Starting phenix.real_space_refine on Wed Feb 4 13:23:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lq1_63290/02_2026/9lq1_63290.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lq1_63290/02_2026/9lq1_63290.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lq1_63290/02_2026/9lq1_63290.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lq1_63290/02_2026/9lq1_63290.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lq1_63290/02_2026/9lq1_63290.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lq1_63290/02_2026/9lq1_63290.map" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 6 6.06 5 S 82 5.16 5 C 6782 2.51 5 N 1865 2.21 5 O 1914 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10649 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3526 Classifications: {'peptide': 440} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 417} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 890 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 8, 'TRANS': 97} Chain: "E" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 899 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "F" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3526 Classifications: {'peptide': 440} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 417} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 907 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "C" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 895 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 97} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 611 SG CYS A 549 93.396 40.270 47.070 1.00 85.67 S ATOM 645 SG CYS A 554 90.929 39.623 44.052 1.00 56.15 S ATOM 858 SG CYS A 583 92.406 36.754 46.224 1.00 86.12 S ATOM 884 SG CYS A 586 94.289 38.700 43.634 1.00 77.32 S ATOM 527 SG CYS A 537 85.231 31.555 53.250 1.00 66.14 S ATOM 548 SG CYS A 540 82.758 29.582 55.230 1.00 69.17 S ATOM 685 SG CYS A 559 86.272 30.450 56.674 1.00 86.17 S ATOM 707 SG CYS A 562 85.914 27.764 54.194 1.00 76.00 S ATOM 214 SG CYS A 497 76.885 21.647 54.066 1.00 79.59 S ATOM 336 SG CYS A 514 74.488 22.024 50.611 1.00 72.17 S ATOM 359 SG CYS A 517 76.501 24.843 51.693 1.00 73.27 S ATOM 5926 SG CYS F 549 64.822 107.151 47.138 1.00 91.09 S ATOM 5960 SG CYS F 554 67.231 107.763 44.069 1.00 61.22 S ATOM 6173 SG CYS F 583 65.962 110.664 46.294 1.00 92.89 S ATOM 6199 SG CYS F 586 63.955 108.751 43.721 1.00 71.72 S ATOM 5529 SG CYS F 497 81.552 125.700 53.913 1.00 77.13 S ATOM 5651 SG CYS F 514 83.758 125.556 50.624 1.00 67.23 S ATOM 5674 SG CYS F 517 82.192 122.285 51.878 1.00 72.74 S ATOM 5842 SG CYS F 537 73.208 115.596 53.353 1.00 63.51 S ATOM 5863 SG CYS F 540 75.561 117.785 55.270 1.00 63.40 S ATOM 6000 SG CYS F 559 72.097 116.653 56.782 1.00 84.34 S ATOM 6022 SG CYS F 562 72.260 119.346 54.479 1.00 73.48 S Time building chain proxies: 2.67, per 1000 atoms: 0.25 Number of scatterers: 10649 At special positions: 0 Unit cell: (159.5, 148.5, 83.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 6 29.99 S 82 16.00 O 1914 8.00 N 1865 7.00 C 6782 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 541.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 586 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 583 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 554 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 549 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 559 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 540 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 537 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 562 " pdb=" ZN A1003 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 497 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 514 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 517 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 586 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 554 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 583 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 549 " pdb=" ZN F1002 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 497 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 514 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 517 " pdb=" ZN F1003 " pdb="ZN ZN F1003 " - pdb=" SG CYS F 559 " pdb="ZN ZN F1003 " - pdb=" SG CYS F 540 " pdb="ZN ZN F1003 " - pdb=" SG CYS F 562 " pdb="ZN ZN F1003 " - pdb=" SG CYS F 537 " Number of angles added : 24 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2448 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 11 sheets defined 28.3% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 473 through 485 Processing helix chain 'A' and resid 489 through 493 removed outlier: 4.095A pdb=" N ILE A 493 " --> pdb=" O ILE A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 525 Processing helix chain 'A' and resid 560 through 567 Processing helix chain 'A' and resid 570 through 578 Processing helix chain 'A' and resid 600 through 608 Processing helix chain 'A' and resid 609 through 611 No H-bonds generated for 'chain 'A' and resid 609 through 611' Processing helix chain 'A' and resid 627 through 631 Processing helix chain 'A' and resid 644 through 654 removed outlier: 3.527A pdb=" N LEU A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 677 Processing helix chain 'A' and resid 691 through 698 Processing helix chain 'A' and resid 717 through 721 Processing helix chain 'A' and resid 730 through 742 Processing helix chain 'A' and resid 762 through 774 Processing helix chain 'A' and resid 783 through 785 No H-bonds generated for 'chain 'A' and resid 783 through 785' Processing helix chain 'A' and resid 814 through 818 removed outlier: 3.554A pdb=" N CYS A 818 " --> pdb=" O LEU A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 841 Processing helix chain 'A' and resid 860 through 868 removed outlier: 4.038A pdb=" N ARG A 866 " --> pdb=" O THR A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 892 Processing helix chain 'A' and resid 894 through 903 Processing helix chain 'A' and resid 904 through 908 Processing helix chain 'B' and resid 63 through 68 Processing helix chain 'E' and resid 63 through 68 Processing helix chain 'F' and resid 474 through 485 Processing helix chain 'F' and resid 489 through 493 removed outlier: 4.174A pdb=" N ILE F 