Starting phenix.real_space_refine on Fri Dec 27 21:02:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zx8_15007/12_2024/7zx8_15007.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zx8_15007/12_2024/7zx8_15007.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zx8_15007/12_2024/7zx8_15007.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zx8_15007/12_2024/7zx8_15007.map" model { file = "/net/cci-nas-00/data/ceres_data/7zx8_15007/12_2024/7zx8_15007.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zx8_15007/12_2024/7zx8_15007.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 11 6.06 5 P 126 5.49 5 Mg 1 5.21 5 S 276 5.16 5 C 30886 2.51 5 N 8718 2.21 5 O 9516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 124 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 49534 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 11274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1423, 11274 Classifications: {'peptide': 1423} Link IDs: {'PCIS': 3, 'PTRANS': 67, 'TRANS': 1352} Chain breaks: 4 Chain: "B" Number of atoms: 9076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1136, 9076 Classifications: {'peptide': 1136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 53, 'TRANS': 1082} Chain breaks: 2 Chain: "C" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2059 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "D" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1050 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "E" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1721 Classifications: {'peptide': 209} Modifications used: {'COO': 1} 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} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "G" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1351 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} 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: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 928 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 507 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} 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: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 373 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "M" Number of atoms: 2301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2301 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 15, 'TRANS': 282} Chain breaks: 1 Chain: "N" Number of atoms: 1316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1316 Classifications: {'DNA': 63} Link IDs: {'rna3p': 62} Chain breaks: 1 Chain: "O" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1422 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain: "Q" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1138 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 7, 'TRANS': 130} Chain breaks: 1 Chain: "R" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1788 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain breaks: 1 Chain: "T" Number of atoms: 1253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1253 Classifications: {'DNA': 63} Link IDs: {'rna3p': 62} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DG:plan': 1, ' DG:plan2': 1} Unresolved non-hydrogen planarities: 14 Chain: "U" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 734 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain breaks: 1 Chain: "V" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 785 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 1, 'TRANS': 94} Chain: "a" Number of atoms: 1807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1807 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 207} Chain breaks: 1 Chain: "b" Number of atoms: 2972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2972 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 17, 'TRANS': 346} Chain breaks: 2 Chain: "c" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2517 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 9, 'TRANS': 293} Chain breaks: 1 Chain: "d" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 408 Classifications: {'peptide': 50} Link IDs: {'TRANS': 49} 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: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "b" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 464 SG CYS A 71 61.735 98.064 127.094 1.00182.78 S ATOM 486 SG CYS A 74 61.491 99.102 130.662 1.00184.17 S ATOM 533 SG CYS A 81 64.719 97.807 129.341 1.00170.01 S ATOM 768 SG CYS A 111 59.221 51.185 130.069 1.00217.66 S ATOM 796 SG CYS A 114 55.513 50.609 131.293 1.00218.09 S ATOM 1109 SG CYS A 154 58.421 48.356 132.202 1.00215.02 S ATOM 1132 SG CYS A 184 56.519 48.652 128.785 1.00213.61 S ATOM 19919 SG CYS B1119 55.404 86.973 140.778 1.00173.90 S ATOM 19941 SG CYS B1122 57.497 84.667 138.664 1.00173.94 S ATOM 20056 SG CYS B1137 55.479 87.383 137.076 1.00184.30 S ATOM 20077 SG CYS B1140 53.827 84.383 138.616 1.00185.93 S ATOM 21044 SG CYS C 88 108.534 146.750 141.160 1.00 67.79 S ATOM 21057 SG CYS C 90 106.778 145.861 137.840 1.00 75.24 S ATOM 21092 SG CYS C 94 109.717 147.785 137.791 1.00 67.09 S ATOM 21114 SG CYS C 97 109.985 144.206 138.782 1.00 59.31 S ATOM 28400 SG CYS I 17 114.638 29.160 109.070 1.00146.35 S ATOM 28424 SG CYS I 20 111.961 30.926 107.561 1.00149.56 S ATOM 28585 SG CYS I 39 111.364 29.175 110.900 1.00154.10 S ATOM 28610 SG CYS I 42 111.900 27.045 107.153 1.00155.91 S ATOM 28962 SG CYS I 86 149.084 48.805 128.434 1.00 93.47 S ATOM 28986 SG CYS I 89 151.777 49.989 126.067 1.00 98.92 S ATOM 29190 SG CYS I 114 148.739 52.045 126.495 1.00 90.07 S ATOM 29225 SG CYS I 119 148.605 48.768 124.706 1.00 93.84 S ATOM 29336 SG CYS J 7 129.586 119.593 140.023 1.00 40.76 S ATOM 29360 SG CYS J 10 130.649 122.280 142.524 1.00 42.98 S ATOM 29624 SG CYS J 44 131.800 118.612 142.842 1.00 37.57 S ATOM 29630 SG CYS J 45 133.092 121.022 140.352 1.00 39.55 S ATOM 30750 SG CYS L 19 109.058 119.568 101.581 1.00 69.08 S ATOM 30769 SG CYS L 22 110.820 122.302 99.718 1.00 73.32 S ATOM 30886 SG CYS L 36 107.401 121.593 98.962 1.00 77.28 S ATOM 30912 SG CYS L 39 109.888 119.084 98.032 1.00 79.71 S ATOM 31094 SG CYS M 15 68.612 122.085 135.003 1.00156.52 S ATOM 31241 SG CYS M 34 71.628 123.388 133.213 1.00139.22 S ATOM 31263 SG CYS M 37 71.251 123.737 137.040 1.00138.53 S ATOM 45010 SG CYS b 221 118.395 98.334 25.476 1.00245.67 S ATOM 45807 SG CYS b 317 114.802 97.859 27.186 1.00246.80 S ATOM 46129 SG CYS b 354 130.689 77.448 28.243 1.00255.98 S ATOM 46153 SG CYS b 357 134.194 77.023 27.702 1.00253.53 S ATOM 46344 SG CYS b 380 132.192 77.922 25.124 1.00252.00 S ATOM 46365 SG CYS b 383 132.857 74.554 25.877 1.00249.55 S Time building chain proxies: 18.83, per 1000 atoms: 0.38 Number of scatterers: 49534 At special positions: 0 Unit cell: (176.4, 195.3, 225.75, 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 11 29.99 S 276 16.00 P 126 15.00 Mg 1 11.99 O 9516 8.00 N 8718 7.00 C 30886 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: 9.18 Conformation dependent library (CDL) restraints added in 4.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " 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 ZN A2001 " - pdb=" SG CYS A 81 " 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 154 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " 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 I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " 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 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" NE2 HIS M 18 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 37 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 34 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 15 " pdb=" ZN b 500 " pdb="ZN ZN b 500 " - pdb=" NE2 HIS b 313 " pdb="ZN ZN b 500 " - pdb=" SG CYS b 221 " pdb="ZN ZN b 500 " - pdb=" SG CYS b 317 " pdb=" ZN b 501 " pdb="ZN ZN b 501 " - pdb=" SG CYS b 380 " pdb="ZN ZN b 501 " - pdb=" SG CYS b 354 " pdb="ZN ZN b 501 " - pdb=" SG CYS b 383 " pdb="ZN ZN b 501 " - pdb=" SG CYS b 357 " Number of angles added : 54 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11038 Finding SS restraints... Secondary structure from input PDB file: 212 helices and 58 sheets defined 43.2% alpha, 15.3% beta 52 base pairs and 105 stacking pairs defined. Time for finding SS restraints: 13.30 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 134 Processing helix chain 'A' and resid 136 through 151 removed outlier: 3.534A pdb=" N THR A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 227 Processing helix chain 'A' and resid 229 through 236 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 257 through 261 Processing helix chain 'A' and resid 274 through 297 Processing helix chain 'A' and resid 299 through 319 removed outlier: 3.632A 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 381 through 388 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 434 through 439 removed outlier: 3.603A pdb=" N LEU A 438 " --> pdb=" O LYS A 434 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 539 through 549 Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 588 through 596 Processing helix chain 'A' and resid 610 through 614 removed outlier: 3.517A pdb=" N GLU A 613 " --> pdb=" O PRO A 610 " (cutoff:3.500A) removed outlier: 3.875A 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 661 Processing helix chain 'A' and resid 661 through 684 removed outlier: 4.113A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.572A 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 removed outlier: 3.527A pdb=" N LEU A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 772 Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 832 through 869 removed outlier: 3.535A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE A 860 " --> pdb=" O GLU A 856 " (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 Processing helix chain 'A' and resid 935 through 945 removed outlier: 3.935A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN A 945 " --> pdb=" O ASP A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.709A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1020 Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1080 removed outlier: 3.548A pdb=" N ILE A1080 " --> pdb=" O PHE A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1097 Processing helix chain 'A' and resid 1098 through 1102 Processing helix chain 'A' and resid 1119 through 1129 removed outlier: 3.726A pdb=" N ARG A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1162 removed outlier: 3.577A pdb=" N ILE A1157 " --> pdb=" O ARG A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1199 removed outlier: 4.352A pdb=" N TRP A1192 " --> pdb=" O GLU A1188 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N VAL A1195 " --> pdb=" O GLU A1191 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR A1196 " --> pdb=" O TRP A1192 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N MET A1199 " --> pdb=" O VAL A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1225 Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1262 through 1267 removed outlier: 3.606A pdb=" N GLU A1266 " --> pdb=" O MET A1262 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1295 Processing helix chain 'A' and resid 1342 through 1349 removed outlier: 3.520A pdb=" N SER A1348 " --> pdb=" O MET A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1370 Processing helix chain 'A' and resid 1370 through 1388 Processing helix chain 'A' and resid 1394 through 1407 removed outlier: 3.580A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 Processing helix chain 'A' and resid 1425 through 1433 Processing helix chain 'A' and resid 1434 through 1445 Processing helix chain 'A' and resid 1453 through 1460 removed outlier: 3.572A pdb=" N ASN A1457 " --> pdb=" O GLY A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1469 Processing helix chain 'A' and resid 1476 through 1482 removed outlier: 3.855A pdb=" N TYR A1482 " --> pdb=" O GLU A1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 38 removed outlier: 4.462A pdb=" N GLN B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLU B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 53 through 62 Processing helix chain 'B' and resid 109 through 117 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 246 through 253 Processing helix chain 'B' and resid 269 through 277 Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 294 through 308 removed outlier: 3.704A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 313 through 324 removed outlier: 3.806A 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: 3.630A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 437 through 451 Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 495 through 500 removed outlier: 3.730A pdb=" N ARG B 499 " --> pdb=" O LEU B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 557 through 562 removed outlier: 3.701A pdb=" N ALA B 562 " --> pdb=" O ALA B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 594 Processing helix chain 'B' and resid 636 through 645 Processing helix chain 'B' and resid 652 through 659 removed outlier: 3.767A pdb=" N LEU B 656 " --> pdb=" O SER B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 671 removed outlier: 3.618A pdb=" N GLU B 671 " --> pdb=" O THR B 