Starting phenix.real_space_refine on Wed Aug 27 01:27:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xrm_38607/08_2025/8xrm_38607.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xrm_38607/08_2025/8xrm_38607.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xrm_38607/08_2025/8xrm_38607.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xrm_38607/08_2025/8xrm_38607.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xrm_38607/08_2025/8xrm_38607.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xrm_38607/08_2025/8xrm_38607.map" } resolution = 3.13 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= 0.002 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: 7 Type Number sf(0) Gaussians Zn 10 6.06 5 P 98 5.49 5 Mg 1 5.21 5 S 260 5.16 5 C 28028 2.51 5 N 7871 2.21 5 O 8604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 44872 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 11088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1400, 11088 Classifications: {'peptide': 1400} Link IDs: {'PTRANS': 69, 'TRANS': 1330} Chain breaks: 6 Chain: "B" Number of atoms: 9061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1133, 9061 Classifications: {'peptide': 1133} Link IDs: {'PTRANS': 53, 'TRANS': 1079} Chain breaks: 3 Chain: "C" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2082 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 15, 'TRANS': 243} Chain breaks: 1 Chain: "D" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1015 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 123} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1715 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 636 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "G" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1333 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 918 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 388 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "M" Number of atoms: 6742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6742 Classifications: {'peptide': 818} Link IDs: {'PTRANS': 33, 'TRANS': 784} Chain breaks: 11 Chain: "N" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 694 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain breaks: 1 Chain: "P" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 452 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 6} Link IDs: {'rna2p': 7, 'rna3p': 13} Chain: "Q" Number of atoms: 488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 488 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "T" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 889 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "Y" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 911 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "Z" Number of atoms: 3810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3810 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 17, 'TRANS': 460} Chain breaks: 6 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 464 SG CYS A 71 108.432 68.496 69.235 1.00 84.50 S ATOM 486 SG CYS A 74 110.264 71.074 67.592 1.00 84.34 S ATOM 533 SG CYS A 81 107.938 72.092 70.107 1.00 73.66 S ATOM 768 SG CYS A 111 71.223 70.299 37.404 1.00104.23 S ATOM 796 SG CYS A 114 73.346 68.801 35.566 1.00103.95 S ATOM 1109 SG CYS A 184 69.919 66.927 35.418 1.00123.50 S ATOM 19719 SG CYS B1119 107.262 75.767 52.376 1.00 79.61 S ATOM 19741 SG CYS B1122 103.903 75.184 52.830 1.00 79.85 S ATOM 19856 SG CYS B1137 106.548 72.947 54.287 1.00 97.95 S ATOM 19877 SG CYS B1140 105.182 73.068 50.852 1.00111.58 S ATOM 20844 SG CYS C 88 128.326 107.973 124.414 1.00 86.72 S ATOM 20857 SG CYS C 90 127.982 104.492 124.225 1.00 96.25 S ATOM 20892 SG CYS C 94 127.660 105.817 127.453 1.00 78.68 S ATOM 20914 SG CYS C 97 124.888 106.237 125.101 1.00 74.40 S ATOM 28163 SG CYS I 17 15.638 82.199 72.916 1.00134.75 S ATOM 28348 SG CYS I 39 18.009 81.439 70.201 1.00141.25 S ATOM 28373 SG CYS I 42 14.579 79.751 70.441 1.00145.06 S ATOM 28725 SG CYS I 86 22.783 118.945 97.186 1.00134.61 S ATOM 28749 SG CYS I 89 21.629 118.390 100.768 1.00137.30 S ATOM 28953 SG CYS I 114 25.033 116.480 99.916 1.00124.34 S ATOM 28988 SG CYS I 119 21.788 115.514 98.420 1.00135.00 S ATOM 29089 SG CYS J 7 95.001 117.860 122.494 1.00 32.70 S ATOM 29377 SG CYS J 44 93.779 121.625 121.959 1.00 38.37 S ATOM 29383 SG CYS J 45 94.633 120.215 125.278 1.00 36.83 S ATOM 30545 SG CYS L 19 92.974 73.353 126.416 1.00103.81 S ATOM 30681 SG CYS L 36 94.277 70.446 128.114 1.00112.73 S ATOM 30707 SG CYS L 39 90.711 70.484 127.833 1.00116.33 S ATOM 38803 SG CYS Q 26 48.823 56.186 58.183 1.00175.38 S ATOM 38827 SG CYS Q 29 51.647 54.632 56.161 1.00176.44 S ATOM 38988 SG CYS Q 50 50.381 57.786 54.858 1.00176.98 S ATOM 39008 SG CYS Q 53 48.321 54.883 54.628 1.00176.15 S ATOM 40259 SG CYS Y 16 69.500 20.407 67.657 1.00259.04 S ATOM 40281 SG CYS Y 19 66.345 22.296 67.235 1.00253.01 S ATOM 40393 SG CYS Y 33 66.444 19.492 69.834 1.00259.41 S Time building chain proxies: 8.66, per 1000 atoms: 0.19 Number of scatterers: 44872 At special positions: 0 Unit cell: (195.04, 185.5, 155.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 10 29.99 S 260 16.00 P 98 15.00 Mg 1 11.99 O 8604 8.00 N 7871 7.00 C 28028 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: 3.11 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 184 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb=" ZN Q 200 " pdb="ZN ZN Q 200 " - pdb=" SG CYS Q 26 " pdb="ZN ZN Q 200 " - pdb=" SG CYS Q 50 " pdb="ZN ZN Q 200 " - pdb=" SG CYS Q 29 " pdb="ZN ZN Q 200 " - pdb=" SG CYS Q 53 " pdb=" ZN Y 201 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 16 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 33 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 19 " Number of angles added : 27 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10084 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 61 sheets defined 40.3% alpha, 16.8% beta 43 base pairs and 74 stacking pairs defined. Time for finding SS restraints: 5.40 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 59 through 63 removed outlier: 3.782A pdb=" N GLY A 63 " --> pdb=" O PRO A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 136 through 150 removed outlier: 4.351A pdb=" N GLY A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 227 removed outlier: 3.643A pdb=" N ARG A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 237 Processing helix chain 'A' and resid 244 through 249 removed outlier: 3.846A pdb=" N ILE A 249 " --> pdb=" O GLU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 297 removed outlier: 3.546A pdb=" N LYS A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 319 removed outlier: 3.840A pdb=" N VAL A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 344 Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 382 through 386 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.731A pdb=" N TYR A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 521 through 524 Processing helix chain 'A' and resid 538 through 549 removed outlier: 3.958A pdb=" N LEU A 542 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR A 543 " --> pdb=" O GLN A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.859A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 614 removed outlier: 3.562A pdb=" N GLU A 613 " --> pdb=" O PRO A 610 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP A 614 " --> pdb=" O ASP A 611 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 610 through 614' Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 660 Processing helix chain 'A' and resid 661 through 684 removed outlier: 3.520A pdb=" N LEU A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.648A pdb=" N ILE A 693 " --> pdb=" O GLY A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 760 Processing helix chain 'A' and resid 764 through 772 Processing helix chain 'A' and resid 777 through 786 removed outlier: 3.715A pdb=" N ILE A 781 " --> pdb=" O SER A 777 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER A 782 " --> pdb=" O LYS A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 869 removed outlier: 3.611A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 851 " --> pdb=" O LEU A 847 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR A 859 " --> pdb=" O ALA A 855 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A 867 " --> pdb=" O ARG A 863 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET A 868 " --> pdb=" O LEU A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 926 through 934 removed outlier: 3.694A pdb=" N THR A 933 " --> pdb=" O ALA A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 945 removed outlier: 3.731A pdb=" N LYS A 940 " --> pdb=" O GLU A 936 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.658A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 Processing helix chain 'A' and resid 1005 through 1020 removed outlier: 3.699A pdb=" N VAL A1009 " --> pdb=" O HIS A1005 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL A1010 " --> pdb=" O PRO A1006 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU A1015 " --> pdb=" O GLU A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1051 through 1057 Processing helix chain 'A' and resid 1061 through 1078 removed outlier: 3.631A pdb=" N GLU A1073 " --> pdb=" O LEU A1069 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A1074 " --> pdb=" O GLY A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1097 removed outlier: 3.548A pdb=" N LEU A1090 " --> pdb=" O MET A1086 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1101 Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1144 through 1149 removed outlier: 3.955A pdb=" N SER A1147 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1160 removed outlier: 3.583A pdb=" N ALA A1154 " --> pdb=" O ASP A1150 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A1160 " --> pdb=" O ASP A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1169 No H-bonds generated for 'chain 'A' and resid 1166 through 1169' Processing helix chain 'A' and resid 1188 through 1195 Processing helix chain 'A' and resid 1217 through 1225 Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1282 through 1296 removed outlier: 3.592A pdb=" N ARG A1286 " --> pdb=" O ASP A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1348 Processing helix chain 'A' and resid 1361 through 1369 Processing helix chain 'A' and resid 1370 through 1388 removed outlier: 3.676A pdb=" N ILE A1386 " --> pdb=" O LEU A1382 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1405 removed outlier: 3.952A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 removed outlier: 3.526A pdb=" N ASN A1420 " --> pdb=" O ARG A1416 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1433 removed outlier: 3.802A pdb=" N SER A1431 " --> pdb=" O LEU A1427 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE A1432 " --> pdb=" O MET A1428 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU A1433 " --> pdb=" O LYS A1429 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1446 Processing helix chain 'A' and resid 1453 through 1460 removed outlier: 3.802A pdb=" N ASN A1457 " --> pdb=" O GLY A1453 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A1460 " --> pdb=" O GLU A1456 " (cutoff:3.500A) Processing helix chain 'A' and resid 1478 through 1482 removed outlier: 3.504A pdb=" N TYR A1482 " --> pdb=" O LYS A1479 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 37 removed outlier: 4.505A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 62 removed outlier: 5.346A pdb=" N VAL B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N GLN B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA B 62 " --> pdb=" O ILE