraints excluded: chain B residue 640 PHE Chi-restraints excluded: chain B residue 739 HIS Chi-restraints excluded: chain B residue 764 SER Chi-restraints excluded: chain B residue 833 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: [21, 9, 127, 63, 30, 51, 131, 119, 32, 76, 29] chunk 21 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 127 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 30 optimal weight: 0.0870 chunk 51 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 chunk 119 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 overall best weight: 2.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 692 GLN ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.130368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.086390 restraints weight = 40184.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.088996 restraints weight = 20437.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.090455 restraints weight = 14084.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.091565 restraints weight = 11496.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.091881 restraints weight = 10160.052| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13005 Z= 0.202 Angle : 0.671 11.879 17606 Z= 0.322 Chirality : 0.042 0.160 1853 Planarity : 0.004 0.048 2281 Dihedral : 4.666 41.613 1758 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.01 % Allowed : 14.73 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: 1563 helix: 0.32 (0.23), residues: 533 sheet: -1.30 (0.50), residues: 118 loop : -0.39 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 792 TYR 0.016 0.002 TYR D 724 PHE 0.022 0.002 PHE D 731 TRP 0.015 0.001 TRP D 313 HIS 0.013 0.001 HIS D 739 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 (12969) covalent geometry : angle 0.62969 / 0.32 (17552) hydrogen bonds : bond 0.03476 / 2.30 ( 424) hydrogen bonds : angle 5.34049 / 3.81 ( 1158) metal coordination : bond 0.00690 / 0.49 ( 36) metal coordination : angle 4.22898 / 3.08 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 167 time to evaluate : 0.478 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: A 683 TYR cc_start: 0.8314 (OUTLIER) cc_final: 0.7537 (t80) REVERT: A 754 LEU cc_start: 0.9290 (tt) cc_final: 0.8735 (mp) REVERT: A 757 ASN cc_start: 0.8077 (t0) cc_final: 0.7794 (t0) REVERT: A 793 TYR cc_start: 0.7713 (m-80) cc_final: 0.7329 (m-80) REVERT: A 902 PHE cc_start: 0.9382 (m-10) cc_final: 0.9165 (m-10) REVERT: A 909 PHE cc_start: 0.7925 (m-80) cc_final: 0.7368 (m-80) REVERT: C 513 MET cc_start: 0.8194 (tmm) cc_final: 0.7895 (tmm) REVERT: C 548 MET cc_start: 0.7971 (mmp) cc_final: 0.7670 (mmp) REVERT: C 557 CYS cc_start: 0.7017 (m) cc_final: 0.6442 (m) REVERT: C 731 PHE cc_start: 0.8921 (t80) cc_final: 0.8641 (t80) REVERT: C 885 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.7299 (ttp-170) REVERT: D 306 TRP cc_start: 0.7400 (m100) cc_final: 0.6548 (m100) REVERT: D 329 MET cc_start: 0.8467 (tpp) cc_final: 0.8164 (tmm) REVERT: D 577 LYS cc_start: 0.9300 (ptpp) cc_final: 0.9095 (ptpp) REVERT: D 606 GLN cc_start: 0.9189 (mm110) cc_final: 0.8371 (tm-30) REVERT: D 715 ILE cc_start: 0.9587 (tp) cc_final: 0.9243 (mm) REVERT: D 882 ARG cc_start: 0.8658 (ptm-80) cc_final: 0.8255 (ptm-80) REVERT: D 887 ARG cc_start: 0.9288 (OUTLIER) cc_final: 0.8441 (tmm-80) REVERT: B 536 TYR cc_start: 0.7821 (OUTLIER) cc_final: 0.7615 (t80) REVERT: B 548 MET cc_start: 0.3974 (mmt) cc_final: 0.3339 (mtm) REVERT: B 615 GLN cc_start: 0.7898 (tm-30) cc_final: 0.7424 (tm-30) REVERT: B 669 SER cc_start: 0.8630 (m) cc_final: 0.8412 (p) REVERT: B 768 ASP cc_start: 0.8823 (m-30) cc_final: 0.8448 (m-30) REVERT: B 793 TYR cc_start: 0.8364 (m-80) cc_final: 0.8095 (m-80) REVERT: B 880 MET cc_start: 0.1067 (mtm) cc_final: -0.1075 (ttm) outliers start: 40 outliers final: 18 residues processed: 195 average time/residue: 0.1233 time to fit residues: 34.1901 Evaluate side-chains 177 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 759 VAL Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 834 THR Chi-restraints excluded: chain C residue 851 PHE Chi-restraints excluded: chain C residue 861 CYS Chi-restraints excluded: chain C residue 875 THR Chi-restraints excluded: chain C residue 885 ARG Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain D residue 789 HIS Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 834 THR Chi-restraints excluded: chain D residue 859 LEU Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 887 ARG Chi-restraints excluded: chain B residue 536 TYR Chi-restraints excluded: chain B residue 640 PHE Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain B residue 764 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: [120, 9, 55, 143, 70, 105, 110, 98, 71, 100, 118] chunk 120 optimal weight: 20.0000 chunk 9 optimal weight: 20.0000 chunk 55 optimal weight: 0.0980 chunk 143 optimal weight: 0.6980 chunk 70 optimal weight: 50.0000 chunk 105 optimal weight: 0.7980 chunk 110 optimal weight: 0.6980 chunk 98 optimal weight: 0.0770 chunk 71 optimal weight: 0.0770 chunk 100 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 789 HIS ** D 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.133249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.089436 restraints weight = 39224.