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 667 through 671' Processing helix chain 'B' and resid 678 through 683 Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 707 through 711 Processing helix chain 'B' and resid 713 through 717 removed outlier: 3.552A pdb=" N ASN B 717 " --> pdb=" O PRO B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 730 removed outlier: 3.739A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 766 Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 970 through 976 removed outlier: 4.759A pdb=" N SER B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.717A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 removed outlier: 3.581A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1058 Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1153 through 1165 Processing helix chain 'C' and resid 27 through 41 Processing helix chain 'C' and resid 60 through 71 Processing helix chain 'C' and resid 77 through 82 removed outlier: 3.842A 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 271 Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 72 Processing helix chain 'D' and resid 76 through 90 removed outlier: 3.686A pdb=" N LYS D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'E' and resid 3 through 24 removed outlier: 3.564A pdb=" N TYR E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 45 Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 121 removed outlier: 3.711A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 137 through 142 removed outlier: 6.198A pdb=" N THR E 140 " --> pdb=" O ILE E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'H' and resid 83 through 88 Processing helix chain 'H' and resid 130 through 133 removed outlier: 3.833A pdb=" N HIS H 133 " --> pdb=" O ASN H 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 130 through 133' Processing helix chain 'I' and resid 63 through 68 removed outlier: 3.919A pdb=" N GLN I 67 " --> pdb=" O ASP I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.538A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 52 removed outlier: 3.734A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 115 Processing helix chain 'M' and resid 89 through 93 Processing helix chain 'M' and resid 108 through 128 removed outlier: 3.543A pdb=" N ILE M 128 " --> pdb=" O MET M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 149 Processing helix chain 'M' and resid 155 through 171 Processing helix chain 'M' and resid 176 through 183 removed outlier: 3.604A pdb=" N VAL M 183 " --> pdb=" O GLU M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 187 through 203 Processing helix chain 'M' and resid 210 through 213 Processing helix chain 'M' and resid 214 through 223 Processing helix chain 'M' and resid 225 through 243 Processing helix chain 'M' and resid 249 through 264 Processing helix chain 'M' and resid 270 through 279 Processing helix chain 'M' and resid 281 through 293 Processing helix chain 'M' and resid 295 through 300 Processing helix chain 'M' and resid 309 through 313 Processing helix chain 'O' and resid 179 through 187 Processing helix chain 'O' and resid 226 through 244 Processing helix chain 'O' and resid 269 through 277 removed outlier: 3.643A pdb=" N LEU O 273 " --> pdb=" O ARG O 269 " (cutoff:3.500A) Processing helix chain 'O' and resid 317 through 334 removed outlier: 3.540A pdb=" N ILE O 321 " --> pdb=" O VAL O 317 " (cutoff:3.500A) Proline residue: O 330 - end of helix Processing helix chain 'Q' and resid 5 through 9 Processing helix chain 'Q' and resid 34 through 36 No H-bonds generated for 'chain 'Q' and resid 34 through 36' Processing helix chain 'Q' and resid 156 through 166 removed outlier: 3.819A pdb=" N GLU Q 162 " --> pdb=" O GLU Q 158 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU Q 165 " --> pdb=" O GLU Q 161 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ARG Q 166 " --> pdb=" O GLU Q 162 " (cutoff:3.500A) Processing helix chain 'Q' and resid 174 through 180 removed outlier: 3.926A pdb=" N GLN Q 178 " --> pdb=" O PHE Q 174 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG Q 180 " --> pdb=" O ILE Q 176 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 14 Processing helix chain 'R' and resid 24 through 35 Processing helix chain 'R' and resid 59 through 64 Processing helix chain 'R' and resid 122 through 137 removed outlier: 3.890A pdb=" N ARG R 126 " --> pdb=" O GLU R 122 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU R 127 " --> pdb=" O ASN R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 159 through 173 Processing helix chain 'R' and resid 179 through 194 removed outlier: 3.848A pdb=" N LYS R 193 " --> pdb=" O SER R 189 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS R 194 " --> pdb=" O ALA R 190 " (cutoff:3.500A) Processing helix chain 'R' and resid 198 through 207 removed outlier: 3.787A pdb=" N ASP R 204 " --> pdb=" O LYS R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 221 removed outlier: 3.687A pdb=" N ILE R 220 " --> pdb=" O ILE R 216 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 33 removed outlier: 4.865A pdb=" N ASP U 27 " --> pdb=" O ASN U 23 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ILE U 28 " --> pdb=" O ASP U 24 " (cutoff:3.500A) Processing helix chain 'U' and resid 35 through 51 removed outlier: 3.751A pdb=" N MET U 51 " --> pdb=" O GLU U 47 " (cutoff:3.500A) Processing helix chain 'U' and resid 360 through 363 Processing helix chain 'V' and resid 9 through 25 Processing helix chain 'V' and resid 29 through 51 removed outlier: 3.570A pdb=" N ALA V 49 " --> pdb=" O ASN V 45 " (cutoff:3.500A) Processing helix chain 'a' and resid 6 through 22 removed outlier: 3.535A pdb=" N ASP a 10 " --> pdb=" O GLY a 6 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR a 21 " --> pdb=" O ARG a 17 " (cutoff:3.500A) Processing helix chain 'a' and resid 25 through 37 removed outlier: 3.531A pdb=" N PHE a 29 " --> pdb=" O ARG a 25 " (cutoff:3.500A) Processing helix chain 'a' and resid 38 through 41 Processing helix chain 'a' and resid 48 through 67 Processing helix chain 'a' and resid 71 through 87 Processing helix chain 'a' and resid 100 through 117 removed outlier: 3.527A pdb=" N ASP a 105 " --> pdb=" O LEU a 101 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU a 106 " --> pdb=" O LYS a 102 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS a 109 " --> pdb=" O ASP a 105 " (cutoff:3.500A) Processing helix chain 'a' and resid 119 through 132 Processing helix chain 'a' and resid 166 through 172 removed outlier: 3.660A pdb=" N LYS a 170 " --> pdb=" O ASP a 166 " (cutoff:3.500A) Processing helix chain 'a' and resid 173 through 195 removed outlier: 3.547A pdb=" N VAL a 193 " --> pdb=" O ASN a 189 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N SER a 195 " --> pdb=" O LYS a 191 " (cutoff:3.500A) Processing helix chain 'a' and resid 202 through 206 removed outlier: 3.723A pdb=" N SER a 206 " --> pdb=" O LYS a 203 " (cutoff:3.500A) Processing helix chain 'a' and resid 211 through 232 Processing helix chain 'b' and resid 45 through 55 Processing helix chain 'b' and resid 77 through 91 removed outlier: 3.633A pdb=" N ARG b 81 " --> pdb=" O ALA b 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 93 through 104 Processing helix chain 'b' and resid 127 through 143 Processing helix chain 'b' and resid 150 through 161 removed outlier: 3.531A pdb=" N PHE b 155 " --> pdb=" O ARG b 151 " (cutoff:3.500A) Processing helix chain 'b' and resid 193 through 198 removed outlier: 4.026A pdb=" N GLU b 197 " --> pdb=" O HIS b 193 " (cutoff:3.500A) Processing helix chain 'b' and resid 214 through 219 Processing helix chain 'b' and resid 242 through 247 Processing helix chain 'b' and resid 269 through 280 removed outlier: 4.503A pdb=" N THR b 273 " --> pdb=" O ASP b 269 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE b 274 " --> pdb=" O LEU b 270 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TRP b 277 " --> pdb=" O THR b 273 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER b 280 " --> pdb=" O GLU b 276 " (cutoff:3.500A) Processing helix chain 'b' and resid 380 through 388 removed outlier: 3.551A pdb=" N HIS b 388 " --> pdb=" O PHE b 384 " (cutoff:3.500A) Processing helix chain 'c' and resid 82 through 123 removed outlier: 4.229A pdb=" N CYS c 86 " --> pdb=" O ASP c 82 " (cutoff:3.500A) Processing helix chain 'c' and resid 162 through 170 Processing helix chain 'c' and resid 176 through 180 Processing helix chain 'c' and resid 185 through 223 removed outlier: 3.533A pdb=" N LYS c 189 " --> pdb=" O LYS c 185 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA c 190 " --> pdb=" O ASN c 186 " (cutoff:3.500A) Proline residue: c 207 - end of helix removed outlier: 3.606A pdb=" N LYS c 221 " --> pdb=" O GLN c 217 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N SER c 223 " --> pdb=" O GLN c 219 " (cutoff:3.500A) Processing helix chain 'c' and resid 224 through 247 Processing helix chain 'c' and resid 249 through 255 removed outlier: 3.691A pdb=" N GLY c 255 " --> pdb=" O GLU c 251 " (cutoff:3.500A) Processing helix chain 'c' and resid 262 through 269 removed outlier: 3.650A pdb=" N ASN c 268 " --> pdb=" O GLU c 264 " (cutoff:3.500A) Processing helix chain 'c' and resid 276 through 287 Processing helix chain 'c' and resid 298 through 313 Processing helix chain 'c' and resid 316 through 324 Processing helix chain 'c' and resid 329 through 339 Processing helix chain 'c' and resid 340 through 345 removed outlier: 6.293A pdb=" N ALA c 343 " --> pdb=" O HIS c 340 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU c 344 " --> pdb=" O ASN c 341 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS c 345 " --> pdb=" O LYS c 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 340 through 345' Processing helix chain 'c' and resid 350 through 364 Processing helix chain 'c' and resid 371 through 377 Processing helix chain 'c' and resid 383 through 394 Processing helix chain 'd' and resid 4 through 45 Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 16 removed outlier: 4.453A 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 95 removed outlier: 7.066A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 10.666A pdb=" N LYS A 92 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 10.304A pdb=" N ILE A 249 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 190 through 194 removed outlier: 4.282A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 264 through 265 Processing sheet with id=AA6, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.789A pdb=" N LEU B1084 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1060 through 1062 removed outlier: 3.594A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.708A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 526 through 527 removed outlier: 3.627A pdb=" N ARG A 532 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AB2, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.133A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 602 through 605 removed outlier: 6.883A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB5, first strand: chain 'A' and resid 792 through 793 Processing sheet with id=AB6, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AB7, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB8, first strand: chain 'A' and resid 1307 through 1310 removed outlier: 3.662A pdb=" N LEU A1139 " --> pdb=" O THR A1338 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1164 through 1165 Processing sheet with id=AC1, first strand: chain 'A' and resid 1243 through 1247 removed outlier: 4.367A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AC3, first strand: chain 'A' and resid 1471 through 1475 Processing sheet with id=AC4, first strand: chain 'B' and resid 65 through 68 removed outlier: 5.362A pdb=" N TYR B 84 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE B 133 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N LEU B 86 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N THR B 131 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ALA B 122 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY B 150 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LEU B 124 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N PHE B 148 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N VAL B 126 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS B 146 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AC6, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC7, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.503A pdb=" N ALA B 196 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 205 through 208 removed outlier: 3.561A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 531 through 532 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 632 through 633 current: chain 'B' and resid 695 through 696 Processing sheet with id=AD1, first strand: chain 'B' and resid 551 through 552 removed outlier: 5.463A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 747 through 751 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 808 through 817 current: chain 'B' and resid 902 through 911 removed outlier: 7.872A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 917 through 927 current: chain 'L' and resid 25 through 27 Processing sheet with