B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 269 through 277 Processing helix chain 'B' and resid 281 through 287 removed outlier: 3.683A pdb=" N HIS B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 308 Proline residue: B 303 - end of helix removed outlier: 3.664A pdb=" N ALA B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 324 removed outlier: 3.595A pdb=" N ARG B 324 " --> pdb=" O PHE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 357 through 377 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 425 removed outlier: 3.797A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG B 425 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 437 through 451 removed outlier: 3.852A pdb=" N SER B 441 " --> pdb=" O THR B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 459 Processing helix chain 'B' and resid 474 through 482 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 538 through 548 removed outlier: 3.626A pdb=" N GLU B 547 " --> pdb=" O GLU B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 594 removed outlier: 3.661A pdb=" N MET B 584 " --> pdb=" O PRO B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 645 Processing helix chain 'B' and resid 645 through 650 removed outlier: 3.590A pdb=" N ASN B 649 " --> pdb=" O GLU B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 667 through 672 removed outlier: 4.065A pdb=" N THR B 672 " --> pdb=" O LEU B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 683 Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.583A pdb=" N LEU B 704 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 removed outlier: 3.833A pdb=" N ILE B 710 " --> pdb=" O CYS B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 717 removed outlier: 3.808A pdb=" N ASN B 717 " --> pdb=" O PRO B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 730 removed outlier: 4.038A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 removed outlier: 3.718A pdb=" N GLU B 765 " --> pdb=" O ARG B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 970 through 976 removed outlier: 4.647A pdb=" N SER B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.852A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 removed outlier: 3.611A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1087 through 1097 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1152 through 1165 Processing helix chain 'C' and resid 27 through 41 removed outlier: 3.748A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 removed outlier: 3.501A pdb=" N LEU C 70 " --> pdb=" O HIS C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 82 removed outlier: 3.813A pdb=" N LYS C 81 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 270 removed outlier: 3.925A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 27 removed outlier: 3.633A pdb=" N GLU D 27 " --> pdb=" O LYS D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 51 removed outlier: 3.594A pdb=" N ALA D 51 " --> pdb=" O GLN D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 71 removed outlier: 3.847A pdb=" N MET D 62 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE D 71 " --> pdb=" O TYR D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 89 removed outlier: 3.612A pdb=" N ILE D 80 " --> pdb=" O ASN D 76 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA D 81 " --> pdb=" O ARG D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 removed outlier: 3.979A pdb=" N ALA D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS D 99 " --> pdb=" O PHE D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 123 through 137 Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.539A pdb=" N ASP E 34 " --> pdb=" O GLN E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 45 removed outlier: 3.502A pdb=" N PHE E 40 " --> pdb=" O THR E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 59 removed outlier: 4.064A pdb=" N LEU E 58 " --> pdb=" O ARG E 55 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR E 59 " --> pdb=" O THR E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 97 removed outlier: 3.924A pdb=" N VAL E 89 " --> pdb=" O LYS E 85 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N TYR E 90 " --> pdb=" O THR E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 121 removed outlier: 3.538A pdb=" N MET E 121 " --> pdb=" O SER E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 136 Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 166 through 170 removed outlier: 3.659A pdb=" N LEU E 170 " --> pdb=" O GLU E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 removed outlier: 3.509A pdb=" N GLN F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'F' and resid 121 through 123 No H-bonds generated for 'chain 'F' and resid 121 through 123' Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 22 through 35 Processing helix chain 'H' and resid 83 through 88 removed outlier: 3.728A pdb=" N GLN H 87 " --> pdb=" O ARG H 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 67 Processing helix chain 'I' and resid 69 through 75 Processing helix chain 'J' and resid 17 through 26 Processing helix chain 'J' and resid 30 through 38 removed outlier: 4.142A pdb=" N ASP J 36 " --> pdb=" O GLY J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 52 removed outlier: 4.089A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 61 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.572A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE K 10 " --> pdb=" O PHE K 7 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 52 removed outlier: 4.338A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS K 52 " --> pdb=" O SER K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 removed outlier: 3.595A pdb=" N SER K 96 " --> pdb=" O THR K 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 267 through 272 Processing helix chain 'M' and resid 273 through 280 Processing helix chain 'M' and resid 283 through 291 removed outlier: 3.774A pdb=" N ASN M 287 " --> pdb=" O THR M 283 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU M 288 " --> pdb=" O ASP M 284 " (cutoff:3.500A) Processing helix chain 'M' and resid 295 through 301 Processing helix chain 'M' and resid 311 through 325 Processing helix chain 'M' and resid 356 through 368 Processing helix chain 'M' and resid 372 through 380 Processing helix chain 'M' and resid 380 through 385 removed outlier: 3.775A pdb=" N VAL M 384 " --> pdb=" O ARG M 380 " (cutoff:3.500A) Processing helix chain 'M' and resid 389 through 427 Processing helix chain 'M' and resid 444 through 453 Processing helix chain 'M' and resid 456 through 471 removed outlier: 3.598A pdb=" N TYR M 470 " --> pdb=" O HIS M 466 " (cutoff:3.500A) Processing helix chain 'M' and resid 522 through 530 removed outlier: 3.808A pdb=" N ILE M 526 " --> pdb=" O ASP M 522 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA M 530 " --> pdb=" O ILE M 526 " (cutoff:3.500A) Processing helix chain 'M' and resid 532 through 539 removed outlier: 3.721A pdb=" N ALA M 536 " --> pdb=" O LEU M 532 " (cutoff:3.500A) Processing helix chain 'M' and resid 542 through 552 Processing helix chain 'M' and resid 565 through 573 removed outlier: 3.502A pdb=" N LEU M 569 " --> pdb=" O GLU M 565 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP M 572 " --> pdb=" O GLU M 568 " (cutoff:3.500A) Processing helix chain 'M' and resid 580 through 598 removed outlier: 3.618A pdb=" N VAL M 584 " --> pdb=" O THR M 580 " (cutoff:3.500A) Processing helix chain 'M' and resid 599 through 613 Processing helix chain 'M' and resid 622 through 626 removed outlier: 3.540A pdb=" N ARG M 625 " --> pdb=" O LYS M 622 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS M 626 " --> pdb=" O LYS M 623 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 622 through 626' Processing helix chain 'M' and resid 632 through 636 removed outlier: 4.424A pdb=" N SER M 636 " --> pdb=" O TYR M 633 " (cutoff:3.500A) Processing helix chain 'M' and resid 646 through 648 No H-bonds generated for 'chain 'M' and resid 646 through 648' Processing helix chain 'M' and resid 651 through 662 Processing helix chain 'M' and resid 685 through 693 removed outlier: 4.167A pdb=" N ILE M 689 " --> pdb=" O TYR M 685 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN M 691 " --> pdb=" O GLU M 687 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N PHE M 692 " --> pdb=" O GLU M 688 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR M 693 " --> pdb=" O ILE M 689 " (cutoff:3.500A) Processing helix chain 'M' and resid 700 through 720 removed outlier: 3.561A pdb=" N GLU M 704 " --> pdb=" O HIS M 700 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TRP M 705 " --> pdb=" O GLN M 701 " (cutoff:3.500A) Processing helix chain 'M' and resid 720 through 754 Processing helix chain 'M' and resid 825 through 843 Processing helix chain 'M' and resid 854 through 872 removed outlier: 3.643A pdb=" N GLN M 858 " --> pdb=" O ASN M 854 " (cutoff:3.500A) Processing helix chain 'M' and resid 887 through 896 removed outlier: 3.598A pdb=" N ILE M 891 " --> pdb=" O ASN M 887 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU M 892 " --> pdb=" O GLU M 888 " (cutoff:3.500A) Processing helix chain 'M' and resid 896 through 903 Processing helix chain 'M' and resid 907 through 922 Processing helix chain 'M' and resid 922 through 931 Processing helix chain 'M' and resid 933 through 940 removed outlier: 3.603A pdb=" N LEU M 940 " --> pdb=" O ASP M 936 " (cutoff:3.500A) Processing helix chain 'M' and resid 950 through 970 Processing helix chain 'M' and resid 973 through 979 Processing helix chain 'M' and resid 980 through 989 removed outlier: 5.192A pdb=" N ALA M 984 " --> pdb=" O TYR M 981 " (cutoff:3.500A) Processing helix chain 'M' and resid 993 through 1008 Processing helix chain 'M' and resid 1015 through 1021 Processing helix chain 'M' and resid 1024 through 1032 Processing helix chain 'M' and resid 1051 through 1056 removed outlier: 3.676A pdb=" N SER M1056 " --> pdb=" O LEU M1053 " (cutoff:3.500A) Processing helix chain 'M' and resid 1059 through 1063 Processing helix chain 'M' and resid 1119 through 1132 Processing helix chain 'M' and resid 1145 through 1155 Processing helix chain 'M' and resid 1252 through 1256 removed outlier: 4.236A pdb=" N GLU M1255 " --> pdb=" O ARG M1252 " (cutoff:3.500A) Processing helix chain 'M' and resid 1282 through 1286 Processing helix chain 'M' and resid 1302 through 1312 Processing helix chain 'Q' and resid 66 through 83 Processing helix chain 'Y' and resid 2 through 6 removed outlier: 3.754A pdb=" N THR Y 5 " --> pdb=" O ALA Y 2 " (cutoff:3.500A) Processing helix chain 'Y' and resid 25 through 32 Processing helix chain 'Y' and resid 36 through 41 Processing helix chain 'Y' and resid 45 through 52 Processing helix chain 'Y' and resid 65 through 68 Processing helix chain 'Y' and resid 69 through 75 removed outlier: 3.512A pdb=" N LYS Y 73 " --> pdb=" O SER Y 69 " (cutoff:3.500A) Processing helix chain 'Y' and resid 94 through 105 Processing helix chain 'Z' and resid 188 through 204 Processing helix chain 'Z' and resid 231 through 240 Processing helix chain 'Z' and resid 259 through 264 removed outlier: 4.171A pdb=" N LEU Z 264 " --> pdb=" O MET Z 260 " (cutoff:3.500A) Processing helix chain 'Z' and resid 341 through 349 Processing helix chain 'Z' and resid 389 through 396 Processing helix chain 'Z' and resid 514 through 516 No H-bonds generated for 'chain 'Z' and resid 514 through 516' Processing helix chain 'Z' and resid 573 through 575 No H-bonds generated for 'chain 'Z' and resid 573 through 575' Processing helix chain 'Z' and resid 631 through 633 No H-bonds generated for 'chain 'Z' and resid 631 through 633' Processing helix chain 'Z' and