Starting phenix.real_space_refine on Sun Aug 9 06:14:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/29rf_57322/08_2026/29rf_57322.cif Found real_map, /net/cci-nas-00/data/ceres_data/29rf_57322/08_2026/29rf_57322.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/29rf_57322/08_2026/29rf_57322.map" default_real_map = "/net/cci-nas-00/data/ceres_data/29rf_57322/08_2026/29rf_57322.map" model { file = "/net/cci-nas-00/data/ceres_data/29rf_57322/08_2026/29rf_57322.cif" } default_model = "/net/cci-nas-00/data/ceres_data/29rf_57322/08_2026/29rf_57322.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.055 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 20237 2.51 5 N 5638 2.21 5 O 6248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s 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: 32370 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 10993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1396, 10993 Classifications: {'peptide': 1396} Link IDs: {'PCIS': 1, 'PTRANS': 63, 'TRANS': 1331} 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: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 223 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 1} Link IDs: {'rna3p': 9} 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 457 SG CYS A 67 57.603 69.955 83.851 1.00 25.42 S ATOM 479 SG CYS A 70 57.064 73.278 82.087 1.00 27.13 S ATOM 532 SG CYS A 77 60.581 71.671 82.259 1.00 19.17 S ATOM 762 SG CYS A 107 75.414 79.655 127.349 1.00 32.13 S ATOM 786 SG CYS A 110 73.168 82.655 126.778 1.00 36.70 S ATOM 1091 SG CYS A 148 75.824 82.663 129.476 1.00 42.90 S ATOM 1190 SG CYS A 167 72.596 80.563 129.862 1.00 45.27 S ATOM 19767 SG CYS B1163 58.932 86.000 92.011 1.00 11.49 S ATOM 19785 SG CYS B1166 61.451 83.636 93.538 1.00 10.46 S ATOM 19910 SG CYS B1182 57.970 82.464 92.260 1.00 22.03 S ATOM 19929 SG CYS B1185 58.368 84.502 95.513 1.00 22.32 S ATOM 20917 SG CYS C 86 86.427 60.666 20.223 1.00 31.69 S ATOM 20934 SG CYS C 88 84.592 58.288 22.545 1.00 45.81 S ATOM 20967 SG CYS C 92 86.547 56.939 19.636 1.00 25.09 S ATOM 20990 SG CYS C 95 88.378 58.472 22.674 1.00 21.09 S ATOM 28575 SG CYS I 7 133.938 48.954 135.530 1.00 53.15 S ATOM 28600 SG CYS I 10 130.292 48.358 135.101 1.00 52.60 S ATOM 28766 SG CYS I 29 131.456 51.744 136.518 1.00 58.08 S ATOM 28790 SG CYS I 32 131.787 48.680 138.633 1.00 55.57 S ATOM 29117 SG CYS I 75 159.084 58.344 99.123 1.00 44.76 S ATOM 29139 SG CYS I 78 160.792 55.021 98.765 1.00 49.53 S ATOM 29355 SG CYS I 103 157.198 55.288 97.650 1.00 31.25 S ATOM 29375 SG CYS I 106 158.144 55.368 101.352 1.00 38.26 S ATOM 29494 SG CYS J 7 115.850 59.515 38.815 1.00 9.24 S ATOM 29517 SG CYS J 10 116.088 61.172 35.408 1.00 6.74 S ATOM 29797 SG CYS J 45 118.714 61.845 38.137 1.00 8.75 S ATOM 29803 SG CYS J 46 118.580 58.609 36.114 1.00 7.67 S ATOM 30926 SG CYS L 31 90.585 27.699 55.326 1.00 35.48 S ATOM 30946 SG CYS L 34 91.677 24.834 53.096 1.00 39.73 S ATOM 31050 SG CYS L 48 88.072 25.050 54.473 1.00 40.61 S ATOM 31073 SG CYS L 51 91.091 24.195 56.733 1.00 48.88 S Time building chain proxies: 5.83, per 1000 atoms: 0.18 Number of scatterers: 32370 At special positions: 0 Unit cell: (172.165, 155.923, 158.089, 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 6248 8.00 N 5638 7.00 C 20237 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: 2.59 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 77 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 167 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " 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 29 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " 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 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7386 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 46 sheets defined 38.0% alpha, 18.8% beta 25 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 3.90 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' 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 removed outlier: 3.632A pdb=" N HIS A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 221 Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.744A pdb=" N ILE A 235 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 283 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: 3.840A 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 524 through 535 removed outlier: 3.622A pdb=" N LEU A 528 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 Processing helix chain 'A' and resid 574 through 582 removed outlier: 4.249A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.660A 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 removed outlier: 3.529A pdb=" N HIS A 659 