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.092153 restraints weight = 19857.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.094005 restraints weight = 13642.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.094798 restraints weight = 10943.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.095546 restraints weight = 9816.581| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13005 Z= 0.109 Angle : 0.606 11.321 17606 Z= 0.288 Chirality : 0.041 0.167 1853 Planarity : 0.004 0.043 2281 Dihedral : 4.477 39.953 1758 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.88 % Allowed : 16.00 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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 (0.22), residues: 1563 helix: 0.47 (0.23), residues: 536 sheet: -1.12 (0.47), residues: 126 loop : -0.36 (0.21), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 556 TYR 0.016 0.001 TYR B 724 PHE 0.021 0.002 PHE B 902 TRP 0.010 0.001 TRP C 795 HIS 0.005 0.001 HIS D 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (12969) covalent geometry : angle 0.57051 / 0.29 (17552) hydrogen bonds : bond 0.02959 / 1.99 ( 424) hydrogen bonds : angle 5.00996 / 3.57 ( 1158) metal coordination : bond 0.00442 / 0.32 ( 36) metal coordination : angle 3.72149 / 2.72 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.415 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: A 683 TYR cc_start: 0.8440 (OUTLIER) cc_final: 0.7650 (t80) REVERT: A 754 LEU cc_start: 0.9274 (tt) cc_final: 0.8728 (mp) REVERT: A 757 ASN cc_start: 0.7551 (t0) cc_final: 0.7134 (t0) REVERT: A 767 ARG cc_start: 0.9246 (mtm180) cc_final: 0.8984 (mtm-85) REVERT: A 779 MET cc_start: 0.7050 (tpt) cc_final: 0.6749 (tpt) REVERT: A 793 TYR cc_start: 0.7898 (m-80) cc_final: 0.7510 (m-80) REVERT: A 909 PHE cc_start: 0.7986 (m-80) cc_final: 0.7554 (m-80) REVERT: C 513 MET cc_start: 0.8079 (tmm) cc_final: 0.7680 (tmm) REVERT: C 548 MET cc_start: 0.7925 (mmp) cc_final: 0.7661 (mmp) REVERT: C 674 MET cc_start: 0.8115 (tpp) cc_final: 0.7805 (tpp) REVERT: C 731 PHE cc_start: 0.8775 (t80) cc_final: 0.8390 (t80) REVERT: D 306 TRP cc_start: 0.7429 (m100) cc_final: 0.6561 (m100) REVERT: D 577 LYS cc_start: 0.9292 (ptpp) cc_final: 0.9074 (ptpp) REVERT: D 606 GLN cc_start: 0.9183 (mm110) cc_final: 0.8234 (tm-30) REVERT: D 715 ILE cc_start: 0.9563 (tp) cc_final: 0.9223 (mm) REVERT: D 721 LYS cc_start: 0.9197 (mtpp) cc_final: 0.8798 (mtpt) REVERT: D 779 MET cc_start: 0.8348 (ttp) cc_final: 0.8069 (ppp) REVERT: D 882 ARG cc_start: 0.8580 (ptm-80) cc_final: 0.8223 (ptm-80) REVERT: D 887 ARG cc_start: 0.9245 (OUTLIER) cc_final: 0.8386 (tmm-80) REVERT: B 513 MET cc_start: 0.6969 (ttm) cc_final: 0.5948 (mmm) REVERT: B 536 TYR cc_start: 0.7636 (OUTLIER) cc_final: 0.7430 (t80) REVERT: B 548 MET cc_start: 0.4068 (mmt) cc_final: 0.3305 (mtm) REVERT: B 767 ARG cc_start: 0.8926 (ptp-170) cc_final: 0.8695 (ptp90) REVERT: B 768 ASP cc_start: 0.8747 (m-30) cc_final: 0.8360 (m-30) REVERT: B 769 ILE cc_start: 0.9422 (mm) cc_final: 0.9122 (mt) REVERT: B 880 MET cc_start: 0.0471 (mtm) cc_final: -0.1631 (ttm) outliers start: 25 outliers final: 14 residues processed: 201 average time/residue: 0.1222 time to fit residues: 34.6656 Evaluate side-chains 174 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 834 THR Chi-restraints excluded: chain C residue 851 PHE Chi-restraints excluded: chain C residue 861 CYS Chi-restraints excluded: chain C residue 875 THR Chi-restraints excluded: chain D residue 484 ARG Chi-restraints excluded: chain D residue 739 HIS Chi-restraints excluded: chain D residue 789 HIS Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 887 ARG Chi-restraints excluded: chain B residue 536 TYR Chi-restraints excluded: chain B residue 640 PHE Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 779 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: [24, 128, 19, 48, 6, 81, 49, 11, 3, 30, 113] chunk 24 optimal weight: 20.0000 chunk 128 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 81 optimal weight: 0.0370 chunk 49 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 overall best weight: 2.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 757 ASN C 611 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.130411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.086712 restraints weight = 39857.