493 " --> pdb=" O ILE F 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 514 through 525 removed outlier: 3.889A pdb=" N ASN F 519 " --> pdb=" O GLN F 515 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N CYS F 520 " --> pdb=" O ASN F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 567 removed outlier: 3.520A pdb=" N VAL F 563 " --> pdb=" O CYS F 559 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 578 removed outlier: 3.590A pdb=" N ALA F 574 " --> pdb=" O GLY F 570 " (cutoff:3.500A) Processing helix chain 'F' and resid 600 through 609 removed outlier: 3.877A pdb=" N PHE F 609 " --> pdb=" O LEU F 605 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 631 Processing helix chain 'F' and resid 644 through 654 removed outlier: 3.621A pdb=" N LEU F 648 " --> pdb=" O ALA F 644 " (cutoff:3.500A) Processing helix chain 'F' and resid 666 through 677 Processing helix chain 'F' and resid 691 through 698 Processing helix chain 'F' and resid 726 through 742 removed outlier: 4.225A pdb=" N GLU F 733 " --> pdb=" O ARG F 729 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE F 734 " --> pdb=" O LEU F 730 " (cutoff:3.500A) Processing helix chain 'F' and resid 762 through 774 Processing helix chain 'F' and resid 783 through 785 No H-bonds generated for 'chain 'F' and resid 783 through 785' Processing helix chain 'F' and resid 814 through 818 removed outlier: 3.570A pdb=" N CYS F 818 " --> pdb=" O LEU F 815 " (cutoff:3.500A) Processing helix chain 'F' and resid 836 through 840 Processing helix chain 'F' and resid 860 through 868 removed outlier: 3.859A pdb=" N ARG F 866 " --> pdb=" O THR F 862 " (cutoff:3.500A) Processing helix chain 'F' and resid 883 through 892 removed outlier: 3.529A pdb=" N ARG F 887 " --> pdb=" O LEU F 883 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER F 892 " --> pdb=" O LEU F 888 " (cutoff:3.500A) Processing helix chain 'F' and resid 894 through 903 Processing helix chain 'F' and resid 904 through 908 Processing helix chain 'D' and resid 63 through 68 Processing helix chain 'C' and resid 63 through 68 Processing sheet with id=AA1, first strand: chain 'A' and resid 504 through 505 Processing sheet with id=AA2, first strand: chain 'A' and resid 546 through 548 removed outlier: 3.953A pdb=" N PHE A 558 " --> pdb=" O LEU A 547 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 591 through 592 Processing sheet with id=AA4, first strand: chain 'A' and resid 682 through 683 removed outlier: 7.540A pdb=" N ILE A 634 " --> pdb=" O ASP A 658 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N TYR A 660 " --> pdb=" O ILE A 634 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL A 636 " --> pdb=" O TYR A 660 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ALA A 662 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N SER A 638 " --> pdb=" O ALA A 662 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N ILE A 705 " --> pdb=" O ARG A 635 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU A 637 " --> pdb=" O ILE A 705 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL A 704 " --> pdb=" O LEU A 754 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N GLU A 756 " --> pdb=" O VAL A 704 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 824 through 825 Processing sheet with id=AA6, first strand: chain 'B' and resid 17 through 22 removed outlier: 6.867A pdb=" N VAL B 25 " --> pdb=" O TRP B 21 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU B 50 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ILE B 39 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ARG B 48 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ILE B 41 " --> pdb=" O GLN B 46 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N GLN B 46 " --> pdb=" O ILE B 41 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 46 through 53 current: chain 'B' and resid 83 through 86 removed outlier: 5.643A pdb=" N LEU B 94 " --> pdb=" O GLU B 109 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLU B 109 " --> pdb=" O LEU B 94 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TYR B 96 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 107 " --> pdb=" O TYR B 96 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 103 through 110 current: chain 'E' and resid 25 through 28 removed outlier: 3.760A pdb=" N ALA E 33 " --> pdb=" O GLU E 54 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU E 50 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ILE E 39 " --> pdb=" O ARG E 48 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ARG E 48 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE E 41 " --> pdb=" O GLN E 46 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N GLN E 46 " --> pdb=" O ILE E 41 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 46 through 54 current: chain 'E' and resid 83 through 86 removed outlier: 5.587A pdb=" N LEU E 94 " --> pdb=" O GLU E 109 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLU E 109 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TYR E 96 " --> pdb=" O LEU E 107 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 504 through 505 Processing sheet with id=AA8, first strand: chain 'F' and resid 591 through 592 Processing sheet with id=AA9, first strand: chain 'F' and resid 682 through 683 removed outlier: 7.488A pdb=" N ILE F 634 " --> pdb=" O ASP F 658 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N TYR F 660 " --> pdb=" O ILE F 634 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL F 636 " --> pdb=" O TYR F 660 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ALA F 662 " --> pdb=" O VAL F 636 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N SER F 638 " --> pdb=" O ALA F 662 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 824 through 825 Processing sheet with id=AB2, first strand: chain 'D' and resid 9 through 10 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 9 through 10 current: chain 'D' and resid 25 through 27 removed outlier: 6.897A pdb=" N LEU D 50 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE D 39 " --> pdb=" O ARG D 48 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG D 48 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ILE D 41 " --> pdb=" O GLN D 46 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N