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 removed outlier: 3.512A pdb=" N ILE A 670 " --> pdb=" O GLY A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 698 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 Processing helix chain 'A' and resid 793 through 797 removed outlier: 3.517A pdb=" N LYS A 797 " --> pdb=" O PRO A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 846 removed outlier: 3.617A pdb=" N GLU A 822 " --> pdb=" O MET A 818 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR A 831 " --> pdb=" O THR A 827 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A 833 " --> pdb=" O VAL A 829 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR A 836 " --> pdb=" O ALA A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 874 through 878 removed outlier: 3.771A pdb=" N ILE A 878 " --> pdb=" O ALA A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 909 through 913 removed outlier: 3.519A pdb=" N LEU A 913 " --> pdb=" O PRO A 910 " (cutoff:3.500A) 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 972 Processing helix chain 'A' and resid 982 through 995 removed outlier: 3.638A pdb=" N GLU A 995 " --> pdb=" O LYS A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1015 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 1057 removed outlier: 3.647A pdb=" N VAL A1057 " --> pdb=" O PHE A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1079 removed outlier: 3.529A pdb=" N LEU A1067 " --> pdb=" O MET A1063 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU A1074 " --> pdb=" O GLN A1070 " (cutoff:3.500A) Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1096 through 1107 removed outlier: 3.706A pdb=" N ARG A1100 " --> pdb=" O SER A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1139 Processing helix chain 'A' and resid 1143 through 1146 No H-bonds generated for 'chain 'A' and resid 1143 through 1146' Processing helix chain 'A' and resid 1166 through 1175 removed outlier: 3.626A pdb=" N SER A1175 " --> pdb=" O GLN A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1185 removed outlier: 3.603A pdb=" N GLU A1182 " --> pdb=" O ASP A1178 " (cutoff:3.500A) 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 1271 removed outlier: 3.826A pdb=" N ILE A1271 " --> pdb=" O MET A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1317 removed outlier: 3.570A pdb=" N MET A1317 " --> pdb=" O LEU A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1340 Processing helix chain 'A' and resid 1340 through 1357 Processing helix chain 'A' and resid 1358 through 1360 No H-bonds generated for 'chain 'A' and resid 1358 through 1360' Processing helix chain 'A' and resid 1364 through 1375 removed outlier: 3.916A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1401 removed outlier: 3.531A pdb=" N SER A1401 " --> pdb=" O LEU A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1431 removed outlier: 3.746A pdb=" N ASN A1427 " --> pdb=" O GLY A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1439 Processing helix chain 'B' and resid 29 through 37 removed outlier: 4.117A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 64 removed outlier: 3.505A pdb=" N LEU B 48 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (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 158 through 160 No H-bonds generated for 'chain 'B' and resid 158 through 160' 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 303 removed outlier: 3.936A pdb=" N TYR B 303 " --> pdb=" O GLU B 299 " (cutoff:3.500A) 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: 3.628A pdb=" N ARG B 348 " --> pdb=" O LYS B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 390 removed outlier: 3.544A pdb=" N LYS B 374 " --> pdb=" O PHE B 370 " (cutoff:3.500A) 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: 3.510A pdb=" N GLU B 437 " --> pdb=" O GLN B 433 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU B 438 " --> pdb=" O ARG B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.802A 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 508 through 513 removed outlier: 4.001A pdb=" N ARG B 512 " --> pdb=" O LEU B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 592 through 607 Processing helix chain 'B' and resid 654 through 667 removed outlier: 3.505A 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: 3.627A pdb=" N GLU B 699 " --> pdb=" O GLU B 696 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 removed outlier: 3.654A pdb=" N LEU B 710 " --> pdb=" O PRO B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.789A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 762 removed outlier: 3.508A pdb=" N ASN B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 774 Processing helix chain 