resid 639 through 641 No H-bonds generated for 'chain 'Z' and resid 639 through 641' Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 16 removed outlier: 4.659A pdb=" N ARG B1150 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 94 removed outlier: 10.280A pdb=" N LEU A 90 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 10.723A pdb=" N LYS A 92 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL A 252 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 190 through 194 Processing sheet with id=AA5, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.524A pdb=" N LYS A 357 " --> pdb=" O PHE B1086 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1060 through 1061 removed outlier: 6.010A pdb=" N VAL A 378 " --> pdb=" O ARG A 475 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU A 477 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N VAL A 380 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 484 " --> pdb=" O THR A 368 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.765A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 526 through 527 removed outlier: 3.797A pdb=" N ARG A 532 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AB1, first strand: chain 'A' and resid 602 through 605 removed outlier: 3.743A pdb=" N MET A 637 " --> pdb=" O VAL A 629 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB3, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.894A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB5, first strand: chain 'A' and resid 1335 through 1337 removed outlier: 3.940A pdb=" N THR A1358 " --> pdb=" O THR A1140 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1164 through 1165 removed outlier: 6.747A pdb=" N THR A1164 " --> pdb=" O LEU A1298 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1244 through 1247 removed outlier: 3.566A pdb=" N ASN A1244 " --> pdb=" O ARG A1260 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU A1211 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ILE A1175 " --> pdb=" O LEU A1211 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ARG A1213 " --> pdb=" O THR A1173 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N THR A1173 " --> pdb=" O ARG A1213 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLU A1215 " --> pdb=" O ALA A1171 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1471 through 1475 Processing sheet with id=AB9, first strand: chain 'B' and resid 83 through 84 removed outlier: 3.656A pdb=" N ARG B 83 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 84 removed outlier: 3.656A pdb=" N ARG B 83 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ALA B 122 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N GLY B 150 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N LEU B 124 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N PHE B 148 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N VAL B 126 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS B 146 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU B 138 " --> pdb=" O LYS B 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC3, first strand: chain 'B' and resid 391 through 394 Processing sheet with id=AC4, first strand: chain 'B' and resid 206 through 208 removed outlier: 3.644A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC6, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC7, first strand: chain 'B' and resid 551 through 552 removed outlier: 5.502A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 748 through 751 removed outlier: 6.659A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD1, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 7.387A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AD3, first strand: chain 'B' and resid 865 through 867 removed outlier: 6.756A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1127 through 1129 Processing sheet with id=AD5, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.530A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TYR C 230 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE C 184 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.774A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 73 through 74 removed outlier: 4.030A pdb=" N ILE C 128 " --> pdb=" O ILE C 74 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AD9, first strand: chain 'E' and resid 26 through 27 removed outlier: 4.676A pdb=" N ALA E 63 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLN E 71 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N LEU E 103 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE E 73 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL E 105 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N PHE E 75 " --> pdb=" O VAL E 105 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ALA E 102 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N PHE E 130 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 147 through 150 Processing sheet with id=AE2, first strand: chain 'G' and resid 5 through 13 removed outlier: 6.856A pdb=" N ASN G 53 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS G 71 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ILE G 51 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LYS G 73 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA G 47 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N PHE G 77 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N VAL G 45 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 5 through 13 Processing sheet with id=AE4, first strand: chain 'G' and resid 84 through 92 removed outlier: 5.732A pdb=" N VAL G 89 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLU G 100 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN G 91 " --> pdb=" O PHE G 98 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER G 105 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N GLY G 161 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N PHE G 107 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 117 through 120 Processing sheet with id=AE6, first strand: chain 'H' and resid 90 through 91 removed outlier: 3.938A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ARG H 27 " --> pdb=" O ILE H 15 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ILE H 15 " --> pdb=" O ARG H 27 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 25 through 29 Processing sheet with id=AE8, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AE9, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF1, first strand: chain 'M' and resid 640 through 644 removed outlier: 3.550A pdb=" N ASN M 642 " --> pdb=" O LEU M 616 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N LEU M 616 " --> pdb=" O ASN M 642 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 805 through 811 removed outlier: 6.249A pdb=" N LEU M 782 " --> pdb=" O THR M 849 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ALA M 851 " --> pdb=" O LEU M 782 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ILE M 784 " --> pdb=" O ALA M 851 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL M 848 " --> pdb=" O GLU M 883 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL M 885 " --> pdb=" O VAL M 848 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL M 850 " --> pdb=" O VAL M 885 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 971 through 972 removed outlier: 6.184A pdb=" N VAL M 971 " --> pdb=" O LYS M1036 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'M' and resid 1166 through 1173 removed outlier: 6.841A pdb=" N LYS M1229 " --> pdb=" O THR M1172 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR M1237 " --> pdb=" O ALA M1277 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEU M1279 " --> pdb=" O THR M1237 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N SER M1276 " --> pdb=" O ILE M1270 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ILE M1270 " --> pdb=" O SER M1276 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASP M1278 " --> pdb=" O MET M1268 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG M1266 " --> pdb=" O THR M1280 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Q' and resid 23 through 24 removed outlier: 3.603A pdb=" N PHE Q 24 " --> pdb=" O CYS Q 35 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Y' and resid 22 through 24 Processing sheet with id=AF7, first strand: chain 'Y' and resid 57 through 58 Processing sheet with id=AF8, first strand: chain 'Y' and resid 83 through 85 removed outlier: 3.711A pdb=" N VAL Z 215 " --> pdb=" O ALA Y 62 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER Z 214 " --> pdb=" O GLU Z 228 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN Z 253 " --> pdb=" O THR Z 181 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Y' and resid 115 through 116 removed outlier: 5.941A pdb=" N ILE Y 115 " --> pdb=" O LYS Z 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'Z' and resid 352 through 354 removed outlier: 4.883A pdb=" N TYR Z 366 " --> pdb=" O PHE Z 373 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N THR Z 302 " --> pdb=" O VAL Z 296 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL Z 296 " --> pdb=" O THR Z 302 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N SER Z 304 " --> pdb=" O ASP Z 294 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Z' and resid 453 through 454 Processing sheet with id=AG3, first strand: chain 'Z' and resid 510 through 513 removed outlier: 6.814A pdb=" N PHE Z 503 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ILE Z 492 " --> pdb=" O PHE Z 503 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Z' and resid 567 through 571 removed outlier: 3.557A pdb=" N VAL Z 568 " --> pdb=" O VAL Z 560 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N THR Z 557 " --> pdb=" O LEU Z 553 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N LEU Z 553 " --> pdb=" O THR Z 557 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N GLN Z 559 " --> pdb=" O VAL Z 551 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR Z 576 " --> pdb=" O GLN Z 541 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Z' and resid 586 through 587 removed outlier: 3.656A pdb=" N ALA Z 586 " --> pdb=" O ILE Z 594 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE Z 594 " --> pdb=" O ALA Z 586 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'Z' and resid 635 through 638 removed outlier: 7.068A pdb=" N PHE Z 623 " --> pdb=" O ARG Z 615 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY Z 612 " --> pdb=" O VAL Z 600 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL Z 600 " --> pdb=" O GLY Z 612 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Z' and resid 742 through 746 removed outlier: 3.820A pdb=" N ASP Z 726 " --> pdb=" O ARG Z 733 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLU Z 735 " --> pdb=" O VAL Z 724 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N VAL Z 724 " --> pdb=" O GLU Z 735 " (cutoff:3.500A) 1769 hydrogen bonds defined for protein. 