Starting phenix.real_space_refine on Sun Aug 9 06:41:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sb2_54710/08_2026/9sb2_54710.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sb2_54710/08_2026/9sb2_54710.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sb2_54710/08_2026/9sb2_54710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sb2_54710/08_2026/9sb2_54710.map" model { file = "/net/cci-nas-00/data/ceres_data/9sb2_54710/08_2026/9sb2_54710.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sb2_54710/08_2026/9sb2_54710.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.043 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 8 6.06 5 P 56 5.49 5 Mg 1 5.21 5 S 182 5.16 5 C 20257 2.51 5 N 5644 2.21 5 O 6254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32402 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 11025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1400, 11025 Classifications: {'peptide': 1400} Link IDs: {'PCIS': 1, 'PTRANS': 63, 'TRANS': 1335} Chain breaks: 7 Chain: "B" Number of atoms: 9268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1164, 9268 Classifications: {'peptide': 1164} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 1113} Chain breaks: 4 Chain: "C" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2095 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain: "D" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1327 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 164} Chain breaks: 2 Chain: "E" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1744 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1340 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1077 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Chain: "I" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 926 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 904 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "N" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 334 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "R" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 246 Classifications: {'RNA': 11} Modifications used: {'rna3p_pur': 10, 'rna3p_pyr': 1} Link IDs: {'rna3p': 10} Chain: "T" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 537 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} 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: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {' ZN': 1, 'PPV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 457 SG CYS A 67 58.167 70.418 85.366 1.00 65.87 S ATOM 479 SG CYS A 70 57.634 73.593 83.263 1.00 61.23 S ATOM 532 SG CYS A 77 61.129 71.977 83.533 1.00 51.93 S ATOM 762 SG CYS A 107 75.507 80.438 128.556 1.00102.59 S ATOM 786 SG CYS A 110 73.362 83.402 127.880 1.00 94.48 S ATOM 1091 SG CYS A 148 76.066 83.546 130.650 1.00 98.35 S ATOM 1190 SG CYS A 167 72.787 81.538 131.048 1.00106.29 S ATOM 19799 SG CYS B1163 59.497 86.186 93.209 1.00 55.05 S ATOM 19817 SG CYS B1166 62.070 83.900 94.613 1.00 55.21 S ATOM 19942 SG CYS B1182 58.676 82.526 93.367 1.00 63.67 S ATOM 19961 SG CYS B1185 58.949 84.487 96.645 1.00 75.78 S ATOM 20949 SG CYS C 86 85.058 60.911 21.177 1.00112.13 S ATOM 20966 SG CYS C 88 83.743 58.275 23.524 1.00139.43 S ATOM 20999 SG CYS C 92 85.627 57.194 20.488 1.00 98.81 S ATOM 21022 SG CYS C 95 87.508 58.915 23.344 1.00 88.00 S ATOM 28607 SG CYS I 7 135.209 48.756 136.264 1.00160.06 S ATOM 28632 SG CYS I 10 131.657 47.876 135.562 1.00151.22 S ATOM 28798 SG CYS I 29 132.475 51.383 136.886 1.00168.92 S ATOM 28822 SG CYS I 32 132.780 48.447 139.195 1.00171.73 S ATOM 29149 SG CYS I 75 159.913 58.904 97.993 1.00136.84 S ATOM 29171 SG CYS I 78 161.790 55.690 97.892 1.00152.72 S ATOM 29387 SG CYS I 103 158.090 55.751 96.762 1.00151.91 S ATOM 29407 SG CYS I 106 158.923 56.020 100.374 1.00134.99 S ATOM 29526 SG CYS J 7 115.441 59.450 39.170 1.00 37.83 S ATOM 29549 SG CYS J 10 115.716 61.283 35.865 1.00 34.51 S ATOM 29829 SG CYS J 45 118.459 61.681 38.447 1.00 55.52 S ATOM 29835 SG CYS J 46 118.060 58.449 36.487 1.00 42.08 S ATOM 30958 SG CYS L 31 89.938 27.629 55.767 1.00105.03 S ATOM 30978 SG CYS L 34 90.684 24.800 53.342 1.00132.04 S ATOM 31082 SG CYS L 48 87.335 24.954 55.250 1.00112.34 S ATOM 31105 SG CYS L 51 90.619 24.074 57.014 1.00114.73 S Time building chain proxies: 6.72, per 1000 atoms: 0.21 Number of scatterers: 32402 At special positions: 0 Unit cell: (173.25, 155.925, 160.256, 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 8 29.99 S 182 16.00 P 56 15.00 Mg 1 11.99 O 6254 8.00 N 5644 7.00 C 20257 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: 2.47 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 148 " pdb=" ZN B1302 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1182 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " Number of angles added : 45 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7394 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 44 sheets defined 38.0% alpha, 19.1% beta 28 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 4.31 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 95 through 104 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 203 through 213 Processing helix chain 'A' and resid 215 through 221 Processing helix chain 'A' and resid 230 through 233 Processing helix chain 'A' and resid 260 through 283 removed outlier: 3.666A pdb=" N GLY A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 305 Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.526A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 525 through 536 removed outlier: 3.948A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 574 through 582 removed outlier: 3.867A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 661 Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 672 through 699 Processing helix chain 'A' and resid 709 through 737 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 removed outlier: 3.518A pdb=" N ILE A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 797 Processing helix chain 'A' and resid 809 through 845 removed outlier: 3.970A pdb=" N GLU A 822 " --> pdb=" O MET A 818 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU A 824 " --> pdb=" O GLY A 820 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR A 831 " --> pdb=" O THR A 827 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLU A 833 " --> pdb=" O VAL A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 909 through 913 Processing helix chain 'A' and resid 915 through 920 Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 959 through 969 Processing helix chain 'A' and resid 982 through 994 removed outlier: 3.514A pdb=" N GLN A 994 " --> pdb=" O VAL A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 997 No H-bonds generated for 'chain 'A' and resid 995 through 997' Processing helix chain 'A' and resid 1004 through 1015 removed outlier: 3.565A pdb=" N VAL A1015 " --> pdb=" O GLN A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1038 through 1056 Processing helix chain 'A' and resid 1063 through 1081 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1097 through 1107 Processing helix chain 'A' and resid 1130 through 1139 Processing helix chain 'A' and resid 1166 through 1175 removed outlier: 3.544A pdb=" N SER A1175 " --> pdb=" O GLN A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1185 Processing helix chain 'A' and resid 1198 through 1206 Processing helix chain 'A' and resid 1208 through 1221 Processing helix chain 'A' and resid 1257 through 1270 Processing helix chain 'A' and resid 1312 through 1317 removed outlier: 3.608A pdb=" N MET A1317 " --> pdb=" O LEU A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1339 Processing helix chain 'A' and resid 1340 through 1357 Processing helix chain 'A' and resid 1364 through 1376 removed outlier: 3.930A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1401 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1431 removed outlier: 3.605A pdb=" N ASN A1427 " --> pdb=" O GLY A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1439 Processing helix chain 'A' and resid 1446 through 1452 removed outlier: 3.768A pdb=" N LYS A1452 " --> pdb=" O GLU A1448 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 37 removed outlier: 4.205A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 57 Processing helix chain 'B' and resid 57 through 66 removed outlier: 4.338A pdb=" N ASP B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 293 through 302 Processing helix chain 'B' and resid 308 through 321 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 344 through 359 removed outlier: 3.507A pdb=" N ARG B 348 " --> pdb=" O LYS