id=AD3, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD4, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 6.920A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AD6, first strand: chain 'B' and resid 865 through 867 removed outlier: 3.800A pdb=" N ILE B 867 " --> pdb=" O THR B 894 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 956 through 957 Processing sheet with id=AD8, first strand: chain 'B' and resid 1067 through 1068 removed outlier: 6.779A pdb=" N ILE B1067 " --> pdb=" O ASP M 47 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'B' and resid 1127 through 1129 Processing sheet with id=AE1, first strand: chain 'C' and resid 8 through 14 removed outlier: 5.738A pdb=" N VAL C 9 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLU C 24 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ILE C 11 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE C 22 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLY C 181 " --> pdb=" O GLU C 234 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.965A pdb=" N ARG C 162 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ILE C 52 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N TYR C 164 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N VAL C 50 " --> pdb=" O TYR C 164 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LYS C 166 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ASP C 48 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLY C 168 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA C 46 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AE4, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.535A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 2 through 13 current: chain 'G' and resid 43 through 54 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 43 through 54 current: chain 'G' and resid 66 through 77 Processing sheet with id=AE5, first strand: chain 'E' and resid 60 through 63 removed outlier: 4.280A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ALA E 102 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N PHE E 130 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 81 through 82 Processing sheet with id=AE7, first strand: chain 'E' and resid 147 through 150 Processing sheet with id=AE8, first strand: chain 'G' and resid 84 through 92 removed outlier: 3.750A pdb=" N VAL G 88 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU G 97 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N SER G 105 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N GLY G 161 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N PHE G 107 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE G 160 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 118 through 119 Processing sheet with id=AF1, first strand: chain 'I' and resid 24 through 29 removed outlier: 3.616A pdb=" N ASP I 29 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE I 34 " --> pdb=" O ASP I 29 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AF3, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF4, first strand: chain 'M' and resid 24 through 26 removed outlier: 4.315A pdb=" N MET M 32 " --> pdb=" O VAL M 41 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'O' and resid 190 through 191 removed outlier: 6.484A pdb=" N LEU O 165 " --> pdb=" O GLY O 260 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLY O 260 " --> pdb=" O LEU O 165 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASN O 167 " --> pdb=" O MET O 258 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N MET O 258 " --> pdb=" O ASN O 167 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL O 169 " --> pdb=" O GLN O 256 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ASN O 173 " --> pdb=" O ASP O 252 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ASP O 252 " --> pdb=" O ASN O 173 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Q' and resid 11 through 17 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 11 through 17 current: chain 'Q' and resid 98 through 102 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 109 through 114 current: chain 'Q' and resid 135 through 149 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 135 through 149 current: chain 'R' and resid 52 through 58 removed outlier: 10.609A pdb=" N THR R 52 " --> pdb=" O LEU R 85 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N LEU R 85 " --> pdb=" O THR R 52 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL R 54 " --> pdb=" O PHE R 83 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 81 through 86 current: chain 'R' and resid 104 through 116 Processing sheet with id=AF7, first strand: chain 'R' and resid 222 through 224 Processing sheet with id=AF8, first strand: chain 'U' and resid 333 through 345 removed outlier: 6.356A pdb=" N VAL U 334 " --> pdb=" O MET U 358 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N MET U 358 " --> pdb=" O VAL U 334 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL U 336 " --> pdb=" O GLY U 356 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLY U 356 " --> pdb=" O VAL U 336 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLN U 338 " --> pdb=" O LYS U 354 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N HIS U 352 " --> pdb=" O ASP U 340 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE U 342 " --> pdb=" O LYS U 350 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LYS U 350 " --> pdb=" O ILE U 342 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ARG U 344 " --> pdb=" O LYS U 348 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LYS U 348 " --> pdb=" O ARG U 344 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 365 through 367 current: chain 'V' and resid 55 through 64 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 55 through 64 current: chain 'V' and resid 71 through 82 removed outlier: 6.525A pdb=" N ASP V 91 " --> pdb=" O ASP V 78 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLU V 80 " --> pdb=" O LYS V 89 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LYS V 89 " --> pdb=" O GLU V 80 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ARG V 82 " --> pdb=" O LEU V 87 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU V 87 " --> pdb=" O ARG V 82 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'a' and resid 97 through 99 removed outlier: 5.857A pdb=" N ILE a 97 " --> pdb=" O HIS a 136 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'b' and resid 43 through 44 Processing sheet with id=AG2, first strand: chain 'b' and resid 201 through 206 removed outlier: 3.920A pdb=" N ASP b 325 " --> pdb=" O SER b 183 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASN b 185 " --> pdb=" O ILE b 323 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ILE b 323 " --> pdb=" O ASN b 185 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'b' and resid 289 through 291 removed outlier: 6.285A pdb=" N PHE b 258 " --> pdb=" O ALA b 291 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N CYS b 317 " --> pdb=" O HIS b 313 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'b' and resid 377 through 379 2062 hydrogen bonds defined for protein. 5790 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 127 hydrogen bonds 254 hydrogen bond angles 0 basepair planarities 52 basepair parallelities 105 stacking parallelities Total time for adding SS restraints: 20.73 Time building geometry restraints manager: 10.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 15565 1.34 - 1.46: 8779 1.46 - 1.58: 25705 1.58 - 1.70: 248 1.70 - 1.82: 434 Bond restraints: 50731 Sorted by residual: bond pdb=" C1' DG N -7 " pdb=" N9 DG N -7 " ideal model delta sigma weight residual 1.460 1.357 0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C1' DG N -9 " pdb=" N9 DG N -9 " ideal model delta sigma weight residual 1.460 1.358 0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" C1' DA T -9 " pdb=" N9 DA T -9 " ideal model delta sigma weight residual 1.460 1.363 0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" C1' DG T 5 " pdb=" N9 DG T 5 " ideal model delta sigma weight residual 1.460 1.367 0.093 2.00e-02 2.50e+03 2.14e+01 bond pdb=" C1' DA T 3 " pdb=" N9 DA T 3 " ideal model delta sigma weight residual 1.460 1.373 0.087 2.00e-02 2.50e+03 1.90e+01 ... (remaining 50726 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 67834 2.05 - 4.10: 1082 4.10 - 6.15: 81 6.15 - 8.20: 15 8.20 - 10.25: 3 Bond angle restraints: 69015 Sorted by residual: angle pdb=" C MET a 140 " pdb=" N PRO a 141 " pdb=" CA PRO a 141 " ideal model delta sigma weight residual 119.76 128.88 -9.12 1.03e+00 9.43e-01 7.83e+01 angle pdb=" N LYS c 393 " pdb=" CA LYS c 393 " pdb=" C LYS c 393 " ideal model delta sigma weight residual 112.23 121.79 -9.56 1.26e+00 6.30e-01 5.76e+01 angle pdb=" N VAL a 24 " pdb=" CA VAL a 24 " pdb=" C VAL a 24 " ideal model delta sigma weight residual 113.10 106.99 6.11 9.70e-01 1.06e+00 3.96e+01 angle pdb=" C TYR A 669 " pdb=" CA TYR A 669 " pdb=" CB TYR A 669 " ideal model delta sigma weight residual 110.79 102.60 8.19 1.66e+00 3.63e-01 2.43e+01 angle pdb=" N ALA a 139 " pdb=" CA ALA a 139 " pdb=" C ALA a 139 " ideal model delta sigma weight residual 110.80 100.55 10.25 2.13e+00 2.20e-01 2.32e+01 ... (remaining 69010 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.28: 28797 28.28 - 56.56: 1646 56.56 - 84.84: 223 84.84 - 113.13: 25 113.13 - 141.41: 2 Dihedral angle restraints: 30693 sinusoidal: 13660 harmonic: 17033 Sorted by residual: dihedral pdb=" CA LYS O 297 " pdb=" C LYS O 297 " pdb=" N PRO O 298 " pdb=" CA PRO O 298 " ideal model delta harmonic sigma weight residual 180.00 152.68 27.32 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA LEU b 212 " pdb=" C LEU b 212 " pdb=" N THR b 213 " pdb=" CA THR b 213 " ideal model delta harmonic sigma weight residual -180.00 -154.68 -25.32 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA ASN A1129 " pdb=" C ASN A1129 " pdb=" N ILE A1130 " pdb=" CA ILE A1130 " ideal model delta harmonic sigma weight residual -180.00 -155.10 -24.90 0 5.00e+00 4.00e-02 2.48e+01 ... (remaining 30690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 6706 0.067 - 0.133: 861 0.133 - 0.200: 59 0.200 - 0.266: 8 0.266 - 0.333: 5 Chirality restraints: 7639 Sorted by residual: chirality pdb=" CA LYS c 393 " pdb=" N LYS c 393 " pdb=" C LYS c 393 " pdb=" CB LYS c 393 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" C3' DA N -12 " pdb=" C4' DA N -12 " pdb=" O3' DA N -12 " pdb=" C2' DA N -12 " both_signs ideal model delta sigma weight residual False -2.66 -2.34 -0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CA TYR A 669 " pdb=" N TYR A 669 " pdb=" C TYR A 669 " pdb=" CB TYR A 669 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 7636 not shown) Planarity restraints: 8512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU V 48 " 0.032 2.00e-02 2.50e+03 6.50e-02 4.23e+01 pdb=" C LEU V 48 " -0.112 2.00e-02 2.50e+03 pdb=" O LEU V 48 " 0.043 2.00e-02 2.50e+03 pdb=" N ALA V 49 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY b 315 " -0.019 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" C GLY b 315 " 0.065 2.00e-02 2.50e+03 pdb=" O GLY b 315 " -0.024 2.00e-02 2.50e+03 pdb=" N ASP b 316 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR a 138 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C THR a 138 " 0.062 2.00e-02 2.50e+03 pdb=" O THR a 138 " -0.024 2.00e-02 2.50e+03 pdb=" N ALA a 139 " -0.021 2.00e-02 2.50e+03 ... (remaining 8509 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.29: 66 2.29 - 2.94: 22106 2.94 - 3.59: 75626 3.59 - 4.25: 125442 4.25 - 4.90: 204512 Nonbonded interactions: 427752 Sorted by model distance: nonbonded pdb=" OE2 GLU a 27 " pdb=" CG2 VAL b 103 " model vdw 1.635 3.460 nonbonded pdb=" OG SER U 16 " pdb=" NH1 ARG V 51 " model vdw 1.702 3.120 nonbonded pdb=" OG SER U 16 " pdb=" CZ ARG V 51 " model vdw 1.941 3.270 nonbonded pdb=" OD1 ASP A 497 " pdb="MG MG A2003 " model vdw 2.083 2.170 nonbonded pdb=" OD1 ASP A 499 " pdb="MG MG A2003 " model vdw 2.107 2.170 ... (remaining 427747 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=0.00 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: 3.340 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: 0.040 Extract box with map and model: 1.410 Check model and map are aligned: 0.270 Set scattering table: 0.350 Process input model: 99.050 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.140 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:10.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 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 : 0.005 0.103 50731 Z= 0.295 Angle : 0.615 10.251 69015 Z= 0.379 Chirality : 0.045 0.333 7639 Planarity : 0.003 0.065 8512 Dihedral : 17.022 141.407 19655 Min Nonbonded Distance : 1.635 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.15 % Allowed : 1.59 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.11), residues: 5767 helix: 1.21 (0.11), residues: 2215 sheet: 0.27 (0.17), residues: 873 loop : -0.36 (0.12), residues: 2679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP c 317 HIS 0.007 0.001 HIS M 18 PHE 0.031 0.001 PHE A 458 TYR 0.043 0.001 TYR B1048 ARG 0.005 0.000 ARG A 483 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 904 residues out of total 5173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 896 time to evaluate : 4.