4908 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 116 hydrogen bonds 232 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 74 stacking parallelities Total time for adding SS restraints: 12.15 Time building geometry restraints manager: 4.33 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: 11435 1.33 - 1.45: 9299 1.45 - 1.58: 24573 1.58 - 1.70: 193 1.70 - 1.83: 407 Bond restraints: 45907 Sorted by residual: bond pdb=" C ILE Z 550 " pdb=" N VAL Z 551 " ideal model delta sigma weight residual 1.329 1.282 0.047 9.40e-03 1.13e+04 2.50e+01 bond pdb=" CA VAL Z 551 " pdb=" CB VAL Z 551 " ideal model delta sigma weight residual 1.544 1.494 0.050 1.17e-02 7.31e+03 1.83e+01 bond pdb=" N GLN I 98 " pdb=" CA GLN I 98 " ideal model delta sigma weight residual 1.452 1.502 -0.050 1.22e-02 6.72e+03 1.66e+01 bond pdb=" CZ ARG F 51 " pdb=" NH2 ARG F 51 " ideal model delta sigma weight residual 1.330 1.282 0.048 1.30e-02 5.92e+03 1.39e+01 bond pdb=" CA LYS Z 597 " pdb=" C LYS Z 597 " ideal model delta sigma weight residual 1.522 1.578 -0.056 1.51e-02 4.39e+03 1.38e+01 ... (remaining 45902 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 57764 2.19 - 4.37: 4099 4.37 - 6.56: 503 6.56 - 8.75: 35 8.75 - 10.93: 2 Bond angle restraints: 62403 Sorted by residual: angle pdb=" N VAL B 330 " pdb=" CA VAL B 330 " pdb=" C VAL B 330 " ideal model delta sigma weight residual 111.62 118.74 -7.12 7.90e-01 1.60e+00 8.12e+01 angle pdb=" C PRO B 81 " pdb=" N PRO B 82 " pdb=" CA PRO B 82 " ideal model delta sigma weight residual 120.21 127.88 -7.67 9.60e-01 1.09e+00 6.38e+01 angle pdb=" CA VAL B 330 " pdb=" C VAL B 330 " pdb=" N THR B 331 " ideal model delta sigma weight residual 117.15 123.05 -5.90 7.80e-01 1.64e+00 5.72e+01 angle pdb=" N GLY A 297 " pdb=" CA GLY A 297 " pdb=" C GLY A 297 " ideal model delta sigma weight residual 112.49 103.70 8.79 1.21e+00 6.83e-01 5.28e+01 angle pdb=" N SER A 480 " pdb=" CA SER A 480 " pdb=" C SER A 480 " ideal model delta sigma weight residual 113.15 121.09 -7.94 1.19e+00 7.06e-01 4.45e+01 ... (remaining 62398 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.35: 26970 35.35 - 70.71: 868 70.71 - 106.06: 45 106.06 - 141.42: 0 141.42 - 176.77: 5 Dihedral angle restraints: 27888 sinusoidal: 12326 harmonic: 15562 Sorted by residual: dihedral pdb=" O4' C P 4 " pdb=" C1' C P 4 " pdb=" N1 C P 4 " pdb=" C2 C P 4 " ideal model delta sinusoidal sigma weight residual -128.00 48.77 -176.77 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA GLU B 818 " pdb=" C GLU B 818 " pdb=" N SER B 819 " pdb=" CA SER B 819 " ideal model delta harmonic sigma weight residual -180.00 -150.05 -29.95 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" C5' C P 4 " pdb=" C4' C P 4 " pdb=" C3' C P 4 " pdb=" O3' C P 4 " ideal model delta sinusoidal sigma weight residual 147.00 107.19 39.81 1 8.00e+00 1.56e-02 3.48e+01 ... (remaining 27885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 5952 0.091 - 0.183: 858 0.183 - 0.274: 123 0.274 - 0.365: 36 0.365 - 0.456: 5 Chirality restraints: 6974 Sorted by residual: chirality pdb=" C3' G P 12 " pdb=" C4' G P 12 " pdb=" O3' G P 12 " pdb=" C2' G P 12 " both_signs ideal model delta sigma weight residual False -2.48 -2.02 -0.46 2.00e-01 2.50e+01 5.21e+00 chirality pdb=" CA LYS A 910 " pdb=" N LYS A 910 " pdb=" C LYS A 910 " pdb=" CB LYS A 910 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 4.99e+00 chirality pdb=" CA SER B 719 " pdb=" N SER B 719 " pdb=" C SER B 719 " pdb=" CB SER B 719 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.32e+00 ... (remaining 6971 not shown) Planarity restraints: 7728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP M 403 " 0.108 2.00e-02 2.50e+03 6.52e-02 1.06e+02 pdb=" CG TRP M 403 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP M 403 " -0.093 2.00e-02 2.50e+03 pdb=" CD2 TRP M 403 " -0.019 2.00e-02 2.50e+03 pdb=" NE1 TRP M 403 " -0.039 2.00e-02 2.50e+03 pdb=" CE2 TRP M 403 " 0.022 2.00e-02 2.50e+03 pdb=" CE3 TRP M 403 " -0.084 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 403 " 0.086 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 403 " -0.051 2.00e-02 2.50e+03 pdb=" CH2 TRP M 403 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 41 " 0.118 2.00e-02 2.50e+03 6.35e-02 8.06e+01 pdb=" CG TYR L 41 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR L 41 " -0.053 2.00e-02 2.50e+03 pdb=" CD2 TYR L 41 " -0.061 2.00e-02 2.50e+03 pdb=" CE1 TYR L 41 " -0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR L 41 " -0.025 2.00e-02 2.50e+03 pdb=" CZ TYR L 41 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR L 41 " 0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1048 " -0.117 2.00e-02 2.50e+03 6.26e-02 7.83e+01 pdb=" CG TYR B1048 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR B1048 " 0.061 2.00e-02 2.50e+03 pdb=" CD2 TYR B1048 " 0.044 2.00e-02 2.50e+03 pdb=" CE1 TYR B1048 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR B1048 " 0.035 2.00e-02 2.50e+03 pdb=" CZ TYR B1048 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR B1048 " -0.091 2.00e-02 2.50e+03 ... (remaining 7725 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 53 2.46 - 3.07: 28693 3.07 - 3.68: 67394 3.68 - 4.29: 98962 4.29 - 4.90: 164477 Nonbonded interactions: 359579 Sorted by model distance: nonbonded pdb=" OP1 C P 21 " pdb="MG MG A2003 " model vdw 1.851 2.170 nonbonded pdb=" OD1 ASP A 497 " pdb="MG MG A2003 " model vdw 1.895 2.170 nonbonded pdb=" OH TYR M 379 " pdb=" O GLY M1033 " model vdw 2.212 3.040 nonbonded pdb=" NZ LYS B 847 " pdb=" OE2 GLU Z 735 " model vdw 2.224 3.120 nonbonded pdb=" OG1 THR E 36 " pdb=" OE1 GLU E 39 " model vdw 2.300 3.040 ... (remaining 359574 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.470 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: 0.030 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 47.560 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 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 : 0.008 0.344 45942 Z= 0.477 Angle : 1.140 19.929 62430 Z= 0.729 Chirality : 0.066 0.456 6974 Planarity : 0.010 0.124 7728 Dihedral : 15.889 176.771 17804 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.04 % Allowed : 11.15 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.25 (0.12), residues: 5255 helix: 0.87 (0.13), residues: 1839 sheet: -0.55 (0.18), residues: 775 loop : -0.74 (0.12), residues: 2641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.001 ARG B 859 TYR 0.118 0.008 TYR L 41 PHE 0.094 0.006 PHE M 539 TRP 0.108 0.008 TRP M 403 HIS 0.032 0.002 HIS Z 737 Details of bonding type rmsd covalent geometry : bond 0.00779 (45907) covalent geometry : angle 1.12548 (62403) hydrogen bonds : bond 0.16602 ( 1872) hydrogen bonds : angle 6.47869 ( 5140) metal coordination : bond 0.12238 ( 35) metal coordination : angle 8.87976 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 4739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 385 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8115 (tpp) cc_final: 0.7575 (tpp) REVERT: A 1459 MET cc_start: 0.8880 (mtt) cc_final: 0.8623 (mtt) REVERT: B 677 MET cc_start: 0.8919 (tpp) cc_final: 0.8618 (tpp) REVERT: D 39 MET cc_start: 0.8238 (mmm) cc_final: 0.8017 (mmm) REVERT: D 75 LYS cc_start: 0.9127 (mmmm) cc_final: 0.8905 (mmtm) REVERT: E 117 SER cc_start: 0.9079 (m) cc_final: 0.8841 (p) REVERT: E 151 MET cc_start: 0.8854 (mtp) cc_final: 0.8633 (mtt) REVERT: G 3 TYR cc_start: 0.7863 (m-80) cc_final: 0.7150 (m-80) REVERT: G 142 GLU cc_start: 0.7576 (mp0) cc_final: 0.7305 (mp0) REVERT: G 144 ARG cc_start: 0.7764 (mmt90) cc_final: 0.7501 (ttm110) REVERT: H 126 GLN cc_start: 0.8376 (tt0) cc_final: 0.8168 (tt0) REVERT: I 18 GLN cc_start: 0.8210 (tp40) cc_final: 0.7888 (mm-40) REVERT: I 29 ASP cc_start: 0.7274 (t0) cc_final: 0.6888 (t70) REVERT: I 58 ILE cc_start: 0.7924 (tt) cc_final: 0.7635 (tp) REVERT: I 92 LYS cc_start: 0.8465 (ptpp) cc_final: 0.8077 (ptmm) REVERT: J 48 MET cc_start: 0.9084 (mmm) cc_final: 0.8532 (mmm) REVERT: J 66 GLU cc_start: 0.6529 (mt-10) cc_final: 0.6115 (mp0) REVERT: K 102 GLU cc_start: 0.8003 (tt0) cc_final: 0.7761 (tt0) REVERT: L 44 MET cc_start: 0.8373 (mmm) cc_final: 0.8170 (mmt) REVERT: M 271 MET cc_start: 0.6198 (mmt) cc_final: 0.5984 (mmm) REVERT: M 366 MET cc_start: 0.7610 (mtm) cc_final: 0.7349 (mtt) REVERT: M 522 ASP cc_start: 0.7624 (m-30) cc_final: 0.7256 (t0) REVERT: M 523 MET cc_start: 0.4451 (mtt) cc_final: 0.3719 (tpp) REVERT: M 962 PHE cc_start: 0.7684 (m-80) cc_final: 0.7241 (m-10) REVERT: Q 32 GLU cc_start: 0.8489 (pm20) cc_final: 0.8073 (pt0) REVERT: Y 9 ASP cc_start: 0.6117 (p0) cc_final: 0.5873 (p0) REVERT: Y 29 GLU cc_start: 0.6507 (tt0) cc_final: 0.6237 (tp30) REVERT: Y 34 ASP cc_start: 0.6767 (m-30) cc_final: 0.6342 (m-30) REVERT: Y 64 MET cc_start: 0.4980 (tpp) cc_final: 0.4480 (tmm) REVERT: Y 98 VAL cc_start: 0.7817 (t) cc_final: 0.7588 (t) REVERT: Z 250 TRP cc_start: 0.6245 (m100) cc_final: 0.5324 (m-10) REVERT: Z 254 MET cc_start: 0.7221 (tpt) cc_final: 0.6005 (ttt) REVERT: Z 563 MET cc_start: 0.5490 (ptm) cc_final: 0.4747 (ppp) outliers start: 2 outliers final: 1 residues processed: 387 average time/residue: 0.2622 time to fit residues: 161.7098 Evaluate side-chains 257 residues out of total 4739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 256 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 283 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 394 optimal weight: 5.9990 chunk 430 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 265 optimal weight: 0.9980 chunk 523 optimal weight: 40.0000 chunk 497 optimal weight: 5.9990 chunk 414 optimal weight: 30.0000 chunk 310 optimal weight: 0.1980 chunk 488 optimal weight: 1.9990 chunk 366 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 ASN B 144 HIS B 593 GLN B 838 GLN I 22 ASN ** M 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 466 HIS M 948 HIS M1151 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.093330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.053821 restraints weight = 144969.636| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.61 r_work: 0.2822 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 45942 Z= 0.159 Angle : 0.587 9.109 62430 Z= 0.309 Chirality : 0.044 0.214 6974 Planarity : 0.004 0.059 7728 Dihedral : 14.019 177.941 6949 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.59 % Allowed : 12.19 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % 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 aren not related in a simple way. whole: 0.06 (0.12), residues: 5255 helix: 1.20 (0.12), residues: 1868 sheet: -0.50 (0.18), residues: 751 loop : -0.59 (0.12), residues: 2636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 103 TYR 0.026 0.001 TYR Q 71 PHE 0.019 0.002 PHE D 95 TRP 0.031 0.002 TRP M 319 HIS 0.006 0.001 HIS I 60 Details of bonding type rmsd covalent geometry : bond 0.00365 (45907) covalent geometry : angle 0.57957 (62403) hydrogen bonds : bond 0.04456 ( 1872) hydrogen bonds : angle 4.92964 ( 5140) metal coordination : bond 0.00775 ( 35) metal coordination : angle 4.36872 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 4739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 279 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8978 (tpp) cc_final: 0.8180 (tpp) REVERT: A 266 MET cc_start: 0.6010 (tpp) cc_final: 0.5787 (mmm) REVERT: A 1247 PHE cc_start: 0.7222 (p90) cc_final: 0.6586 (p90) REVERT: A 1262 MET cc_start: 0.6815 (mpp) cc_final: 0.6455 (mpp) REVERT: B 677 MET cc_start: 0.9149 (tpp) cc_final: 0.8944 (tpp) REVERT: B 1165 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.8971 (mtp) REVERT: C 213 GLU cc_start: 0.8630 (mp0) cc_final: 0.8341 (tp30) REVERT: D 39 MET cc_start: 0.8618 (mmm) cc_final: 0.8340 (mmm) REVERT: D 75 LYS cc_start: 0.9205 (mmmm) cc_final: 0.8784 (mmtm) REVERT: G 3 TYR cc_start: 0.7792 (m-80) cc_final: 0.7090 (m-80) REVERT: G 100 GLU cc_start: 0.7462 (tm-30) cc_final: 0.7232 (tm-30) REVERT: G 131 MET cc_start: 0.8186 (pmm) cc_final: 0.7971 (pmm) REVERT: G 142 GLU cc_start: 0.7466 (mp0) cc_final: 0.7215 (mp0) REVERT: H 126 GLN cc_start: 0.8892 (tt0) cc_final: 0.8503 (tt0) REVERT: I 18 GLN cc_start: 0.8322 (tp40) cc_final: 0.7734 (mm-40) REVERT: I 46 GLN cc_start: 0.7805 (mt0) cc_final: 0.7361 (mt0) REVERT: I 103 ARG cc_start: 0.4344 (OUTLIER) cc_final: 0.3747 (tpt170) REVERT: K 102 GLU cc_start: 0.8671 (tt0) cc_final: 0.8380 (tt0) REVERT: L 16 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.7996 (tt) REVERT: L 25 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7437 (pt0) REVERT: M 271 MET cc_start: 0.6467 (mmt) cc_final: 0.6198 (tpt) REVERT: M 523 MET cc_start: 0.4418 (mtt) cc_final: 0.4054 (tpp) REVERT: M 962 PHE cc_start: 0.7889 (m-80) cc_final: 0.7275 (m-10) REVERT: Q 32 GLU cc_start: 0.8676 (pm20) cc_final: 0.8174 (pt0) REVERT: Q 38 LYS cc_start: 0.8595 (ttpt) cc_final: 0.8073 (tppt) REVERT: Y 34 ASP cc_start: 0.6887 (m-30) cc_final: 0.6551 (m-30) REVERT: Z 250 TRP cc_start: 0.6473 (m100) cc_final: 0.5514 (m-10) REVERT: Z 563 MET cc_start: 0.5521 (ptm) cc_final: 0.4738 (ppp) REVERT: Z 635 MET cc_start: 0.4645 (OUTLIER) cc_final: 0.4429 (tpt) outliers start: 75 outliers final: 21 residues processed: 341 average time/residue: 0.2493 time to fit residues: 141.4293 Evaluate side-chains 273 residues out of total 4739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 248 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain B residue 1165 MET Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 67 GLN Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain K residue 103 GLU Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain Y residue 102 LYS Chi-restraints excluded: chain Z residue 635 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 146 optimal weight: 5.9990 chunk 186 optimal weight: 7.9990 chunk 334 optimal weight: 6.9990 chunk 358 optimal weight: 9.9990 chunk 90 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 321 optimal weight: 9.9990 chunk 458 optimal weight: 5.9990 chunk 522 optimal weight: 0.0030 chunk 261 optimal weight: 0.9990 chunk 423 optimal weight: 9.