GLN D 46 " --> pdb=" O ILE D 41 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 46 through 53 current: chain 'D' and resid 83 through 85 removed outlier: 5.518A pdb=" N LEU D 94 " --> pdb=" O GLU D 109 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLU D 109 " --> pdb=" O LEU D 94 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TYR D 96 " --> pdb=" O LEU D 107 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 103 through 110 current: chain 'C' and resid 25 through 28 removed outlier: 3.760A pdb=" N ALA C 33 " --> pdb=" O GLU C 54 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU C 50 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE C 39 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ARG C 48 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ILE C 41 " --> pdb=" O GLN C 46 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLN C 46 " --> pdb=" O ILE C 41 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 46 through 54 current: chain 'C' and resid 83 through 86 removed outlier: 5.357A pdb=" N LEU C 94 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLU C 109 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR C 96 " --> pdb=" O LEU C 107 " (cutoff:3.500A) 285 hydrogen bonds defined for protein. 744 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: 1.59 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3255 1.33 - 1.45: 1608 1.45 - 1.57: 5934 1.57 - 1.69: 0 1.69 - 1.81: 118 Bond restraints: 10915 Sorted by residual: bond pdb=" N GLY E 8 " pdb=" CA GLY E 8 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.34e+00 bond pdb=" N GLY B 8 " pdb=" CA GLY B 8 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.14e+00 bond pdb=" C ARG D 60 " pdb=" N PRO D 61 " ideal model delta sigma weight residual 1.330 1.359 -0.029 1.22e-02 6.72e+03 5.49e+00 bond pdb=" N GLU C 9 " pdb=" CA GLU C 9 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.11e+00 bond pdb=" N GLU F 473 " pdb=" CA GLU F 473 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 ... (remaining 10910 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 13834 1.15 - 2.31: 801 2.31 - 3.46: 116 3.46 - 4.61: 38 4.61 - 5.76: 6 Bond angle restraints: 14795 Sorted by residual: angle pdb=" C ASP A 614 " pdb=" CA ASP A 614 " pdb=" CB ASP A 614 " ideal model delta sigma weight residual 116.63 110.87 5.76 1.16e+00 7.43e-01 2.47e+01 angle pdb=" CA PRO D 61 " pdb=" C PRO D 61 " pdb=" O PRO D 61 " ideal model delta sigma weight residual 122.08 117.37 4.71 1.28e+00 6.10e-01 1.35e+01 angle pdb=" N ARG C 44 " pdb=" CA ARG C 44 " pdb=" CB ARG C 44 " ideal model delta sigma weight residual 110.98 107.12 3.86 1.32e+00 5.74e-01 8.54e+00 angle pdb=" CA ASP A 614 " pdb=" C ASP A 614 " pdb=" N GLN A 615 " ideal model delta sigma weight residual 119.63 117.33 2.30 8.10e-01 1.52e+00 8.05e+00 angle pdb=" CA PRO D 112 " pdb=" N PRO D 112 " pdb=" CD PRO D 112 " ideal model delta sigma weight residual 112.00 108.16 3.84 1.40e+00 5.10e-01 7.54e+00 ... (remaining 14790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 5782 17.60 - 35.20: 609 35.20 - 52.80: 116 52.80 - 70.39: 32 70.39 - 87.99: 17 Dihedral angle restraints: 6556 sinusoidal: 2761 harmonic: 3795 Sorted by residual: dihedral pdb=" CA ASP A 614 " pdb=" C ASP A 614 " pdb=" N GLN A 615 " pdb=" CA GLN A 615 " ideal model delta harmonic sigma weight residual 180.00 -158.58 -21.42 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA GLU F 545 " pdb=" C GLU F 545 " pdb=" N VAL F 546 " pdb=" CA VAL F 546 " ideal model delta harmonic sigma weight residual 180.00 -159.87 -20.13 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA ILE F 715 " pdb=" C ILE F 715 " pdb=" N VAL F 716 " pdb=" CA VAL F 716 " ideal model delta harmonic sigma weight residual -180.00 -160.43 -19.57 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 6553 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 856 0.028 - 0.056: 493 0.056 - 0.084: 122 0.084 - 0.112: 73 0.112 - 0.140: 29 Chirality restraints: 1573 Sorted by residual: chirality pdb=" CA VAL F 704 " pdb=" N VAL F 704 " pdb=" C VAL F 704 " pdb=" CB VAL F 704 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.91e-01 chirality pdb=" CA VAL A 704 " pdb=" N VAL A 704 " pdb=" C VAL A 704 " pdb=" CB VAL A 704 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CA ILE E 39 " pdb=" N ILE E 39 " pdb=" C ILE E 39 " pdb=" CB ILE E 39 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01 ... (remaining 1570 not shown) Planarity restraints: 1921 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 111 " 0.040 5.00e-02 4.00e+02 5.90e-02 5.57e+00 pdb=" N PRO D 112 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO D 112 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 112 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 63 " 0.037 5.00e-02 4.00e+02 5.66e-02 5.12e+00 pdb=" N PRO D 64 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 64 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 64 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE F 848 " 0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO F 849 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO F 849 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 849 " 0.021 5.00e-02 4.00e+02 ... (remaining 1918 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 56 2.52 - 3.11: 7502 3.11 - 3.71: 14580 3.71 - 4.30: 20354 4.30 - 4.90: 36090 Nonbonded interactions: 78582 Sorted by model distance: nonbonded pdb=" O TYR A 623 " pdb=" OH TYR A 908 " model vdw 1.923 3.040 nonbonded pdb=" O GLY F 642 " pdb=" OG SER F 669 " model vdw 1.964 3.040 nonbonded pdb=" OH TYR E 26 " pdb=" O PRO E 73 " model vdw 2.000 3.040 nonbonded pdb=" OH TYR C 26 " pdb=" O PRO C 73 " model vdw 2.014 3.040 nonbonded pdb=" OG SER D 86 " pdb=" OD1 ASP D 88 " model vdw 2.016 3.040 ... (remaining 78577 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' } ncs_group { reference = (chain 'B' and resid 9 through 113) selection = (chain 'C' and resid 9 through 113) selection = (chain 'D' and resid 9 through 113) selection = (chain 'E' and resid 9 through 113) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.540 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.010 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10937 Z= 0.178 