B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 390 Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 438 removed outlier: 3.874A pdb=" N GLU B 438 " --> pdb=" O ARG B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 448 removed outlier: 3.530A pdb=" N ILE B 448 " --> pdb=" O MET B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.570A pdb=" N THR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 495 Processing helix chain 'B' and resid 509 through 513 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 592 through 607 Processing helix chain 'B' and resid 654 through 667 removed outlier: 3.516A pdb=" N ILE B 658 " --> pdb=" O ARG B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.756A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.692A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'B' and resid 763 through 775 removed outlier: 4.157A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 788 removed outlier: 3.641A pdb=" N ARG B 788 " --> pdb=" O TYR B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.479A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.865A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1061 Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1153 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.593A pdb=" N GLN C 79 " --> pdb=" O ASP C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 204 through 210 removed outlier: 4.058A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU C 210 " --> pdb=" O CYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 266 removed outlier: 3.657A pdb=" N ASP C 266 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 73 Processing helix chain 'D' and resid 118 through 127 removed outlier: 3.522A pdb=" N ASP D 127 " --> pdb=" O LEU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 132 removed outlier: 4.336A pdb=" N GLN D 132 " --> pdb=" O LEU D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 150 Processing helix chain 'D' and resid 156 through 171 removed outlier: 4.221A pdb=" N VAL D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER D 169 " --> pdb=" O GLN D 165 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N THR D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 196 through 199 Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'E' and resid 4 through 27 removed outlier: 3.575A pdb=" N GLY E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 44 Processing helix chain 'E' and resid 54 through 59 removed outlier: 3.919A pdb=" N SER E 59 " --> pdb=" O LYS E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 92 through 103 Processing helix chain 'E' and resid 117 through 124 Processing helix chain 'E' and resid 138 through 141 Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'G' and resid 50 through 54 removed outlier: 3.521A pdb=" N ILE G 54 " --> pdb=" O TYR G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 52 Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 52 removed outlier: 3.944A pdb=" N ASN K 44 " --> pdb=" O HIS K 40 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 91 removed outlier: 11.246A pdb=" N LYS A 88 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N CYS A 238 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 177 Processing sheet with id=AA4, first strand: chain 'A' and resid 343 through 345 removed outlier: 3.562A pdb=" N LEU B1128 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.664A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.763A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 512 through 513 Processing sheet with id=AA8, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AA9, first strand: chain 'A' and resid 588 through 590 removed outlier: 7.014A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AB2, first strand: chain 'A' and resid 849 through 850 removed outlier: 6.846A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 879 through 882 Processing sheet with id=AB4, first strand: chain 'A' and resid 1282 through 1292 removed outlier: 3.667A pdb=" N THR A1308 " --> pdb=" O LEU A1116 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A1116 " --> pdb=" O THR A1308 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.352A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL A1242 " --> pdb=" O TRP A1191 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TRP A1191 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU A1192 " --> pdb=" O ILE A1152 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE A1152 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ARG A1194 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER A1150 " --> pdb=" O ARG A1194 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLU A1196 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR I 44 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 48 through 49 removed outlier: 4.743A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ARG G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N VAL G 48 " --> pdb=" O ARG G 75 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL G 77 " --> pdb=" O LEU G 46 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 143 through 147 removed outlier: 5.500A pdb=" N VAL A1443 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY G 59 " --> pdb=" O ILE A1445 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 69 through 73 removed outlier: 5.820A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS B 134 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR B 136 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ALA B 153 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLU B 138 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N LEU B 151 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 69 through 73 removed outlier: 5.820A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AC2, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC3, first strand: chain 'B' and resid 404 through 407 removed outlier: 6.137A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 224 through 227 removed outlier: 3.716A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC6, first strand: chain 'B' and resid 650 through 651 removed outlier: 3.941A pdb=" N GLU B 650 " --> pdb=" O GLU B 641 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N CYS B 741 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 564 through 565 removed outlier: 7.156A pdb=" N VAL B 580 " --> pdb=" O HIS B 587 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL B 589 " --> pdb=" O THR B 578 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N THR B 578 " --> pdb=" O VAL B 589 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 792 through 793 removed outlier: 7.014A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 792 through 793 removed outlier: 7.014A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD2, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 7.014A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 873 through 874 removed outlier: 3.798A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD5, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD6, first strand: chain 'C' and resid 7 through 13 removed outlier: 5.441A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.885A pdb=" N GLU C 152 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASN C 54 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LYS C 154 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 111 through 114 removed outlier: 3.504A pdb=" N CYS C 145 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AE1, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.331A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.811A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 86 through 95 removed outlier: 5.786A pdb=" N VAL G 91 " --> pdb=" O GLN G 102 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N GLN G 102 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER G 93 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LYS G 107 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ALA G 159 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N HIS G 158 " --> pdb=" O CYS G 150 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N CYS G 150 " --> pdb=" O HIS G 158 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ILE G 160 " --> pdb=" O GLU G 148 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE G 143 " --> pdb=" O GLY G 89 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY G 89 " --> pdb=" O ILE G 143 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL G 145 " --> pdb=" O VAL G 87 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL G 87 " --> pdb=" O VAL G 145 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.595A pdb=" N THR G 120 " --> pdb=" O GLN G 131 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.753A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY H 99 " --> pdb=" O ALA H 140 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG H 145 " --> pdb=" O THR H 56 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 15 through 19 Processing sheet with id=AE7, first strand: chain 'I' and resid 70 through 71 removed outlier: 4.148A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 19 through 24 removed outlier: 4.549A pdb=" N ALA K 30 " --> pdb=" O ASP K 24 " (cutoff:3.500A) 1317 hydrogen bonds defined for protein. 