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ILE cc_start: 0.8745 (mm) cc_final: 0.8475 (mm) REVERT: A 78 MET cc_start: 0.7630 (ttm) cc_final: 0.6863 (ttp) REVERT: A 238 MET cc_start: 0.8420 (mtt) cc_final: 0.7553 (mmm) REVERT: A 329 MET cc_start: 0.8588 (mmt) cc_final: 0.8259 (mmp) REVERT: A 346 LYS cc_start: 0.7331 (tttt) cc_final: 0.7064 (tttm) REVERT: A 735 GLN cc_start: 0.8557 (mt0) cc_final: 0.8224 (mt0) REVERT: A 1164 THR cc_start: 0.7794 (m) cc_final: 0.7449 (p) REVERT: A 1228 MET cc_start: 0.8564 (mmm) cc_final: 0.8081 (ttm) REVERT: A 1301 ILE cc_start: 0.8369 (mt) cc_final: 0.8095 (mp) REVERT: B 206 TYR cc_start: 0.7459 (m-80) cc_final: 0.6796 (m-80) REVERT: B 285 LEU cc_start: 0.7923 (mp) cc_final: 0.7384 (mt) REVERT: B 288 ILE cc_start: 0.8675 (mt) cc_final: 0.8423 (mp) REVERT: B 896 LEU cc_start: 0.7807 (tp) cc_final: 0.7031 (tp) REVERT: B 1165 MET cc_start: 0.8409 (mtm) cc_final: 0.8119 (mtt) REVERT: E 115 LYS cc_start: 0.9628 (ttmt) cc_final: 0.9407 (pttm) REVERT: F 71 LEU cc_start: 0.9057 (tp) cc_final: 0.8675 (tp) REVERT: F 86 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7681 (mp0) REVERT: G 3 TYR cc_start: 0.5563 (m-80) cc_final: 0.4751 (m-80) REVERT: G 7 LEU cc_start: 0.8523 (mt) cc_final: 0.8088 (mm) REVERT: G 12 LEU cc_start: 0.8433 (tp) cc_final: 0.8190 (mt) REVERT: G 117 MET cc_start: -0.5111 (mmm) cc_final: -0.6186 (ttm) REVERT: I 23 MET cc_start: 0.8181 (tpp) cc_final: 0.7797 (tpt) REVERT: I 25 TYR cc_start: 0.8262 (m-80) cc_final: 0.7592 (m-80) REVERT: I 40 ARG cc_start: 0.7862 (mtt-85) cc_final: 0.7502 (mtt-85) REVERT: M 52 TRP cc_start: 0.6644 (p90) cc_final: 0.6063 (p90) REVERT: M 115 MET cc_start: 0.8516 (ttp) cc_final: 0.8144 (tmm) REVERT: M 120 GLU cc_start: 0.8248 (tp30) cc_final: 0.8003 (tm-30) REVERT: M 124 MET cc_start: 0.8857 (mtm) cc_final: 0.8500 (mtp) REVERT: O 221 CYS cc_start: 0.8794 (t) cc_final: 0.8491 (t) REVERT: O 282 SER cc_start: 0.9040 (m) cc_final: 0.8768 (p) REVERT: Q 47 LEU cc_start: 0.8199 (tp) cc_final: 0.7942 (tp) REVERT: Q 99 LEU cc_start: 0.9043 (tp) cc_final: 0.8801 (tm) REVERT: Q 155 LEU cc_start: 0.8824 (mp) cc_final: 0.8601 (mm) REVERT: Q 156 THR cc_start: 0.8477 (m) cc_final: 0.7662 (p) REVERT: Q 162 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8727 (mp0) REVERT: R 201 ASP cc_start: 0.9024 (m-30) cc_final: 0.8723 (m-30) REVERT: U 361 ASN cc_start: 0.9099 (m-40) cc_final: 0.8673 (p0) REVERT: U 373 ASP cc_start: 0.9093 (t0) cc_final: 0.8462 (t0) REVERT: V 8 ASN cc_start: 0.9363 (m-40) cc_final: 0.9134 (m110) REVERT: V 66 ARG cc_start: 0.8630 (ttm110) cc_final: 0.8384 (ttt180) REVERT: V 73 THR cc_start: 0.9281 (m) cc_final: 0.9054 (p) REVERT: c 354 ASP cc_start: 0.0714 (m-30) cc_final: -0.0868 (m-30) REVERT: c 379 MET cc_start: -0.1437 (mtp) cc_final: -0.1721 (ptp) outliers start: 8 outliers final: 6 residues processed: 900 average time/residue: 1.3966 time to fit residues: 1550.6171 Evaluate side-chains 511 residues out of total 5173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 505 time to evaluate : 4.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain R residue 204 ASP Chi-restraints excluded: chain b residue 194 LYS Chi-restraints excluded: chain c residue 396 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 493 optimal weight: 50.0000 chunk 442 optimal weight: 9.9990 chunk 245 optimal weight: 6.9990 chunk 151 optimal weight: 0.9990 chunk 298 optimal weight: 0.0070 chunk 236 optimal weight: 1.9990 chunk 457 optimal weight: 10.0000 chunk 177 optimal weight: 5.9990 chunk 278 optimal weight: 2.9990 chunk 340 optimal weight: 1.9990 chunk 530 optimal weight: 5.9990 overall best weight: 1.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1077 ASN ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1251 ASN ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 111 ASN B 452 ASN B 503 ASN B1115 GLN B1117 HIS C 108 ASN C 217 GLN C 260 GLN E 210 GLN G 122 ASN H 131 ASN I 50 ASN ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 ASN K 89 ASN ** O 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 141 HIS ** Q 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 194 HIS U 352 HIS V 31 GLN V 45 ASN V 77 ASN ** c 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 50731 Z= 0.327 Angle : 0.688 11.794 69015 Z= 0.362 Chirality : 0.045 0.226 7639 Planarity : 0.005 0.072 8512 Dihedral : 15.533 149.364 7749 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.01 % Allowed : 11.19 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.11), residues: 5767 helix: 1.28 (0.11), residues: 2275 sheet: 0.24 (0.17), residues: 860 loop : -0.33 (0.12), residues: 2632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP c 184 HIS 0.012 0.001 HIS c 314 PHE 0.026 0.002 PHE R 188 TYR 0.028 0.002 TYR V 3 ARG 0.008 0.001 ARG G 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 5173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 608 time to evaluate : 4.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ILE cc_start: 0.9006 (mm) cc_final: 0.8605 (mm) REVERT: A 58 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8006 (mmm) REVERT: A 238 MET cc_start: 0.8335 (mtt) cc_final: 0.7544 (mmm) REVERT: A 329 MET cc_start: 0.8655 (mmt) cc_final: 0.8338 (mmm) REVERT: A 749 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7568 (ttm-80) REVERT: A 863 ARG cc_start: 0.8111 (mtm-85) cc_final: 0.7773 (mmm-85) REVERT: A 1164 THR cc_start: 0.8038 (m) cc_final: 0.7692 (p) REVERT: A 1192 TRP cc_start: 0.7979 (p-90) cc_final: 0.7598 (p-90) REVERT: A 1228 MET cc_start: 0.8527 (mmm) cc_final: 0.8139 (ttm) REVERT: A 1361 ASP cc_start: 0.8705 (t0) cc_final: 0.8436 (t0) REVERT: A 1439 LEU cc_start: 0.8828 (mt) cc_final: 0.8566 (mt) REVERT: B 95 LYS cc_start: 0.7921 (mmpt) cc_final: 0.6726 (ptpt) REVERT: B 206 TYR cc_start: 0.7691 (m-80) cc_final: 0.7000 (m-80) REVERT: B 238 SER cc_start: 0.7361 (m) cc_final: 0.7144 (m) REVERT: B 341 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7398 (tm-30) REVERT: B 1071 ASN cc_start: 0.8027 (m-40) cc_final: 0.7756 (m-40) REVERT: F 71 LEU cc_start: 0.9270 (tp) cc_final: 0.9060 (tt) REVERT: F 80 MET cc_start: 0.7706 (tpp) cc_final: 0.7180 (mpp) REVERT: F 90 LEU cc_start: 0.8515 (tm) cc_final: 0.8206 (mt) REVERT: F 125 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8746 (mp) REVERT: G 3 TYR cc_start: 0.5164 (m-80) cc_final: 0.4918 (m-80) REVERT: G 67 LEU cc_start: 0.8831 (tm) cc_final: 0.8591 (tm) REVERT: G 104 MET cc_start: 0.3341 (ppp) cc_final: 0.1545 (mtm) REVERT: G 117 MET cc_start: -0.4804 (mmm) cc_final: -0.5952 (ttm) REVERT: I 23 MET cc_start: 0.8182 (tpp) cc_final: 0.7810 (tpt) REVERT: M 25 GLU cc_start: 0.6922 (tt0) cc_final: 0.6330 (tm-30) REVERT: M 107 MET cc_start: 0.7394 (mtt) cc_final: 0.7133 (mmp) REVERT: M 115 MET cc_start: 0.8384 (ttp) cc_final: 0.7993 (tmm) REVERT: O 173 ASN cc_start: 0.9310 (t0) cc_final: 0.8913 (t0) REVERT: O 193 ASN cc_start: 0.9592 (t0) cc_final: 0.9374 (t0) REVERT: O 271 GLU cc_start: 0.9209 (pm20) cc_final: 0.8612 (pm20) REVERT: O 282 SER cc_start: 0.9081 (m) cc_final: 0.8746 (p) REVERT: Q 138 PHE cc_start: 0.6112 (m-80) cc_final: 0.5872 (m-10) REVERT: Q 158 GLU cc_start: 0.7745 (pm20) cc_final: 0.7267 (pm20) REVERT: Q 166 ARG cc_start: 0.5358 (OUTLIER) cc_final: 0.4751 (ptm160) REVERT: R 194 HIS cc_start: 0.8707 (t70) cc_final: 0.8373 (t-90) REVERT: R 201 ASP cc_start: 0.9269 (m-30) cc_final: 0.9001 (m-30) REVERT: U 24 ASP cc_start: 0.7679 (m-30) cc_final: 0.7175 (p0) REVERT: U 40 MET cc_start: 0.8841 (tpt) cc_final: 0.7814 (mmm) REVERT: U 337 CYS cc_start: 0.7814 (p) cc_final: 0.7571 (p) REVERT: U 360 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8091 (tp) REVERT: U 361 ASN cc_start: 0.9115 (m-40) cc_final: 0.8800 (p0) REVERT: V 66 ARG cc_start: 0.8919 (ttm110) cc_final: 0.8578 (ttt180) REVERT: b 174 MET cc_start: 0.3732 (tpt) cc_final: 0.3282 (tpt) REVERT: c 91 MET cc_start: 0.7844 (mmp) cc_final: 0.7594 (mmp) REVERT: c 146 MET cc_start: 0.7476 (OUTLIER) cc_final: 0.7048 (mpt) REVERT: c 253 LEU cc_start: 0.5097 (OUTLIER) cc_final: 0.4875 (mm) outliers start: 104 outliers final: 31 residues processed: 670 average time/residue: 1.3392 time to fit residues: 1127.0941 Evaluate side-chains 517 residues out of total 5173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 478 time to evaluate : 4.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 749 ARG Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 1002 SER Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 438 ARG Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 106 ARG Chi-restraints excluded: chain M residue 277 ILE Chi-restraints excluded: chain Q residue 128 THR Chi-restraints excluded: chain Q residue 166 ARG Chi-restraints excluded: chain R residue 204 ASP Chi-restraints excluded: chain R residue 219 GLU Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain U residue 360 LEU Chi-restraints excluded: chain U residue 365 TYR Chi-restraints excluded: chain V residue 16 GLN Chi-restraints excluded: chain V residue 50 GLN Chi-restraints excluded: chain c residue 146 MET Chi-restraints excluded: chain c residue 253 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 294 optimal weight: 6.9990 chunk 164 optimal weight: 6.9990 chunk 441 optimal weight: 4.9990 chunk 361 optimal weight: 0.5980 chunk 146 optimal weight: 0.6980 chunk 531 optimal weight: 20.0000 chunk 573 optimal weight: 20.0000 chunk 473 optimal weight: 10.0000 chunk 526 optimal weight: 50.0000 chunk 181 optimal weight: 1.9990 chunk 426 optimal weight: 7.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1332 GLN ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 GLN ** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN B 968 ASN B1115 GLN C 114 HIS ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN F 72 GLN ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 ASN ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 HIS ** O 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 285 GLN ** c 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 369 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 50731 Z= 0.482 Angle : 0.694 12.301 69015 Z= 0.362 Chirality : 0.046 0.204 7639 Planarity : 0.005 0.054 8512 Dihedral : 15.497 144.664 7736 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.73 % Allowed : 13.03 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.11), residues: 5767 helix: 1.19 (0.11), residues: 2286 sheet: 0.08 (0.17), residues: 863 loop : -0.45 (0.12), residues: 2618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP a 104 HIS 0.011 0.001 HIS a 223 PHE 0.022 0.002 PHE A 592 TYR 0.029 0.002 TYR R 212 ARG 0.012 0.001 ARG I 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 5173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 519 time to evaluate : 4.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 LEU cc_start: 0.9480 (mt) cc_final: 0.9089 (mt) REVERT: A 238 MET cc_start: 0.8418 (mtt) cc_final: 0.7644 (mmm) REVERT: A 329 MET cc_start: 0.8586 (mmt) cc_final: 0.8253 (mmm) REVERT: A 347 GLU cc_start: 0.8120 (tp30) cc_final: 0.7903 (tp30) REVERT: A 749 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.7634 (ttm-80) REVERT: A 1228 MET cc_start: 0.8620 (mmm) cc_final: 0.8253 (ttt) REVERT: A 1361 ASP cc_start: 0.8865 (t0) cc_final: 0.8549 (t0) REVERT: A 1428 MET cc_start: 0.7303 (OUTLIER) cc_final: 0.7069 (mmm) REVERT: A 1439 LEU cc_start: 0.8847 (mt) cc_final: 0.8615 (mt) REVERT: B 238 SER cc_start: 0.8055 (m) cc_final: 0.7778 (p) REVERT: B 288 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8799 (mp) REVERT: B 300 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8205 (mtp) REVERT: B 341 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7582 (tm-30) REVERT: B 603 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8436 (mtm) REVERT: B 613 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7822 (mtt-85) REVERT: B 1071 ASN cc_start: 0.8298 (m-40) cc_final: 0.7889 (m110) REVERT: D 39 MET cc_start: 0.9143 (tpt) cc_final: 0.8380 (tpp) REVERT: D 43 HIS cc_start: 0.9460 (OUTLIER) cc_final: 0.9026 (m-70) REVERT: E 108 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8207 (pp30) REVERT: E 126 ILE cc_start: 0.9041 (mp) cc_final: 0.8773 (pp) REVERT: F 102 ILE cc_start: 0.9424 (OUTLIER) cc_final: 0.9118 (mm) REVERT: G 21 ASN cc_start: 0.8459 (m110) cc_final: 0.7966 (t0) REVERT: G 104 MET cc_start: 0.4874 (ppp) cc_final: 0.2191 (mtm) REVERT: G 117 MET cc_start: -0.4650 (mmm) cc_final: -0.5920 (ttm) REVERT: H 103 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7670 (pm20) REVERT: M 107 MET cc_start: 0.7580 (mtt) cc_final: 0.7302 (mmp) REVERT: M 115 MET cc_start: 0.8266 (ttp) cc_final: 0.7966 (tmm) REVERT: M 194 CYS cc_start: 0.9000 (m) cc_final: 0.8703 (m) REVERT: O 173 ASN cc_start: 0.9350 (t0) cc_final: 0.8992 (t0) REVERT: O 193 ASN cc_start: 0.9626 (t0) cc_final: 0.9421 (t0) REVERT: O 258 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.7920 (pmm) REVERT: O 271 GLU cc_start: 0.9233 (pm20) cc_final: 0.8707 (pm20) REVERT: O 282 SER cc_start: 0.9060 (m) cc_final: 0.8732 (p) REVERT: O 317 VAL cc_start: 0.9194 (OUTLIER) cc_final: 0.8930 (p) REVERT: Q 125 TYR cc_start: 0.7416 (m-80) cc_final: 0.7148 (m-10) REVERT: Q 155 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.7760 (tp) REVERT: R 43 LEU cc_start: 0.8371 (mt) cc_final: 0.8118 (tm) REVERT: R 194 HIS cc_start: 0.8681 (t70) cc_final: 0.8383 (t70) REVERT: R 212 TYR cc_start: 0.7699 (t80) cc_final: 0.7426 (t80) REVERT: U 24 ASP cc_start: 0.7881 (m-30) cc_final: 0.7532 (p0) REVERT: U 39 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7314 (mt) REVERT: U 40 MET cc_start: 0.8542 (tpt) cc_final: 0.7806 (mmp) REVERT: U 337 CYS cc_start: 0.7639 (p) cc_final: 0.7291 (p) REVERT: U 351 PHE cc_start: 0.9087 (m-80) cc_final: 0.8811 (m-80) REVERT: U 353 LEU cc_start: 0.8917 (mm) cc_final: 0.8558 (mm) REVERT: U 360 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8332 (tp) REVERT: U 361 ASN cc_start: 0.9118 (m-40) cc_final: 0.8889 (p0) REVERT: U 367 PHE cc_start: 0.8228 (p90) cc_final: 0.7636 (p90) REVERT: V 72 TRP cc_start: 0.9365 (m100) cc_final: 0.8898 (m100) REVERT: V 82 ARG cc_start: 0.8286 (mmm160) cc_final: 0.7996 (mmm160) REVERT: a 211 ASP cc_start: 0.8924 (p0) cc_final: 0.8680 (t0) REVERT: b 174 MET cc_start: 0.4125 (tpt) cc_final: 0.3620 (tpt) REVERT: c 91 MET cc_start: 0.8001 (mmp) cc_final: 0.7754 (mmp) REVERT: c 141 TYR cc_start: 0.7816 (t80) cc_final: 0.7320 (t80) REVERT: c 146 MET cc_start: 0.7555 (OUTLIER) cc_final: 0.7124 (mpt) REVERT: c 216 HIS cc_start: 0.9288 (m-70) cc_final: 0.9023 (m-70) REVERT: c 364 MET cc_start: 0.0365 (pp-130) cc_final: 0.0130 (pp-130) outliers start: 141 outliers final: 50 residues processed: 611 average time/residue: 1.2791 time to fit residues: 985.4992 Evaluate side-chains 511 residues out of total 5173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 444 time to evaluate : 4.