Angle : 0.667 13.629 14819 Z= 0.365 Chirality : 0.041 0.140 1573 Planarity : 0.004 0.059 1921 Dihedral : 15.688 87.992 4108 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.26 % Allowed : 12.24 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.67 (0.23), residues: 1295 helix: 0.58 (0.30), residues: 312 sheet: 0.04 (0.31), residues: 258 loop : -1.09 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 792 TYR 0.011 0.001 TYR A 793 PHE 0.012 0.001 PHE A 755 TRP 0.010 0.001 TRP B 34 HIS 0.011 0.002 HIS E 97 Details of bonding type rmsd covalent geometry : bond 0.00387 (10915) covalent geometry : angle 0.62302 (14795) hydrogen bonds : bond 0.21592 ( 285) hydrogen bonds : angle 6.61451 ( 744) metal coordination : bond 0.00719 ( 22) metal coordination : angle 5.93213 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 157 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 513 MET cc_start: 0.7912 (ttm) cc_final: 0.7606 (ttm) REVERT: A 536 TYR cc_start: 0.7282 (m-80) cc_final: 0.7044 (m-10) REVERT: A 621 LYS cc_start: 0.7732 (tttt) cc_final: 0.7374 (ptpt) REVERT: A 696 GLN cc_start: 0.8273 (tp-100) cc_final: 0.7594 (mt0) REVERT: A 748 ASP cc_start: 0.7574 (m-30) cc_final: 0.6950 (t70) REVERT: A 899 ARG cc_start: 0.8075 (ttt90) cc_final: 0.7756 (ttm110) REVERT: A 911 CYS cc_start: 0.8287 (p) cc_final: 0.8054 (m) REVERT: B 19 TRP cc_start: 0.7392 (m-10) cc_final: 0.6859 (m100) REVERT: B 43 ASP cc_start: 0.6851 (m-30) cc_final: 0.6571 (m-30) REVERT: E 75 MET cc_start: 0.5876 (mmm) cc_final: 0.5631 (mmp) REVERT: F 513 MET cc_start: 0.7978 (ttm) cc_final: 0.7727 (ttt) REVERT: F 792 ARG cc_start: 0.8261 (mtt-85) cc_final: 0.7347 (mtt90) REVERT: C 94 LEU cc_start: 0.6773 (tt) cc_final: 0.6247 (mp) outliers start: 3 outliers final: 2 residues processed: 159 average time/residue: 0.1382 time to fit residues: 29.4143 Evaluate side-chains 130 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 128 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain C residue 54 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 0.0670 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 35 optimal weight: 0.7980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 696 GLN A 789 HIS ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 HIS F 613 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.233118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.210817 restraints weight = 11481.193| |-----------------------------------------------------------------------------| r_work (start): 0.4436 rms_B_bonded: 1.23 r_work: 0.4121 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10937 Z= 0.116 Angle : 0.600 13.892 14819 Z= 0.293 Chirality : 0.042 0.141 1573 Planarity : 0.004 0.054 1921 Dihedral : 5.519 88.725 1460 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.05 % Allowed : 12.76 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.29 (0.23), residues: 1295 helix: 0.96 (0.30), residues: 314 sheet: 0.27 (0.31), residues: 268 loop : -0.90 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 891 TYR 0.012 0.001 TYR C 26 PHE 0.011 0.001 PHE A 755 TRP 0.012 0.001 TRP D 21 HIS 0.008 0.001 HIS F 739 Details of bonding type rmsd covalent geometry : bond 0.00257 (10915) covalent geometry : angle 0.55072 (14795) hydrogen bonds : bond 0.03836 ( 285) hydrogen bonds : angle 4.85442 ( 744) metal coordination : bond 0.00556 ( 22) metal coordination : angle 5.96264 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 513 MET cc_start: 0.8363 (ttm) cc_final: 0.8018 (ttt) REVERT: A 748 ASP cc_start: 0.7417 (m-30) cc_final: 0.6822 (t70) REVERT: F 513 MET cc_start: 0.8484 (ttm) cc_final: 0.7994 (ttm) REVERT: F 548 MET cc_start: 0.6826 (OUTLIER) cc_final: 0.6350 (mtt) REVERT: F 613 HIS cc_start: 0.7264 (OUTLIER) cc_final: 0.7005 (t-90) REVERT: F 792 ARG cc_start: 0.8186 (mtt-85) cc_final: 0.7467 (mtt90) REVERT: C 94 LEU cc_start: 0.6943 (tt) cc_final: 0.6465 (mp) outliers start: 24 outliers final: 12 residues processed: 146 average time/residue: 0.1092 time to fit residues: 22.6957 Evaluate side-chains 129 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 696 GLN Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 548 MET Chi-restraints excluded: chain F residue 613 HIS Chi-restraints excluded: chain F residue 763 VAL Chi-restraints excluded: chain F residue 862 THR Chi-restraints excluded: chain F residue 867 VAL Chi-restraints excluded: chain F residue 911 CYS Chi-restraints excluded: chain D residue 25 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 127 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 4 optimal weight: 8.9990 chunk 101 optimal weight: 0.8980 chunk 62 optimal weight: 10.0000 chunk 27 optimal weight: 0.0470 chunk 35 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 696 GLN A 886 GLN E 97 HIS F 613 HIS F 789 HIS F 847 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.232380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.205863 restraints weight = 11413.320| |-----------------------------------------------------------------------------| r_work (start): 0.4390 rms_B_bonded: 1.35 r_work: 0.4044 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10937 Z= 0.111 Angle : 0.576 13.402 14819 Z= 0.278 Chirality : 0.042 0.140 1573 Planarity : 0.004 0.052 1921 Dihedral : 5.011 87.397 1456 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.74 % Allowed : 13.36 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.20 (0.24), residues: 1295 helix: 1.10 (0.31), residues: 312 sheet: 0.31 (0.31), residues: 266 loop : -0.87 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 48 TYR 0.011 0.001 TYR F 793 PHE 0.010 0.001 PHE A 755 TRP 0.015 0.001 TRP B 19 HIS 0.013 0.001 HIS F 613 Details of bonding type rmsd covalent geometry : bond 0.00259 (10915) covalent geometry : angle 0.52825 (14795) hydrogen bonds : bond 0.03643 ( 285) hydrogen bonds : angle 4.60102 ( 744) metal coordination : bond 0.00563 ( 22) metal coordination : angle 5.73478 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: A 478 ARG cc_start: 0.7626 (tpp80) cc_final: 0.7205 (ptt180) REVERT: A 513 MET cc_start: 0.8382 (ttm) cc_final: 0.8023 (ttt) REVERT: A 635 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7878 (mtt-85) REVERT: A 696 GLN cc_start: 0.7841 (tp40) cc_final: 0.7267 (mt0) REVERT: A 748 ASP cc_start: 0.7205 (m-30) cc_final: 0.6622 (t0) REVERT: B 43 ASP cc_start: 0.6108 (m-30) cc_final: 0.5888 (m-30) REVERT: F 513 MET cc_start: 0.8483 (ttm) cc_final: 0.7980 (ttm) REVERT: F 548 MET cc_start: 0.6558 (OUTLIER) cc_final: 0.6090 (mtt) REVERT: F 792 ARG cc_start: 0.8076 (mtt-85) cc_final: 0.7392 (mtt90) REVERT: F 805 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7813 (tt) REVERT: C 94 LEU cc_start: 0.6934 (tt) cc_final: 0.6151 (mp) outliers start: 32 outliers final: 16 residues processed: 141 average time/residue: 0.1041 time to fit residues: 21.2887 Evaluate side-chains 135 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 635 ARG Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 810 ASN Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 548 MET Chi-restraints excluded: chain F residue 588 HIS Chi-restraints excluded: chain F residue 763 VAL Chi-restraints excluded: chain F residue 805 LEU Chi-restraints excluded: chain F residue 862 THR Chi-restraints excluded: chain F residue 867 VAL Chi-restraints excluded: chain F residue 911 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 44 optimal weight: 0.0040 chunk 86 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 81 optimal weight: 0.4980 chunk 98 optimal weight: 0.6980 chunk 62 optimal weight: 9.9990 chunk 15 optimal weight: 0.6980 chunk 73 optimal weight: 9.9990 chunk 95 optimal weight: 0.0670 chunk 118 optimal weight: 0.9980 overall best weight: 0.3930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 GLN ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 HIS F 613 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.234041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.213990 restraints weight = 11448.649| |-----------------------------------------------------------------------------| r_work (start): 0.4464 rms_B_bonded: 1.05 r_work: 0.4183 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10937 Z= 0.093 Angle : 0.540 12.227 14819 Z= 0.259 Chirality : 0.041 0.181 1573 Planarity : 0.004 0.049 1921 Dihedral : 4.743 80.188 1456 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.31 % Allowed : 14.38 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.04 (0.24), residues: 1295 helix: 1.24 (0.31), residues: 312 sheet: 0.63 (0.32), residues: 261 loop : -0.86 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 17 TYR 0.009 0.001 TYR F 793 PHE 0.008 0.001 PHE A 755 TRP 0.021 0.001 TRP B 19 HIS 0.007 0.001 HIS F 739 Details of bonding type rmsd covalent geometry : bond 0.00201 (10915) covalent geometry : angle 0.49563 (14795) hydrogen bonds : bond 0.02938 ( 285) hydrogen bonds : angle 4.38348 ( 744) metal coordination : bond 0.00493 ( 22) metal coordination : angle 5.35018 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 513 MET cc_start: 0.8251 (ttm) cc_final: 0.7777 (ttm) REVERT: A 635 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7800 (mtt-85) REVERT: A 748 ASP cc_start: 0.7404 (m-30) cc_final: 0.6837 (t0) REVERT: A 792 ARG cc_start: 0.8011 (mmt90) cc_final: 0.7664 (mtt90) REVERT: A 899 ARG cc_start: 0.7537 (ttm110) cc_final: 0.7178 (ttm110) REVERT: B 17 ARG cc_start: 0.7726 (mtm110) cc_final: 0.7438 (mtp180) REVERT: E 75 MET cc_start: 0.5238 (mmp) cc_final: 0.4840 (tpt) REVERT: E 76 TRP cc_start: 0.6007 (OUTLIER) cc_final: 0.5799 (m100) REVERT: F 493 ILE cc_start: 0.6803 (OUTLIER) cc_final: 0.6578 (pt) REVERT: F 513 MET cc_start: 0.8453 (ttm) cc_final: 0.7905 (ttm) REVERT: F 548 MET cc_start: 0.6540 (OUTLIER) cc_final: 0.6068 (mtt) REVERT: F 790 ARG cc_start: 0.7556 (mtp85) cc_final: 0.7141 (mtp180) REVERT: F 805 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7768 (tt) REVERT: C 94 LEU cc_start: 0.6730 (tt) cc_final: 0.6134 (mp) outliers start: 27 outliers final: 13 residues processed: 139 average time/residue: 0.1162 time to fit residues: 22.6448 Evaluate side-chains 135 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 635 ARG Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 810 ASN Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain E residue 76 TRP Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 548 MET Chi-restraints excluded: chain F residue 588 HIS Chi-restraints excluded: chain F residue 763 VAL Chi-restraints excluded: chain F residue 805 LEU Chi-restraints excluded: chain F residue 862 THR Chi-restraints excluded: chain F residue 911 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 22 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 113 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 101 optimal weight: 0.0670 chunk 82 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 886 GLN B 77 GLN ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 HIS F 613 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.230815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.209640 restraints weight = 11346.091| |-----------------------------------------------------------------------------| r_work (start): 0.4423 rms_B_bonded: 1.05 r_work: 0.4136 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.4023 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10937 Z= 0.127 Angle : 0.584 13.123 14819 Z= 0.280 Chirality : 0.042 0.144 1573 Planarity : 0.005 0.054 1921 Dihedral : 4.770 69.759 1456 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.34 % Allowed : 13.78 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.19 (0.24), residues: 1295 helix: 1.09 (0.31), residues: 314 sheet: 0.61 (0.33), residues: 246 loop : -0.94 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 478 TYR 0.015 0.001 TYR F 793 PHE 0.010 0.001 PHE D 24 TRP 0.020 0.001 TRP B 19 HIS 0.008 0.001 HIS E 97 Details of bonding type rmsd covalent geometry : bond 0.00308 (10915) covalent geometry : angle 0.53560 (14795) hydrogen bonds : bond 0.03701 ( 285) hydrogen bonds : angle 4.36308 ( 744) metal coordination : bond 0.00578 ( 22) metal coordination : angle 5.80432 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 125 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 513 MET cc_start: 0.8328 (ttm) cc_final: 0.7843 (ttm) REVERT: A 635 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7799 (mtt-85) REVERT: A 792 ARG cc_start: 0.8200 (mmt90) cc_final: 0.7907 (mtt90) REVERT: B 43 ASP