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 GLN ** M 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 895 ASN Y 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.092838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.053345 restraints weight = 142773.727| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.59 r_work: 0.2811 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 45942 Z= 0.151 Angle : 0.544 9.821 62430 Z= 0.286 Chirality : 0.043 0.212 6974 Planarity : 0.004 0.077 7728 Dihedral : 13.867 177.230 6948 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.74 % Allowed : 12.57 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % 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 aren not related in a simple way. whole: 0.24 (0.12), residues: 5255 helix: 1.41 (0.12), residues: 1866 sheet: -0.45 (0.18), residues: 735 loop : -0.53 (0.12), residues: 2654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 103 TYR 0.013 0.001 TYR J 29 PHE 0.017 0.001 PHE Y 28 TRP 0.039 0.001 TRP A1192 HIS 0.004 0.001 HIS B 749 Details of bonding type rmsd covalent geometry : bond 0.00344 (45907) covalent geometry : angle 0.53918 (62403) hydrogen bonds : bond 0.03948 ( 1872) hydrogen bonds : angle 4.59281 ( 5140) metal coordination : bond 0.00572 ( 35) metal coordination : angle 3.52907 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 4739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 268 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8912 (mmt) cc_final: 0.8480 (mmt) REVERT: A 78 MET cc_start: 0.9172 (tpp) cc_final: 0.8239 (tpp) REVERT: A 266 MET cc_start: 0.6108 (tpp) cc_final: 0.5816 (mmm) REVERT: A 1233 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8607 (tm-30) REVERT: A 1247 PHE cc_start: 0.7185 (p90) cc_final: 0.6500 (p90) REVERT: B 388 TYR cc_start: 0.9209 (OUTLIER) cc_final: 0.8862 (m-80) REVERT: C 213 GLU cc_start: 0.8889 (mp0) cc_final: 0.8324 (tm-30) REVERT: D 26 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7860 (t80) REVERT: D 39 MET cc_start: 0.8627 (mmm) cc_final: 0.8320 (mmm) REVERT: D 75 LYS cc_start: 0.9136 (mmmm) cc_final: 0.8728 (mmtm) REVERT: E 186 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8706 (ptpp) REVERT: G 142 GLU cc_start: 0.7643 (mp0) cc_final: 0.7371 (mp0) REVERT: I 18 GLN cc_start: 0.8552 (tp40) cc_final: 0.8131 (mm-40) REVERT: I 43 ASP cc_start: 0.8295 (t70) cc_final: 0.7754 (p0) REVERT: I 46 GLN cc_start: 0.7787 (mt0) cc_final: 0.7433 (mt0) REVERT: K 102 GLU cc_start: 0.8948 (tt0) cc_final: 0.8647 (tt0) REVERT: L 16 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.7877 (tt) REVERT: L 31 ARG cc_start: 0.6991 (mmt180) cc_final: 0.6755 (mmt-90) REVERT: M 523 MET cc_start: 0.4633 (mtt) cc_final: 0.4111 (tpp) REVERT: M 962 PHE cc_start: 0.7920 (m-80) cc_final: 0.7307 (m-10) REVERT: Q 32 GLU cc_start: 0.8682 (pm20) cc_final: 0.8203 (pt0) REVERT: Q 62 THR cc_start: 0.8332 (OUTLIER) cc_final: 0.8130 (t) REVERT: Y 57 PHE cc_start: 0.4877 (p90) cc_final: 0.4586 (p90) REVERT: Z 250 TRP cc_start: 0.6559 (m100) cc_final: 0.5586 (m-10) REVERT: Z 451 MET cc_start: 0.7408 (mmt) cc_final: 0.7163 (mmm) REVERT: Z 563 MET cc_start: 0.5597 (ptm) cc_final: 0.4834 (ppp) REVERT: Z 635 MET cc_start: 0.4355 (tpt) cc_final: 0.4148 (tpt) outliers start: 82 outliers final: 33 residues processed: 341 average time/residue: 0.2457 time to fit residues: 140.2504 Evaluate side-chains 290 residues out of total 4739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 252 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain D residue 26 PHE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 186 LYS Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 103 GLU Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain M residue 302 SER Chi-restraints excluded: chain M residue 805 VAL Chi-restraints excluded: chain M residue 1272 ILE Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 62 THR Chi-restraints excluded: chain Z residue 278 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 161 optimal weight: 7.9990 chunk 469 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 chunk 510 optimal weight: 20.0000 chunk 66 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 456 optimal weight: 7.9990 chunk 407 optimal weight: 7.9990 chunk 401 optimal weight: 30.0000 chunk 475 optimal weight: 8.9990 chunk 394 optimal weight: 20.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN A1194 ASN ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 GLN ** B 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN G 24 ASN M 405 GLN M 921 GLN M1310 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.090618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.050647 restraints weight = 143202.992| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.57 r_work: 0.2727 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.094 45942 Z= 0.329 Angle : 0.679 15.216 62430 Z= 0.351 Chirality : 0.048 0.251 6974 Planarity : 0.005 0.076 7728 Dihedral : 14.030 176.492 6948 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.79 % Allowed : 12.93 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: -0.02 (0.12), residues: 5255 helix: 1.13 (0.12), residues: 1876 sheet: -0.64 (0.18), residues: 761 loop : -0.60 (0.12), residues: 2618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 83 TYR 0.023 0.002 TYR B 814 PHE 0.030 0.002 PHE B 935 TRP 0.030 0.002 TRP A1192 HIS 0.007 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00785 (45907) covalent geometry : angle 0.66769 (62403) hydrogen bonds : bond 0.05063 ( 1872) hydrogen bonds : angle 4.82098 ( 5140) metal coordination : bond 0.01226 ( 35) metal coordination : angle 5.89447 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 4739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 254 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 MET cc_start: 0.6298 (tpp) cc_final: 0.6016 (mmm) REVERT: A 660 MET cc_start: 0.9403 (OUTLIER) cc_final: 0.8488 (mmm) REVERT: A 952 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9222 (mt) REVERT: A 1182 GLN cc_start: 0.8390 (pp30) cc_final: 0.7836 (pm20) REVERT: A 1233 GLU cc_start: 0.8828 (tm-30) cc_final: 0.8614 (tm-30) REVERT: A 1247 PHE cc_start: 0.7327 (p90) cc_final: 0.6510 (p90) REVERT: A 1351 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.7910 (t0) REVERT: B 51 ILE cc_start: 0.9488 (OUTLIER) cc_final: 0.9164 (tp) REVERT: B 151 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8439 (mtmm) REVERT: B 285 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9219 (mp) REVERT: B 388 TYR cc_start: 0.9409 (OUTLIER) cc_final: 0.9151 (m-80) REVERT: B 1145 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8723 (pm20) REVERT: D 26 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.7937 (t80) REVERT: D 39 MET cc_start: 0.8633 (mmm) cc_final: 0.8308 (mmm) REVERT: D 75 LYS cc_start: 0.9190 (mmmm) cc_final: 0.8848 (mmtm) REVERT: D 122 PHE cc_start: 0.7185 (m-80) cc_final: 0.6889 (m-80) REVERT: E 186 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8700 (ptpp) REVERT: F 68 THR cc_start: 0.9553 (OUTLIER) cc_final: 0.9349 (p) REVERT: G 67 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8884 (pt) REVERT: G 83 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7109 (mm-30) REVERT: G 118 GLU cc_start: 0.8762 (tp30) cc_final: 0.8153 (pm20) REVERT: G 142 GLU cc_start: 0.7793 (mp0) cc_final: 0.7501 (mp0) REVERT: H 133 HIS cc_start: 0.9129 (OUTLIER) cc_final: 0.8581 (t70) REVERT: I 18 GLN cc_start: 0.8996 (tp40) cc_final: 0.8402 (mm-40) REVERT: I 19 GLU cc_start: 0.8937 (pt0) cc_final: 0.8375 (pm20) REVERT: I 33 ARG cc_start: 0.7401 (mtt-85) cc_final: 0.6947 (ptm160) REVERT: I 43 ASP cc_start: 0.8495 (t70) cc_final: 0.8015 (p0) REVERT: I 46 GLN cc_start: 0.7776 (mt0) cc_final: 0.7420 (mt0) REVERT: I 68 ILE cc_start: 0.8558 (mm) cc_final: 0.8252 (mt) REVERT: K 68 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8323 (mp0) REVERT: M 271 MET cc_start: 0.6326 (tpt) cc_final: 0.6089 (mmm) REVERT: M 523 MET cc_start: 0.4548 (mtt) cc_final: 0.3933 (tpp) REVERT: M 556 ARG cc_start: 0.7196 (OUTLIER) cc_final: 0.6957 (ttp80) REVERT: M 920 ILE cc_start: 0.6894 (OUTLIER) cc_final: 0.6399 (pt) REVERT: M 962 PHE cc_start: 0.8013 (m-80) cc_final: 0.7402 (m-10) REVERT: M 1286 LEU cc_start: 0.3669 (OUTLIER) cc_final: 0.3247 (tt) REVERT: M 1310 HIS cc_start: 0.4752 (OUTLIER) cc_final: 0.4441 (t-170) REVERT: Q 32 GLU cc_start: 0.8745 (pm20) cc_final: 0.8277 (pt0) REVERT: Y 57 PHE cc_start: 0.5210 (p90) cc_final: 0.4975 (p90) REVERT: Z 250 TRP cc_start: 0.6534 (m100) cc_final: 0.5650 (m-10) REVERT: Z 508 MET cc_start: 0.7549 (tpp) cc_final: 0.6989 (tpp) REVERT: Z 635 MET cc_start: 0.4169 (tpt) cc_final: 0.3960 (tpt) outliers start: 132 outliers final: 56 residues processed: 370 average time/residue: 0.2266 time to fit residues: 142.6051 Evaluate side-chains 315 residues out of total 4739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 241 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 660 MET Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1351 ASP Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 840 MET Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain B residue 1145 GLN Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 26 PHE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 186 LYS Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 107 PHE Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 103 GLU Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain M residue 302 SER Chi-restraints excluded: chain M residue 556 ARG Chi-restraints excluded: chain M residue 805 VAL Chi-restraints excluded: chain M residue 920 ILE Chi-restraints excluded: chain M residue 1272 ILE Chi-restraints excluded: chain M residue 1286 LEU Chi-restraints excluded: chain M residue 1310 HIS Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Z residue 536 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 477 optimal weight: 40.0000 chunk 108 optimal weight: 1.9990 chunk 336 optimal weight: 5.9990 chunk 486 optimal weight: 4.9990 chunk 188 optimal weight: 0.3980 