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.089350 restraints weight = 20240.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.090915 restraints weight = 13896.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.091943 restraints weight = 11238.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.092169 restraints weight = 9980.633| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13005 Z= 0.177 Angle : 0.649 12.715 17606 Z= 0.309 Chirality : 0.042 0.165 1853 Planarity : 0.004 0.054 2281 Dihedral : 4.629 41.170 1758 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.10 % Allowed : 17.81 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: -0.30 (0.21), residues: 1563 helix: 0.46 (0.23), residues: 533 sheet: -1.23 (0.45), residues: 131 loop : -0.37 (0.21), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 556 TYR 0.015 0.001 TYR D 724 PHE 0.020 0.002 PHE D 731 TRP 0.009 0.001 TRP C 581 HIS 0.007 0.001 HIS D 739 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (12969) covalent geometry : angle 0.60614 / 0.31 (17552) hydrogen bonds : bond 0.03108 / 2.05 ( 424) hydrogen bonds : angle 5.08778 / 3.64 ( 1158) metal coordination : bond 0.00583 / 0.42 ( 36) metal coordination : angle 4.25149 / 2.95 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 0.407 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: A 683 TYR cc_start: 0.8419 (OUTLIER) cc_final: 0.7689 (t80) REVERT: A 754 LEU cc_start: 0.9286 (tt) cc_final: 0.8777 (mp) REVERT: A 779 MET cc_start: 0.7174 (tpt) cc_final: 0.6838 (tpt) REVERT: A 793 TYR cc_start: 0.7946 (m-80) cc_final: 0.7709 (m-10) REVERT: A 909 PHE cc_start: 0.8210 (m-80) cc_final: 0.7856 (m-80) REVERT: C 513 MET cc_start: 0.8169 (tmm) cc_final: 0.7825 (tmm) REVERT: C 731 PHE cc_start: 0.8895 (t80) cc_final: 0.8488 (t80) REVERT: D 306 TRP cc_start: 0.7440 (m100) cc_final: 0.6517 (m100) REVERT: D 345 MET cc_start: 0.6040 (ppp) cc_final: 0.5730 (ppp) REVERT: D 577 LYS cc_start: 0.9296 (ptpp) cc_final: 0.9088 (ptpp) REVERT: D 606 GLN cc_start: 0.9231 (mm110) cc_final: 0.8345 (tm-30) REVERT: D 607 MET cc_start: 0.8793 (tpp) cc_final: 0.8569 (tpp) REVERT: D 715 ILE cc_start: 0.9608 (tp) cc_final: 0.9238 (mm) REVERT: D 721 LYS cc_start: 0.9307 (mtpp) cc_final: 0.8897 (mtpt) REVERT: D 739 HIS cc_start: 0.7590 (OUTLIER) cc_final: 0.7258 (t70) REVERT: D 833 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8581 (pp) REVERT: D 882 ARG cc_start: 0.8625 (ptm-80) cc_final: 0.8228 (ptm-80) REVERT: D 887 ARG cc_start: 0.9275 (OUTLIER) cc_final: 0.8410 (tmm-80) REVERT: B 513 MET cc_start: 0.6669 (ttm) cc_final: 0.6449 (ttm) REVERT: B 536 TYR cc_start: 0.7917 (OUTLIER) cc_final: 0.7637 (t80) REVERT: B 548 MET cc_start: 0.4067 (mmt) cc_final: 0.3310 (mtm) REVERT: B 767 ARG cc_start: 0.8979 (ptp-170) cc_final: 0.8764 (ptp90) REVERT: B 768 ASP cc_start: 0.8737 (m-30) cc_final: 0.8307 (m-30) REVERT: B 769 ILE cc_start: 0.9499 (mm) cc_final: 0.9223 (mt) REVERT: B 880 MET cc_start: 0.0611 (mtm) cc_final: -0.1513 (ttm) outliers start: 28 outliers final: 18 residues processed: 181 average time/residue: 0.1216 time to fit residues: 31.2129 Evaluate side-chains 177 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 759 VAL Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 834 THR Chi-restraints excluded: chain C residue 851 PHE Chi-restraints excluded: chain C residue 861 CYS Chi-restraints excluded: chain C residue 875 THR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 739 HIS Chi-restraints excluded: chain D residue 789 HIS Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 833 ILE Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 887 ARG Chi-restraints excluded: chain B residue 536 TYR Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain B residue 761 MET Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 779 MET Chi-restraints excluded: chain B residue 798 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: [156, 35, 45, 12, 98, 50, 145, 148, 78, 105, 8] chunk 156 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 98 optimal weight: 0.0980 chunk 50 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 chunk 148 optimal weight: 8.9990 chunk 78 optimal weight: 40.0000 chunk 105 optimal weight: 0.9980 chunk 8 optimal weight: 20.0000 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.130299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.086407 restraints weight = 39607.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.089000 restraints weight = 20527.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.090718 restraints weight = 14293.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.091467 restraints weight = 11564.