'B' and resid 775 through 777 No H-bonds generated for 'chain 'B' and resid 775 through 777' Processing helix chain 'B' and resid 806 through 810 removed outlier: 3.737A pdb=" N GLU B 810 " --> pdb=" O ARG B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.559A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.915A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1061 removed outlier: 3.551A pdb=" N GLU B1061 " --> pdb=" O LYS B1057 " (cutoff:3.500A) 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 removed outlier: 3.554A pdb=" N LEU C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 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 removed outlier: 3.558A pdb=" N GLU C 200 " --> pdb=" O ASP C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 210 removed outlier: 3.844A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 266 Processing helix chain 'D' and resid 51 through 73 Processing helix chain 'D' and resid 118 through 127 Processing helix chain 'D' and resid 128 through 132 removed outlier: 4.093A 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 167 removed outlier: 4.208A pdb=" N VAL D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 179 Processing helix chain 'D' and resid 180 through 182 No H-bonds generated for 'chain 'D' and resid 180 through 182' Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 196 through 199 removed outlier: 3.826A pdb=" N ASN D 199 " --> pdb=" O PRO D 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 196 through 199' Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'E' and resid 4 through 26 Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 44 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 91 through 103 removed outlier: 3.669A pdb=" N THR E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS E 103 " --> pdb=" O HIS E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 124 Processing helix chain 'E' and resid 138 through 141 removed outlier: 3.504A pdb=" N VAL E 141 " --> pdb=" O ALA E 138 " (cutoff:3.500A) No H-bonds generated for '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 171 through 175 removed outlier: 3.621A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) 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 34 removed outlier: 3.609A pdb=" N LEU G 31 " --> pdb=" O LYS G 27 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU G 32 " --> pdb=" O THR G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 54 removed outlier: 3.723A pdb=" N ILE G 54 " --> pdb=" O TYR G 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 93 removed outlier: 3.542A pdb=" N ASP H 92 " --> pdb=" O LEU H 89 " (cutoff:3.500A) 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 42 through 53 removed outlier: 3.690A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP K 53 " --> pdb=" O GLU K 49 " (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 82 through 90 removed outlier: 6.822A pdb=" N THR A 237 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 173 through 177 removed outlier: 3.633A pdb=" N THR A 173 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER A 184 " --> pdb=" O THR A 173 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 343 through 344 removed outlier: 3.522A pdb=" N LYS A 343 " --> pdb=" O PHE B1130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.773A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N MET A 456 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL A 364 " --> pdb=" O LYS A 461 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE A 463 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N VAL A 366 " --> pdb=" O ILE A 463 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 375 through 379 removed outlier: 6.293A pdb=" N LYS A 431 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL A 405 " --> pdb=" O LYS A 431 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLU A 433 " --> pdb=" O LYS A 403 " (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: 6.892A 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: 6.915A 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 1284 through 1292 Processing sheet with id=AB5, first strand: chain 'A' and resid 1141 through 1142 removed outlier: 4.000A pdb=" N ARG A1274 " --> pdb=" O THR A1141 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1224 through 1227 removed outlier: 4.952A pdb=" N VAL A1242 " --> pdb=" O TRP A1191 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N TRP A1191 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU A1192 " --> pdb=" O ILE A1152 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE A1152 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ARG A1194 