chunk 28 optimal weight: 9.9990 chunk 391 optimal weight: 9.9990 chunk 392 optimal weight: 6.9990 chunk 419 optimal weight: 5.9990 chunk 264 optimal weight: 2.9990 chunk 527 optimal weight: 40.0000 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN M 921 GLN M 956 ASN M1310 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.091198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.051598 restraints weight = 142699.222| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.55 r_work: 0.2753 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 45942 Z= 0.219 Angle : 0.585 11.791 62430 Z= 0.305 Chirality : 0.044 0.194 6974 Planarity : 0.004 0.136 7728 Dihedral : 13.945 177.361 6948 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.20 % Allowed : 13.75 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.08 (0.12), residues: 5255 helix: 1.23 (0.12), residues: 1881 sheet: -0.56 (0.18), residues: 746 loop : -0.58 (0.12), residues: 2628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG Q 43 TYR 0.014 0.001 TYR G 68 PHE 0.019 0.002 PHE B 935 TRP 0.025 0.002 TRP A1192 HIS 0.020 0.001 HIS M1310 Details of bonding type rmsd covalent geometry : bond 0.00521 (45907) covalent geometry : angle 0.57776 (62403) hydrogen bonds : bond 0.04208 ( 1872) hydrogen bonds : angle 4.61493 ( 5140) metal coordination : bond 0.00775 ( 35) metal coordination : angle 4.59165 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 4739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 249 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 MET cc_start: 0.6386 (tpp) cc_final: 0.6068 (mmm) REVERT: A 1182 GLN cc_start: 0.8400 (pp30) cc_final: 0.7799 (pm20) REVERT: A 1233 GLU cc_start: 0.8920 (tm-30) cc_final: 0.8709 (tm-30) REVERT: A 1351 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7873 (t0) REVERT: B 51 ILE cc_start: 0.9407 (OUTLIER) cc_final: 0.9104 (tp) REVERT: B 276 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8832 (mp) REVERT: B 297 MET cc_start: 0.9055 (mtp) cc_final: 0.8836 (mtp) REVERT: B 388 TYR cc_start: 0.9384 (OUTLIER) cc_final: 0.9113 (m-80) REVERT: B 422 PHE cc_start: 0.7868 (OUTLIER) cc_final: 0.7564 (t80) REVERT: B 1101 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8651 (mt0) REVERT: B 1145 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8727 (pm20) REVERT: D 26 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.7945 (t80) REVERT: D 39 MET cc_start: 0.8766 (mmm) cc_final: 0.8440 (mmm) REVERT: D 75 LYS cc_start: 0.9193 (mmmm) cc_final: 0.8783 (mmtm) REVERT: E 186 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8624 (ptpp) REVERT: G 118 GLU cc_start: 0.8843 (tp30) cc_final: 0.8336 (pm20) REVERT: G 142 GLU cc_start: 0.7760 (mp0) cc_final: 0.7464 (mp0) REVERT: H 133 HIS cc_start: 0.9168 (OUTLIER) cc_final: 0.8573 (t70) REVERT: I 18 GLN cc_start: 0.9143 (tp40) cc_final: 0.8636 (mm-40) REVERT: I 33 ARG cc_start: 0.7380 (mtt-85) cc_final: 0.7024 (ptm160) REVERT: I 43 ASP cc_start: 0.8517 (t70) cc_final: 0.7965 (p0) REVERT: I 46 GLN cc_start: 0.7770 (mt0) cc_final: 0.7435 (mt0) REVERT: I 68 ILE cc_start: 0.8483 (mm) cc_final: 0.8192 (mt) REVERT: K 68 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8266 (mp0) REVERT: M 271 MET cc_start: 0.6275 (tpt) cc_final: 0.6065 (mmm) REVERT: M 523 MET cc_start: 0.4444 (mtt) cc_final: 0.3863 (tpt) REVERT: M 920 ILE cc_start: 0.6817 (OUTLIER) cc_final: 0.6200 (pt) REVERT: M 958 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8290 (mt) REVERT: M 962 PHE cc_start: 0.8043 (m-80) cc_final: 0.7437 (m-10) REVERT: M 1161 PHE cc_start: 0.4482 (OUTLIER) cc_final: 0.4249 (m-80) REVERT: M 1310 HIS cc_start: 0.4408 (OUTLIER) cc_final: 0.4017 (t-170) REVERT: Q 32 GLU cc_start: 0.8811 (pm20) cc_final: 0.8281 (pt0) REVERT: Y 104 ARG cc_start: 0.6180 (tmm160) cc_final: 0.5687 (tpt-90) REVERT: Z 250 TRP cc_start: 0.6474 (m100) cc_final: 0.5580 (m-10) REVERT: Z 451 MET cc_start: 0.7381 (mmm) cc_final: 0.6997 (mmm) REVERT: Z 508 MET cc_start: 0.7500 (tpp) cc_final: 0.6971 (tpp) outliers start: 104 outliers final: 55 residues processed: 339 average time/residue: 0.2331 time to fit residues: 134.5262 Evaluate side-chains 310 residues out of total 4739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 240 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1351 ASP Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain B residue 1101 GLN Chi-restraints excluded: chain B residue 1145 GLN Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 26 PHE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 186 LYS Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 107 PHE Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain I residue 67 GLN Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 103 GLU Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain M residue 302 SER Chi-restraints excluded: chain M residue 805 VAL Chi-restraints excluded: chain M residue 920 ILE Chi-restraints excluded: chain M residue 958 LEU Chi-restraints excluded: chain M residue 960 CYS Chi-restraints excluded: chain M residue 1018 VAL Chi-restraints excluded: chain M residue 1161 PHE Chi-restraints excluded: chain M residue 1272 ILE Chi-restraints excluded: chain M residue 1310 HIS Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Z residue 536 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 526 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 533 optimal weight: 10.0000 chunk 372 optimal weight: 2.9990 chunk 517 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 513 optimal weight: 20.0000 chunk 313 optimal weight: 0.0770 chunk 79 optimal weight: 1.9990 chunk 325 optimal weight: 6.9990 chunk 309 optimal weight: 0.9980 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 ASN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.091866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.052458 restraints weight = 142858.079| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.53 r_work: 0.2783 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 45942 Z= 0.138 Angle : 0.535 8.601 62430 Z= 0.280 Chirality : 0.042 0.176 6974 Planarity : 0.004 0.046 7728 Dihedral : 13.849 177.899 6948 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.03 % Allowed : 14.11 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.22 (0.12), residues: 5255 helix: 1.40 (0.12), residues: 1887 sheet: -0.50 (0.18), residues: 744 loop : -0.54 (0.12), residues: 2624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG Q 43 TYR 0.015 0.001 TYR Q 71 PHE 0.015 0.001 PHE D 61 TRP 0.024 0.001 TRP A1192 HIS 0.013 0.001 HIS M 632 Details of bonding type rmsd covalent geometry : bond 0.00322 (45907) covalent geometry : angle 0.52979 (62403) hydrogen bonds : bond 0.03702 ( 1872) hydrogen bonds : angle 4.42848 ( 5140) metal coordination : bond 0.00484 ( 35) metal coordination : angle 3.70397 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 4739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 246 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8943 (mmt) cc_final: 0.8430 (mmt) REVERT: A 266 MET cc_start: 0.6413 (tpp) cc_final: 0.6125 (mmm) REVERT: A 567 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9138 (tt) REVERT: A 1182 GLN cc_start: 0.8442 (pp30) cc_final: 0.7800 (mp10) REVERT: A 1233 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8678 (tm-30) REVERT: B 51 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.9062 (tp) REVERT: B 151 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8247 (mtmm) REVERT: B 297 MET cc_start: 0.9062 (mtp) cc_final: 0.8856 (mtp) REVERT: B 388 TYR cc_start: 0.9231 (OUTLIER) cc_final: 0.8966 (m-80) REVERT: B 677 MET cc_start: 0.9281 (tpp) cc_final: 0.8924 (tpp) REVERT: D 26 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.7983 (t80) REVERT: D 39 MET cc_start: 0.8752 (mmm) cc_final: 0.8419 (mmm) REVERT: D 75 LYS cc_start: 0.9191 (mmmm) cc_final: 0.8804 (mmtm) REVERT: E 186 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8640 (ptpp) REVERT: F 68 THR cc_start: 0.9579 (OUTLIER) cc_final: 0.9344 (p) REVERT: G 118 GLU cc_start: 0.9044 (tp30) cc_final: 0.8471 (pm20) REVERT: G 142 GLU cc_start: 0.7769 (mp0) cc_final: 0.7461 (mp0) REVERT: H 133 HIS cc_start: 0.9136 (OUTLIER) cc_final: 0.8513 (t70) REVERT: I 18 GLN cc_start: 0.9160 (tp40) cc_final: 0.8700 (mm-40) REVERT: I 28 GLU cc_start: 0.6926 (pm20) cc_final: 0.6205 (pt0) REVERT: I 43 ASP cc_start: 0.8488 (t70) cc_final: 0.7937 (p0) REVERT: I 46 GLN cc_start: 0.7800 (mt0) cc_final: 0.7462 (mt0) REVERT: I 68 ILE cc_start: 0.8468 (mm) cc_final: 0.8164 (mt) REVERT: I 103 ARG cc_start: 0.5081 (tpm170) cc_final: 0.4081 (tpt170) REVERT: K 68 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8226 (mp0) REVERT: L 25 GLU cc_start: 0.8463 (tt0) cc_final: 0.8169 (tt0) REVERT: M 366 MET cc_start: 0.7449 (mtt) cc_final: 0.6820 (mtt) REVERT: M 523 MET cc_start: 0.4450 (mtt) cc_final: 0.3853 (tpt) REVERT: M 894 MET cc_start: 0.8175 (ptt) cc_final: 0.7861 (mtm) REVERT: M 920 ILE cc_start: 0.6830 (OUTLIER) cc_final: 0.6232 (pt) REVERT: M 958 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8276 (mt) REVERT: M 962 PHE cc_start: 0.8135 (m-80) cc_final: 0.7556 (m-10) REVERT: M 1161 PHE cc_start: 0.4543 (OUTLIER) cc_final: 0.4287 (m-80) REVERT: M 1233 ASP cc_start: 0.6481 (OUTLIER) cc_final: 0.5352 (t0) REVERT: M 1286 LEU cc_start: 0.3382 (OUTLIER) cc_final: 0.2972 (tt) REVERT: Q 32 GLU cc_start: 0.8781 (pm20) cc_final: 0.8407 (pt0) REVERT: Y 104 ARG cc_start: 0.6172 (tmm160) cc_final: 0.5633 (tpt-90) REVERT: Z 250 TRP cc_start: 0.6459 (m100) cc_final: 0.5570 (m-10) REVERT: Z 508 MET cc_start: 0.7605 (tpp) cc_final: 0.7035 (tpp) outliers start: 96 outliers final: 54 residues processed: 331 average time/residue: 0.2268 time to fit residues: 127.6185 Evaluate side-chains 308 residues out of total 4739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 240 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain D residue 26 PHE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 186 LYS Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 107 PHE Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain I residue 67 GLN Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 103 GLU Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain M residue 302 SER Chi-restraints excluded: chain M residue 805 VAL Chi-restraints excluded: chain M residue 920 ILE Chi-restraints excluded: chain M residue 958 LEU Chi-restraints excluded: chain M residue 960 CYS Chi-restraints excluded: chain M residue 1018 VAL Chi-restraints excluded: chain M residue 1161 PHE Chi-restraints excluded: chain M residue 1233 ASP Chi-restraints excluded: chain M residue 1272 ILE Chi-restraints excluded: chain M residue 1286 LEU Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 45 THR Chi-restraints excluded: chain Z residue 536 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 249 optimal weight: 6.9990 chunk 157 optimal weight: 1.9990 chunk 316 optimal weight: 5.9990 chunk 348 optimal weight: 20.0000 chunk 528 optimal weight: 30.0000 chunk 532 optimal weight: 9.9990 chunk 280 optimal weight: 3.9990 chunk 170 optimal weight: 10.0000 chunk 310 optimal weight: 3.9990 chunk 441 optimal weight: 6.9990 chunk 393 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 704 ASN ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 HIS ** B 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1097 HIS B1101 GLN ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 121 HIS M1310 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.090193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.050653 restraints weight = 142032.745| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.54 r_work: 0.2723 