3636 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 74 hydrogen bonds 148 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 9.44 Time building geometry restraints manager: 3.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.44: 13965 1.44 - 1.67: 18821 1.67 - 1.90: 295 1.90 - 2.13: 1 2.13 - 2.36: 4 Bond restraints: 33086 Sorted by residual: bond pdb=" CA THR D 133 " pdb=" CB THR D 133 " ideal model delta sigma weight residual 1.529 2.088 -0.559 1.58e-02 4.01e+03 1.25e+03 bond pdb=" CD2 PHE D 70 " pdb=" CE2 PHE D 70 " ideal model delta sigma weight residual 1.382 2.359 -0.977 3.00e-02 1.11e+03 1.06e+03 bond pdb=" CE1 PHE D 70 " pdb=" CZ PHE D 70 " ideal model delta sigma weight residual 1.382 2.341 -0.959 3.00e-02 1.11e+03 1.02e+03 bond pdb=" CD1 PHE D 70 " pdb=" CE1 PHE D 70 " ideal model delta sigma weight residual 1.382 2.328 -0.946 3.00e-02 1.11e+03 9.94e+02 bond pdb=" CE2 PHE D 70 " pdb=" CZ PHE D 70 " ideal model delta sigma weight residual 1.382 2.327 -0.945 3.00e-02 1.11e+03 9.92e+02 ... (remaining 33081 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.94: 44876 4.94 - 9.87: 21 9.87 - 14.81: 2 14.81 - 19.75: 2 19.75 - 24.69: 1 Bond angle restraints: 44902 Sorted by residual: angle pdb=" CA THR D 133 " pdb=" CB THR D 133 " pdb=" CG2 THR D 133 " ideal model delta sigma weight residual 110.50 135.19 -24.69 1.70e+00 3.46e-01 2.11e+02 angle pdb=" CA THR D 133 " pdb=" CB THR D 133 " pdb=" OG1 THR D 133 " ideal model delta sigma weight residual 109.60 128.15 -18.55 1.50e+00 4.44e-01 1.53e+02 angle pdb=" OG1 THR D 133 " pdb=" CB THR D 133 " pdb=" CG2 THR D 133 " ideal model delta sigma weight residual 109.30 92.25 17.05 2.00e+00 2.50e-01 7.27e+01 angle pdb=" N THR D 133 " pdb=" CA THR D 133 " pdb=" C THR D 133 " ideal model delta sigma weight residual 111.14 102.03 9.11 1.08e+00 8.57e-01 7.11e+01 angle pdb=" C THR D 133 " pdb=" CA THR D 133 " pdb=" CB THR D 133 " ideal model delta sigma weight residual 110.90 124.08 -13.18 1.58e+00 4.01e-01 6.96e+01 ... (remaining 44897 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.78: 19547 25.78 - 51.57: 487 51.57 - 77.35: 99 77.35 - 103.14: 5 103.14 - 128.92: 1 Dihedral angle restraints: 20139 sinusoidal: 8723 harmonic: 11416 Sorted by residual: dihedral pdb=" C THR D 133 " pdb=" N THR D 133 " pdb=" CA THR D 133 " pdb=" CB THR D 133 " ideal model delta harmonic sigma weight residual -122.00 -141.48 19.48 0 2.50e+00 1.60e-01 6.07e+01 dihedral pdb=" N THR D 133 " pdb=" C THR D 133 " pdb=" CA THR D 133 " pdb=" CB THR D 133 " ideal model delta harmonic sigma weight residual 123.40 139.28 -15.88 0 2.50e+00 1.60e-01 4.03e+01 dihedral pdb=" C4' G R 9 " pdb=" C3' G R 9 " pdb=" O3' G R 9 " pdb=" P A R 10 " ideal model delta sinusoidal sigma weight residual 220.00 91.08 128.92 1 3.50e+01 8.16e-04 1.28e+01 ... (remaining 20136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.193: 5052 0.193 - 0.387: 0 0.387 - 0.580: 0 0.580 - 0.773: 0 0.773 - 0.966: 1 Chirality restraints: 5053 Sorted by residual: chirality pdb=" CB THR D 133 " pdb=" CA THR D 133 " pdb=" OG1 THR D 133 " pdb=" CG2 THR D 133 " both_signs ideal model delta sigma weight residual False 2.55 1.59 0.97 2.00e-01 2.50e+01 2.34e+01 chirality pdb=" CB VAL A1094 " pdb=" CA VAL A1094 " pdb=" CG1 VAL A1094 " pdb=" CG2 VAL A1094 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.31e-01 chirality pdb=" C3' G R 9 " pdb=" C4' G R 9 " pdb=" O3' G R 9 " pdb=" C2' G R 9 " both_signs ideal model delta sigma weight residual False -2.48 -2.30 -0.18 2.00e-01 2.50e+01 8.16e-01 ... (remaining 5050 not shown) Planarity restraints: 5627 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 70 " 0.001 2.00e-02 2.50e+03 5.31e-02 4.93e+01 pdb=" CG PHE D 70 " 0.005 2.00e-02 2.50e+03 pdb=" CD1 PHE D 70 " -0.061 2.00e-02 2.50e+03 pdb=" CD2 PHE D 70 " 0.075 2.00e-02 2.50e+03 pdb=" CE1 PHE D 70 " 0.026 2.00e-02 2.50e+03 pdb=" CE2 PHE D 70 " -0.089 2.00e-02 2.50e+03 pdb=" CZ PHE D 70 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 133 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.59e+00 pdb=" C THR D 133 " 0.041 2.00e-02 2.50e+03 pdb=" O THR D 133 " -0.015 2.00e-02 2.50e+03 pdb=" N THR D 134 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 244 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.19e+00 pdb=" N PRO A 245 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 245 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 245 " -0.029 5.00e-02 4.00e+02 ... (remaining 5624 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 288 2.60 - 3.18: 26905 3.18 - 3.75: 49628 3.75 - 4.33: 70556 4.33 - 4.90: 117419 Nonbonded interactions: 264796 Sorted by model distance: nonbonded pdb=" OD1 ASP A 481 " pdb="MG MG A1801 " model vdw 2.028 2.170 nonbonded pdb=" CE2 PHE D 70 " pdb=" OG1 THR D 133 " model vdw 2.044 3.340 nonbonded pdb=" O3' A R 18 " pdb="MG MG A1801 " model vdw 2.059 2.170 nonbonded pdb=" O LYS B 801 " pdb=" OG1 THR J 52 " model vdw 2.115 3.040 nonbonded pdb=" OD1 ASP A 483 " pdb="MG MG A1801 " model vdw 2.148 2.170 ... (remaining 264791 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.870 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.780 Check model and map are aligned: 0.170 Set scattering table: 0.160 Process input model: 39.100 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 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 : 0.012 0.977 33118 Z= 0.464 Angle : 0.516 24.687 44947 Z= 0.313 Chirality : 0.043 0.966 5053 Planarity : 0.003 0.053 5627 Dihedral : 11.551 128.924 12745 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.83 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.14), residues: 3882 helix: 1.84 (0.15), residues: 1332 sheet: 0.50 (0.22), residues: 587 loop : -0.19 (0.14), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 348 TYR 0.023 0.001 TYR K 61 PHE 0.089 0.001 PHE D 70 TRP 0.018 0.001 TRP A1044 HIS 0.006 0.001 HIS L 53 Details of bonding type rmsd/Z covalent geometry : bond 0.01187 / 0.46 (33086) covalent geometry : angle 0.51249 / 0.31 (44902) hydrogen bonds : bond 0.18009 / 12.20 ( 1369) hydrogen bonds : angle 6.25661 / 4.57 ( 3784) metal coordination : bond 0.00234 / 0.16 ( 32) metal coordination : angle 2.09283 / 1.45 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 3462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 811 time to evaluate : 1.322 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: A 592 ASP cc_start: 0.7548 (m-30) cc_final: 0.6854 (m-30) REVERT: A 596 THR cc_start: 0.8526 (p) cc_final: 0.8133 (t) REVERT: A 731 ARG cc_start: 0.7605 (mmt180) cc_final: 0.7127 (mtm110) REVERT: A 1124 HIS cc_start: 0.6308 (p90) cc_final: 0.6089 (p90) REVERT: A 1133 LEU cc_start: 0.8277 (mt) cc_final: 0.8040 (tp) REVERT: A 1143 LEU cc_start: 0.8509 (tp) cc_final: 0.8032 (tt) REVERT: A 1225 PHE cc_start: 0.7804 (t80) cc_final: 0.7594 (t80) REVERT: A 1284 MET cc_start: 0.8058 (ttm) cc_final: 0.7718 (ttm) REVERT: A 1432 GLN cc_start: 0.8573 (mt0) cc_final: 0.8346 (mt0) REVERT: A 1453 TYR cc_start: 0.7439 (m-80) cc_final: 0.7234 (m-80) REVERT: B 270 LYS cc_start: 0.7848 (mtmm) cc_final: 0.7461 (mtmm) REVERT: B 302 CYS cc_start: 0.8585 (t) cc_final: 0.8329 (t) REVERT: B 570 VAL cc_start: 0.8055 (t) cc_final: 0.7806 (m) REVERT: B 618 ASP cc_start: 0.8205 (t0) cc_final: 0.7720 (t70) REVERT: B 935 ARG cc_start: 0.6904 (tmt-80) cc_final: 0.6515 (ttt180) REVERT: C 53 THR cc_start: 0.8245 (t) cc_final: 0.8021 (t) REVERT: D 39 ASN cc_start: 0.5247 (p0) cc_final: 0.4420 (p0) REVERT: D 61 GLU cc_start: 0.8076 (pt0) cc_final: 0.7194 (tm-30) REVERT: F 127 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7954 (mt-10) REVERT: F 154 ASP cc_start: 0.7934 (t0) cc_final: 0.7490 (p0) REVERT: G 141 SER cc_start: 0.6025 (t) cc_final: 0.5793 (p) REVERT: G 144 ARG cc_start: 0.5655 (ttm170) cc_final: 0.5253 (mpt180) REVERT: H 16 ASP cc_start: 0.8180 (t0) cc_final: 0.7955 (p0) REVERT: H 22 LYS cc_start: 0.9001 (mttp) cc_final: 0.8610 (mttm) REVERT: I 13 MET cc_start: 0.4945 (ptt) cc_final: 0.4672 (ptp) REVERT: I 61 ASP cc_start: 0.6490 (t0) cc_final: 0.6128 (t0) REVERT: I 91 ARG cc_start: 0.6892 (mmp-170) cc_final: 0.6629 (ttm110) outliers start: 0 outliers final: 0 residues processed: 811 average time/residue: 0.2411 time to fit residues: 301.1686 Evaluate side-chains 437 residues out of total 3462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 437 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.2980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.0030 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 overall best weight: 2.