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 749 ARG Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1257 LEU Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1428 MET Chi-restraints excluded: chain A residue 1482 TYR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 438 ARG Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 613 ARG Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain K residue 106 ARG Chi-restraints excluded: chain O residue 220 VAL Chi-restraints excluded: chain O residue 258 MET Chi-restraints excluded: chain O residue 317 VAL Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 128 THR Chi-restraints excluded: chain Q residue 155 LEU Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain R residue 204 ASP Chi-restraints excluded: chain R residue 219 GLU Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain U residue 360 LEU Chi-restraints excluded: chain U residue 365 TYR Chi-restraints excluded: chain V residue 16 GLN Chi-restraints excluded: chain a residue 38 PHE Chi-restraints excluded: chain a residue 136 HIS Chi-restraints excluded: chain b residue 409 THR Chi-restraints excluded: chain c residue 146 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 524 optimal weight: 50.0000 chunk 399 optimal weight: 0.9980 chunk 275 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 253 optimal weight: 4.9990 chunk 356 optimal weight: 0.7980 chunk 533 optimal weight: 40.0000 chunk 564 optimal weight: 5.9990 chunk 278 optimal weight: 0.7980 chunk 505 optimal weight: 8.9990 chunk 152 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 ASN ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 GLN ** B 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN E 210 GLN H 133 HIS ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 ASN ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 263 GLN ** O 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 48 ASN ** a 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 202 GLN ** c 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 37 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 50731 Z= 0.239 Angle : 0.612 13.044 69015 Z= 0.319 Chirality : 0.043 0.289 7639 Planarity : 0.004 0.093 8512 Dihedral : 15.431 146.258 7736 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.24 % Allowed : 15.10 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.11), residues: 5767 helix: 1.30 (0.11), residues: 2285 sheet: 0.05 (0.17), residues: 863 loop : -0.40 (0.12), residues: 2619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP a 63 HIS 0.008 0.001 HIS B1060 PHE 0.023 0.002 PHE c 283 TYR 0.021 0.001 TYR A 669 ARG 0.011 0.000 ARG V 7 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 5173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 499 time to evaluate : 4.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.8325 (mmt) cc_final: 0.8098 (mmt) REVERT: A 85 PHE cc_start: 0.7224 (m-80) cc_final: 0.6524 (m-10) REVERT: A 236 LEU cc_start: 0.9492 (mt) cc_final: 0.9108 (mt) REVERT: A 238 MET cc_start: 0.8439 (mtt) cc_final: 0.7685 (mmm) REVERT: A 329 MET cc_start: 0.8668 (mmt) cc_final: 0.8310 (mmm) REVERT: A 347 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7762 (tp30) REVERT: A 749 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7606 (ttm-80) REVERT: A 1228 MET cc_start: 0.8518 (mmm) cc_final: 0.8181 (ttm) REVERT: A 1260 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6911 (mtt90) REVERT: A 1361 ASP cc_start: 0.8876 (t0) cc_final: 0.8532 (t0) REVERT: A 1460 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8901 (tt) REVERT: A 1472 ASP cc_start: 0.7894 (m-30) cc_final: 0.7572 (m-30) REVERT: B 238 SER cc_start: 0.8132 (m) cc_final: 0.7863 (p) REVERT: B 341 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7206 (tm-30) REVERT: B 442 ASP cc_start: 0.8116 (m-30) cc_final: 0.7886 (m-30) REVERT: B 890 ARG cc_start: 0.6561 (OUTLIER) cc_final: 0.6287 (ttp-170) REVERT: B 1071 ASN cc_start: 0.8315 (m-40) cc_final: 0.7901 (m110) REVERT: E 108 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8209 (pp30) REVERT: E 126 ILE cc_start: 0.9050 (mp) cc_final: 0.8794 (pp) REVERT: E 210 GLN cc_start: 0.7337 (mt0) cc_final: 0.7080 (pp30) REVERT: F 102 ILE cc_start: 0.9395 (OUTLIER) cc_final: 0.9162 (mm) REVERT: G 1 MET cc_start: 0.7869 (ptt) cc_final: 0.7623 (pp-130) REVERT: G 67 LEU cc_start: 0.8566 (tm) cc_final: 0.8357 (tm) REVERT: G 104 MET cc_start: 0.4629 (ppp) cc_final: 0.2057 (ptp) REVERT: G 117 MET cc_start: -0.4622 (mmm) cc_final: -0.5937 (ttm) REVERT: I 50 ASN cc_start: 0.7791 (t160) cc_final: 0.7526 (p0) REVERT: I 82 GLU cc_start: 0.7394 (pp20) cc_final: 0.7004 (pp20) REVERT: K 93 ASP cc_start: 0.7278 (m-30) cc_final: 0.7074 (m-30) REVERT: M 107 MET cc_start: 0.7564 (mtt) cc_final: 0.7289 (mmp) REVERT: M 115 MET cc_start: 0.8133 (ttp) cc_final: 0.7793 (tmm) REVERT: M 194 CYS cc_start: 0.8913 (m) cc_final: 0.8710 (m) REVERT: O 173 ASN cc_start: 0.9331 (t0) cc_final: 0.8970 (t0) REVERT: O 222 THR cc_start: 0.8821 (p) cc_final: 0.8450 (t) REVERT: O 258 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.7746 (pmm) REVERT: O 271 GLU cc_start: 0.9236 (pm20) cc_final: 0.8753 (pm20) REVERT: O 278 GLN cc_start: 0.8848 (pm20) cc_final: 0.8583 (mp10) REVERT: O 282 SER cc_start: 0.9031 (m) cc_final: 0.8705 (p) REVERT: Q 47 LEU cc_start: 0.8268 (tm) cc_final: 0.7754 (pt) REVERT: Q 155 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7572 (tp) REVERT: Q 158 GLU cc_start: 0.8140 (mp0) cc_final: 0.7836 (mp0) REVERT: R 43 LEU cc_start: 0.8522 (mt) cc_final: 0.8151 (tm) REVERT: R 194 HIS cc_start: 0.8592 (t70) cc_final: 0.8266 (t70) REVERT: R 219 GLU cc_start: 0.9216 (OUTLIER) cc_final: 0.8832 (pp20) REVERT: U 39 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7289 (mt) REVERT: U 40 MET cc_start: 0.8481 (tpt) cc_final: 0.7804 (mmp) REVERT: U 360 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8347 (tp) REVERT: V 66 ARG cc_start: 0.8747 (ttm110) cc_final: 0.8384 (ttm110) REVERT: V 67 PHE cc_start: 0.8618 (t80) cc_final: 0.8411 (t80) REVERT: V 82 ARG cc_start: 0.8203 (mmm160) cc_final: 0.7884 (mmm160) REVERT: V 94 LYS cc_start: 0.9311 (tptp) cc_final: 0.8994 (tppt) REVERT: a 211 ASP cc_start: 0.8885 (p0) cc_final: 0.8634 (t0) REVERT: b 174 MET cc_start: 0.4040 (tpt) cc_final: 0.3495 (tpt) REVERT: b 359 MET cc_start: 0.7103 (pmm) cc_final: 0.6590 (pmm) REVERT: c 91 MET cc_start: 0.8143 (mmp) cc_final: 0.7876 (mmp) REVERT: c 105 ASN cc_start: 0.7750 (m-40) cc_final: 0.7440 (m110) REVERT: c 141 TYR cc_start: 0.7780 (OUTLIER) cc_final: 0.7465 (t80) REVERT: c 146 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.7088 (mpt) REVERT: c 209 LEU cc_start: 0.9227 (mt) cc_final: 0.8670 (pp) REVERT: c 364 MET cc_start: -0.0034 (pp-130) cc_final: -0.0416 (pp-130) outliers start: 116 outliers final: 41 residues processed: 572 average time/residue: 1.2647 time to fit residues: 919.0082 Evaluate side-chains 499 residues out of total 5173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 443 time to evaluate : 4.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 749 ARG Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1260 ARG Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1482 TYR Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 890 ARG Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain G residue 3 TYR Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain O residue 258 MET Chi-restraints excluded: chain Q residue 128 THR Chi-restraints excluded: chain Q residue 155 LEU Chi-restraints excluded: chain R residue 172 ASP Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain R residue 204 ASP Chi-restraints excluded: chain R residue 219 GLU Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain U residue 360 LEU Chi-restraints excluded: chain V residue 16 GLN Chi-restraints excluded: chain V residue 50 GLN Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain a residue 136 HIS Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain b residue 388 HIS Chi-restraints excluded: chain b residue 409 THR Chi-restraints excluded: chain c residue 141 TYR Chi-restraints excluded: chain c residue 146 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 470 optimal weight: 20.0000 chunk 320 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 420 optimal weight: 10.0000 chunk 232 optimal weight: 3.9990 chunk 481 optimal weight: 7.9990 chunk 390 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 288 optimal weight: 50.0000 chunk 506 optimal weight: 20.0000 chunk 142 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 861 GLN ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 GLN B 227 ASN ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 GLN B 452 ASN ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 GLN ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 63 ASN V 77 ASN ** c 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 50731 Z= 0.314 Angle : 0.629 13.582 69015 Z= 0.325 Chirality : 0.044 0.293 7639 Planarity : 0.004 0.060 8512 Dihedral : 15.339 148.410 7736 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.53 % Allowed : 15.75 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.11), residues: 5767 helix: 1.38 (0.11), residues: 2269 sheet: 0.11 (0.17), residues: 861 loop : -0.46 (0.12), residues: 2637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP a 104 HIS 0.027 0.001 HIS b 281 PHE 0.023 0.002 PHE B 320 TYR 0.029 0.002 TYR R 212 ARG 0.015 0.000 ARG L 37 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 5173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 472 time to evaluate : 4.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.8390 (mmt) cc_final: 0.8067 (mmm) REVERT: A 85 PHE cc_start: 0.7406 (m-80) cc_final: 0.6697 (m-80) REVERT: A 236 LEU cc_start: 0.9506 (mt) cc_final: 0.9180 (mt) REVERT: A 238 MET cc_start: 0.8456 (mtt) cc_final: 0.7715 (mmm) REVERT: A 329 MET cc_start: 0.8727 (mmt) cc_final: 0.8402 (mmm) REVERT: A 347 GLU cc_start: 0.8086 (tp30) cc_final: 0.7797 (tp30) REVERT: A 749 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7642 (ttm-80) REVERT: A 1228 MET cc_start: 0.8534 (mmm) cc_final: 0.8274 (ttm) REVERT: A 1361 ASP cc_start: 0.8913 (t0) cc_final: 0.8664 (t0) REVERT: A 1422 GLN cc_start: 0.7958 (tm-30) cc_final: 0.7681 (tm-30) REVERT: A 1460 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8647 (tt) REVERT: A 1472 ASP cc_start: 0.7941 (m-30) cc_final: 0.7601 (m-30) REVERT: B 238 SER cc_start: 0.8384 (m) cc_final: 0.8055 (p) REVERT: B 341 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7352 (tm-30) REVERT: B 613 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7797 (mtt-85) REVERT: B 1071 ASN cc_start: 0.8471 (m-40) cc_final: 0.7999 (m110) REVERT: E 108 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8226 (pp30) REVERT: E 121 MET cc_start: 0.7030 (tpp) cc_final: 0.6733 (tpp) REVERT: E 126 ILE cc_start: 0.9077 (mp) cc_final: 0.8832 (pp) REVERT: F 75 MET cc_start: 0.8725 (mtm) cc_final: 0.8502 (mtm) REVERT: F 102 ILE cc_start: 0.9420 (mm) cc_final: 0.9167 (mm) REVERT: F 127 ASP cc_start: 0.6508 (OUTLIER) cc_final: 0.6246 (p0) REVERT: G 1 MET cc_start: 0.8123 (ptt) cc_final: 0.7653 (pp-130) REVERT: G 60 GLN cc_start: 0.8361 (mm-40) cc_final: 0.8058 (mm110) REVERT: G 63 ARG cc_start: 0.7234 (tmm-80) cc_final: 0.6950 (ttp80) REVERT: G 104 MET cc_start: 0.4874 (ppp) cc_final: 0.2051 (ptp) REVERT: G 117 MET cc_start: -0.4407 (mmm) cc_final: -0.5848 (ttm) REVERT: I 50 ASN cc_start: 0.7722 (t160) cc_final: 0.7304 (p0) REVERT: L 44 MET cc_start: 0.8530 (mmm) cc_final: 0.7923 (mmm) REVERT: M 107 MET cc_start: 0.7568 (mtt) cc_final: 0.7268 (mpp) REVERT: M 115 MET cc_start: 0.8136 (ttp) cc_final: 0.7808 (tmm) REVERT: M 126 ASP cc_start: 0.8168 (t0) cc_final: 0.7904 (t0) REVERT: O 173 ASN cc_start: 0.9366 (t0) cc_final: 0.9026 (t0) REVERT: O 222 THR cc_start: 0.8659 (p) cc_final: 0.8458 (t) REVERT: O 271 GLU cc_start: 0.9238 (pm20) cc_final: 0.8725 (pm20) REVERT: O 282 SER cc_start: 0.9032 (m) cc_final: 0.8723 (p) REVERT: Q 44 GLN cc_start: 0.7662 (OUTLIER) cc_final: 0.7423 (tm-30) REVERT: Q 125 TYR cc_start: 0.7413 (m-10) cc_final: 0.7109 (m-10) REVERT: Q 155 LEU cc_start: 0.8224 (mm) cc_final: 0.7395 (tp) REVERT: R 43 LEU cc_start: 0.8522 (mt) cc_final: 0.8168 (tm) REVERT: R 194 HIS cc_start: 0.8580 (t70) cc_final: 0.8260 (t70) REVERT: R 219 GLU cc_start: 0.9241 (OUTLIER) cc_final: 0.8911 (mp0) REVERT: U 40 MET cc_start: 0.8570 (tpt) cc_final: 0.7941 (mmm) REVERT: U 353 LEU cc_start: 0.8609 (mm) cc_final: 0.7933 (mm) REVERT: V 82 ARG cc_start: 0.8098 (mmm160) cc_final: 0.7814 (mmm160) REVERT: V 94 LYS cc_start: 0.9314 (tptp) cc_final: 0.8991 (tppt) REVERT: a 190 MET cc_start: 0.0952 (pmt) cc_final: 0.0728 (pmm) REVERT: a 211 ASP cc_start: 0.8902 (p0) cc_final: 0.8649 (t0) REVERT: b 174 MET cc_start: 0.3889 (tpt) cc_final: 0.3344 (tpt) REVERT: c 91 MET cc_start: 0.8201 (mmp) cc_final: 0.7929 (mmp) REVERT: c 105 ASN cc_start: 0.7697 (m-40) cc_final: 0.7402 (m110) REVERT: c 141 TYR cc_start: 0.7815 (t80) cc_final: 0.7462 (t80) REVERT: c 216 HIS cc_start: 0.9235 (m-70) cc_final: 0.8892 (m-70) REVERT: c 364 MET cc_start: -0.0319 (pp-130) cc_final: -0.0757 (pp-130) REVERT: c 379 MET cc_start: -0.1455 (OUTLIER) cc_final: -0.1724 (pmt) outliers start: 131 outliers final: 56 residues processed: 565 average time/residue: 1.2746 time to fit residues: 913.1376 Evaluate side-chains 484 residues out of total 5173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 419 time to evaluate : 4.