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.091538 restraints weight = 10440.514| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13005 Z= 0.187 Angle : 0.667 12.732 17606 Z= 0.316 Chirality : 0.042 0.169 1853 Planarity : 0.004 0.052 2281 Dihedral : 4.715 41.935 1758 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.55 % Allowed : 17.96 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: -0.38 (0.21), residues: 1563 helix: 0.38 (0.23), residues: 534 sheet: -1.21 (0.46), residues: 126 loop : -0.42 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 556 TYR 0.015 0.001 TYR C 683 PHE 0.032 0.002 PHE D 331 TRP 0.014 0.001 TRP D 860 HIS 0.007 0.001 HIS D 739 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 (12969) covalent geometry : angle 0.62121 / 0.31 (17552) hydrogen bonds : bond 0.03116 / 2.02 ( 424) hydrogen bonds : angle 5.16050 / 3.69 ( 1158) metal coordination : bond 0.00628 / 0.44 ( 36) metal coordination : angle 4.40581 / 3.13 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 0.566 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: A 683 TYR cc_start: 0.8443 (OUTLIER) cc_final: 0.7718 (t80) REVERT: A 754 LEU cc_start: 0.9290 (tt) cc_final: 0.8818 (mp) REVERT: A 801 MET cc_start: 0.7608 (mtt) cc_final: 0.7206 (mmt) REVERT: A 902 PHE cc_start: 0.9306 (m-10) cc_final: 0.9062 (m-80) REVERT: A 909 PHE cc_start: 0.8127 (m-80) cc_final: 0.7682 (m-80) REVERT: C 513 MET cc_start: 0.8303 (tmm) cc_final: 0.7900 (tmm) REVERT: C 607 MET cc_start: 0.9222 (tpp) cc_final: 0.9003 (tpp) REVERT: C 731 PHE cc_start: 0.8851 (t80) cc_final: 0.8588 (t80) REVERT: D 306 TRP cc_start: 0.7457 (m100) cc_final: 0.6476 (m100) REVERT: D 329 MET cc_start: 0.7356 (OUTLIER) cc_final: 0.7148 (ppp) REVERT: D 345 MET cc_start: 0.6095 (ppp) cc_final: 0.5790 (ppp) REVERT: D 523 GLU cc_start: 0.8493 (mt-10) cc_final: 0.7652 (mt-10) REVERT: D 606 GLN cc_start: 0.9221 (mm110) cc_final: 0.8358 (tm-30) REVERT: D 607 MET cc_start: 0.8806 (tpp) cc_final: 0.8557 (tpp) REVERT: D 715 ILE cc_start: 0.9643 (tp) cc_final: 0.9275 (mm) REVERT: D 721 LYS cc_start: 0.9309 (mtpp) cc_final: 0.8907 (mtpt) REVERT: D 739 HIS cc_start: 0.7554 (OUTLIER) cc_final: 0.7242 (t-90) REVERT: D 756 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7722 (tm-30) REVERT: D 761 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.7287 (ppp) REVERT: D 833 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8620 (pp) REVERT: D 860 TRP cc_start: 0.8285 (m-10) cc_final: 0.7497 (m-90) REVERT: D 882 ARG cc_start: 0.8451 (ptm-80) cc_final: 0.8065 (ptm-80) REVERT: D 887 ARG cc_start: 0.9265 (OUTLIER) cc_final: 0.8263 (tmm-80) REVERT: B 536 TYR cc_start: 0.7999 (OUTLIER) cc_final: 0.7690 (t80) REVERT: B 548 MET cc_start: 0.4033 (mmt) cc_final: 0.3281 (mtm) REVERT: B 767 ARG cc_start: 0.9040 (ptp-170) cc_final: 0.8819 (ptp90) REVERT: B 768 ASP cc_start: 0.8731 (m-30) cc_final: 0.8323 (m-30) REVERT: B 769 ILE cc_start: 0.9540 (mm) cc_final: 0.9261 (mt) REVERT: B 801 MET cc_start: 0.7655 (mtp) cc_final: 0.7354 (mtp) REVERT: B 880 MET cc_start: 0.0580 (mtm) cc_final: -0.1533 (ttm) outliers start: 34 outliers final: 22 residues processed: 178 average time/residue: 0.1116 time to fit residues: 28.6563 Evaluate side-chains 185 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 834 THR Chi-restraints excluded: chain C residue 851 PHE Chi-restraints excluded: chain C residue 861 CYS Chi-restraints excluded: chain C residue 875 THR Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 329 MET Chi-restraints excluded: chain D residue 331 PHE Chi-restraints excluded: chain D residue 484 ARG Chi-restraints excluded: chain D residue 739 HIS Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain D residue 761 MET Chi-restraints excluded: chain D residue 789 HIS Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 833 ILE Chi-restraints excluded: chain D residue 834 THR Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 887 ARG Chi-restraints excluded: chain B residue 536 TYR Chi-restraints excluded: chain B residue 640 PHE Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain B residue 761 MET Chi-restraints excluded: chain B residue 779 MET Chi-restraints excluded: chain B residue 798 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: [39, 20, 74, 136, 150, 93, 117, 98, 92, 125, 9] chunk 39 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 150 optimal weight: 0.2980 chunk 93 optimal weight: 0.8980 chunk 117 optimal weight: 0.7980 chunk 98 optimal weight: 0.0470 chunk 92 optimal weight: 0.6980 chunk 125 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 797 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.132535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.088824 restraints weight = 39174.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.091639 restraints weight = 20048.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.093362 restraints weight = 13764.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.094153 restraints weight = 11155.