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 45942 Z= 0.305 Angle : 0.655 12.602 62430 Z= 0.338 Chirality : 0.046 0.237 6974 Planarity : 0.005 0.050 7728 Dihedral : 13.958 177.508 6948 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.37 % Allowed : 14.09 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: 0.04 (0.12), residues: 5255 helix: 1.20 (0.12), residues: 1881 sheet: -0.58 (0.18), residues: 745 loop : -0.61 (0.12), residues: 2629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 181 TYR 0.022 0.002 TYR B 811 PHE 0.027 0.002 PHE B 935 TRP 0.026 0.002 TRP A1192 HIS 0.007 0.001 HIS M 632 Details of bonding type rmsd covalent geometry : bond 0.00728 (45907) covalent geometry : angle 0.64684 (62403) hydrogen bonds : bond 0.04807 ( 1872) hydrogen bonds : angle 4.64887 ( 5140) metal coordination : bond 0.01024 ( 35) metal coordination : angle 5.12284 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 4739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 243 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 266 MET cc_start: 0.6516 (tpp) cc_final: 0.6213 (mmm) REVERT: A 660 MET cc_start: 0.9371 (OUTLIER) cc_final: 0.8466 (mmm) REVERT: A 1351 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.7918 (t0) REVERT: B 51 ILE cc_start: 0.9480 (OUTLIER) cc_final: 0.9156 (tp) REVERT: B 151 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8324 (mtmm) REVERT: B 276 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8923 (mp) REVERT: B 677 MET cc_start: 0.9258 (tpp) cc_final: 0.8905 (tpp) REVERT: B 1145 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8769 (pm20) REVERT: C 260 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8414 (tt0) REVERT: D 16 ASP cc_start: 0.7259 (t0) cc_final: 0.7052 (t0) REVERT: D 26 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.7921 (t80) REVERT: D 39 MET cc_start: 0.8750 (mmm) cc_final: 0.8432 (mmm) REVERT: D 75 LYS cc_start: 0.9194 (mmmm) cc_final: 0.8832 (mmtm) REVERT: E 186 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8730 (ptpp) REVERT: F 68 THR cc_start: 0.9585 (OUTLIER) cc_final: 0.9334 (p) REVERT: G 118 GLU cc_start: 0.9080 (tp30) cc_final: 0.8487 (pm20) REVERT: G 142 GLU cc_start: 0.7837 (mp0) cc_final: 0.7512 (mp0) REVERT: H 133 HIS cc_start: 0.9111 (OUTLIER) cc_final: 0.8473 (t70) REVERT: I 18 GLN cc_start: 0.9226 (tp40) cc_final: 0.8791 (mm-40) REVERT: I 28 GLU cc_start: 0.7018 (pm20) cc_final: 0.6359 (pt0) REVERT: I 43 ASP cc_start: 0.8569 (t70) cc_final: 0.8110 (p0) REVERT: I 46 GLN cc_start: 0.7829 (mt0) cc_final: 0.7337 (mt0) REVERT: I 62 VAL cc_start: 0.5061 (OUTLIER) cc_final: 0.4850 (m) REVERT: I 68 ILE cc_start: 0.8671 (mm) cc_final: 0.8404 (mt) REVERT: I 103 ARG cc_start: 0.5020 (tpm170) cc_final: 0.3984 (tpt170) REVERT: K 8 GLU cc_start: 0.9153 (mm-30) cc_final: 0.8919 (mm-30) REVERT: K 68 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8317 (mp0) REVERT: L 25 GLU cc_start: 0.8577 (tt0) cc_final: 0.8248 (tt0) REVERT: M 271 MET cc_start: 0.6343 (tpt) cc_final: 0.6122 (mmm) REVERT: M 523 MET cc_start: 0.4611 (mtt) cc_final: 0.3966 (tpt) REVERT: M 958 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8428 (mt) REVERT: M 962 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.7479 (m-10) REVERT: M 1161 PHE cc_start: 0.4608 (OUTLIER) cc_final: 0.4351 (m-80) REVERT: M 1233 ASP cc_start: 0.6816 (OUTLIER) cc_final: 0.5437 (t0) REVERT: M 1286 LEU cc_start: 0.3282 (OUTLIER) cc_final: 0.2858 (tt) REVERT: M 1310 HIS cc_start: 0.4714 (OUTLIER) cc_final: 0.4303 (t-170) REVERT: Y 104 ARG cc_start: 0.6207 (tmm160) cc_final: 0.5675 (tpt-90) REVERT: Z 250 TRP cc_start: 0.6507 (m100) cc_final: 0.5626 (m-10) outliers start: 112 outliers final: 67 residues processed: 343 average time/residue: 0.1992 time to fit residues: 116.4293 Evaluate side-chains 322 residues out of total 4739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 236 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 660 MET Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 865 ILE Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1351 ASP Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1463 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain B residue 840 MET Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain B residue 1145 GLN Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain D residue 26 PHE Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 186 LYS Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 107 PHE Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 67 GLN Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 103 GLU Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain M residue 302 SER Chi-restraints excluded: chain M residue 805 VAL Chi-restraints excluded: chain M residue 950 VAL Chi-restraints excluded: chain M residue 958 LEU Chi-restraints excluded: chain M residue 960 CYS Chi-restraints excluded: chain M residue 962 PHE Chi-restraints excluded: chain M residue 1018 VAL Chi-restraints excluded: chain M residue 1161 PHE Chi-restraints excluded: chain M residue 1233 ASP Chi-restraints excluded: chain M residue 1272 ILE Chi-restraints excluded: chain M residue 1286 LEU Chi-restraints excluded: chain M residue 1310 HIS Chi-restraints excluded: chain Q residue 45 THR Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Z residue 536 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 5 optimal weight: 0.9990 chunk 525 optimal weight: 40.0000 chunk 482 optimal weight: 30.0000 chunk 80 optimal weight: 1.9990 chunk 490 optimal weight: 0.9990 chunk 184 optimal weight: 2.9990 chunk 372 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 140 optimal weight: 6.9990 chunk 284 optimal weight: 1.9990 chunk 190 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1182 GLN A1194 ASN ** B 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.091938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.053129 restraints weight = 142673.190| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.94 r_work: 0.2766 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 45942 Z= 0.116 Angle : 0.535 12.377 62430 Z= 0.279 Chirality : 0.042 0.175 6974 Planarity : 0.004 0.046 7728 Dihedral : 13.828 178.059 6948 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.82 % Allowed : 14.83 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.27 (0.12), residues: 5255 helix: 1.45 (0.12), residues: 1888 sheet: -0.48 (0.18), residues: 740 loop : -0.53 (0.12), residues: 2627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 43 TYR 0.014 0.001 TYR A 669 PHE 0.016 0.001 PHE Z 503 TRP 0.024 0.001 TRP A1192 HIS 0.025 0.001 HIS M1310 Details of bonding type rmsd covalent geometry : bond 0.00256 (45907) covalent geometry : angle 0.53139 (62403) hydrogen bonds : bond 0.03467 ( 1872) hydrogen bonds : angle 4.33793 ( 5140) metal coordination : bond 0.00362 ( 35) metal coordination : angle 3.17023 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 4739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 247 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8742 (mmt) cc_final: 0.8540 (mmt) REVERT: A 266 MET cc_start: 0.6554 (tpp) cc_final: 0.6273 (tpp) REVERT: A 567 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9073 (tt) REVERT: A 1351 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7943 (t0) REVERT: B 51 ILE cc_start: 0.9328 (OUTLIER) cc_final: 0.9037 (tp) REVERT: B 53 MET cc_start: 0.9128 (mmm) cc_final: 0.8888 (mmm) REVERT: B 276 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8811 (mp) REVERT: B 677 MET cc_start: 0.9170 (tpp) cc_final: 0.8801 (tpp) REVERT: B 1076 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8127 (tt0) REVERT: D 26 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.7965 (t80) REVERT: D 39 MET cc_start: 0.8775 (mmm) cc_final: 0.8403 (mmm) REVERT: D 75 LYS cc_start: 0.9196 (mmmm) cc_final: 0.8769 (mmtm) REVERT: E 186 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8602 (ptpp) REVERT: G 118 GLU cc_start: 0.9020 (tp30) cc_final: 0.8375 (pm20) REVERT: G 142 GLU cc_start: 0.7746 (mp0) cc_final: 0.7444 (mp0) REVERT: G 164 MET cc_start: 0.8698 (mmp) cc_final: 0.6926 (ppp) REVERT: H 133 HIS cc_start: 0.8987 (OUTLIER) cc_final: 0.8276 (t70) REVERT: I 18 GLN cc_start: 0.9249 (tp40) cc_final: 0.8877 (mm-40) REVERT: I 28 GLU cc_start: 0.7100 (pm20) cc_final: 0.6426 (pt0) REVERT: I 33 ARG cc_start: 0.7379 (mtt-85) cc_final: 0.6874 (ptm160) REVERT: I 43 ASP cc_start: 0.8559 (t70) cc_final: 0.8107 (p0) REVERT: I 46 GLN cc_start: 0.7803 (mt0) cc_final: 0.7240 (mt0) REVERT: I 68 ILE cc_start: 0.8591 (mm) cc_final: 0.8325 (mt) REVERT: K 68 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8022 (mp0) REVERT: L 25 GLU cc_start: 0.8458 (tt0) cc_final: 0.8069 (tt0) REVERT: M 366 MET cc_start: 0.7468 (mtt) cc_final: 0.6815 (mtt) REVERT: M 523 MET cc_start: 0.4638 (mtt) cc_final: 0.4121 (tpt) REVERT: M 958 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8323 (mt) REVERT: M 960 CYS cc_start: 0.8387 (OUTLIER) cc_final: 0.7310 (m) REVERT: M 962 PHE cc_start: 0.8021 (OUTLIER) cc_final: 0.7495 (m-10) REVERT: M 1161 PHE cc_start: 0.4624 (OUTLIER) cc_final: 0.4352 (m-80) REVERT: M 1286 LEU cc_start: 0.3264 (OUTLIER) cc_final: 0.2867 (tt) REVERT: M 1310 HIS cc_start: 0.3979 (OUTLIER) cc_final: 0.3581 (t-90) REVERT: Z 250 TRP cc_start: 0.6427 (m100) cc_final: 0.5523 (m-10) REVERT: Z 254 MET cc_start: 0.8270 (tpp) cc_final: 0.7513 (ttt) outliers start: 86 outliers final: 46 residues processed: 321 average time/residue: 0.1865 time to fit residues: 102.4901 Evaluate side-chains 300 residues out of total 4739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 239 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1019 LYS Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1351 ASP Chi-restraints excluded: chain A residue 1463 LEU Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain B residue 1076 GLU Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain D residue 26 PHE Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 186 LYS Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 107 PHE Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain I residue 67 GLN Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 103 GLU Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain M residue 805 VAL Chi-restraints excluded: chain M residue 958 LEU Chi-restraints excluded: chain M residue 960 CYS Chi-restraints excluded: chain M residue 962 PHE Chi-restraints excluded: chain M residue 986 ILE Chi-restraints excluded: chain M residue 1018 VAL Chi-restraints excluded: chain M residue 1161 PHE Chi-restraints excluded: chain M residue 1286 LEU Chi-restraints excluded: chain M residue 1310 HIS Chi-restraints excluded: chain Q residue 45 THR Chi-restraints excluded: chain Z residue 536 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 18 optimal weight: 0.9990 chunk 334 optimal weight: 6.9990 chunk 143 optimal weight: 0.9990 chunk 406 optimal weight: 6.9990 chunk 438 optimal weight: 7.9990 chunk 125 optimal weight: 0.9980 chunk 232 optimal weight: 0.9990 chunk 383 optimal weight: 30.0000 chunk 351 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 611 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.091948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.053204 restraints weight = 142557.245| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.92 r_work: 0.2769 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 45942 Z= 0.127 Angle : 0.528 11.580 62430 Z= 0.273 Chirality : 0.042 0.174 6974 Planarity : 0.004 0.047 7728 Dihedral : 13.754 178.492 6948 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.71 % Allowed : 15.07 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.35 (0.12), residues: 5255 helix: 