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 ASN ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 169 ASN A 316 GLN A 358 ASN A 640 GLN ** A 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 GLN ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1265 ASN A1432 GLN B 366 GLN B 433 GLN B 740 HIS D 9 GLN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 ASN F 100 GLN H 52 GLN I 108 HIS L 66 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.140336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.102808 restraints weight = 48519.598| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.19 r_work: 0.3172 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 1.039 33118 Z= 0.482 Angle : 0.640 24.631 44947 Z= 0.332 Chirality : 0.047 0.819 5053 Planarity : 0.005 0.062 5627 Dihedral : 11.676 130.886 4891 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.40 % Favored : 96.50 % Rotamer: Outliers : 1.62 % Allowed : 7.08 % Favored : 91.31 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.14), residues: 3882 helix: 1.56 (0.14), residues: 1361 sheet: 0.27 (0.21), residues: 583 loop : -0.33 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1239 TYR 0.017 0.001 TYR G 44 PHE 0.076 0.002 PHE D 70 TRP 0.013 0.001 TRP A1044 HIS 0.010 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.01265 / 0.48 (33086) covalent geometry : angle 0.60668 / 0.33 (44902) hydrogen bonds : bond 0.04826 / 3.28 ( 1369) hydrogen bonds : angle 4.94011 / 3.55 ( 3784) metal coordination : bond 0.01197 / 0.90 ( 32) metal coordination : angle 6.51676 / 4.08 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 3462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 441 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8216 (mm-30) REVERT: A 596 THR cc_start: 0.8778 (p) cc_final: 0.8412 (t) REVERT: A 731 ARG cc_start: 0.7544 (mmt180) cc_final: 0.6980 (mtm110) REVERT: A 1124 HIS cc_start: 0.6456 (p90) cc_final: 0.6003 (p90) REVERT: A 1143 LEU cc_start: 0.8526 (tp) cc_final: 0.8070 (tt) REVERT: A 1198 ASP cc_start: 0.6934 (t0) cc_final: 0.6653 (t0) REVERT: A 1225 PHE cc_start: 0.7741 (t80) cc_final: 0.7473 (t80) REVERT: A 1284 MET cc_start: 0.8437 (ttm) cc_final: 0.8222 (ttm) REVERT: A 1444 MET cc_start: 0.8886 (mmm) cc_final: 0.8485 (mtp) REVERT: B 101 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8054 (mmt) REVERT: B 270 LYS cc_start: 0.7749 (mtmm) cc_final: 0.7313 (mtmm) REVERT: B 308 TRP cc_start: 0.7943 (p-90) cc_final: 0.7668 (p-90) REVERT: B 310 MET cc_start: 0.8460 (ttm) cc_final: 0.8238 (ttm) REVERT: B 468 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7081 (tm-30) REVERT: B 618 ASP cc_start: 0.8157 (t0) cc_final: 0.7714 (t0) REVERT: B 686 ASN cc_start: 0.7921 (p0) cc_final: 0.7684 (m-40) REVERT: D 61 GLU cc_start: 0.8005 (pt0) cc_final: 0.7222 (tm-30) REVERT: F 119 ARG cc_start: 0.8696 (tpp80) cc_final: 0.8141 (mpt-90) REVERT: F 127 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7817 (mt-10) REVERT: F 154 ASP cc_start: 0.8031 (t0) cc_final: 0.7539 (p0) REVERT: G 141 SER cc_start: 0.6024 (t) cc_final: 0.5744 (p) REVERT: G 144 ARG cc_start: 0.5446 (ttm170) cc_final: 0.5064 (mpt180) REVERT: H 16 ASP cc_start: 0.8331 (t0) cc_final: 0.7773 (p0) REVERT: I 13 MET cc_start: 0.5239 (ptt) cc_final: 0.4858 (ptp) REVERT: I 45 ARG cc_start: 0.7947 (ttt90) cc_final: 0.7556 (ttt-90) REVERT: I 61 ASP cc_start: 0.6589 (t0) cc_final: 0.6198 (t0) REVERT: I 98 VAL cc_start: 0.8458 (t) cc_final: 0.8167 (p) REVERT: L 54 ARG cc_start: 0.7650 (ptp-170) cc_final: 0.7394 (ptp-170) outliers start: 56 outliers final: 37 residues processed: 483 average time/residue: 0.2134 time to fit residues: 164.6231 Evaluate side-chains 431 residues out of total 3462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 393 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 1138 ILE Chi-restraints excluded: chain A residue 1334 ASP Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 682 SER Chi-restraints excluded: chain B residue 938 SER Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 9 GLN Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 155 SER Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 78 CYS Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain L residue 64 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 341 optimal weight: 20.0000 chunk 71 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 332 optimal weight: 8.9990 chunk 72 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 chunk 316 optimal weight: 4.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1265 ASN A1432 GLN B 366 GLN B 572 HIS B 573 GLN D 9 GLN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 GLN I 108 HIS ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.140733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.103065 restraints weight = 48170.430| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.23 r_work: 0.3181 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.029 33118 Z= 0.459 Angle : 0.583 24.415 44947 Z= 0.302 Chirality : 0.044 0.786 5053 Planarity : 0.004 0.054 5627 Dihedral : 11.711 130.246 4891 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.89 % Favored : 97.01 % Rotamer: Outliers : 1.44 % Allowed : 8.93 % Favored : 89.63 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.14), residues: 3882 helix: 1.60 (0.14), residues: 1365 sheet: 0.19 (0.21), residues: 579 loop : -0.34 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1239 TYR 0.017 0.001 TYR A1453 PHE 0.081 0.002 PHE D 70 TRP 0.013 0.001 TRP A1044 HIS 0.006 0.001 HIS I 108 Details of bonding type rmsd/Z covalent geometry : bond 0.01213 / 0.46 (33086) covalent geometry : angle 0.55224 / 0.30 (44902) hydrogen bonds : bond 0.04173 / 2.82 ( 1369) hydrogen bonds : angle 4.61496 / 3.31 ( 3784) metal coordination : bond 0.00597 / 0.40 ( 32) metal coordination : angle 5.94138 / 3.86 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 3462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 428 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7388 (pt0) REVERT: A 542 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8151 (mm-30) REVERT: A 596 THR cc_start: 0.8706 (p) cc_final: 0.8378 (t) REVERT: A 731 ARG cc_start: 0.7539 (mmt180) cc_final: 0.6915 (mtp180) REVERT: A 1078 GLN cc_start: 0.7985 (mm110) cc_final: 0.7632 (mm-40) REVERT: A 1124 HIS cc_start: 0.6365 (p90) cc_final: 0.5963 (p90) REVERT: A 1143 LEU cc_start: 0.8517 (tp) cc_final: 0.8105 (tt) REVERT: A 1151 GLU cc_start: 0.5786 (pm20) cc_final: 0.5519 (pm20) REVERT: A 1198 ASP cc_start: 0.6816 (t0) cc_final: 0.6613 (t0) REVERT: A 1225 PHE cc_start: 0.7817 (t80) cc_final: 0.7565 (t80) REVERT: A 1444 MET cc_start: 0.8980 (mmm) cc_final: 0.8516 (mtp) REVERT: B 101 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8073 (mmt) REVERT: B 308 TRP cc_start: 0.8026 (p-90) cc_final: 0.7712 (p-90) REVERT: B 618 ASP cc_start: 0.8152 (t0) cc_final: 0.7598 (t70) REVERT: B 686 ASN cc_start: 0.7870 (p0) cc_final: 0.7660 (m110) REVERT: C 152 GLU cc_start: 0.8049 (tt0) cc_final: 0.7667 (pt0) REVERT: C 195 GLN cc_start: 0.8895 (mp10) cc_final: 0.8638 (mp10) REVERT: D 61 GLU cc_start: 0.8044 (pt0) cc_final: 0.7498 (tt0) REVERT: F 127 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7801 (mt-10) REVERT: F 154 ASP cc_start: 0.8033 (t0) cc_final: 0.7522 (p0) REVERT: G 21 ARG cc_start: 0.7906 (mtm180) cc_final: 0.7637 (ptm160) REVERT: G 141 SER cc_start: 0.5996 (t) cc_final: 0.5701 (p) REVERT: G 144 ARG cc_start: 0.5398 (ttm170) cc_final: 0.5124 (mpt180) REVERT: H 16 ASP cc_start: 0.8321 (t0) cc_final: 0.7713 (p0) REVERT: I 28 GLU cc_start: 0.7233 (pp20) cc_final: 0.6705 (pm20) REVERT: I 30 ARG cc_start: 0.6046 (mpp80) cc_final: 0.5699 (ptt90) REVERT: I 36 GLU cc_start: 0.7227 (tt0) cc_final: 0.6949 (tt0) REVERT: I 61 ASP cc_start: 0.6752 (t0) cc_final: 0.6351 (t0) REVERT: I 98 VAL cc_start: 0.8425 (t) cc_final: 0.8188 (p) REVERT: K 49 GLU cc_start: 0.8839 (tp30) cc_final: 0.8632 (tp30) outliers start: 50 outliers final: 34 residues processed: 460 average time/residue: 0.2127 time to fit