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.094370 restraints weight = 10020.311| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13005 Z= 0.107 Angle : 0.632 12.388 17606 Z= 0.293 Chirality : 0.041 0.170 1853 Planarity : 0.004 0.049 2281 Dihedral : 4.489 39.149 1758 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.10 % Allowed : 18.33 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: -0.26 (0.21), residues: 1563 helix: 0.48 (0.23), residues: 533 sheet: -1.09 (0.46), residues: 126 loop : -0.36 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 556 TYR 0.014 0.001 TYR B 724 PHE 0.024 0.001 PHE D 331 TRP 0.013 0.001 TRP C 795 HIS 0.004 0.001 HIS D 739 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (12969) covalent geometry : angle 0.58643 / 0.29 (17552) hydrogen bonds : bond 0.02840 / 1.90 ( 424) hydrogen bonds : angle 5.00616 / 3.58 ( 1158) metal coordination : bond 0.00477 / 0.35 ( 36) metal coordination : angle 4.29243 / 3.12 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.553 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: A 683 TYR cc_start: 0.8460 (OUTLIER) cc_final: 0.7631 (t80) REVERT: A 754 LEU cc_start: 0.9283 (tt) cc_final: 0.8752 (mp) REVERT: A 767 ARG cc_start: 0.9239 (mtm180) cc_final: 0.8985 (mtm-85) REVERT: A 779 MET cc_start: 0.7737 (tpt) cc_final: 0.7233 (tpp) REVERT: A 902 PHE cc_start: 0.9304 (m-10) cc_final: 0.9097 (m-10) REVERT: A 909 PHE cc_start: 0.8036 (m-80) cc_final: 0.7592 (m-80) REVERT: C 513 MET cc_start: 0.8280 (tmm) cc_final: 0.7859 (tmm) REVERT: C 731 PHE cc_start: 0.8747 (t80) cc_final: 0.8314 (t80) REVERT: C 879 ASN cc_start: 0.8826 (p0) cc_final: 0.8603 (m-40) REVERT: D 306 TRP cc_start: 0.7424 (m100) cc_final: 0.6492 (m100) REVERT: D 345 MET cc_start: 0.5818 (ppp) cc_final: 0.5479 (ppp) REVERT: D 606 GLN cc_start: 0.9180 (mm110) cc_final: 0.8291 (tm-30) REVERT: D 715 ILE cc_start: 0.9600 (tp) cc_final: 0.9259 (mm) REVERT: D 721 LYS cc_start: 0.9279 (mtpp) cc_final: 0.8865 (mtpt) REVERT: D 739 HIS cc_start: 0.7599 (OUTLIER) cc_final: 0.7328 (t-90) REVERT: D 833 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8511 (pp) REVERT: D 882 ARG cc_start: 0.8395 (ptm-80) cc_final: 0.7995 (ptm-80) REVERT: D 887 ARG cc_start: 0.9241 (OUTLIER) cc_final: 0.8253 (tmm-80) REVERT: B 682 MET cc_start: 0.6846 (mpp) cc_final: 0.6644 (mpp) REVERT: B 767 ARG cc_start: 0.8958 (ptp-170) cc_final: 0.8728 (ptp90) REVERT: B 768 ASP cc_start: 0.8634 (m-30) cc_final: 0.8221 (m-30) REVERT: B 769 ILE cc_start: 0.9483 (mm) cc_final: 0.9186 (mt) REVERT: B 801 MET cc_start: 0.7733 (mtp) cc_final: 0.7464 (mtp) REVERT: B 880 MET cc_start: 0.0528 (mtm) cc_final: -0.1200 (ttm) REVERT: B 885 ARG cc_start: 0.8622 (ttm170) cc_final: 0.8017 (ttm170) outliers start: 28 outliers final: 18 residues processed: 184 average time/residue: 0.1135 time to fit residues: 30.5263 Evaluate side-chains 178 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 834 THR Chi-restraints excluded: chain C residue 851 PHE Chi-restraints excluded: chain C residue 861 CYS Chi-restraints excluded: chain C residue 875 THR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 331 PHE Chi-restraints excluded: chain D residue 484 ARG Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 739 HIS Chi-restraints excluded: chain D residue 789 HIS Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 833 ILE Chi-restraints excluded: chain D residue 887 ARG Chi-restraints excluded: chain B residue 640 PHE Chi-restraints excluded: chain B residue 761 MET Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 779 MET Chi-restraints excluded: chain B residue 798 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: [78, 153, 10, 6, 28, 95, 125, 53, 75, 17, 65] chunk 78 optimal weight: 40.0000 chunk 153 optimal weight: 30.0000 chunk 10 optimal weight: 6.9990 chunk 6 optimal weight: 40.0000 chunk 28 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 125 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 65 optimal weight: 30.0000 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 GLN ** 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 = 0.4345 r_free = 0.4345 target = 0.129066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.085595 restraints weight = 39273.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.088237 restraints weight = 20363.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.089562 restraints weight = 14108.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.090547 restraints weight = 11654.