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N SER A1150 " --> pdb=" O ARG A1194 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU A1196 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR I 44 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 143 through 147 removed outlier: 3.524A 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: 5.447A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR B 136 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA B 153 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N GLU B 138 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 5.733A 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: 5.447A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.501A 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: 6.308A 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: 3.790A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER B 242 " --> pdb=" O SER B 252 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 252 " --> pdb=" O SER B 242 " (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: 3.833A pdb=" N GLU B 650 " --> pdb=" O GLU B 641 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 564 through 565 removed outlier: 5.509A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 792 through 796 removed outlier: 6.951A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.617A 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 796 removed outlier: 6.951A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.236A 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: 7.044A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 910 through 913 removed outlier: 3.555A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD5, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD6, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD7, first strand: chain 'C' and resid 7 through 13 removed outlier: 5.413A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TYR C 229 " --> pdb=" O PHE C 178 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE C 178 " --> pdb=" O TYR C 229 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ASN C 231 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILE C 176 " --> pdb=" O ASN C 231 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLU C 233 " --> pdb=" O ALA C 174 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.632A pdb=" N GLU C 152 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N THR C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LYS C 154 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N VAL C 51 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR C 156 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N VAL C 49 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL C 158 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 111 through 114 removed outlier: 6.325A pdb=" N THR C 111 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LYS C 146 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL C 113 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 37 through 38 removed outlier: 3.783A pdb=" N GLN D 37 " --> pdb=" O GLU D 45 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.307A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLY E 108 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N PHE E 135 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N PHE E 110 " --> pdb=" O PHE E 135 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.698A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE E 178 " --> pdb=" O MET E 215 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 2 through 13 removed outlier: 3.831A pdb=" N PHE G 3 " --> pdb=" O VAL G 78 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL G 78 " --> pdb=" O PHE G 3 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS G 5 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA G 76 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL G 77 " --> pdb=" O CYS G 47 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 86 through 94 removed outlier: 4.168A pdb=" N THR G 90 " --> pdb=" O GLN G 102 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL G 92 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N GLY G 161 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N PHE G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE G 143 " --> pdb=" O GLY G 89 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLY G 89 " --> pdb=" O ILE G 143 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL G 145 " --> pdb=" O VAL G 87 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL G 87 " --> pdb=" O VAL G 145 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 151 through 152 Processing sheet