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 749 ARG Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1482 TYR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 613 ARG Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain G residue 3 TYR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain O residue 220 VAL Chi-restraints excluded: chain Q residue 14 TYR Chi-restraints excluded: chain Q residue 44 GLN Chi-restraints excluded: chain Q residue 128 THR Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 204 ASP Chi-restraints excluded: chain R residue 219 GLU Chi-restraints excluded: chain U residue 334 VAL Chi-restraints excluded: chain U residue 365 TYR Chi-restraints excluded: chain V residue 16 GLN Chi-restraints excluded: chain V residue 50 GLN Chi-restraints excluded: chain a residue 136 HIS Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain b residue 388 HIS Chi-restraints excluded: chain b residue 409 THR Chi-restraints excluded: chain c residue 379 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 189 optimal weight: 1.9990 chunk 508 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 331 optimal weight: 0.3980 chunk 139 optimal weight: 5.9990 chunk 565 optimal weight: 30.0000 chunk 469 optimal weight: 40.0000 chunk 261 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 186 optimal weight: 0.6980 chunk 296 optimal weight: 0.0050 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 189 ASN Q 44 GLN ** Q 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 352 HIS ** b 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 50731 Z= 0.196 Angle : 0.611 15.032 69015 Z= 0.314 Chirality : 0.042 0.223 7639 Planarity : 0.004 0.057 8512 Dihedral : 15.253 151.280 7736 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.97 % Allowed : 16.90 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.11), residues: 5767 helix: 1.45 (0.11), residues: 2272 sheet: 0.10 (0.17), residues: 876 loop : -0.41 (0.12), residues: 2619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A1192 HIS 0.020 0.001 HIS b 281 PHE 0.026 0.001 PHE V 74 TYR 0.022 0.001 TYR E 8 ARG 0.010 0.000 ARG L 37 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 5173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 465 time to evaluate : 4.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.8247 (mmt) cc_final: 0.8004 (mmt) REVERT: A 85 PHE cc_start: 0.7430 (m-80) cc_final: 0.6885 (m-80) REVERT: A 236 LEU cc_start: 0.9507 (mt) cc_final: 0.8408 (mt) REVERT: A 238 MET cc_start: 0.8453 (mtt) cc_final: 0.7887 (mpt) REVERT: A 329 MET cc_start: 0.8800 (mmt) cc_final: 0.8529 (mmm) REVERT: A 347 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7732 (tp30) REVERT: A 865 ILE cc_start: 0.8916 (mm) cc_final: 0.8650 (mt) REVERT: A 1164 THR cc_start: 0.8489 (m) cc_final: 0.8047 (p) REVERT: A 1247 PHE cc_start: 0.9030 (p90) cc_final: 0.8784 (p90) REVERT: A 1361 ASP cc_start: 0.8895 (t0) cc_final: 0.8642 (t0) REVERT: A 1422 GLN cc_start: 0.7808 (tm-30) cc_final: 0.7549 (tm-30) REVERT: A 1472 ASP cc_start: 0.7919 (m-30) cc_final: 0.7584 (m-30) REVERT: B 238 SER cc_start: 0.8352 (m) cc_final: 0.8034 (p) REVERT: B 281 ASP cc_start: 0.8221 (m-30) cc_final: 0.7729 (m-30) REVERT: B 341 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7354 (tm-30) REVERT: B 1071 ASN cc_start: 0.8464 (m-40) cc_final: 0.7987 (m110) REVERT: B 1089 MET cc_start: 0.8612 (mmm) cc_final: 0.8411 (mmp) REVERT: E 108 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8189 (pp30) REVERT: E 126 ILE cc_start: 0.9055 (mp) cc_final: 0.8833 (pp) REVERT: F 71 LEU cc_start: 0.8968 (tt) cc_final: 0.8751 (tt) REVERT: F 102 ILE cc_start: 0.9372 (OUTLIER) cc_final: 0.9156 (mm) REVERT: G 1 MET cc_start: 0.8097 (ptt) cc_final: 0.7518 (pp-130) REVERT: G 63 ARG cc_start: 0.7242 (tmm-80) cc_final: 0.6865 (tmm-80) REVERT: G 67 LEU cc_start: 0.8820 (tm) cc_final: 0.8521 (tm) REVERT: G 104 MET cc_start: 0.4838 (ppp) cc_final: 0.2016 (ptp) REVERT: G 117 MET cc_start: -0.4480 (mmm) cc_final: -0.5902 (ttm) REVERT: I 50 ASN cc_start: 0.7729 (t160) cc_final: 0.7288 (p0) REVERT: I 93 GLU cc_start: 0.8225 (tp30) cc_final: 0.7432 (tp30) REVERT: K 93 ASP cc_start: 0.7304 (m-30) cc_final: 0.7086 (m-30) REVERT: L 21 GLU cc_start: 0.7630 (tt0) cc_final: 0.7409 (pt0) REVERT: L 44 MET cc_start: 0.8498 (mmm) cc_final: 0.7913 (mmm) REVERT: M 107 MET cc_start: 0.7554 (OUTLIER) cc_final: 0.7304 (mpp) REVERT: M 115 MET cc_start: 0.8134 (ttp) cc_final: 0.7749 (tmm) REVERT: M 126 ASP cc_start: 0.8142 (t0) cc_final: 0.7843 (t0) REVERT: M 146 TYR cc_start: 0.7098 (t80) cc_final: 0.6881 (t80) REVERT: M 215 MET cc_start: 0.8547 (mmm) cc_final: 0.8254 (mmm) REVERT: O 173 ASN cc_start: 0.9375 (t0) cc_final: 0.9026 (t0) REVERT: O 179 ASP cc_start: 0.9433 (t0) cc_final: 0.9174 (p0) REVERT: O 222 THR cc_start: 0.8771 (p) cc_final: 0.8397 (t) REVERT: O 271 GLU cc_start: 0.9251 (pm20) cc_final: 0.8783 (pm20) REVERT: O 282 SER cc_start: 0.9019 (m) cc_final: 0.8716 (p) REVERT: Q 44 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7703 (tm-30) REVERT: Q 47 LEU cc_start: 0.8315 (tm) cc_final: 0.7716 (pt) REVERT: Q 125 TYR cc_start: 0.7285 (m-10) cc_final: 0.6944 (m-10) REVERT: R 43 LEU cc_start: 0.8508 (mt) cc_final: 0.8140 (tm) REVERT: R 194 HIS cc_start: 0.8547 (t70) cc_final: 0.8221 (t70) REVERT: R 212 TYR cc_start: 0.7652 (t80) cc_final: 0.6851 (t80) REVERT: R 219 GLU cc_start: 0.9199 (OUTLIER) cc_final: 0.8872 (mp0) REVERT: U 39 LEU cc_start: 0.6681 (mt) cc_final: 0.6108 (mm) REVERT: U 40 MET cc_start: 0.8614 (tpt) cc_final: 0.8109 (mmm) REVERT: U 351 PHE cc_start: 0.8955 (m-80) cc_final: 0.8748 (m-80) REVERT: U 353 LEU cc_start: 0.8538 (mm) cc_final: 0.7895 (mm) REVERT: U 367 PHE cc_start: 0.8249 (p90) cc_final: 0.7600 (p90) REVERT: U 369 LYS cc_start: 0.9005 (pmtt) cc_final: 0.8177 (pmtt) REVERT: U 373 ASP cc_start: 0.8578 (t0) cc_final: 0.8282 (t0) REVERT: V 59 ARG cc_start: 0.8382 (mmm-85) cc_final: 0.8047 (mmm160) REVERT: V 74 PHE cc_start: 0.9345 (m-10) cc_final: 0.9138 (m-10) REVERT: V 82 ARG cc_start: 0.7989 (mmm160) cc_final: 0.7773 (mmm160) REVERT: V 94 LYS cc_start: 0.9320 (tptp) cc_final: 0.8984 (tppt) REVERT: a 169 MET cc_start: 0.4330 (pmt) cc_final: 0.4079 (pmm) REVERT: a 211 ASP cc_start: 0.8891 (p0) cc_final: 0.8637 (t0) REVERT: b 174 MET cc_start: 0.3874 (tpt) cc_final: 0.3348 (tpt) REVERT: b 237 GLN cc_start: 0.2143 (OUTLIER) cc_final: 0.1658 (pm20) REVERT: b 359 MET cc_start: 0.6554 (pmm) cc_final: 0.6213 (pmm) REVERT: c 91 MET cc_start: 0.8310 (mmp) cc_final: 0.8087 (mmp) REVERT: c 105 ASN cc_start: 0.7642 (m-40) cc_final: 0.7304 (m110) REVERT: c 141 TYR cc_start: 0.7770 (OUTLIER) cc_final: 0.7468 (t80) REVERT: c 146 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.6981 (mmm) REVERT: c 364 MET cc_start: -0.0445 (pp-130) cc_final: -0.0869 (pp-130) REVERT: c 379 MET cc_start: -0.0574 (ptt) cc_final: -0.0899 (pmt) outliers start: 102 outliers final: 53 residues processed: 528 average time/residue: 1.2765 time to fit residues: 858.5582 Evaluate side-chains 495 residues out of total 5173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 432 time to evaluate : 4.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1482 TYR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 107 MET Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain Q residue 14 TYR Chi-restraints excluded: chain Q residue 44 GLN Chi-restraints excluded: chain Q residue 128 THR Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 204 ASP Chi-restraints excluded: chain R residue 219 GLU Chi-restraints excluded: chain U residue 334 VAL Chi-restraints excluded: chain U residue 337 CYS Chi-restraints excluded: chain U residue 355 ASP Chi-restraints excluded: chain U residue 365 TYR Chi-restraints excluded: chain V residue 16 GLN Chi-restraints excluded: chain V residue 50 GLN Chi-restraints excluded: chain a residue 70 TYR Chi-restraints excluded: chain a residue 136 HIS Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain b residue 237 GLN Chi-restraints excluded: chain b residue 388 HIS Chi-restraints excluded: chain b residue 409 THR Chi-restraints excluded: chain c residue 141 TYR Chi-restraints excluded: chain c residue 146 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 544 optimal weight: 30.0000 chunk 63 optimal weight: 0.8980 chunk 321 optimal weight: 0.9980 chunk 412 optimal weight: 20.0000 chunk 319 optimal weight: 40.0000 chunk 475 optimal weight: 0.1980 chunk 315 optimal weight: 8.9990 chunk 562 optimal weight: 20.0000 chunk 352 optimal weight: 7.9990 chunk 343 optimal weight: 4.9990 chunk 259 optimal weight: 1.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 ASN A1190 GLN ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 GLN ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 GLN ** Q 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 352 HIS U 361 ASN b 152 GLN ** b 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 338 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 50731 Z= 0.315 Angle : 0.643 12.822 69015 Z= 0.328 Chirality : 0.043 0.200 7639 Planarity : 0.004 0.051 8512 Dihedral : 15.135 152.250 7736 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.20 % Allowed : 17.24 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.11), residues: 5767 helix: 1.43 (0.11), residues: 2277 sheet: 0.09 (0.17), residues: 871 loop : -0.42 (0.12), residues: 2619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A1192 HIS 0.017 0.001 HIS b 281 PHE 0.020 0.002 PHE A 458 TYR 0.022 0.002 TYR I 25 ARG 0.008 0.000 ARG c 166 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 5173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 458 time to evaluate : 4.