cc_start: 0.6060 (m-30) cc_final: 0.5782 (m-30) REVERT: B 76 TRP cc_start: 0.8643 (OUTLIER) cc_final: 0.8238 (m-90) REVERT: E 76 TRP cc_start: 0.6258 (OUTLIER) cc_final: 0.5973 (m100) REVERT: F 513 MET cc_start: 0.8473 (ttm) cc_final: 0.7922 (ttm) REVERT: F 790 ARG cc_start: 0.7757 (mtp85) cc_final: 0.7319 (mtp180) REVERT: F 805 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7964 (tt) REVERT: C 76 TRP cc_start: 0.6511 (OUTLIER) cc_final: 0.4611 (m-10) outliers start: 39 outliers final: 25 residues processed: 154 average time/residue: 0.1051 time to fit residues: 22.9261 Evaluate side-chains 152 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 635 ARG Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 810 ASN Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 911 CYS Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 76 TRP Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 76 TRP Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 588 HIS Chi-restraints excluded: chain F residue 705 ILE Chi-restraints excluded: chain F residue 763 VAL Chi-restraints excluded: chain F residue 805 LEU Chi-restraints excluded: chain F residue 862 THR Chi-restraints excluded: chain F residue 867 VAL Chi-restraints excluded: chain F residue 911 CYS Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 76 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 122 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 0.0000 chunk 20 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 HIS ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 HIS F 613 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.229329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.208229 restraints weight = 11462.216| |-----------------------------------------------------------------------------| r_work (start): 0.4413 rms_B_bonded: 1.10 r_work: 0.4138 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.4031 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10937 Z= 0.146 Angle : 0.615 14.383 14819 Z= 0.292 Chirality : 0.043 0.147 1573 Planarity : 0.005 0.051 1921 Dihedral : 4.834 60.873 1456 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.60 % Allowed : 14.21 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.23), residues: 1295 helix: 0.97 (0.31), residues: 312 sheet: 0.46 (0.33), residues: 245 loop : -1.04 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 604 TYR 0.014 0.001 TYR F 793 PHE 0.010 0.002 PHE F 827 TRP 0.016 0.001 TRP B 19 HIS 0.006 0.001 HIS F 506 Details of bonding type rmsd covalent geometry : bond 0.00359 (10915) covalent geometry : angle 0.56074 (14795) hydrogen bonds : bond 0.03938 ( 285) hydrogen bonds : angle 4.41772 ( 744) metal coordination : bond 0.00668 ( 22) metal coordination : angle 6.30477 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 129 time to evaluate : 0.325 Fit side-chains REVERT: A 513 MET cc_start: 0.8391 (ttm) cc_final: 0.7855 (ttm) REVERT: A 635 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7780 (mtt-85) REVERT: A 792 ARG cc_start: 0.8260 (mmt90) cc_final: 0.7977 (mtt90) REVERT: B 43 ASP cc_start: 0.6131 (m-30) cc_final: 0.5823 (m-30) REVERT: B 76 TRP cc_start: 0.8659 (OUTLIER) cc_final: 0.8282 (m-90) REVERT: E 75 MET cc_start: 0.5453 (mmp) cc_final: 0.5114 (tpt) REVERT: E 76 TRP cc_start: 0.6606 (OUTLIER) cc_final: 0.5002 (m-10) REVERT: F 513 MET cc_start: 0.8531 (ttm) cc_final: 0.7995 (ttm) REVERT: F 790 ARG cc_start: 0.7747 (mtp85) cc_final: 0.7292 (mtp180) REVERT: F 805 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8053 (tt) REVERT: C 76 TRP cc_start: 0.6842 (OUTLIER) cc_final: 0.4595 (m-10) outliers start: 42 outliers final: 28 residues processed: 158 average time/residue: 0.1032 time to fit residues: 22.6982 Evaluate side-chains 153 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 635 ARG Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 810 ASN Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 867 VAL Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 911 CYS Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 76 TRP Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 76 TRP Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 548 MET Chi-restraints excluded: chain F residue 588 HIS Chi-restraints excluded: chain F residue 705 ILE Chi-restraints excluded: chain F residue 729 ARG Chi-restraints excluded: chain F residue 739 HIS Chi-restraints excluded: chain F residue 763 VAL Chi-restraints excluded: chain F residue 805 LEU Chi-restraints excluded: chain F residue 862 THR Chi-restraints excluded: chain F residue 867 VAL Chi-restraints excluded: chain F residue 911 CYS Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 76 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 101 optimal weight: 0.0030 chunk 98 optimal weight: 0.2980 chunk 14 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 78 optimal weight: 0.0970 chunk 115 optimal weight: 0.9980 chunk 46 optimal weight: 0.4980 chunk 69 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 overall best weight: 0.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 97 HIS F 613 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.232791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.211072 restraints weight = 11372.400| |-----------------------------------------------------------------------------| r_work (start): 0.4438 rms_B_bonded: 1.16 r_work: 0.4143 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10937 Z= 0.084 Angle : 0.532 12.403 14819 Z= 0.254 Chirality : 0.041 0.155 1573 Planarity : 0.004 0.047 1921 Dihedral : 4.457 53.279 1456 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.40 % Allowed : 15.15 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.13 (0.24), residues: 1295 helix: 1.18 (0.31), residues: 312 sheet: 0.69 (0.34), residues: 241 loop : -0.94 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 83 TYR 0.008 0.001 TYR F 793 PHE 0.008 0.001 PHE A 755 TRP 0.012 0.001 TRP D 21 HIS 0.007 0.001 HIS E 97 Details of bonding type rmsd covalent geometry : bond 0.00181 (10915) covalent geometry : angle 0.48272 (14795) hydrogen bonds : bond 0.02698 ( 285) hydrogen bonds : angle 4.24066 ( 744) metal coordination : bond 0.00489 ( 22) metal coordination : angle 5.57597 