residues: 155.9581 Evaluate side-chains 429 residues out of total 3462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 394 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1309 ASP Chi-restraints excluded: chain A residue 1334 ASP Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 810 GLU Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 9 GLN Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 155 SER Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain L residue 64 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 370 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 chunk 214 optimal weight: 3.9990 chunk 212 optimal weight: 4.9990 chunk 381 optimal weight: 3.9990 chunk 178 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 304 optimal weight: 10.0000 chunk 330 optimal weight: 4.9990 chunk 236 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1211 GLN A1265 ASN A1270 ASN B 255 GLN B 366 GLN B 440 HIS B 667 GLN D 9 GLN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 HIS ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.137138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.098951 restraints weight = 48760.529| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.20 r_work: 0.3125 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 1.031 33118 Z= 0.499 Angle : 0.640 24.542 44947 Z= 0.333 Chirality : 0.047 0.811 5053 Planarity : 0.005 0.057 5627 Dihedral : 11.863 130.848 4891 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.84 % Favored : 96.03 % Rotamer: Outliers : 2.20 % Allowed : 9.56 % Favored : 88.24 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.13), residues: 3882 helix: 1.41 (0.14), residues: 1359 sheet: 0.06 (0.21), residues: 562 loop : -0.45 (0.14), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1366 TYR 0.015 0.002 TYR J 44 PHE 0.078 0.002 PHE D 70 TRP 0.012 0.001 TRP H 79 HIS 0.010 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.01305 / 0.50 (33086) covalent geometry : angle 0.61434 / 0.33 (44902) hydrogen bonds : bond 0.04416 / 2.97 ( 1369) hydrogen bonds : angle 4.61580 / 3.30 ( 3784) metal coordination : bond 0.00807 / 0.58 ( 32) metal coordination : angle 5.64983 / 3.64 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 394 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.7743 (t0) cc_final: 0.7407 (t70) REVERT: A 149 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7494 (pt0) REVERT: A 293 GLU cc_start: 0.7908 (tt0) cc_final: 0.7697 (tp30) REVERT: A 731 ARG cc_start: 0.7656 (mmt180) cc_final: 0.7067 (mtm110) REVERT: A 1113 THR cc_start: 0.8934 (OUTLIER) cc_final: 0.8590 (p) REVERT: A 1124 HIS cc_start: 0.6428 (p90) cc_final: 0.6139 (p-80) REVERT: A 1143 LEU cc_start: 0.8531 (tp) cc_final: 0.8082 (tt) REVERT: A 1198 ASP cc_start: 0.6896 (t0) cc_final: 0.6647 (t0) REVERT: B 101 MET cc_start: 0.8558 (mmt) cc_final: 0.8112 (mmt) REVERT: B 186 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7887 (mt-10) REVERT: B 308 TRP cc_start: 0.8143 (p-90) cc_final: 0.7715 (p-90) REVERT: B 618 ASP cc_start: 0.8120 (t0) cc_final: 0.7647 (t0) REVERT: D 61 GLU cc_start: 0.8153 (pt0) cc_final: 0.7556 (tt0) REVERT: E 93 MET cc_start: 0.7824 (tpp) cc_final: 0.7616 (tpp) REVERT: F 127 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7904 (mt-10) REVERT: F 154 ASP cc_start: 0.8140 (t0) cc_final: 0.7540 (p0) REVERT: G 21 ARG cc_start: 0.7975 (mtm180) cc_final: 0.7653 (ptm160) REVERT: G 141 SER cc_start: 0.5921 (t) cc_final: 0.5625 (p) REVERT: G 144 ARG cc_start: 0.5405 (ttm170) cc_final: 0.4959 (mpt180) REVERT: H 16 ASP cc_start: 0.8384 (t0) cc_final: 0.7599 (p0) REVERT: H 22 LYS cc_start: 0.8946 (mttm) cc_final: 0.8475 (mttm) REVERT: I 30 ARG cc_start: 0.6086 (mpp80) cc_final: 0.5869 (ptt-90) REVERT: I 36 GLU cc_start: 0.7091 (tt0) cc_final: 0.6834 (tt0) REVERT: I 61 ASP cc_start: 0.6797 (t0) cc_final: 0.6305 (t0) REVERT: K 24 ASP cc_start: 0.7893 (t0) cc_final: 0.7692 (t70) outliers start: 76 outliers final: 56 residues processed: 442 average time/residue: 0.2119 time to fit residues: 149.3811 Evaluate side-chains 421 residues out of total 3462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 363 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1309 ASP Chi-restraints excluded: chain A residue 1334 ASP Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain A residue 1447 GLU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 682 SER Chi-restraints excluded: chain B residue 810 GLU Chi-restraints excluded: chain B residue 837 ASP Chi-restraints excluded: chain B residue 938 SER Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 9 GLN Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 155 SER Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain H residue 14 GLU Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 48 ARG Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain L residue 64 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 98 optimal weight: 0.6980 chunk 341 optimal weight: 5.9990 chunk 132 optimal weight: 0.5980 chunk 214 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 251 optimal weight: 6.9990 chunk 351 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 390 optimal weight: 20.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 GLN ** A 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1265 ASN A1270 ASN B 366 GLN C 102 GLN D 9 GLN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 HIS I 108 HIS I 114 GLN L 53 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.137678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.100601 restraints weight = 48270.609| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.09 r_work: 0.3148 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.027 33118 Z= 0.462 Angle : 0.575 24.381 44947 Z= 0.302 Chirality : 0.045 0.800 5053 Planarity : 0.004 0.055 5627 Dihedral : 11.836 130.330 4891 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.04 % Favored : 96.83 % Rotamer: Outliers : 1.88 % Allowed : 10.83 % Favored : 87.29 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.14), residues: 3882 helix: 1.52 (0.14), residues: 1357 sheet: 0.04 (0.21), residues: 581 loop : -0.43 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 45 TYR 0.013 0.001 TYR J 44 PHE 0.079 0.002 PHE D 70 TRP 0.012 0.001 TRP A1044 HIS 0.006 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.01221 / 0.46 (33086) covalent geometry : angle 0.55198 / 0.30 (44902) hydrogen bonds : bond 0.03925 / 2.63 ( 1369) hydrogen bonds : angle 4.43794 / 3.18 ( 3784) metal coordination : bond 0.00622 / 0.44 ( 32) metal coordination : angle 5.13941 / 3.36 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 390 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.7734 (t0) cc_final: 0.7427 (t70) REVERT: A 149 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7400 (pt0) REVERT: A 731 ARG cc_start: 0.7589 (mmt180) cc_final: 0.7019 (mtm110) REVERT: A 1113 THR cc_start: 0.8744 (OUTLIER) cc_final: 0.8368 (p) REVERT: A 1124 HIS cc_start: 0.6398 (p90) cc_final: 0.6176 (p-80) REVERT: A 1143 LEU cc_start: 0.8572 (tp) cc_final: 0.7824 (tt) REVERT: A 1198 ASP cc_start: 0.7027 (t0) cc_final: 0.6773 (t0) REVERT: A 1225 PHE cc_start: 0.7562 (t80) cc_final: 0.7309 (t80) REVERT: B 101 MET cc_start: 0.8558 (mmt) cc_final: 0.8163 (mmt) REVERT: B 308 TRP cc_start: 0.8144 (p-90) cc_final: 0.7707 (p-90) REVERT: B 310 MET cc_start: 0.8705 (ttm) cc_final: 0.8500 (mtm) REVERT: B 326 ASP cc_start: 0.5658 (t70) cc_final: 0.5414 (p0) REVERT: B 618 ASP cc_start: 0.8083 (t0) cc_final: 0.7541 (t70) REVERT: D 61 GLU cc_start: 0.8160 (pt0) cc_final: 0.7556 (tt0) REVERT: E 93 MET cc_start: 0.7754 (tpp) cc_final: 0.7553 (tpp) REVERT: F 127 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7852 (mt-10) REVERT: F 154 ASP cc_start: 0.8151 (t0) cc_final: 0.7549 (p0) REVERT: G 21 ARG cc_start: 0.7995 (mtm180) cc_final: 0.7570 (ptm160) REVERT: G 141 SER cc_start: 0.5979 (t) cc_final: 0.5677 (p) REVERT: G 144 ARG cc_start: 0.4944 (ttm170) cc_final: 0.4532 (mpt180) REVERT: H 16 ASP cc_start: 0.8329 (t0) cc_final: 0.7616 (p0) REVERT: H 22 LYS cc_start: 0.8897 (mttm) cc_final: 0.8500 (mttm) REVERT: I 4 PHE cc_start: 0.5779 (OUTLIER) cc_final: 0.5167 (m-10) REVERT: I 36 GLU cc_start: 0.7112 (tt0) cc_final: 0.6836 (tt0) REVERT: I 61 ASP cc_start: 0.6783 (t0) cc_final: 0.6297 (t0) REVERT: K 24 ASP cc_start: 0.7801 (t0) cc_final: 0.7552 (t70) outliers start: 65 outliers final: 47 residues processed: 433 average time/residue: 0.2073 time to fit residues: 143.3842 Evaluate side-chains 416 residues out of total 3462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 367 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 706 HIS Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1265 ASN Chi-restraints excluded: chain A residue 1334 ASP Chi-restraints excluded: chain A residue 1447 GLU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 810 GLU Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 155 SER Chi-restraints excluded: chain H residue 14 GLU Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 4 PHE Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain L residue 64 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 342 optimal weight: 20.0000 chunk 365 optimal weight: 10.0000 chunk 155 optimal weight: 0.9980 chunk 304 optimal weight: 10.0000 chunk 165 optimal weight: 0.8980 chunk 232 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 383 optimal weight: 4.9990 chunk 318 optimal weight: 8.9990 chunk 60 optimal weight: 7.9990 chunk 199 optimal weight: 1.