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.8366 (mmt) cc_final: 0.8061 (mmt) REVERT: A 85 PHE cc_start: 0.7437 (m-80) cc_final: 0.6882 (m-80) REVERT: A 236 LEU cc_start: 0.9518 (mt) cc_final: 0.8434 (mt) REVERT: A 238 MET cc_start: 0.8422 (mtt) cc_final: 0.7909 (mpt) REVERT: A 329 MET cc_start: 0.8707 (mmt) cc_final: 0.8347 (mmm) REVERT: A 347 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7806 (tp30) REVERT: A 1164 THR cc_start: 0.8527 (m) cc_final: 0.8048 (p) REVERT: A 1361 ASP cc_start: 0.8901 (t0) cc_final: 0.8621 (OUTLIER) REVERT: B 238 SER cc_start: 0.8736 (m) cc_final: 0.8328 (p) REVERT: B 281 ASP cc_start: 0.8254 (m-30) cc_final: 0.7809 (m-30) REVERT: B 341 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7447 (tm-30) REVERT: B 442 ASP cc_start: 0.8252 (m-30) cc_final: 0.7888 (m-30) REVERT: B 890 ARG cc_start: 0.6808 (OUTLIER) cc_final: 0.6397 (ttm170) REVERT: B 1071 ASN cc_start: 0.8537 (m-40) cc_final: 0.8053 (m110) REVERT: B 1172 MET cc_start: 0.7254 (mpm) cc_final: 0.6812 (mpm) REVERT: C 94 CYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7261 (p) REVERT: E 108 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8242 (pp30) REVERT: E 121 MET cc_start: 0.7385 (tpp) cc_final: 0.7037 (tpp) REVERT: E 126 ILE cc_start: 0.9087 (mp) cc_final: 0.8880 (pp) REVERT: E 151 MET cc_start: 0.8276 (ttm) cc_final: 0.8062 (mtp) REVERT: G 1 MET cc_start: 0.7794 (ptt) cc_final: 0.7490 (pp-130) REVERT: G 67 LEU cc_start: 0.8888 (tm) cc_final: 0.8394 (tp) REVERT: G 104 MET cc_start: 0.4850 (ppp) cc_final: 0.1971 (ptp) REVERT: G 117 MET cc_start: -0.4556 (mmm) cc_final: -0.5824 (ttm) REVERT: H 103 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7842 (pm20) REVERT: I 50 ASN cc_start: 0.7789 (t160) cc_final: 0.7330 (p0) REVERT: L 44 MET cc_start: 0.8536 (mmm) cc_final: 0.7938 (mmm) REVERT: M 107 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.7318 (mpp) REVERT: M 115 MET cc_start: 0.8136 (ttp) cc_final: 0.7767 (tmm) REVERT: O 173 ASN cc_start: 0.9387 (t0) cc_final: 0.9046 (t0) REVERT: O 179 ASP cc_start: 0.9449 (t0) cc_final: 0.9190 (p0) REVERT: O 222 THR cc_start: 0.8745 (p) cc_final: 0.8363 (t) REVERT: O 271 GLU cc_start: 0.9257 (pm20) cc_final: 0.8795 (pm20) REVERT: O 282 SER cc_start: 0.9036 (m) cc_final: 0.8732 (p) REVERT: Q 125 TYR cc_start: 0.7432 (m-10) cc_final: 0.7163 (m-10) REVERT: Q 155 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7510 (mm) REVERT: R 43 LEU cc_start: 0.8521 (mt) cc_final: 0.8157 (tm) REVERT: R 164 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8428 (pp20) REVERT: R 194 HIS cc_start: 0.8526 (t70) cc_final: 0.8216 (t70) REVERT: R 219 GLU cc_start: 0.9182 (OUTLIER) cc_final: 0.8892 (mp0) REVERT: U 39 LEU cc_start: 0.6629 (mt) cc_final: 0.6240 (mm) REVERT: U 40 MET cc_start: 0.8656 (tpt) cc_final: 0.8150 (mmm) REVERT: U 341 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8529 (tmmt) REVERT: U 353 LEU cc_start: 0.8444 (mm) cc_final: 0.7795 (mm) REVERT: U 367 PHE cc_start: 0.8238 (p90) cc_final: 0.7704 (p90) REVERT: V 66 ARG cc_start: 0.8822 (ttm110) cc_final: 0.8392 (ttm110) REVERT: V 74 PHE cc_start: 0.9343 (m-80) cc_final: 0.9096 (m-10) REVERT: V 94 LYS cc_start: 0.9286 (tptp) cc_final: 0.8924 (tppt) REVERT: a 169 MET cc_start: 0.4246 (pmt) cc_final: 0.3998 (pmm) REVERT: a 190 MET cc_start: 0.1762 (pmt) cc_final: 0.1496 (pmm) REVERT: a 211 ASP cc_start: 0.8892 (p0) cc_final: 0.8632 (t0) REVERT: b 174 MET cc_start: 0.3794 (tpt) cc_final: 0.3295 (tpt) REVERT: b 237 GLN cc_start: 0.2570 (OUTLIER) cc_final: 0.2102 (pm20) REVERT: b 359 MET cc_start: 0.6709 (pmm) cc_final: 0.6432 (pmm) REVERT: c 105 ASN cc_start: 0.7721 (m-40) cc_final: 0.7366 (m110) REVERT: c 141 TYR cc_start: 0.7736 (OUTLIER) cc_final: 0.7526 (t80) REVERT: c 216 HIS cc_start: 0.9234 (m-70) cc_final: 0.8864 (m-70) REVERT: c 364 MET cc_start: -0.0701 (pp-130) cc_final: -0.1119 (pp-130) REVERT: c 379 MET cc_start: -0.1264 (ptt) cc_final: -0.1636 (pmt) outliers start: 114 outliers final: 54 residues processed: 535 average time/residue: 1.2854 time to fit residues: 876.0016 Evaluate side-chains 487 residues out of total 5173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 422 time to evaluate : 4.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1482 TYR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 890 ARG Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain I residue 53 ILE Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 107 MET Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain O residue 220 VAL Chi-restraints excluded: chain Q residue 14 TYR Chi-restraints excluded: chain Q residue 128 THR Chi-restraints excluded: chain Q residue 155 LEU Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 219 GLU Chi-restraints excluded: chain U residue 337 CYS Chi-restraints excluded: chain U residue 341 LYS Chi-restraints excluded: chain U residue 355 ASP Chi-restraints excluded: chain U residue 365 TYR Chi-restraints excluded: chain U residue 366 ILE Chi-restraints excluded: chain V residue 16 GLN Chi-restraints excluded: chain V residue 50 GLN Chi-restraints excluded: chain a residue 136 HIS Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain b residue 237 GLN Chi-restraints excluded: chain b residue 388 HIS Chi-restraints excluded: chain b residue 409 THR Chi-restraints excluded: chain c residue 141 TYR Chi-restraints excluded: chain c residue 146 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 348 optimal weight: 0.6980 chunk 224 optimal weight: 0.0980 chunk 336 optimal weight: 0.2980 chunk 169 optimal weight: 0.0870 chunk 110 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 357 optimal weight: 0.0970 chunk 383 optimal weight: 9.9990 chunk 278 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 442 optimal weight: 8.9990 overall best weight: 0.2356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN B 537 GLN B 817 GLN ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 60 GLN ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 289 GLN c 293 ASN c 295 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 50731 Z= 0.172 Angle : 0.640 13.937 69015 Z= 0.324 Chirality : 0.043 0.226 7639 Planarity : 0.004 0.047 8512 Dihedral : 15.020 152.009 7734 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.95 % Allowed : 18.06 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.11), residues: 5767 helix: 1.48 (0.11), residues: 2270 sheet: 0.14 (0.17), residues: 837 loop : -0.38 (0.12), residues: 2660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP c 187 HIS 0.015 0.001 HIS b 281 PHE 0.025 0.001 PHE U 351 TYR 0.034 0.001 TYR R 212 ARG 0.009 0.000 ARG c 166 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 5173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 477 time to evaluate : 4.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.8135 (mmt) cc_final: 0.7859 (mmt) REVERT: A 85 PHE cc_start: 0.7295 (m-80) cc_final: 0.6812 (m-80) REVERT: A 236 LEU cc_start: 0.9511 (mt) cc_final: 0.8447 (mt) REVERT: A 238 MET cc_start: 0.8425 (mtt) cc_final: 0.7892 (mpt) REVERT: A 329 MET cc_start: 0.8787 (mmt) cc_final: 0.8433 (mmm) REVERT: A 347 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7762 (tp30) REVERT: A 865 ILE cc_start: 0.8883 (mm) cc_final: 0.8542 (mt) REVERT: A 1164 THR cc_start: 0.8355 (m) cc_final: 0.7468 (m) REVERT: A 1361 ASP cc_start: 0.8870 (t0) cc_final: 0.8614 (OUTLIER) REVERT: A 1428 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.7175 (mmm) REVERT: B 238 SER cc_start: 0.8476 (m) cc_final: 0.8133 (p) REVERT: B 281 ASP cc_start: 0.8225 (m-30) cc_final: 0.7727 (m-30) REVERT: B 341 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7513 (tm-30) REVERT: B 442 ASP cc_start: 0.8163 (m-30) cc_final: 0.7938 (m-30) REVERT: B 890 ARG cc_start: 0.6723 (OUTLIER) cc_final: 0.6330 (ttm170) REVERT: B 1071 ASN cc_start: 0.8478 (m-40) cc_final: 0.7977 (m110) REVERT: B 1172 MET cc_start: 0.7547 (mpm) cc_final: 0.7160 (mpm) REVERT: C 94 CYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7331 (p) REVERT: E 108 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.8247 (pp30) REVERT: E 151 MET cc_start: 0.8210 (ttm) cc_final: 0.7929 (mtp) REVERT: F 102 ILE cc_start: 0.9411 (OUTLIER) cc_final: 0.9155 (mm) REVERT: G 1 MET cc_start: 0.7679 (ptt) cc_final: 0.7406 (pp-130) REVERT: G 60 GLN cc_start: 0.8254 (mm110) cc_final: 0.7997 (mm110) REVERT: G 67 LEU cc_start: 0.8880 (tm) cc_final: 0.8382 (tp) REVERT: G 104 MET cc_start: 0.4641 (ppp) cc_final: 0.1664 (ptp) REVERT: G 117 MET cc_start: -0.4668 (mmm) cc_final: -0.5870 (ttm) REVERT: I 50 ASN cc_start: 0.7832 (t160) cc_final: 0.7373 (p0) REVERT: L 44 MET cc_start: 0.8484 (mmm) cc_final: 0.7944 (mmm) REVERT: M 107 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.7305 (mpp) REVERT: M 115 MET cc_start: 0.8127 (ttp) cc_final: 0.7743 (tmm) REVERT: O 173 ASN cc_start: 0.9359 (t0) cc_final: 0.8996 (t0) REVERT: O 179 ASP cc_start: 0.9439 (t0) cc_final: 0.9174 (p0) REVERT: O 222 THR cc_start: 0.8608 (p) cc_final: 0.8215 (t) REVERT: O 258 MET cc_start: 0.8803 (mpp) cc_final: 0.7821 (mpp) REVERT: O 271 GLU cc_start: 0.9231 (pm20) cc_final: 0.8822 (pm20) REVERT: O 282 SER cc_start: 0.8945 (m) cc_final: 0.8661 (p) REVERT: Q 125 TYR cc_start: 0.7224 (m-10) cc_final: 0.6912 (m-10) REVERT: R 43 LEU cc_start: 0.8501 (mt) cc_final: 0.8007 (pt) REVERT: R 194 HIS cc_start: 0.8501 (t70) cc_final: 0.8167 (t70) REVERT: U 39 LEU cc_start: 0.6721 (mt) cc_final: 0.6257 (mm) REVERT: U 40 MET cc_start: 0.8640 (tpt) cc_final: 0.8128 (mmm) REVERT: U 341 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8507 (tmmt) REVERT: U 353 LEU cc_start: 0.8381 (mm) cc_final: 0.7732 (mm) REVERT: U 367 PHE cc_start: 0.8202 (p90) cc_final: 0.7674 (p90) REVERT: U 369 LYS cc_start: 0.8971 (pmtt) cc_final: 0.8768 (pmtt) REVERT: U 373 ASP cc_start: 0.8554 (t0) cc_final: 0.7824 (t0) REVERT: V 59 ARG cc_start: 0.8403 (mmm-85) cc_final: 0.7780 (mmm-85) REVERT: a 169 MET cc_start: 0.4196 (pmt) cc_final: 0.3946 (pmm) REVERT: a 190 MET cc_start: 0.1715 (pmt) cc_final: 0.1442 (pmm) REVERT: a 211 ASP cc_start: 0.8880 (p0) cc_final: 0.8620 (t0) REVERT: b 159 MET cc_start: 0.6538 (ppp) cc_final: 0.6107 (ppp) REVERT: b 174 MET cc_start: 0.3649 (tpt) cc_final: 0.3160 (tpt) REVERT: b 204 MET cc_start: 0.1678 (OUTLIER) cc_final: 0.1196 (tpp) REVERT: b 237 GLN cc_start: 0.2402 (OUTLIER) cc_final: 0.1876 (pm20) REVERT: b 359 MET cc_start: 0.6719 (pmm) cc_final: 0.6510 (pmm) REVERT: c 105 ASN cc_start: 0.7816 (m-40) cc_final: 0.7461 (m110) REVERT: c 141 TYR cc_start: 0.8032 (OUTLIER) cc_final: 0.7566 (t80) REVERT: c 142 MET cc_start: 0.8386 (tmt) cc_final: 0.7701 (mmt) REVERT: c 216 HIS cc_start: 0.9188 (m-70) cc_final: 0.8888 (m-70) REVERT: c 364 MET cc_start: -0.0634 (pp-130) cc_final: -0.1062 (pp-130) REVERT: c 379 MET cc_start: -0.1178 (ptt) cc_final: -0.1560 (pmt) outliers start: 101 outliers final: 44 residues processed: 545 average time/residue: 1.2896 time to fit residues: 898.6663 Evaluate side-chains 487 residues out of total 5173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 432 time to evaluate : 4.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1428 MET Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 890 ARG Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 107 MET Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain O residue 220 VAL Chi-restraints excluded: chain Q residue 14 TYR Chi-restraints excluded: chain Q residue 128 THR Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 219 GLU Chi-restraints excluded: chain U residue 334 VAL Chi-restraints excluded: chain U residue 337 CYS Chi-restraints excluded: chain U residue 341 LYS Chi-restraints excluded: chain U residue 365 TYR Chi-restraints excluded: chain V residue 16 GLN Chi-restraints excluded: chain V residue 50 GLN Chi-restraints excluded: chain a residue 136 HIS Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain b residue 204 MET Chi-restraints excluded: chain b residue 206 VAL Chi-restraints excluded: chain b residue 237 GLN Chi-restraints excluded: chain b residue 388 HIS Chi-restraints excluded: chain b residue 409 THR Chi-restraints excluded: chain c residue 141 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 512 optimal weight: 1.9990 chunk 539 optimal weight: 6.9990 chunk 491 optimal weight: 30.0000 chunk 524 optimal weight: 30.0000 chunk 315 optimal weight: 5.9990 chunk 228 optimal weight: 0.0770 chunk 411 optimal weight: 50.0000 chunk 160 optimal weight: 3.9990 chunk 473 optimal weight: 10.0000 chunk 496 optimal weight: 50.0000 chunk 522 optimal weight: 9.9990 overall best weight: 3.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 HIS A 765 ASN ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 HIS J 61 ASN O 327 ASN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 388 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.092 50731 Z= 0.559 Angle : 0.753 20.536 69015 Z= 0.382 Chirality : 0.048 0.423 7639 Planarity : 0.005 0.053 8512 Dihedral : 15.057 151.568 7734 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.82 % Allowed : 18.46 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.11), residues: 5767 helix: 1.28 (0.11), residues: 2282 sheet: 0.06 (0.17), residues: 882 loop : -0.49 (0.12), residues: 2603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A1192 HIS 0.014 0.001 HIS a 223 PHE 0.022 0.002 PHE A 592 TYR 0.028 0.002 TYR I 25 ARG 0.021 0.001 ARG B 416 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 5173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 431 time to evaluate : 4.