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.340 Fit side-chains REVERT: A 513 MET cc_start: 0.8207 (ttm) cc_final: 0.7764 (ttm) REVERT: A 635 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7739 (mtt-85) REVERT: B 76 TRP cc_start: 0.8504 (OUTLIER) cc_final: 0.8112 (m-90) REVERT: E 76 TRP cc_start: 0.6252 (OUTLIER) cc_final: 0.4536 (m-10) REVERT: F 513 MET cc_start: 0.8418 (ttm) cc_final: 0.7946 (ttm) REVERT: F 729 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7108 (ptp-170) REVERT: F 790 ARG cc_start: 0.7587 (mtp85) cc_final: 0.7245 (mtp180) REVERT: F 805 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7893 (tt) REVERT: C 76 TRP cc_start: 0.6555 (OUTLIER) cc_final: 0.4499 (m-10) outliers start: 28 outliers final: 15 residues processed: 135 average time/residue: 0.0948 time to fit residues: 18.1190 Evaluate side-chains 137 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 635 ARG Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 810 ASN Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 886 GLN Chi-restraints excluded: chain A residue 911 CYS Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 76 TRP Chi-restraints excluded: chain E residue 76 TRP Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain F residue 548 MET Chi-restraints excluded: chain F residue 588 HIS Chi-restraints excluded: chain F residue 729 ARG Chi-restraints excluded: chain F residue 763 VAL Chi-restraints excluded: chain F residue 805 LEU Chi-restraints excluded: chain F residue 810 ASN Chi-restraints excluded: chain F residue 862 THR Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 76 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 44 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 7 optimal weight: 0.0970 chunk 16 optimal weight: 0.0470 chunk 122 optimal weight: 2.9990 chunk 102 optimal weight: 0.0980 chunk 78 optimal weight: 0.0170 chunk 100 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 overall best weight: 0.2114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 97 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.227614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.200099 restraints weight = 11648.035| |-----------------------------------------------------------------------------| r_work (start): 0.4408 rms_B_bonded: 1.47 r_work: 0.4038 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10937 Z= 0.079 Angle : 0.514 10.543 14819 Z= 0.246 Chirality : 0.041 0.157 1573 Planarity : 0.004 0.047 1921 Dihedral : 4.165 44.355 1456 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.05 % Allowed : 15.50 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.10 (0.24), residues: 1295 helix: 1.39 (0.31), residues: 312 sheet: 0.75 (0.33), residues: 251 loop : -0.78 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 790 TYR 0.007 0.001 TYR D 96 PHE 0.006 0.001 PHE A 755 TRP 0.014 0.001 TRP B 19 HIS 0.007 0.001 HIS E 97 Details of bonding type rmsd covalent geometry : bond 0.00169 (10915) covalent geometry : angle 0.47428 (14795) hydrogen bonds : bond 0.02423 ( 285) hydrogen bonds : angle 4.14219 ( 744) metal coordination : bond 0.00434 ( 22) metal coordination : angle 4.94912 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.429 Fit side-chains REVERT: A 513 MET cc_start: 0.8218 (ttm) cc_final: 0.7793 (ttm) REVERT: A 635 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7808 (mtt-85) REVERT: A 748 ASP cc_start: 0.7725 (m-30) cc_final: 0.7177 (t0) REVERT: A 899 ARG cc_start: 0.7724 (ttm110) cc_final: 0.7374 (ttm110) REVERT: B 76 TRP cc_start: 0.8543 (OUTLIER) cc_final: 0.8214 (m-90) REVERT: E 75 MET cc_start: 0.5392 (mmp) cc_final: 0.4962 (tpt) REVERT: E 76 TRP cc_start: 0.6069 (OUTLIER) cc_final: 0.4361 (m-10) REVERT: F 513 MET cc_start: 0.8384 (ttm) cc_final: 0.7951 (ttm) REVERT: F 688 ARG cc_start: 0.8007 (mtt180) cc_final: 0.7756 (mtt180) REVERT: F 729 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.6704 (ptp-170) REVERT: F 790 ARG cc_start: 0.7628 (mtp85) cc_final: 0.7251 (mtp180) REVERT: F 805 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7818 (tt) REVERT: C 76 TRP cc_start: 0.6445 (OUTLIER) cc_final: 0.4446 (m-10) outliers start: 24 outliers final: 17 residues processed: 138 average time/residue: 0.1266 time to fit residues: 23.8845 Evaluate side-chains 140 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 635 ARG Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 810 ASN Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 886 GLN Chi-restraints excluded: chain A residue 911 CYS Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 76 TRP Chi-restraints excluded: chain E residue 76 TRP Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain F residue 548 MET Chi-restraints excluded: chain F residue 588 HIS Chi-restraints excluded: chain F residue 705 ILE Chi-restraints excluded: chain F residue 729 ARG Chi-restraints excluded: chain F residue 763 VAL Chi-restraints excluded: chain F residue 805 LEU Chi-restraints excluded: chain F residue 862 THR Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 76 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 60 optimal weight: 0.4980 chunk 22 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.231506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.209884 restraints weight = 11353.649| |-----------------------------------------------------------------------------| r_work (start): 0.4327 rms_B_bonded: 1.17 r_work: 0.4024 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10937 Z= 0.111 Angle : 0.559 12.288 14819 Z= 0.265 Chirality : 0.042 0.143 1573 Planarity : 0.004 0.049 1921 Dihedral : 4.320 40.990 1456 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.40 % Allowed : 15.41 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.04 (0.24), residues: 1295 helix: 1.31 (0.31), residues: 312 sheet: 0.77 (0.33), residues: 236 loop : -0.90 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 790 TYR 0.011 0.001 TYR F 793 PHE 0.018 0.001 PHE F 732 TRP 0.011 0.001 TRP B 34 HIS 0.006 0.001 HIS E 97 Details of bonding type rmsd covalent geometry : bond 0.00267 (10915) covalent geometry : angle 0.51235 (14795) hydrogen bonds : bond 0.03285 ( 285) hydrogen bonds : angle 4.20286 ( 744) metal coordination : bond 0.00504 ( 22) metal coordination : angle 5.57710 