with id=AE7, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.672A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU H 121 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG H 145 " --> pdb=" O THR H 56 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 15 through 19 removed outlier: 3.585A pdb=" N ARG I 24 " --> pdb=" O ASP I 19 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE I 27 " --> pdb=" O GLU I 36 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU I 36 " --> pdb=" O PHE I 27 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 70 through 71 removed outlier: 3.812A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 21 through 24 removed outlier: 4.611A pdb=" N ALA K 30 " --> pdb=" O ASP K 24 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE K 71 " --> pdb=" O PHE K 35 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LYS K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N TYR K 61 " --> pdb=" O LYS K 72 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLN K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) 1253 hydrogen bonds defined for protein. 3486 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 66 hydrogen bonds 132 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 9.59 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.42: 13592 1.42 - 1.66: 19153 1.66 - 1.89: 304 1.89 - 2.12: 1 2.12 - 2.36: 4 Bond restraints: 33054 Sorted by residual: bond pdb=" CA THR D 133 " pdb=" CB THR D 133 " ideal model delta sigma weight residual 1.528 2.089 -0.561 1.59e-02 3.96e+03 1.24e+03 bond pdb=" CD2 PHE D 70 " pdb=" CE2 PHE D 70 " ideal model delta sigma weight residual 1.382 2.357 -0.975 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 2.342 -0.960 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 2.327 -0.945 3.00e-02 1.11e+03 9.92e+02 bond pdb=" CE2 PHE D 70 " pdb=" CZ PHE D 70 " ideal model delta sigma weight residual 1.382 2.326 -0.944 3.00e-02 1.11e+03 9.91e+02 ... (remaining 33049 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.92: 44829 4.92 - 9.85: 25 9.85 - 14.77: 2 14.77 - 19.70: 2 19.70 - 24.62: 1 Bond angle restraints: 44859 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 110.50 135.12 -24.62 1.70e+00 3.46e-01 2.10e+02 angle pdb=" CA THR D 133 " pdb=" CB THR D 133 " pdb=" OG1 THR D 133 " ideal model delta sigma weight residual 109.60 128.12 -18.52 1.50e+00 4.44e-01 1.52e+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 92.13 17.17 2.00e+00 2.50e-01 7.37e+01 angle pdb=" N THR D 133 " pdb=" CA THR D 133 " pdb=" C THR D 133 " ideal model delta sigma weight residual 111.36 102.12 9.24 1.09e+00 8.42e-01 7.18e+01 angle pdb=" C THR D 133 " pdb=" CA THR D 133 " pdb=" CB THR D 133 " ideal model delta sigma weight residual 110.85 124.17 -13.32 1.70e+00 3.46e-01 6.14e+01 ... (remaining 44854 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.25: 19413 25.25 - 50.50: 585 50.50 - 75.74: 99 75.74 - 100.99: 7 100.99 - 126.24: 4 Dihedral angle restraints: 20108 sinusoidal: 8704 harmonic: 11404 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 -141.50 19.50 0 2.50e+00 1.60e-01 6.09e+01 dihedral pdb=" CA SER I 40 " pdb=" C SER I 40 " pdb=" N PRO I 41 " pdb=" CA PRO I 41 " ideal model delta harmonic sigma weight residual -180.00 -143.21 -36.79 0 5.00e+00 4.00e-02 5.41e+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 123.40 139.14 -15.74 0 2.50e+00 1.60e-01 3.96e+01 ... (remaining 20105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.186: 5044 0.186 - 0.373: 1 0.373 - 0.559: 0 0.559 - 0.745: 0 0.745 - 0.931: 1 Chirality restraints: 5046 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 1.62 0.93 2.00e-01 2.50e+01 2.17e+01 chirality pdb=" C4' GTP T 101 " pdb=" C3' GTP T 101 " pdb=" C5' GTP T 101 " pdb=" O4' GTP T 101 " both_signs ideal model delta sigma weight residual False -2.47 -2.67 0.20 2.00e-01 2.50e+01 9.68e-01 chirality pdb=" CB ILE G 163 " pdb=" CA ILE G 163 " pdb=" CG1 ILE G 163 " pdb=" CG2 ILE G 163 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 6.91e-01 ... (remaining 5043 not shown) Planarity restraints: 5622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 70 " 0.000 2.00e-02 2.50e+03 5.33e-02 4.97e+01 pdb=" CG PHE D 70 " 0.002 2.00e-02 2.50e+03 pdb=" CD1 PHE D 70 " -0.059 2.00e-02 2.50e+03 pdb=" CD2 PHE D 70 " 0.078 2.00e-02 2.50e+03 pdb=" CE1 PHE D 70 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 PHE D 70 " -0.089 2.00e-02 2.50e+03 pdb=" CZ PHE D 70 " 0.041 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 2.41e-02 5.83e+00 pdb=" C THR D 133 " 0.042 2.00e-02 2.50e+03 pdb=" O THR D 133 " -0.016 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 SER I 40 " -0.035 5.00e-02 4.00e+02 