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 GLN B 300 HIS B 366 GLN B 667 GLN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 ASN H 52 GLN I 108 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.135479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.099317 restraints weight = 48420.891| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.18 r_work: 0.3114 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 1.026 33118 Z= 0.491 Angle : 0.620 24.375 44947 Z= 0.324 Chirality : 0.046 0.809 5053 Planarity : 0.004 0.056 5627 Dihedral : 11.891 130.811 4891 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.89 % Favored : 95.98 % Rotamer: Outliers : 2.28 % Allowed : 11.03 % Favored : 86.68 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.13), residues: 3882 helix: 1.44 (0.14), residues: 1354 sheet: -0.08 (0.21), residues: 582 loop : -0.49 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 45 TYR 0.016 0.001 TYR E 187 PHE 0.078 0.002 PHE D 70 TRP 0.011 0.001 TRP A1044 HIS 0.009 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.01288 / 0.49 (33086) covalent geometry : angle 0.59747 / 0.32 (44902) hydrogen bonds : bond 0.04198 / 2.81 ( 1369) hydrogen bonds : angle 4.48709 / 3.21 ( 3784) metal coordination : bond 0.00784 / 0.55 ( 32) metal coordination : angle 5.21527 / 3.44 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 372 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.7760 (t0) cc_final: 0.7466 (t0) REVERT: A 149 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7473 (pt0) REVERT: A 601 LYS cc_start: 0.8574 (mtmt) cc_final: 0.8042 (mmtt) REVERT: A 879 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7545 (mm-30) REVERT: A 912 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7523 (pp) REVERT: A 1113 THR cc_start: 0.8870 (OUTLIER) cc_final: 0.8526 (p) REVERT: A 1124 HIS cc_start: 0.6363 (p90) cc_final: 0.6150 (p-80) REVERT: A 1143 LEU cc_start: 0.8495 (tp) cc_final: 0.8158 (tt) REVERT: A 1198 ASP cc_start: 0.7011 (t0) cc_final: 0.6810 (t0) REVERT: A 1225 PHE cc_start: 0.7712 (t80) cc_final: 0.7499 (t80) REVERT: A 1239 ARG cc_start: 0.5872 (OUTLIER) cc_final: 0.5515 (mtp85) REVERT: B 101 MET cc_start: 0.8643 (mmt) cc_final: 0.8250 (mmt) REVERT: B 186 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7888 (mt-10) REVERT: B 308 TRP cc_start: 0.8203 (p-90) cc_final: 0.7684 (p-90) REVERT: B 310 MET cc_start: 0.8756 (ttm) cc_final: 0.8555 (mtm) REVERT: B 326 ASP cc_start: 0.5669 (t70) cc_final: 0.5203 (p0) REVERT: B 618 ASP cc_start: 0.8145 (t0) cc_final: 0.7606 (t70) REVERT: D 61 GLU cc_start: 0.8188 (pt0) cc_final: 0.7598 (tt0) REVERT: F 127 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7919 (mt-10) REVERT: F 154 ASP cc_start: 0.8193 (t0) cc_final: 0.7560 (p0) REVERT: G 21 ARG cc_start: 0.8035 (mtm180) cc_final: 0.7612 (ptm160) REVERT: G 141 SER cc_start: 0.6162 (t) cc_final: 0.5869 (p) REVERT: H 16 ASP cc_start: 0.8285 (t0) cc_final: 0.7443 (p0) REVERT: H 22 LYS cc_start: 0.8955 (mttm) cc_final: 0.8545 (mttm) REVERT: I 4 PHE cc_start: 0.5874 (OUTLIER) cc_final: 0.5220 (m-10) REVERT: I 36 GLU cc_start: 0.7103 (tt0) cc_final: 0.6755 (tt0) REVERT: I 61 ASP cc_start: 0.6876 (t0) cc_final: 0.6459 (t0) REVERT: K 24 ASP cc_start: 0.7841 (t0) cc_final: 0.7554 (t70) outliers start: 79 outliers final: 61 residues processed: 429 average time/residue: 0.2102 time to fit residues: 144.5378 Evaluate side-chains 429 residues out of total 3462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 362 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 706 HIS Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 879 GLU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1239 ARG Chi-restraints excluded: chain A residue 1309 ASP Chi-restraints excluded: chain A residue 1334 ASP Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain A residue 1447 GLU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 682 SER Chi-restraints excluded: chain B residue 810 GLU Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 938 SER Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 4 PHE Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 48 ARG Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain L residue 64 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 106 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 123 optimal weight: 7.9990 chunk 365 optimal weight: 4.9990 chunk 232 optimal weight: 0.7980 chunk 298 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 47 optimal weight: 0.1980 chunk 264 optimal weight: 0.9980 chunk 302 optimal weight: 2.9990 chunk 297 optimal weight: 10.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 GLN A 881 GLN ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1265 ASN B 366 GLN B 667 GLN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 GLN I 108 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.138210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.101619 restraints weight = 48090.351| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.09 r_work: 0.3161 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.025 33118 Z= 0.451 Angle : 0.558 24.360 44947 Z= 0.294 Chirality : 0.044 0.802 5053 Planarity : 0.004 0.053 5627 Dihedral : 11.807 130.535 4891 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.83 % Favored : 97.04 % Rotamer: Outliers : 1.53 % Allowed : 12.07 % Favored : 86.40 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.14), residues: 3882 helix: 1.67 (0.14), residues: 1353 sheet: -0.07 (0.21), residues: 599 loop : -0.43 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 45 TYR 0.012 0.001 TYR J 44 PHE 0.079 0.001 PHE D 70 TRP 0.014 0.001 TRP B 561 HIS 0.005 0.001 HIS B 587 Details of bonding type rmsd/Z covalent geometry : bond 0.01196 / 0.45 (33086) covalent geometry : angle 0.53812 / 0.29 (44902) hydrogen bonds : bond 0.03639 / 2.43 ( 1369) hydrogen bonds : angle 4.29536 / 3.08 ( 3784) metal coordination : bond 0.00468 / 0.32 ( 32) metal coordination : angle 4.72813 / 3.08 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 395 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8785 (mtt) cc_final: 0.8551 (mtt) REVERT: A 130 ASP cc_start: 0.7694 (t0) cc_final: 0.7414 (t70) REVERT: A 149 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7248 (pt0) REVERT: A 731 ARG cc_start: 0.7585 (mmt180) cc_final: 0.7018 (mtm110) REVERT: A 912 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7498 (pp) REVERT: A 1078 GLN cc_start: 0.8136 (mm110) cc_final: 0.7784 (mm-40) REVERT: A 1113 THR cc_start: 0.8733 (OUTLIER) cc_final: 0.8384 (p) REVERT: A 1143 LEU cc_start: 0.8468 (tp) cc_final: 0.8130 (tt) REVERT: A 1198 ASP cc_start: 0.7108 (t0) cc_final: 0.6846 (t0) REVERT: A 1225 PHE cc_start: 0.7780 (t80) cc_final: 0.7473 (t80) REVERT: A 1239 ARG cc_start: 0.5838 (ttm170) cc_final: 0.5574 (mtp85) REVERT: B 94 LYS cc_start: 0.7575 (tttm) cc_final: 0.7021 (mmmt) REVERT: B 101 MET cc_start: 0.8604 (mmt) cc_final: 0.8244 (mmt) REVERT: B 308 TRP cc_start: 0.8198 (p-90) cc_final: 0.7619 (p-90) REVERT: B 326 ASP cc_start: 0.5569 (t70) cc_final: 0.5228 (p0) REVERT: B 618 ASP cc_start: 0.8091 (t0) cc_final: 0.7619 (t0) REVERT: D 61 GLU cc_start: 0.8154 (pt0) cc_final: 0.7340 (tm-30) REVERT: E 66 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8140 (mt-10) REVERT: F 119 ARG cc_start: 0.8711 (tpp80) cc_final: 0.7994 (mtm180) REVERT: F 154 ASP cc_start: 0.8141 (t0) cc_final: 0.7531 (p0) REVERT: G 21 ARG cc_start: 0.8019 (mtm180) cc_final: 0.7595 (ptm160) REVERT: G 141 SER cc_start: 0.6162 (t) cc_final: 0.5864 (p) REVERT: H 16 ASP cc_start: 0.8229 (t0) cc_final: 0.7464 (p0) REVERT: H 22 LYS cc_start: 0.8908 (mttm) cc_final: 0.8504 (mttm) REVERT: H 27 GLU cc_start: 0.7765 (mp0) cc_final: 0.7547 (mp0) REVERT: I 4 PHE cc_start: 0.5741 (OUTLIER) cc_final: 0.5084 (m-10) REVERT: I 36 GLU cc_start: 0.7100 (tt0) cc_final: 0.6715 (tt0) REVERT: I 61 ASP cc_start: 0.6697 (t0) cc_final: 0.6321 (t0) REVERT: K 24 ASP cc_start: 0.7757 (t0) cc_final: 0.7478 (t70) outliers start: 53 outliers final: 40 residues processed: 429 average time/residue: 0.1997 time to fit residues: 136.9705 Evaluate side-chains 415 residues out of total 3462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 371 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 706 HIS Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1447 GLU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 4 PHE Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain L residue 64 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 44 optimal weight: 0.7980 chunk 255 optimal weight: 3.9990 chunk 264 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 289 optimal weight: 6.9990 chunk 186 optimal weight: 4.9990 chunk 266 optimal weight: 0.0270 chunk 23 optimal weight: 4.9990 chunk 208 optimal weight: 9.9990 chunk 302 optimal weight: 9.9990 chunk 333 optimal weight: 10.0000 overall best weight: 2.