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.091215 restraints weight = 10397.325| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 13005 Z= 0.249 Angle : 0.728 14.787 17606 Z= 0.348 Chirality : 0.043 0.192 1853 Planarity : 0.005 0.043 2281 Dihedral : 4.822 42.441 1758 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.40 % Allowed : 18.26 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: -0.46 (0.21), residues: 1563 helix: 0.40 (0.23), residues: 530 sheet: -1.42 (0.44), residues: 131 loop : -0.50 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 790 TYR 0.024 0.002 TYR B 793 PHE 0.025 0.002 PHE C 701 TRP 0.011 0.002 TRP B 581 HIS 0.007 0.001 HIS D 739 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.25 (12969) covalent geometry : angle 0.67871 / 0.35 (17552) hydrogen bonds : bond 0.03264 / 2.12 ( 424) hydrogen bonds : angle 5.25413 / 3.78 ( 1158) metal coordination : bond 0.00763 / 0.55 ( 36) metal coordination : angle 4.82587 / 3.41 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.480 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: A 683 TYR cc_start: 0.8374 (OUTLIER) cc_final: 0.7615 (t80) REVERT: A 754 LEU cc_start: 0.9316 (tt) cc_final: 0.8778 (mp) REVERT: A 801 MET cc_start: 0.7578 (mmt) cc_final: 0.7294 (mmt) REVERT: A 909 PHE cc_start: 0.8062 (m-80) cc_final: 0.7630 (m-80) REVERT: C 513 MET cc_start: 0.8235 (tmm) cc_final: 0.7817 (tmm) REVERT: C 607 MET cc_start: 0.9268 (tpp) cc_final: 0.9049 (tpp) REVERT: C 667 GLU cc_start: 0.8720 (pm20) cc_final: 0.8496 (pm20) REVERT: D 306 TRP cc_start: 0.7136 (m100) cc_final: 0.6852 (m100) REVERT: D 345 MET cc_start: 0.6112 (ppp) cc_final: 0.5815 (ppp) REVERT: D 383 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7656 (pt) REVERT: D 523 GLU cc_start: 0.8465 (mt-10) cc_final: 0.7656 (mt-10) REVERT: D 606 GLN cc_start: 0.9214 (mm110) cc_final: 0.8394 (tm-30) REVERT: D 715 ILE cc_start: 0.9673 (tp) cc_final: 0.9283 (mm) REVERT: D 721 LYS cc_start: 0.9323 (mtpp) cc_final: 0.8912 (mtpt) REVERT: D 739 HIS cc_start: 0.7720 (OUTLIER) cc_final: 0.7367 (t-90) REVERT: D 756 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7721 (tm-30) REVERT: D 761 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.7294 (ppp) REVERT: D 833 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8594 (pp) REVERT: D 882 ARG cc_start: 0.8508 (ptm-80) cc_final: 0.8043 (ptm-80) REVERT: D 887 ARG cc_start: 0.9292 (OUTLIER) cc_final: 0.8310 (tmm-80) REVERT: B 536 TYR cc_start: 0.7948 (OUTLIER) cc_final: 0.7529 (t80) REVERT: B 767 ARG cc_start: 0.9016 (ptp-170) cc_final: 0.8795 (ptp90) REVERT: B 768 ASP cc_start: 0.8665 (m-30) cc_final: 0.8253 (m-30) REVERT: B 769 ILE cc_start: 0.9571 (mm) cc_final: 0.9294 (mt) REVERT: B 801 MET cc_start: 0.8105 (mtp) cc_final: 0.7723 (mtp) REVERT: B 880 MET cc_start: 0.0575 (mtm) cc_final: -0.1556 (ttm) outliers start: 32 outliers final: 20 residues processed: 176 average time/residue: 0.1125 time to fit residues: 28.1493 Evaluate side-chains 174 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 834 THR Chi-restraints excluded: chain C residue 851 PHE Chi-restraints excluded: chain C residue 861 CYS Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 331 PHE Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain D residue 484 ARG Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 739 HIS Chi-restraints excluded: chain D residue 756 GLU Chi-restraints excluded: chain D residue 761 MET Chi-restraints excluded: chain D residue 789 HIS Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 833 ILE Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 887 ARG Chi-restraints excluded: chain B residue 536 TYR Chi-restraints excluded: chain B residue 640 PHE Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain B residue 761 MET Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 798 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: [3, 103, 99, 127, 149, 22, 94, 57, 89, 105, 18] chunk 3 optimal weight: 9.9990 chunk 103 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 127 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 94 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 105 optimal weight: 0.0980 chunk 18 optimal weight: 10.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 797 ASN B 678 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.130408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.087298 restraints weight = 39680.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.089905 restraints weight = 20267.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.091302 restraints weight = 13986.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.092417 restraints weight = 11480.