1.57 (0.12), residues: 1887 sheet: -0.52 (0.18), residues: 766 loop : -0.48 (0.12), residues: 2602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG Q 43 TYR 0.012 0.001 TYR A 669 PHE 0.014 0.001 PHE D 61 TRP 0.026 0.001 TRP A1192 HIS 0.006 0.001 HIS M1310 Details of bonding type rmsd covalent geometry : bond 0.00297 (45907) covalent geometry : angle 0.52380 (62403) hydrogen bonds : bond 0.03492 ( 1872) hydrogen bonds : angle 4.26965 ( 5140) metal coordination : bond 0.00421 ( 35) metal coordination : angle 3.34717 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 4739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 248 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8739 (mmt) cc_final: 0.8178 (mmt) REVERT: A 266 MET cc_start: 0.6623 (tpp) cc_final: 0.6345 (tpp) REVERT: A 329 MET cc_start: 0.8465 (mtm) cc_final: 0.8199 (mpp) REVERT: A 567 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9077 (tt) REVERT: A 1351 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.8029 (t0) REVERT: A 1440 MET cc_start: 0.9365 (tpp) cc_final: 0.9118 (mmt) REVERT: B 51 ILE cc_start: 0.9354 (OUTLIER) cc_final: 0.9056 (tp) REVERT: B 53 MET cc_start: 0.9102 (mmm) cc_final: 0.8888 (mmm) REVERT: B 151 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8120 (mtmm) REVERT: B 276 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8824 (mp) REVERT: B 677 MET cc_start: 0.9151 (tpp) cc_final: 0.8790 (tpp) REVERT: B 1076 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8114 (tt0) REVERT: D 26 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7938 (t80) REVERT: D 39 MET cc_start: 0.8748 (mmm) cc_final: 0.8403 (mmm) REVERT: D 75 LYS cc_start: 0.9204 (mmmm) cc_final: 0.8776 (mmtm) REVERT: E 186 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8572 (ptpp) REVERT: G 83 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7124 (mm-30) REVERT: G 142 GLU cc_start: 0.7709 (mp0) cc_final: 0.7387 (mp0) REVERT: H 126 GLN cc_start: 0.8888 (tt0) cc_final: 0.8651 (tt0) REVERT: H 133 HIS cc_start: 0.8957 (OUTLIER) cc_final: 0.8274 (t70) REVERT: I 18 GLN cc_start: 0.9261 (tp40) cc_final: 0.8924 (mm-40) REVERT: I 28 GLU cc_start: 0.7072 (pm20) cc_final: 0.6464 (pt0) REVERT: I 43 ASP cc_start: 0.8538 (t70) cc_final: 0.8129 (p0) REVERT: I 46 GLN cc_start: 0.7691 (mt0) cc_final: 0.7361 (pp30) REVERT: I 68 ILE cc_start: 0.8623 (mm) cc_final: 0.8345 (mt) REVERT: I 93 GLU cc_start: 0.8754 (tp30) cc_final: 0.7527 (pm20) REVERT: K 68 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8008 (mp0) REVERT: L 25 GLU cc_start: 0.8389 (tt0) cc_final: 0.7988 (tt0) REVERT: M 366 MET cc_start: 0.7460 (mtt) cc_final: 0.6822 (mtt) REVERT: M 523 MET cc_start: 0.4566 (mtt) cc_final: 0.4061 (tpt) REVERT: M 958 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8348 (mt) REVERT: M 960 CYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7327 (m) REVERT: M 962 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.7587 (m-10) REVERT: M 1161 PHE cc_start: 0.4661 (OUTLIER) cc_final: 0.4403 (m-80) REVERT: M 1233 ASP cc_start: 0.6577 (OUTLIER) cc_final: 0.5504 (t0) REVERT: M 1286 LEU cc_start: 0.3268 (OUTLIER) cc_final: 0.2873 (tt) REVERT: Q 32 GLU cc_start: 0.8543 (pt0) cc_final: 0.8137 (pm20) REVERT: Q 38 LYS cc_start: 0.8580 (ttpt) cc_final: 0.8219 (tttt) REVERT: Z 250 TRP cc_start: 0.6426 (m100) cc_final: 0.5518 (m-10) REVERT: Z 254 MET cc_start: 0.8270 (tpp) cc_final: 0.7211 (ttt) outliers start: 81 outliers final: 48 residues processed: 320 average time/residue: 0.1668 time to fit residues: 90.9664 Evaluate side-chains 305 residues out of total 4739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 241 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1019 LYS Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1351 ASP Chi-restraints excluded: chain A residue 1463 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain B residue 1076 GLU Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain D residue 26 PHE Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 186 LYS Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 107 PHE Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain I residue 67 GLN Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 103 GLU Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain M residue 805 VAL Chi-restraints excluded: chain M residue 958 LEU Chi-restraints excluded: chain M residue 960 CYS Chi-restraints excluded: chain M residue 962 PHE Chi-restraints excluded: chain M residue 986 ILE Chi-restraints excluded: chain M residue 1018 VAL Chi-restraints excluded: chain M residue 1161 PHE Chi-restraints excluded: chain M residue 1233 ASP Chi-restraints excluded: chain M residue 1272 ILE Chi-restraints excluded: chain M residue 1286 LEU Chi-restraints excluded: chain Z residue 536 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 222 optimal weight: 0.5980 chunk 495 optimal weight: 7.9990 chunk 242 optimal weight: 0.0970 chunk 349 optimal weight: 9.9990 chunk 377 optimal weight: 10.0000 chunk 257 optimal weight: 0.9990 chunk 248 optimal weight: 7.9990 chunk 399 optimal weight: 10.0000 chunk 147 optimal weight: 0.4980 chunk 227 optimal weight: 0.7980 chunk 207 optimal weight: 0.7980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 HIS L 26 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.092844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.054017 restraints weight = 143425.313| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.57 r_work: 0.2831 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 45942 Z= 0.097 Angle : 0.515 11.059 62430 Z= 0.265 Chirality : 0.041 0.175 6974 Planarity : 0.004 0.062 7728 Dihedral : 13.663 179.075 6948 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.16 % Allowed : 15.66 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.48 (0.12), residues: 5255 helix: 1.67 (0.12), residues: 1888 sheet: -0.31 (0.18), residues: 760 loop : -0.46 (0.12), residues: 2607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 181 TYR 0.018 0.001 TYR Y 39 PHE 0.013 0.001 PHE B 309 TRP 0.026 0.001 TRP A1192 HIS 0.006 0.001 HIS M 632 Details of bonding type rmsd covalent geometry : bond 0.00215 (45907) covalent geometry : angle 0.51192 (62403) hydrogen bonds : bond 0.03055 ( 1872) hydrogen bonds : angle 4.12263 ( 5140) metal coordination : bond 0.00276 ( 35) metal coordination : angle 2.77228 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 4739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 249 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8904 (mmt) cc_final: 0.8354 (mmt) REVERT: A 1351 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.8223 (t0) REVERT: B 51 ILE cc_start: 0.9302 (OUTLIER) cc_final: 0.9005 (tp) REVERT: B 53 MET cc_start: 0.9288 (mmm) cc_final: 0.9046 (mmm) REVERT: B 151 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8162 (mtmm) REVERT: B 276 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8848 (mp) REVERT: B 677 MET cc_start: 0.9256 (tpp) cc_final: 0.8940 (tpp) REVERT: D 26 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.8054 (t80) REVERT: D 39 MET cc_start: 0.8746 (mmm) cc_final: 0.8449 (mmm) REVERT: D 75 LYS cc_start: 0.9194 (mmmm) cc_final: 0.8855 (mmtm) REVERT: G 83 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7826 (mm-30) REVERT: G 118 GLU cc_start: 0.9084 (tp30) cc_final: 0.8462 (pm20) REVERT: G 129 LYS cc_start: 0.9246 (tmtt) cc_final: 0.8436 (tttt) REVERT: G 142 GLU cc_start: 0.7815 (mp0) cc_final: 0.7496 (mp0) REVERT: G 164 MET cc_start: 0.8591 (mmp) cc_final: 0.6923 (ppp) REVERT: H 133 HIS cc_start: 0.9059 (OUTLIER) cc_final: 0.8410 (t70) REVERT: I 18 GLN cc_start: 0.9266 (tp40) cc_final: 0.8952 (mm-40) REVERT: I 28 GLU cc_start: 0.7196 (pm20) cc_final: 0.6546 (pt0) REVERT: I 43 ASP cc_start: 0.8492 (t70) cc_final: 0.8055 (p0) REVERT: I 46 GLN cc_start: 0.7723 (mt0) cc_final: 0.7426 (pp30) REVERT: I 68 ILE cc_start: 0.8573 (mm) cc_final: 0.8269 (mt) REVERT: I 93 GLU cc_start: 0.8767 (tp30) cc_final: 0.7526 (pm20) REVERT: L 25 GLU cc_start: 0.8446 (tt0) cc_final: 0.8002 (tt0) REVERT: L 31 ARG cc_start: 0.7319 (mmp80) cc_final: 0.7070 (mmp80) REVERT: M 366 MET cc_start: 0.7366 (mtt) cc_final: 0.6694 (mtt) REVERT: M 523 MET cc_start: 0.4905 (mtt) cc_final: 0.4258 (tpt) REVERT: M 958 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8381 (mt) REVERT: M 960 CYS cc_start: 0.8464 (OUTLIER) cc_final: 0.7368 (m) REVERT: M 962 PHE cc_start: 0.8080 (OUTLIER) cc_final: 0.7515 (m-10) REVERT: M 1161 PHE cc_start: 0.4763 (OUTLIER) cc_final: 0.4511 (m-80) REVERT: M 1233 ASP cc_start: 0.6544 (OUTLIER) cc_final: 0.5361 (t0) REVERT: M 1286 LEU cc_start: 0.3199 (OUTLIER) cc_final: 0.2787 (tt) REVERT: Q 38 LYS cc_start: 0.8489 (ttpt) cc_final: 0.8111 (tptt) REVERT: Z 250 TRP cc_start: 0.6438 (m100) cc_final: 0.5505 (m-10) outliers start: 55 outliers final: 32 residues processed: 298 average time/residue: 0.1709 time to fit residues: 85.9485 Evaluate side-chains 288 residues out of total 4739 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 244 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 1019 LYS Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1351 ASP Chi-restraints excluded: chain A residue 1463 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1060 HIS Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain D residue 26 PHE Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 107 PHE Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain I residue 67 GLN Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain K residue 103 GLU Chi-restraints excluded: chain M residue 958 LEU Chi-restraints excluded: chain M residue 960 CYS Chi-restraints excluded: chain M residue 962 PHE Chi-restraints excluded: chain M residue 986 ILE Chi-restraints excluded: chain M residue 1018 VAL Chi-restraints excluded: chain M residue 1161 PHE Chi-restraints excluded: chain M residue 1233 ASP Chi-restraints excluded: chain M residue 1286 LEU Chi-restraints excluded: chain Q residue 45 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 71 optimal weight: 2.9990 chunk 214 optimal weight: 4.9990 chunk 3 optimal weight: 0.0980 chunk 316 optimal weight: 4.9990 chunk 458 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 chunk 188 optimal weight: 0.0050 chunk 186 optimal weight: 0.9980 chunk 390 optimal weight: 20.0000 chunk 526 optimal weight: 6.9990 chunk 105 optimal weight: 0.0870 overall best weight: 0.8374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 HIS L 26 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.092681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.054196 restraints weight = 143598.630| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.96 r_work: 0.2803 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 45942 Z= 0.103 Angle : 0.510 10.884 62430 Z= 0.262 Chirality : 0.041 0.174 6974 Planarity : 0.003 0.046 7728 Dihedral : 13.604 179.445 6948 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.18 % Allowed : 15.53 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.54 (0.12), residues: 5255 helix: 1.75 (0.12), residues: 1882 sheet: -0.34 (0.18), residues: 751 loop : -0.41 (0.12), residues: 2622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Q 43 TYR 0.016 0.001 TYR Y 39 PHE 0.012 0.001 PHE Z 503 TRP 0.026 0.001 TRP A1192 HIS 0.006 0.001 HIS M 632 Details of bonding type rmsd covalent geometry : bond 0.00235 (45907) covalent geometry : angle 0.50631 (62403) hydrogen bonds : bond 0.03092 ( 1872) hydrogen bonds : angle 4.08690 ( 5140) metal coordination : bond 0.00314 ( 35) metal coordination : angle 2.83847 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13769.33 seconds wall clock time: 234 minutes 26.27 seconds (14066.27 seconds total)