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 HIS A 881 GLN ** A1124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1265 ASN B 366 GLN B 667 GLN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 GLN I 108 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.134902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.098520 restraints weight = 48150.687| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.11 r_work: 0.3111 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 1.023 33118 Z= 0.489 Angle : 0.626 24.379 44947 Z= 0.327 Chirality : 0.047 0.813 5053 Planarity : 0.004 0.055 5627 Dihedral : 11.900 131.205 4891 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.76 % Favored : 96.11 % Rotamer: Outliers : 2.11 % Allowed : 11.87 % Favored : 86.02 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.13), residues: 3882 helix: 1.50 (0.14), residues: 1353 sheet: -0.14 (0.21), residues: 582 loop : -0.54 (0.14), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 241 TYR 0.016 0.002 TYR G 25 PHE 0.077 0.002 PHE D 70 TRP 0.011 0.001 TRP B 561 HIS 0.015 0.001 HIS A1124 Details of bonding type rmsd/Z covalent geometry : bond 0.01285 / 0.49 (33086) covalent geometry : angle 0.60560 / 0.33 (44902) hydrogen bonds : bond 0.04182 / 2.79 ( 1369) hydrogen bonds : angle 4.43863 / 3.18 ( 3784) metal coordination : bond 0.00827 / 0.60 ( 32) metal coordination : angle 4.99174 / 3.32 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 377 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8853 (mtt) cc_final: 0.8612 (mtt) REVERT: A 130 ASP cc_start: 0.7764 (t0) cc_final: 0.7478 (t0) REVERT: A 149 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7485 (pt0) REVERT: A 601 LYS cc_start: 0.8624 (mtmt) cc_final: 0.8108 (mmtt) REVERT: A 731 ARG cc_start: 0.7698 (mmt180) cc_final: 0.7070 (mtm110) REVERT: A 879 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7548 (mm-30) REVERT: A 912 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7514 (pp) REVERT: A 1078 GLN cc_start: 0.8142 (mm110) cc_final: 0.7812 (mm-40) REVERT: A 1113 THR cc_start: 0.8857 (OUTLIER) cc_final: 0.8529 (p) REVERT: A 1124 HIS cc_start: 0.6169 (p-80) cc_final: 0.5844 (p-80) REVERT: A 1143 LEU cc_start: 0.8495 (tp) cc_final: 0.8083 (tt) REVERT: A 1198 ASP cc_start: 0.7132 (t0) cc_final: 0.6886 (t0) REVERT: A 1225 PHE cc_start: 0.7836 (t80) cc_final: 0.7584 (t80) REVERT: A 1239 ARG cc_start: 0.5789 (ttm170) cc_final: 0.5581 (mtp85) REVERT: A 1359 ASP cc_start: 0.8452 (p0) cc_final: 0.8203 (p0) REVERT: B 101 MET cc_start: 0.8590 (mmt) cc_final: 0.8207 (mmt) REVERT: B 308 TRP cc_start: 0.8248 (p-90) cc_final: 0.7487 (p-90) REVERT: B 326 ASP cc_start: 0.5670 (t70) cc_final: 0.5321 (p0) REVERT: B 618 ASP cc_start: 0.8128 (t0) cc_final: 0.7667 (t0) REVERT: B 1072 MET cc_start: 0.8827 (mtp) cc_final: 0.8574 (mtp) REVERT: D 61 GLU cc_start: 0.8231 (pt0) cc_final: 0.7493 (tm-30) REVERT: E 66 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8216 (mt-10) REVERT: F 72 LYS cc_start: 0.8483 (ptpp) cc_final: 0.8069 (ptpp) REVERT: F 154 ASP cc_start: 0.8169 (t0) cc_final: 0.7574 (p0) REVERT: G 1 MET cc_start: 0.5703 (ttt) cc_final: 0.5407 (ttm) REVERT: G 21 ARG cc_start: 0.8052 (mtm180) cc_final: 0.7621 (ptm160) REVERT: G 141 SER cc_start: 0.6060 (t) cc_final: 0.5725 (p) REVERT: H 16 ASP cc_start: 0.8286 (t0) cc_final: 0.7414 (p0) REVERT: H 22 LYS cc_start: 0.8910 (mttm) cc_final: 0.8478 (mttm) REVERT: H 27 GLU cc_start: 0.7848 (mp0) cc_final: 0.7627 (mp0) REVERT: I 4 PHE cc_start: 0.5711 (OUTLIER) cc_final: 0.5224 (m-10) REVERT: I 36 GLU cc_start: 0.7112 (tt0) cc_final: 0.6630 (tt0) REVERT: I 61 ASP cc_start: 0.6764 (t0) cc_final: 0.6510 (t0) REVERT: K 24 ASP cc_start: 0.7786 (t0) cc_final: 0.7476 (t70) outliers start: 73 outliers final: 57 residues processed: 429 average time/residue: 0.2222 time to fit residues: 152.4443 Evaluate side-chains 422 residues out of total 3462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 360 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 706 HIS Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 879 GLU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1309 ASP Chi-restraints excluded: chain A residue 1447 GLU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 444 MET Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 563 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 938 SER Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 4 PHE Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain L residue 64 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 205 optimal weight: 0.7980 chunk 294 optimal weight: 20.0000 chunk 95 optimal weight: 6.9990 chunk 196 optimal weight: 2.9990 chunk 387 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 237 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 56 optimal weight: 0.0060 chunk 263 optimal weight: 4.9990 chunk 350 optimal weight: 0.0670 overall best weight: 0.9336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 881 GLN ** A1124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1265 ASN B 366 GLN B 667 GLN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 GLN I 108 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.137576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.100817 restraints weight = 47717.235| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.06 r_work: 0.3153 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.025 33118 Z= 0.453 Angle : 0.567 24.338 44947 Z= 0.300 Chirality : 0.044 0.809 5053 Planarity : 0.004 0.053 5627 Dihedral : 11.819 130.485 4891 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.94 % Favored : 96.93 % Rotamer: Outliers : 1.68 % Allowed : 12.62 % Favored : 85.70 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.14), residues: 3882 helix: 1.65 (0.14), residues: 1353 sheet: -0.06 (0.21), residues: 584 loop : -0.47 (0.14), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 45 TYR 0.013 0.001 TYR J 44 PHE 0.078 0.001 PHE D 70 TRP 0.012 0.001 TRP A1044 HIS 0.020 0.001 HIS A1124 Details of bonding type rmsd/Z covalent geometry : bond 0.01201 / 0.45 (33086) covalent geometry : angle 0.54846 / 0.30 (44902) hydrogen bonds : bond 0.03653 / 2.43 ( 1369) hydrogen bonds : angle 4.25451 / 3.05 ( 3784) metal coordination : bond 0.00483 / 0.34 ( 32) metal coordination : angle 4.54663 / 2.99 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 389 time to evaluate : 1.303 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: A 74 MET cc_start: 0.8790 (mtt) cc_final: 0.8529 (mtt) REVERT: A 130 ASP cc_start: 0.7710 (t0) cc_final: 0.7430 (t70) REVERT: A 149 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7242 (pt0) REVERT: A 601 LYS cc_start: 0.8553 (mtmt) cc_final: 0.8037 (mmtt) REVERT: A 731 ARG cc_start: 0.7608 (mmt180) cc_final: 0.7020 (mtm110) REVERT: A 879 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7287 (mm-30) REVERT: A 912 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7462 (pp) REVERT: A 1078 GLN cc_start: 0.8103 (mm110) cc_final: 0.7822 (mm-40) REVERT: A 1113 THR cc_start: 0.8744 (OUTLIER) cc_final: 0.8399 (p) REVERT: A 1143 LEU cc_start: 0.8446 (tp) cc_final: 0.8131 (tt) REVERT: A 1198 ASP cc_start: 0.7174 (t0) cc_final: 0.6910 (t0) REVERT: A 1225 PHE cc_start: 0.7879 (t80) cc_final: 0.7559 (t80) REVERT: A 1359 ASP cc_start: 0.8083 (p0) cc_final: 0.7771 (p0) REVERT: B 94 LYS cc_start: 0.7476 (tttm) cc_final: 0.6900 (mmmt) REVERT: B 101 MET cc_start: 0.8676 (mmt) cc_final: 0.8281 (mmt) REVERT: B 261 ARG cc_start: 