5.32e-02 4.53e+00 pdb=" N PRO I 41 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO I 41 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO I 41 " -0.029 5.00e-02 4.00e+02 ... (remaining 5619 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 53 2.35 - 2.99: 15925 2.99 - 3.62: 47185 3.62 - 4.26: 75600 4.26 - 4.90: 127168 Nonbonded interactions: 265931 Sorted by model distance: nonbonded pdb=" O3' A R 18 " pdb="MG MG R 101 " model vdw 1.711 2.170 nonbonded pdb=" OD1 ASP A 481 " pdb="MG MG R 101 " model vdw 1.878 2.170 nonbonded pdb=" CE2 PHE D 70 " pdb=" OG1 THR D 133 " model vdw 2.046 3.340 nonbonded pdb=" O LYS B 801 " pdb=" OG1 THR J 52 " model vdw 2.054 3.040 nonbonded pdb=" OG1 THR D 7 " pdb=" OE1 GLU D 32 " model vdw 2.099 3.040 ... (remaining 265926 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: 2.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 37.270 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 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 0.975 33086 Z= 0.498 Angle : 0.590 24.622 44904 Z= 0.360 Chirality : 0.044 0.931 5046 Planarity : 0.004 0.053 5622 Dihedral : 12.332 126.241 12722 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.12 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.13), residues: 3878 helix: 1.23 (0.15), residues: 1311 sheet: -0.02 (0.22), residues: 579 loop : -0.63 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 66 TYR 0.026 0.001 TYR B 797 PHE 0.089 0.002 PHE D 70 TRP 0.012 0.001 TRP A1228 HIS 0.006 0.001 HIS C 188 Details of bonding type rmsd/Z covalent geometry : bond 0.01242 / 0.50 (33054) covalent geometry : angle 0.58439 / 0.36 (44859) hydrogen bonds : bond 0.16938 / 11.50 ( 1295) hydrogen bonds : angle 6.63973 / 4.68 ( 3618) metal coordination : bond 0.00345 / 0.22 ( 32) metal coordination : angle 2.55168 / 1.68 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 746 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 SER cc_start: 0.8065 (t) cc_final: 0.7624 (m) REVERT: A 1109 LYS cc_start: 0.8275 (mptt) cc_final: 0.8003 (mmmt) REVERT: B 597 MET cc_start: 0.8178 (tpt) cc_final: 0.7939 (tpt) REVERT: B 885 MET cc_start: 0.7831 (mmm) cc_final: 0.7555 (mmm) REVERT: B 1125 ASP cc_start: 0.7233 (t0) cc_final: 0.6905 (t0) REVERT: C 224 GLN cc_start: 0.8114 (mt0) cc_final: 0.7899 (mt0) REVERT: F 154 ASP cc_start: 0.7282 (t0) cc_final: 0.7032 (t0) REVERT: H 22 LYS cc_start: 0.8444 (mttp) cc_final: 0.8027 (mttt) REVERT: H 27 GLU cc_start: 0.6947 (mt-10) cc_final: 0.6320 (mt-10) REVERT: I 45 ARG cc_start: 0.8086 (ttt90) cc_final: 0.7666 (ttt90) REVERT: L 70 ARG cc_start: 0.8347 (mtt180) cc_final: 0.8050 (mtt180) outliers start: 0 outliers final: 0 residues processed: 746 average time/residue: 0.2402 time to fit residues: 273.6749 Evaluate side-chains 453 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 453 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 30.0000 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 358 ASN A 517 ASN A 838 GLN A 959 ASN ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 592 ASN B 822 ASN B 862 GLN B1176 ASN B1178 ASN C 203 GLN D 179 GLN E 99 HIS E 143 ASN H 33 GLN I 90 GLN K 96 ASN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.155047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.111669 restraints weight = 40848.893| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.80 r_work: 0.3061 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 1.034 33086 Z= 0.490 Angle : 0.638 24.201 44904 Z= 0.338 Chirality : 0.047 0.799 5046 Planarity : 0.005 0.057 5622 Dihedral : 11.818 123.901 4877 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.33 % Favored : 96.54 % Rotamer: Outliers : 1.16 % Allowed : 7.32 % Favored : 91.53 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 0.59 % 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: 0.01 (0.13), residues: 3878 helix: 1.14 (0.14), residues: 1341 sheet: -0.24 (0.22), residues: 556 loop : -0.67 (0.13), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 996 TYR 0.026 0.002 TYR A 836 PHE 0.079 0.002 PHE D 70 TRP 0.020 0.001 TRP A1228 HIS 0.009 0.001 HIS A 816 Details of bonding type rmsd/Z covalent geometry : bond 0.01284 / 0.49 (33054) covalent geometry : angle 0.62763 / 0.34 (44859) hydrogen bonds : bond 0.04957 / 3.33 ( 1295) hydrogen bonds : angle 5.07681 / 3.60 ( 3618) metal coordination : bond 0.00641 / 0.43 ( 32) metal coordination : angle 3.63922 / 2.46 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 459 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.7914 (tt0) cc_final: 0.7520 (tt0) REVERT: A 486 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8278 (mt-10) REVERT: A 1109 LYS cc_start: 0.8803 (mptt) cc_final: 0.8162 (mmmt) REVERT: A 1225 PHE cc_start: 0.8195 (t80) cc_final: 0.7613 (t80) REVERT: B 319 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7608 (mt-10) REVERT: B 597 MET cc_start: 0.8990 (tpt) cc_final: 0.8728 (tpt) REVERT: B 622 LYS cc_start: 0.8865 (mttt) cc_final: 0.8376 (mtmm) REVERT: B 885 MET cc_start: 0.7922 (mmm) cc_final: 0.7717 (mmm) REVERT: B 908 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7223 (tm-30) REVERT: B 1125 ASP cc_start: 0.8328 (t0) cc_final: 0.7697 (t0) REVERT: C 19 ASP cc_start: 0.8135 (t0) cc_final: 0.7932 (t0) REVERT: E 50 MET cc_start: 0.5739 (pmm) cc_final: 0.5355 (pmm) REVERT: E 57 MET cc_start: 0.7885 (ttm) cc_final: 0.7537 (ttt) REVERT: H 19 ARG cc_start: 0.7769 (mmp80) cc_final: 0.7193 (mtt90) REVERT: H 22 LYS cc_start: 0.8641 (mttp) cc_final: 0.8312 (mttt) REVERT: H 138 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7973 (mt-10) REVERT: I 8 ARG cc_start: 0.7545 (ttp-170) cc_final: 0.7302 (ttp-110) REVERT: L 47 ARG cc_start: 0.7880 (ttp80) cc_final: 0.7581 (ttp80) outliers start: 40 outliers final: 27 residues processed: 491 average time/residue: 0.2341 time to fit residues: 177.3200 Evaluate side-chains 434 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 407 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1112 LYS Chi-restraints excluded: chain A residue 1138 ILE Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 682 SER Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 1149 GLU Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain L residue 65 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 387 optimal weight: 7.9990 chunk 181 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 121 optimal weight: 8.9990 chunk 304 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 191 optimal weight: 3.9990 chunk 218 optimal weight: 4.9990 chunk 382 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 838 GLN A 959 ASN ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN K 96 ASN L 53 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.154042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.110382 restraints weight = 40604.271| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.89 r_work: 0.3057 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 1.024 33086 Z= 0.483 Angle : 0.604 24.219 44904 Z= 0.321 Chirality : 0.046 0.790 5046 Planarity : 0.005 0.053 5622 Dihedral : 11.839 118.854 4877 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.38 % Favored : 96.52 % Rotamer: Outliers : 1.47 % Allowed : 9.46 % Favored : 89.07 % 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: -0.02 (0.13), residues: 3878 helix: 1.13 (0.14), residues: 1351 sheet: -0.29 (0.21), residues: 582 loop : -0.70 (0.14), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 996 TYR 0.022 0.002 TYR A 836 PHE 0.083 0.002 PHE D 70 TRP 0.022 0.001 TRP A1228 HIS 0.009 0.001 HIS C 188 Details of bonding type rmsd/Z covalent geometry : bond 0.01268 / 0.48 (33054) covalent geometry : angle 0.59507 / 0.32 (44859) hydrogen bonds : bond 0.04625 / 3.11 ( 1295) hydrogen bonds : angle 4.76139 / 3.38 ( 3618) metal coordination : bond 0.00559 / 0.39 ( 32) metal coordination : angle 3.36486 / 2.26 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 425 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ASP cc_start: 0.8021 (t0) cc_final: 0.7755 (t0) REVERT: A 317 LYS cc_start: 0.7277 (mttm) cc_final: 0.6866 (mmtt) REVERT: A 486 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8284 (mt-10) REVERT: A 806 ARG cc_start: 0.9086 (OUTLIER) cc_final: 0.8842 (mtt-85) REVERT: A 930 ASP cc_start: 0.7860 (t0) cc_final: 0.7625 (t70) REVERT: A 1109 LYS cc_start: 0.8862 (mptt) cc_final: 0.8208 (mmmt) REVERT: A 1225 PHE cc_start: 0.8204 (t80) cc_final: 0.7801 (t80) REVERT: B 595 ARG cc_start: 0.7584 (ttp-170) cc_final: 0.7372 (ttm170) REVERT: B 597 MET cc_start: 0.8953 (tpt) cc_final: 0.8712 (tpt) REVERT: B 622 LYS cc_start: 0.8909 (mttt) cc_final: 0.8441 (mtmm) REVERT: B 908 GLU cc_start: 0.7528 (tm-30) cc_final: 0.7246 (tm-30) REVERT: B 1125 ASP cc_start: 0.8305 (t0) cc_final: 0.7707 (t0) REVERT: H 8 ASP cc_start: 0.8600 (t0) cc_final: 0.8309 (t0) REVERT: H 19 ARG cc_start: 0.7780 (mmp80) cc_final: 0.7178 (mtt90) REVERT: H 22 LYS cc_start: 0.8616 (mttp) cc_final: 0.8288 (mttt) REVERT: H 27 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7783 (mt-10) REVERT: H 138 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7916 (mt-10) REVERT: L 36 SER cc_start: 0.8854 (m) cc_final: 0.8446 (p) REVERT: L 47 ARG cc_start: 0.7872 (ttp80) cc_final: 0.7626 (ttp80) outliers start: 51 outliers final: 30 residues processed: 466 average time/residue: 0.2243 time to fit