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.8431 (mmt) cc_final: 0.8115 (mmt) REVERT: A 85 PHE cc_start: 0.7516 (m-80) cc_final: 0.7020 (m-80) REVERT: A 236 LEU cc_start: 0.9554 (mt) cc_final: 0.8604 (mt) REVERT: A 238 MET cc_start: 0.8475 (mtt) cc_final: 0.7928 (mpt) REVERT: A 317 MET cc_start: 0.6994 (ttp) cc_final: 0.6791 (tmm) REVERT: A 329 MET cc_start: 0.8669 (mmt) cc_final: 0.8372 (mmm) REVERT: A 347 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7701 (tp30) REVERT: A 749 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.7686 (ttm-80) REVERT: A 1194 ASN cc_start: 0.8911 (m110) cc_final: 0.8626 (p0) REVERT: A 1247 PHE cc_start: 0.9213 (OUTLIER) cc_final: 0.8696 (p90) REVERT: A 1361 ASP cc_start: 0.8919 (t0) cc_final: 0.8631 (OUTLIER) REVERT: A 1428 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.7299 (mmm) REVERT: A 1441 GLU cc_start: 0.8585 (pp20) cc_final: 0.8354 (pp20) REVERT: B 281 ASP cc_start: 0.8450 (m-30) cc_final: 0.7914 (m-30) REVERT: B 315 ASN cc_start: 0.9268 (m-40) cc_final: 0.8992 (m110) REVERT: B 341 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7634 (tm-30) REVERT: B 890 ARG cc_start: 0.6828 (OUTLIER) cc_final: 0.6410 (ttm170) REVERT: B 1071 ASN cc_start: 0.8633 (m-40) cc_final: 0.8173 (m110) REVERT: B 1172 MET cc_start: 0.7648 (mpm) cc_final: 0.7252 (mpm) REVERT: C 94 CYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7262 (p) REVERT: E 72 MET cc_start: 0.8066 (mtp) cc_final: 0.7312 (mtp) REVERT: E 108 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8349 (pp30) REVERT: E 113 SER cc_start: 0.9149 (t) cc_final: 0.8942 (p) REVERT: E 121 MET cc_start: 0.7562 (tpp) cc_final: 0.7308 (tpp) REVERT: E 151 MET cc_start: 0.8438 (ttm) cc_final: 0.8217 (mtp) REVERT: G 1 MET cc_start: 0.7885 (ptt) cc_final: 0.7559 (pp-130) REVERT: G 104 MET cc_start: 0.4648 (ppp) cc_final: 0.1748 (ptp) REVERT: G 117 MET cc_start: -0.4615 (mmm) cc_final: -0.5666 (ttt) REVERT: I 50 ASN cc_start: 0.8057 (t0) cc_final: 0.7531 (p0) REVERT: L 44 MET cc_start: 0.8619 (mmm) cc_final: 0.7989 (mmm) REVERT: M 115 MET cc_start: 0.8180 (ttp) cc_final: 0.7826 (tmm) REVERT: O 173 ASN cc_start: 0.9363 (t0) cc_final: 0.9019 (t0) REVERT: O 222 THR cc_start: 0.8642 (p) cc_final: 0.8225 (t) REVERT: O 258 MET cc_start: 0.8768 (mpp) cc_final: 0.8471 (mpp) REVERT: O 271 GLU cc_start: 0.9257 (pm20) cc_final: 0.8913 (pm20) REVERT: Q 125 TYR cc_start: 0.7765 (m-10) cc_final: 0.7487 (m-10) REVERT: R 43 LEU cc_start: 0.8675 (mt) cc_final: 0.8139 (pt) REVERT: R 164 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8503 (pp20) REVERT: R 165 TYR cc_start: 0.8646 (t80) cc_final: 0.8432 (t80) REVERT: R 194 HIS cc_start: 0.8505 (t70) cc_final: 0.8182 (t70) REVERT: U 24 ASP cc_start: 0.8015 (m-30) cc_final: 0.7206 (p0) REVERT: U 39 LEU cc_start: 0.6500 (mt) cc_final: 0.5991 (mm) REVERT: U 40 MET cc_start: 0.8533 (tpt) cc_final: 0.8047 (mmm) REVERT: U 353 LEU cc_start: 0.8464 (mm) cc_final: 0.7834 (mm) REVERT: U 367 PHE cc_start: 0.8252 (p90) cc_final: 0.7769 (p90) REVERT: U 373 ASP cc_start: 0.8716 (t0) cc_final: 0.8422 (t0) REVERT: V 59 ARG cc_start: 0.8477 (mmm-85) cc_final: 0.8113 (mmm160) REVERT: V 66 ARG cc_start: 0.8851 (ttm110) cc_final: 0.8404 (ttm110) REVERT: V 74 PHE cc_start: 0.9322 (m-10) cc_final: 0.9052 (m-10) REVERT: V 82 ARG cc_start: 0.8112 (tpt170) cc_final: 0.7909 (tpt170) REVERT: V 94 LYS cc_start: 0.9287 (tptp) cc_final: 0.8902 (tppt) REVERT: a 46 MET cc_start: 0.0051 (ttt) cc_final: -0.0877 (tmm) REVERT: a 190 MET cc_start: 0.2082 (pmt) cc_final: 0.1815 (pmm) REVERT: a 211 ASP cc_start: 0.8882 (p0) cc_final: 0.8607 (t0) REVERT: b 174 MET cc_start: 0.3789 (tpt) cc_final: 0.3289 (tpt) REVERT: b 204 MET cc_start: 0.2116 (tpt) cc_final: 0.1575 (tpp) REVERT: b 237 GLN cc_start: 0.2875 (OUTLIER) cc_final: 0.2372 (pm20) REVERT: b 359 MET cc_start: 0.6963 (pmm) cc_final: 0.6705 (pmm) REVERT: c 105 ASN cc_start: 0.7779 (m-40) cc_final: 0.7428 (m110) REVERT: c 141 TYR cc_start: 0.7830 (OUTLIER) cc_final: 0.7258 (t80) REVERT: c 142 MET cc_start: 0.8406 (tmt) cc_final: 0.7903 (mmm) REVERT: c 146 MET cc_start: 0.7966 (mmp) cc_final: 0.7129 (mmp) REVERT: c 216 HIS cc_start: 0.9241 (m-70) cc_final: 0.8938 (m-70) REVERT: c 364 MET cc_start: -0.0570 (pp-130) cc_final: -0.0972 (pp-130) REVERT: c 379 MET cc_start: -0.1143 (ptt) cc_final: -0.1522 (pmt) outliers start: 94 outliers final: 48 residues processed: 499 average time/residue: 1.2773 time to fit residues: 812.5972 Evaluate side-chains 459 residues out of total 5173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 402 time to evaluate : 4.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 749 ARG Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1247 PHE Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1428 MET Chi-restraints excluded: chain A residue 1482 TYR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 890 ARG Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain O residue 220 VAL Chi-restraints excluded: chain Q residue 128 THR Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain U residue 334 VAL Chi-restraints excluded: chain U residue 337 CYS Chi-restraints excluded: chain U residue 365 TYR Chi-restraints excluded: chain U residue 366 ILE Chi-restraints excluded: chain V residue 16 GLN Chi-restraints excluded: chain V residue 50 GLN Chi-restraints excluded: chain a residue 136 HIS Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain b residue 206 VAL Chi-restraints excluded: chain b residue 237 GLN Chi-restraints excluded: chain b residue 409 THR Chi-restraints excluded: chain c residue 141 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 344 optimal weight: 2.9990 chunk 554 optimal weight: 10.0000 chunk 338 optimal weight: 0.8980 chunk 263 optimal weight: 1.9990 chunk 385 optimal weight: 9.9990 chunk 581 optimal weight: 50.0000 chunk 535 optimal weight: 10.0000 chunk 463 optimal weight: 8.9990 chunk 48 optimal weight: 0.6980 chunk 357 optimal weight: 6.9990 chunk 284 optimal weight: 20.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 GLN ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN G 60 GLN ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 ASN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 144 GLN ** R 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 48 ASN ** U 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 361 ASN ** b 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 388 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.5036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 50731 Z= 0.422 Angle : 0.729 21.854 69015 Z= 0.371 Chirality : 0.046 0.482 7639 Planarity : 0.004 0.071 8512 Dihedral : 15.056 152.257 7734 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.43 % Allowed : 19.16 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.11), residues: 5767 helix: 1.24 (0.11), residues: 2275 sheet: 0.03 (0.17), residues: 882 loop : -0.54 (0.12), residues: 2610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A1192 HIS 0.014 0.001 HIS b 281 PHE 0.029 0.002 PHE U 351 TYR 0.041 0.002 TYR b 340 ARG 0.017 0.001 ARG B 416 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11534 Ramachandran restraints generated. 5767 Oldfield, 0 Emsley, 5767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 5173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 427 time to evaluate : 4.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.8421 (mmt) cc_final: 0.8152 (mmt) REVERT: A 85 PHE cc_start: 0.7519 (m-80) cc_final: 0.7025 (m-80) REVERT: A 236 LEU cc_start: 0.9553 (mt) cc_final: 0.8631 (mt) REVERT: A 238 MET cc_start: 0.8456 (mtt) cc_final: 0.7975 (mpt) REVERT: A 329 MET cc_start: 0.8660 (mmt) cc_final: 0.8363 (mmm) REVERT: A 347 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7675 (tp30) REVERT: A 865 ILE cc_start: 0.9122 (mm) cc_final: 0.8864 (mt) REVERT: A 1194 ASN cc_start: 0.8875 (m110) cc_final: 0.8603 (p0) REVERT: A 1244 ASN cc_start: 0.8325 (t0) cc_final: 0.7933 (t0) REVERT: A 1247 PHE cc_start: 0.9148 (OUTLIER) cc_final: 0.8617 (p90) REVERT: A 1279 MET cc_start: 0.7280 (ppp) cc_final: 0.6647 (pp-130) REVERT: A 1361 ASP cc_start: 0.8905 (t0) cc_final: 0.8637 (OUTLIER) REVERT: A 1428 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.7318 (mmm) REVERT: B 281 ASP cc_start: 0.8513 (m-30) cc_final: 0.8017 (m-30) REVERT: B 341 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7629 (tm-30) REVERT: B 890 ARG cc_start: 0.6834 (OUTLIER) cc_final: 0.6427 (ttm170) REVERT: B 1071 ASN cc_start: 0.8615 (m-40) cc_final: 0.8137 (m110) REVERT: B 1172 MET cc_start: 0.7710 (mpm) cc_final: 0.7265 (mpm) REVERT: C 94 CYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7414 (p) REVERT: E 110 MET cc_start: 0.7095 (tmm) cc_final: 0.6854 (tmm) REVERT: E 151 MET cc_start: 0.8377 (ttm) cc_final: 0.8173 (mtp) REVERT: G 1 MET cc_start: 0.8016 (ptt) cc_final: 0.7637 (pp-130) REVERT: G 104 MET cc_start: 0.4609 (ppp) cc_final: 0.1690 (ptp) REVERT: G 117 MET cc_start: -0.4546 (mmm) cc_final: -0.5797 (ttm) REVERT: I 50 ASN cc_start: 0.8167 (t0) cc_final: 0.7752 (t0) REVERT: L 44 MET cc_start: 0.8546 (mmm) cc_final: 0.7958 (mmm) REVERT: M 32 MET cc_start: 0.7519 (mmt) cc_final: 0.7292 (mmm) REVERT: M 102 GLN cc_start: 0.6158 (pm20) cc_final: 0.4667 (tm-30) REVERT: M 115 MET cc_start: 0.8198 (ttp) cc_final: 0.7912 (tmm) REVERT: O 173 ASN cc_start: 0.9370 (t0) cc_final: 0.9029 (t0) REVERT: O 179 ASP cc_start: 0.9248 (t0) cc_final: 0.8885 (p0) REVERT: O 222 THR cc_start: 0.8581 (p) cc_final: 0.8147 (t) REVERT: O 258 MET cc_start: 0.8804 (mpp) cc_final: 0.8429 (mpp) REVERT: O 271 GLU cc_start: 0.9256 (pm20) cc_final: 0.8942 (pm20) REVERT: Q 125 TYR cc_start: 0.7766 (m-10) cc_final: 0.7509 (m-10) REVERT: Q 158 GLU cc_start: 0.8186 (pm20) cc_final: 0.7229 (pm20) REVERT: Q 162 GLU cc_start: 0.8468 (pp20) cc_final: 0.7739 (pm20) REVERT: R 43 LEU cc_start: 0.8697 (mt) cc_final: 0.8261 (tm) REVERT: R 164 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8467 (pp20) REVERT: R 194 HIS cc_start: 0.8457 (t70) cc_final: 0.8148 (t70) REVERT: U 15 ARG cc_start: 0.9063 (tmm160) cc_final: 0.8415 (ppt170) REVERT: U 24 ASP cc_start: 0.8130 (m-30) cc_final: 0.7257 (p0) REVERT: U 39 LEU cc_start: 0.6670 (mt) cc_final: 0.6227 (mm) REVERT: U 40 MET cc_start: 0.8633 (tpt) cc_final: 0.8110 (mmm) REVERT: U 351 PHE cc_start: 0.8977 (m-80) cc_final: 0.8576 (m-80) REVERT: U 353 LEU cc_start: 0.8448 (mm) cc_final: 0.7813 (mm) REVERT: U 367 PHE cc_start: 0.8233 (p90) cc_final: 0.7805 (p90) REVERT: V 41 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.8168 (m-30) REVERT: V 59 ARG cc_start: 0.8479 (mmm-85) cc_final: 0.7937 (mmm160) REVERT: V 66 ARG cc_start: 0.8822 (ttm110) cc_final: 0.8386 (ttm110) REVERT: V 94 LYS cc_start: 0.9290 (tptp) cc_final: 0.8897 (tppt) REVERT: a 46 MET cc_start: 0.0050 (ttt) cc_final: -0.1147 (tmm) REVERT: a 65 TYR cc_start: 0.8231 (t80) cc_final: 0.7611 (t80) REVERT: a 190 MET cc_start: 0.1933 (pmt) cc_final: 0.1677 (pmm) REVERT: a 211 ASP cc_start: 0.8871 (p0) cc_final: 0.8568 (t0) REVERT: b 159 MET cc_start: 0.6444 (ppp) cc_final: 0.5765 (ppp) REVERT: b 174 MET cc_start: 0.3811 (tpt) cc_final: 0.3334 (tpt) REVERT: b 204 MET cc_start: 0.1868 (tpt) cc_final: 0.1624 (tpt) REVERT: b 237 GLN cc_start: 0.2948 (OUTLIER) cc_final: 0.2475 (pm20) REVERT: b 293 MET cc_start: -0.0684 (pp-130) cc_final: -0.0900 (ppp) REVERT: b 359 MET cc_start: 0.7044 (pmm) cc_final: 0.6683 (pmm) REVERT: c 105 ASN cc_start: 0.7791 (m-40) cc_final: 0.7443 (m110) REVERT: c 141 TYR cc_start: 0.7827 (OUTLIER) cc_final: 0.7209 (t80) REVERT: c 142 MET cc_start: 0.8136 (tmt) cc_final: 0.7906 (mmm) REVERT: c 146 MET cc_start: 0.7908 (mmp) cc_final: 0.7006 (mmp) REVERT: c 216 HIS cc_start: 0.9231 (m-70) cc_final: 0.8911 (m-70) REVERT: c 364 MET cc_start: -0.0843 (pp-130) cc_final: -0.1225 (pp-130) REVERT: c 379 MET cc_start: -0.1126 (ptt) cc_final: -0.1479 (pmt) outliers start: 74 outliers final: 48 residues processed: 476 average time/residue: 1.3201 time to fit residues: 798.0917 Evaluate side-chains 464 residues out of total 5173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 408 time to evaluate : 4.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1247 PHE Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1428 MET Chi-restraints excluded: chain A residue 1458 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 890 ARG Chi-restraints excluded: chain C residue 94 CYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 69 ILE Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain L residue 31 ARG Chi-restraints excluded: chain O residue 220 VAL Chi-restraints excluded: chain Q residue 14 TYR Chi-restraints excluded: chain Q residue 128 THR Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain U residue 334 VAL Chi-restraints excluded: chain U residue 337 CYS Chi-restraints excluded: chain U residue 365 TYR Chi-restraints excluded: chain U residue 366 ILE Chi-restraints excluded: chain V residue 16 GLN Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain V residue 50 GLN Chi-restraints excluded: chain a residue 136 HIS Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain b residue 206 VAL Chi-restraints excluded: chain b residue 237 GLN Chi-restraints excluded: chain b residue 409 THR Chi-restraints excluded: chain c residue 141 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 368 optimal weight: 0.8980 chunk 493 optimal weight: 40.0000 chunk 141 optimal weight: 0.9990 chunk 427 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 464 optimal weight: 9.9990 chunk 194 optimal weight: 1.9990 chunk 476 optimal weight: 50.0000 chunk 58 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 361 ASN ** a 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 388 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.146027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.084175 restraints weight = 112602.002| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.46 r_work: 0.2817 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.5137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 50731 Z= 0.270 Angle : 0.702 21.470 69015 Z= 0.357 Chirality : 0.044 0.459 7639 Planarity : 0.004 0.059 8512 Dihedral : 15.001 152.731 7734 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.31 % Allowed : 19.60 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.11), residues: 5767 helix: 1.29 (0.11), residues: 2275 sheet: 0.08 (0.17), residues: 857 loop : -0.52 (0.12), residues: 2635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A1192 HIS 0.013 0.001 HIS b 281 PHE 0.048 0.002 PHE V 74 TYR 0.046 0.002 TYR M 146 ARG 0.018 0.000 ARG L 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14767.31 seconds wall clock time: 257 minutes 12.27 seconds (15432.27 seconds total)