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.092773 restraints weight = 10166.025| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13005 Z= 0.137 Angle : 0.670 13.981 17606 Z= 0.314 Chirality : 0.042 0.197 1853 Planarity : 0.004 0.070 2281 Dihedral : 4.593 40.727 1757 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.03 % Allowed : 18.63 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: -0.34 (0.21), residues: 1563 helix: 0.49 (0.23), residues: 532 sheet: -1.07 (0.45), residues: 129 loop : -0.47 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 556 TYR 0.014 0.001 TYR B 793 PHE 0.024 0.002 PHE D 331 TRP 0.011 0.001 TRP D 860 HIS 0.005 0.001 HIS D 739 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (12969) covalent geometry : angle 0.62283 / 0.31 (17552) hydrogen bonds : bond 0.02935 / 1.92 ( 424) hydrogen bonds : angle 5.09863 / 3.66 ( 1158) metal coordination : bond 0.00516 / 0.37 ( 36) metal coordination : angle 4.51714 / 3.24 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.477 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: A 683 TYR cc_start: 0.8603 (OUTLIER) cc_final: 0.7802 (t80) REVERT: A 754 LEU cc_start: 0.9345 (tt) cc_final: 0.8755 (mp) REVERT: A 767 ARG cc_start: 0.9224 (mtm180) cc_final: 0.8998 (mtm-85) REVERT: A 801 MET cc_start: 0.7562 (mmt) cc_final: 0.7200 (mmt) REVERT: A 909 PHE cc_start: 0.8078 (m-80) cc_final: 0.7641 (m-80) REVERT: C 513 MET cc_start: 0.8350 (tmm) cc_final: 0.7968 (tmm) REVERT: C 607 MET cc_start: 0.9230 (tpp) cc_final: 0.9020 (tpp) REVERT: D 306 TRP cc_start: 0.7559 (m100) cc_final: 0.6813 (m100) REVERT: D 329 MET cc_start: 0.8073 (ppp) cc_final: 0.7556 (mmp) REVERT: D 345 MET cc_start: 0.6066 (ppp) cc_final: 0.5714 (ppp) REVERT: D 523 GLU cc_start: 0.8442 (mt-10) cc_final: 0.7608 (mt-10) REVERT: D 536 TYR cc_start: 0.8420 (m-80) cc_final: 0.8073 (m-80) REVERT: D 606 GLN cc_start: 0.9168 (mm110) cc_final: 0.8319 (tm-30) REVERT: D 715 ILE cc_start: 0.9657 (tp) cc_final: 0.9277 (mm) REVERT: D 721 LYS cc_start: 0.9282 (mtpp) cc_final: 0.8847 (mtpt) REVERT: D 739 HIS cc_start: 0.7671 (OUTLIER) cc_final: 0.7360 (t-90) REVERT: D 833 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8593 (pp) REVERT: D 882 ARG cc_start: 0.8471 (ptm-80) cc_final: 0.7994 (ptm-80) REVERT: B 536 TYR cc_start: 0.8021 (OUTLIER) cc_final: 0.7596 (t80) REVERT: B 767 ARG cc_start: 0.8976 (ptp-170) cc_final: 0.8758 (ptp90) REVERT: B 768 ASP cc_start: 0.8666 (m-30) cc_final: 0.8239 (m-30) REVERT: B 769 ILE cc_start: 0.9514 (mm) cc_final: 0.9258 (mt) REVERT: B 801 MET cc_start: 0.8205 (mtp) cc_final: 0.7871 (mtp) REVERT: B 880 MET cc_start: 0.0524 (mtm) cc_final: -0.1561 (ttm) outliers start: 27 outliers final: 18 residues processed: 177 average time/residue: 0.1135 time to fit residues: 28.9038 Evaluate side-chains 173 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 834 THR Chi-restraints excluded: chain C residue 851 PHE Chi-restraints excluded: chain C residue 861 CYS Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 331 PHE Chi-restraints excluded: chain D residue 484 ARG Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 739 HIS Chi-restraints excluded: chain D residue 789 HIS Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 833 ILE Chi-restraints excluded: chain D residue 834 THR Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain B residue 536 TYR Chi-restraints excluded: chain B residue 640 PHE Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 798 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: [9, 51, 37, 96, 56, 114, 59, 95, 5, 131, 20] chunk 9 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 5 optimal weight: 20.0000 chunk 131 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 797 ASN B 615 GLN B 678 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.129805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.086507 restraints weight = 39842.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.089145 restraints weight = 20166.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.090852 restraints weight = 13825.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.091625 restraints weight = 11189.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.091997 restraints weight = 10035.114| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13005 Z= 0.157 Angle : 0.710 15.584 17606 Z= 0.325 Chirality : 0.043 0.248 1853 Planarity : 0.004 0.033 2281 Dihedral : 4.649 41.217 1757 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.95 % Allowed : 18.93 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: -0.41 (0.21), residues: 1563 helix: 0.39 (0.23), residues: 535 sheet: -1.22 (0.44), residues: 130 loop : -0.46 (0.21), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 556 TYR 0.017 0.001 TYR B 793 PHE 0.033 0.002 PHE A 902 TRP 0.011 0.001 TRP C 581 HIS 0.005 0.001 HIS D 739 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (12969) covalent geometry : angle 0.63946 / 0.32 (17552) hydrogen bonds : bond 0.03050 / 1.98 ( 424) hydrogen bonds : angle 5.17236 / 3.72 ( 1158) metal coordination : bond 0.00565 / 0.38 ( 36) metal coordination : angle 5.61078 / 4.38 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.493 