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 0.428 Fit side-chains REVERT: A 513 MET cc_start: 0.8214 (ttm) cc_final: 0.7760 (ttm) REVERT: A 635 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7754 (mtt-85) REVERT: B 76 TRP cc_start: 0.8585 (OUTLIER) cc_final: 0.8182 (m-90) REVERT: E 76 TRP cc_start: 0.6280 (OUTLIER) cc_final: 0.4315 (m-10) REVERT: F 513 MET cc_start: 0.8377 (ttm) cc_final: 0.7870 (ttm) REVERT: F 688 ARG cc_start: 0.8107 (mtt180) cc_final: 0.7845 (mtt180) REVERT: F 729 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.6981 (ptp-170) REVERT: F 790 ARG cc_start: 0.7589 (mtp85) cc_final: 0.7187 (mtp180) REVERT: F 805 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7923 (tt) REVERT: C 76 TRP cc_start: 0.6630 (OUTLIER) cc_final: 0.4333 (m-10) outliers start: 28 outliers final: 21 residues processed: 135 average time/residue: 0.1109 time to fit residues: 21.2123 Evaluate side-chains 143 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 635 ARG Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 810 ASN Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 76 TRP Chi-restraints excluded: chain E residue 76 TRP Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain F residue 479 LEU Chi-restraints excluded: chain F residue 548 MET Chi-restraints excluded: chain F residue 588 HIS Chi-restraints excluded: chain F residue 705 ILE Chi-restraints excluded: chain F residue 729 ARG Chi-restraints excluded: chain F residue 763 VAL Chi-restraints excluded: chain F residue 805 LEU Chi-restraints excluded: chain F residue 810 ASN Chi-restraints excluded: chain F residue 862 THR Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 76 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 60 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.219743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.192480 restraints weight = 11621.369| |-----------------------------------------------------------------------------| r_work (start): 0.4232 rms_B_bonded: 1.57 r_work: 0.3896 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10937 Z= 0.188 Angle : 0.680 15.111 14819 Z= 0.322 Chirality : 0.045 0.224 1573 Planarity : 0.005 0.051 1921 Dihedral : 4.848 40.696 1456 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.48 % Allowed : 15.58 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.55 (0.23), residues: 1295 helix: 0.75 (0.30), residues: 312 sheet: 0.29 (0.34), residues: 232 loop : -1.09 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 790 TYR 0.014 0.002 TYR F 793 PHE 0.019 0.002 PHE F 732 TRP 0.015 0.002 TRP B 34 HIS 0.009 0.002 HIS F 506 Details of bonding type rmsd covalent geometry : bond 0.00470 (10915) covalent geometry : angle 0.62203 (14795) hydrogen bonds : bond 0.04600 ( 285) hydrogen bonds : angle 4.43198 ( 744) metal coordination : bond 0.00722 ( 22) metal coordination : angle 6.84907 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2590 Ramachandran restraints generated. 1295 Oldfield, 0 Emsley, 1295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.438 Fit side-chains REVERT: A 513 MET cc_start: 0.8330 (ttm) cc_final: 0.7827 (ttm) REVERT: A 578 GLU cc_start: 0.7554 (tt0) cc_final: 0.7279 (tt0) REVERT: A 635 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7752 (mtt-85) REVERT: B 76 TRP cc_start: 0.8650 (OUTLIER) cc_final: 0.8254 (m-90) REVERT: E 76 TRP cc_start: 0.7021 (OUTLIER) cc_final: 0.4384 (m-10) REVERT: F 513 MET cc_start: 0.8450 (ttm) cc_final: 0.7892 (ttm) REVERT: F 790 ARG cc_start: 0.7898 (mtp85) cc_final: 0.7421 (mtp180) REVERT: F 805 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8052 (tt) REVERT: C 76 TRP cc_start: 0.7114 (OUTLIER) cc_final: 0.4376 (m-10) outliers start: 29 outliers final: 23 residues processed: 140 average time/residue: 0.1101 time to fit residues: 21.7751 Evaluate side-chains 147 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 635 ARG Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 810 ASN Chi-restraints excluded: chain A residue 862 THR Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 911 CYS Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 76 TRP Chi-restraints excluded: chain E residue 76 TRP Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain F residue 479 LEU Chi-restraints excluded: chain F residue 548 MET Chi-restraints excluded: chain F residue 588 HIS Chi-restraints excluded: chain F residue 705 ILE Chi-restraints excluded: chain F residue 729 ARG Chi-restraints excluded: chain F residue 763 VAL Chi-restraints excluded: chain F residue 805 LEU Chi-restraints excluded: chain F residue 810 ASN Chi-restraints excluded: chain F residue 862 THR Chi-restraints excluded: chain F residue 867 VAL Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 76 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 61 optimal weight: 10.0000 chunk 107 optimal weight: 0.0970 chunk 4 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 51 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 97 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.229647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.207734 restraints weight = 11403.242| |-----------------------------------------------------------------------------| r_work (start): 0.4342 rms_B_bonded: 1.18 r_work: 0.4033 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10937 Z= 0.122 Angle : 0.596 14.563 14819 Z= 0.281 Chirality : 0.042 0.150 1573 Planarity : 0.004 0.048 1921 Dihedral : 4.613 38.589 1456 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.57 % Allowed : 15.67 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.49 (0.23), residues: 1295 helix: 0.85 (0.31), residues: 312 sheet: 0.52 (0.34), residues: 220 loop : -1.13 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 790 TYR 0.012 0.001 TYR F 793 PHE 0.016 0.001 PHE F 732 TRP 0.013 0.001 TRP D 21 HIS 0.006 0.001 HIS E 97 Details of bonding type rmsd covalent geometry : bond 0.00296 (10915) covalent geometry : angle 0.53829 (14795) hydrogen bonds : bond 0.03592 ( 285) hydrogen bonds : angle 4.31109 ( 744) metal coordination : bond 0.00622 ( 22) metal coordination : angle 6.35608 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2265.59 seconds wall clock time: 39 minutes 31.22 seconds (2371.22 seconds total)