0.7422 (mtp85) cc_final: 0.7118 (mtt-85) REVERT: B 308 TRP cc_start: 0.8271 (p-90) cc_final: 0.7555 (p-90) REVERT: B 326 ASP cc_start: 0.5724 (t70) cc_final: 0.5366 (p0) REVERT: B 618 ASP cc_start: 0.8114 (t0) cc_final: 0.7632 (t0) REVERT: B 665 GLU cc_start: 0.8112 (tt0) cc_final: 0.7863 (tt0) REVERT: B 1072 MET cc_start: 0.8794 (mtp) cc_final: 0.8514 (mtp) REVERT: D 61 GLU cc_start: 0.8215 (pt0) cc_final: 0.7397 (tm-30) REVERT: E 66 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8188 (mt-10) REVERT: F 119 ARG cc_start: 0.8700 (tpp80) cc_final: 0.7963 (mtm180) REVERT: F 154 ASP cc_start: 0.8161 (t0) cc_final: 0.7510 (p0) REVERT: G 21 ARG cc_start: 0.8029 (mtm180) cc_final: 0.7613 (ptm160) REVERT: G 141 SER cc_start: 0.5969 (t) cc_final: 0.5602 (p) REVERT: H 16 ASP cc_start: 0.8254 (t0) cc_final: 0.7364 (p0) REVERT: H 22 LYS cc_start: 0.8891 (mttm) cc_final: 0.8437 (mttm) REVERT: H 27 GLU cc_start: 0.7829 (mp0) cc_final: 0.7598 (mp0) REVERT: I 4 PHE cc_start: 0.5886 (OUTLIER) cc_final: 0.5398 (m-10) REVERT: I 13 MET cc_start: 0.5511 (ttp) cc_final: 0.5225 (ttm) REVERT: I 28 GLU cc_start: 0.7455 (pp20) cc_final: 0.6641 (pm20) REVERT: I 36 GLU cc_start: 0.7205 (tt0) cc_final: 0.6694 (tt0) REVERT: I 61 ASP cc_start: 0.6674 (t0) cc_final: 0.6331 (t0) REVERT: K 24 ASP cc_start: 0.7736 (t0) cc_final: 0.7425 (t70) outliers start: 58 outliers final: 48 residues processed: 427 average time/residue: 0.2221 time to fit residues: 151.3201 Evaluate side-chains 425 residues out of total 3462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 372 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 706 HIS Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 879 GLU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 922 ASP Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1447 GLU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 938 SER Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 4 PHE Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 78 CYS Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain K residue 25 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 365 optimal weight: 7.9990 chunk 317 optimal weight: 0.0980 chunk 74 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 240 optimal weight: 5.9990 chunk 265 optimal weight: 3.9990 chunk 239 optimal weight: 0.9980 chunk 234 optimal weight: 0.9980 chunk 382 optimal weight: 6.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 GLN A 881 GLN ** A1124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1265 ASN B 366 GLN B 667 GLN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 GLN I 108 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.136452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.100424 restraints weight = 48270.644| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.17 r_work: 0.3132 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.022 33118 Z= 0.465 Angle : 0.579 24.338 44947 Z= 0.306 Chirality : 0.045 0.814 5053 Planarity : 0.004 0.054 5627 Dihedral : 11.824 131.350 4891 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.53 % Favored : 96.34 % Rotamer: Outliers : 1.70 % Allowed : 12.65 % Favored : 85.64 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.14), residues: 3882 helix: 1.61 (0.14), residues: 1359 sheet: -0.10 (0.21), residues: 581 loop : -0.49 (0.14), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1366 TYR 0.013 0.001 TYR J 44 PHE 0.077 0.002 PHE D 70 TRP 0.011 0.001 TRP A1044 HIS 0.014 0.001 HIS A1124 Details of bonding type rmsd/Z covalent geometry : bond 0.01229 / 0.47 (33086) covalent geometry : angle 0.56223 / 0.31 (44902) hydrogen bonds : bond 0.03783 / 2.51 ( 1369) hydrogen bonds : angle 4.27350 / 3.06 ( 3784) metal coordination : bond 0.00601 / 0.43 ( 32) metal coordination : angle 4.46913 / 2.97 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7764 Ramachandran restraints generated. 3882 Oldfield, 0 Emsley, 3882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 379 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8821 (mtt) cc_final: 0.8579 (mtt) REVERT: A 130 ASP cc_start: 0.7724 (t0) cc_final: 0.7452 (t0) REVERT: A 149 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7273 (pt0) REVERT: A 601 LYS cc_start: 0.8587 (mtmt) cc_final: 0.8086 (mmtt) REVERT: A 731 ARG cc_start: 0.7631 (mmt180) cc_final: 0.7050 (mtm110) REVERT: A 879 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7348 (mm-30) REVERT: A 912 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7457 (pp) REVERT: A 1078 GLN cc_start: 0.8160 (mm110) cc_final: 0.7912 (mm-40) REVERT: A 1113 THR cc_start: 0.8769 (OUTLIER) cc_final: 0.8433 (p) REVERT: A 1143 LEU cc_start: 0.8460 (tp) cc_final: 0.8139 (tt) REVERT: A 1225 PHE cc_start: 0.7908 (t80) cc_final: 0.7620 (t80) REVERT: B 94 LYS cc_start: 0.7559 (tttm) cc_final: 0.6934 (mmmt) REVERT: B 261 ARG cc_start: 0.7450 (mtp85) cc_final: 0.7142 (mtt-85) REVERT: B 308 TRP cc_start: 0.8237 (p-90) cc_final: 0.8006 (p-90) REVERT: B 326 ASP cc_start: 0.5848 (t70) cc_final: 0.5269 (p0) REVERT: B 618 ASP cc_start: 0.8128 (t0) cc_final: 0.7662 (t0) REVERT: B 665 GLU cc_start: 0.8111 (tt0) cc_final: 0.7861 (tt0) REVERT: B 1072 MET cc_start: 0.8823 (mtp) cc_final: 0.8583 (mtp) REVERT: D 61 GLU cc_start: 0.8220 (pt0) cc_final: 0.7419 (tm-30) REVERT: E 66 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8206 (mt-10) REVERT: F 119 ARG cc_start: 0.8732 (tpp80) cc_final: 0.8035 (mtm180) REVERT: F 154 ASP cc_start: 0.8165 (t0) cc_final: 0.7502 (p0) REVERT: G 21 ARG cc_start: 0.7989 (mtm180) cc_final: 0.7609 (ptm160) REVERT: G 44 TYR cc_start: 0.7752 (m-80) cc_final: 0.7461 (m-10) REVERT: G 141 SER cc_start: 0.5997 (t) cc_final: 0.5618 (p) REVERT: H 16 ASP cc_start: 0.8301 (t0) cc_final: 0.7332 (p0) REVERT: H 22 LYS cc_start: 0.8892 (mttm) cc_final: 0.8440 (mttm) REVERT: I 28 GLU cc_start: 0.7443 (pp20) cc_final: 0.6636 (pm20) REVERT: I 36 GLU cc_start: 0.7216 (tt0) cc_final: 0.6705 (tt0) REVERT: I 61 ASP cc_start: 0.6817 (t0) cc_final: 0.6572 (t0) REVERT: K 24 ASP cc_start: 0.7785 (t0) cc_final: 0.7452 (t70) outliers start: 59 outliers final: 46 residues processed: 418 average time/residue: 0.2246 time to fit residues: 149.8601 Evaluate side-chains 423 residues out of total 3462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 373 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 706 HIS Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 849 MET Chi-restraints excluded: chain A residue 879 GLU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1447 GLU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 938 SER Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 78 CYS Chi-restraints excluded: chain I residue 103 CYS Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain K residue 25 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 279 optimal weight: 5.9990 chunk 222 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 315 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 281 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 302 optimal weight: 10.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 HIS ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 881 GLN ** A1124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1265 ASN B 366 GLN B 667 GLN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 GLN I 108 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.137912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.101937 restraints weight = 48006.251| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.06 r_work: 0.3163 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.022 33118 Z= 0.453 Angle : 0.563 24.320 44947 Z= 0.299 Chirality : 0.044 0.809 5053 Planarity : 0.004 0.085 5627 Dihedral : 11.787 131.069 4891 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.96 % Favored : 96.91 % Rotamer: Outliers : 1.70 % Allowed : 12.56 % Favored : 85.73 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.14), residues: 3882 helix: 1.69 (0.15), residues: 1359 sheet: -0.06 (0.21), residues: 581 loop : -0.46 (0.14), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1239 TYR 0.012 0.001 TYR J 44 PHE 0.078 0.001 PHE D 70 TRP 0.012 0.001 TRP A1044 HIS 0.016 0.001 HIS A1124 Details of bonding type rmsd/Z covalent geometry : bond 0.01200 / 0.45 (33086) covalent geometry : angle 0.54698 / 0.30 (44902) hydrogen bonds : bond 0.03554 / 2.35 ( 1369) hydrogen bonds : angle 4.19666 / 3.01 ( 3784) metal coordination : bond 0.00453 / 0.31 ( 32) metal coordination : angle 4.27406 / 2.82 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9937.05 seconds wall clock time: 170 minutes 14.82 seconds (10214.82 seconds total)