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: A 683 TYR cc_start: 0.8604 (OUTLIER) cc_final: 0.7775 (t80) REVERT: A 754 LEU cc_start: 0.9342 (tt) cc_final: 0.8715 (mp) REVERT: A 767 ARG cc_start: 0.9214 (mtm180) cc_final: 0.8976 (mtm-85) REVERT: A 779 MET cc_start: 0.7188 (tpt) cc_final: 0.6588 (tpp) REVERT: A 797 ASN cc_start: 0.7766 (p0) cc_final: 0.7355 (p0) REVERT: A 801 MET cc_start: 0.7575 (mmt) cc_final: 0.7301 (mmt) REVERT: A 909 PHE cc_start: 0.8142 (m-80) cc_final: 0.7680 (m-80) REVERT: C 513 MET cc_start: 0.8285 (tmm) cc_final: 0.7913 (tmm) REVERT: C 607 MET cc_start: 0.9251 (tpp) cc_final: 0.9042 (tpp) REVERT: D 306 TRP cc_start: 0.7655 (m100) cc_final: 0.7109 (m100) REVERT: D 329 MET cc_start: 0.7841 (ppp) cc_final: 0.7546 (mmp) REVERT: D 345 MET cc_start: 0.5950 (ppp) cc_final: 0.5666 (ppp) REVERT: D 523 GLU cc_start: 0.8437 (mt-10) cc_final: 0.7612 (mt-10) REVERT: D 536 TYR cc_start: 0.8534 (m-80) cc_final: 0.8272 (m-80) REVERT: D 606 GLN cc_start: 0.9198 (mm110) cc_final: 0.8313 (tm-30) REVERT: D 715 ILE cc_start: 0.9664 (tp) cc_final: 0.9284 (mm) REVERT: D 721 LYS cc_start: 0.9271 (mtpp) cc_final: 0.8849 (mtpt) REVERT: D 739 HIS cc_start: 0.7735 (OUTLIER) cc_final: 0.7429 (t-90) REVERT: D 833 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8588 (pp) REVERT: D 882 ARG cc_start: 0.8488 (ptm-80) cc_final: 0.8006 (ptm-80) REVERT: B 536 TYR cc_start: 0.7936 (OUTLIER) cc_final: 0.7592 (t80) REVERT: B 548 MET cc_start: -0.0371 (mtm) cc_final: -0.0611 (mtm) REVERT: B 767 ARG cc_start: 0.8971 (ptp-170) cc_final: 0.8754 (ptp90) REVERT: B 768 ASP cc_start: 0.8700 (m-30) cc_final: 0.8302 (m-30) REVERT: B 769 ILE cc_start: 0.9537 (mm) cc_final: 0.9235 (mt) REVERT: B 880 MET cc_start: 0.0336 (mtm) cc_final: -0.1648 (ttm) outliers start: 26 outliers final: 20 residues processed: 174 average time/residue: 0.1194 time to fit residues: 29.6056 Evaluate side-chains 173 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 655 ILE Chi-restraints excluded: chain C residue 834 THR Chi-restraints excluded: chain C residue 851 PHE Chi-restraints excluded: chain C residue 861 CYS Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 331 PHE Chi-restraints excluded: chain D residue 484 ARG Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 739 HIS Chi-restraints excluded: chain D residue 789 HIS Chi-restraints excluded: chain D residue 808 THR Chi-restraints excluded: chain D residue 833 ILE Chi-restraints excluded: chain D residue 834 THR Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain B residue 536 TYR Chi-restraints excluded: chain B residue 615 GLN Chi-restraints excluded: chain B residue 640 PHE Chi-restraints excluded: chain B residue 678 GLN Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 798 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: [124, 87, 134, 144, 54, 123, 51, 94, 7, 138, 58] chunk 124 optimal weight: 50.0000 chunk 87 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 144 optimal weight: 9.9990 chunk 54 optimal weight: 0.8980 chunk 123 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 138 optimal weight: 10.0000 chunk 58 optimal weight: 0.8980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 615 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.129716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.086741 restraints weight = 39911.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.089364 restraints weight = 20317.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.091052 restraints weight = 13955.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.091828 restraints weight = 11324.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.092133 restraints weight = 10153.088| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.248 13005 Z= 0.274 Angle : 1.112 59.198 17606 Z= 0.615 Chirality : 0.050 0.915 1853 Planarity : 0.004 0.038 2281 Dihedral : 4.645 41.304 1757 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.95 % Allowed : 18.93 % Favored : 79.11 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 3.75 % 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: -0.42 (0.21), residues: 1563 helix: 0.38 (0.23), residues: 535 sheet: -1.23 (0.44), residues: 130 loop : -0.47 (0.21), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.039 0.001 ARG C 729 TYR 0.049 0.002 TYR B 793 PHE 0.034 0.002 PHE A 902 TRP 0.015 0.001 TRP C 601 HIS 0.005 0.001 HIS D 739 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.27 (12969) covalent geometry : angle 1.06903 / 0.61 (17552) hydrogen bonds : bond 0.03081 / 1.98 ( 424) hydrogen bonds : angle 5.19039 / 3.73 ( 1158) metal coordination : bond 0.00546 / 0.39 ( 36) metal coordination : angle 5.60244 / 4.37 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3101.33 seconds wall clock time: 53 minutes 45.25 seconds (3225.25 seconds total)