residues: 162.0527 Evaluate side-chains 426 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 395 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 806 ARG Chi-restraints excluded: chain A residue 1005 GLU Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1138 ILE Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1361 SER Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 963 PHE Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1149 GLU Chi-restraints excluded: chain B residue 1162 ILE Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain L residue 65 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 253 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 255 optimal weight: 2.9990 chunk 375 optimal weight: 0.0570 chunk 296 optimal weight: 7.9990 chunk 219 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 283 optimal weight: 20.0000 chunk 319 optimal weight: 0.7980 chunk 37 optimal weight: 7.9990 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 838 GLN A1033 GLN ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN H 33 GLN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.155866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.112502 restraints weight = 40261.044| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.80 r_work: 0.3079 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.028 33086 Z= 0.455 Angle : 0.545 24.201 44904 Z= 0.293 Chirality : 0.044 0.788 5046 Planarity : 0.004 0.051 5622 Dihedral : 11.781 121.396 4877 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.99 % Favored : 96.91 % Rotamer: Outliers : 1.13 % Allowed : 10.90 % Favored : 87.97 % 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: 0.18 (0.13), residues: 3878 helix: 1.36 (0.14), residues: 1350 sheet: -0.22 (0.21), residues: 571 loop : -0.62 (0.14), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 348 TYR 0.019 0.001 TYR B 666 PHE 0.081 0.001 PHE D 70 TRP 0.013 0.001 TRP A1044 HIS 0.004 0.001 HIS A 816 Details of bonding type rmsd/Z covalent geometry : bond 0.01202 / 0.46 (33054) covalent geometry : angle 0.53711 / 0.29 (44859) hydrogen bonds : bond 0.03913 / 2.64 ( 1295) hydrogen bonds : angle 4.49207 / 3.19 ( 3618) metal coordination : bond 0.00387 / 0.26 ( 32) metal coordination : angle 2.93495 / 1.95 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 421 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.7886 (tt0) cc_final: 0.7515 (tt0) REVERT: A 317 LYS cc_start: 0.7263 (mttm) cc_final: 0.6857 (mmtt) REVERT: A 479 ASN cc_start: 0.8963 (t0) cc_final: 0.8565 (t0) REVERT: A 486 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8245 (mt-10) REVERT: A 1109 LYS cc_start: 0.8831 (mptt) cc_final: 0.8179 (mmmt) REVERT: A 1225 PHE cc_start: 0.8178 (t80) cc_final: 0.7604 (t80) REVERT: B 303 TYR cc_start: 0.7572 (m-80) cc_final: 0.6997 (m-80) REVERT: B 595 ARG cc_start: 0.7592 (ttp-170) cc_final: 0.7365 (ttp-110) REVERT: B 622 LYS cc_start: 0.8871 (mttt) cc_final: 0.8443 (mtmm) REVERT: B 1125 ASP cc_start: 0.8303 (t0) cc_final: 0.7728 (t0) REVERT: H 19 ARG cc_start: 0.7697 (mmp80) cc_final: 0.7152 (mtt180) REVERT: H 22 LYS cc_start: 0.8640 (mttp) cc_final: 0.8313 (mttt) REVERT: H 138 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7942 (mt-10) REVERT: L 36 SER cc_start: 0.8834 (m) cc_final: 0.8489 (p) REVERT: L 47 ARG cc_start: 0.7837 (ttp80) cc_final: 0.7570 (ttp80) outliers start: 39 outliers final: 23 residues processed: 454 average time/residue: 0.2222 time to fit residues: 156.7606 Evaluate side-chains 417 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 394 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1005 GLU Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1138 ILE Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 963 PHE Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1019 SER Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain I residue 105 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 22 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 292 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 244 optimal weight: 0.0570 chunk 256 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 267 optimal weight: 8.9990 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 838 GLN ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN H 33 GLN K 96 ASN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.155576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.112529 restraints weight = 40487.658| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.98 r_work: 0.3065 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.026 33086 Z= 0.458 Angle : 0.544 24.201 44904 Z= 0.291 Chirality : 0.044 0.790 5046 Planarity : 0.004 0.053 5622 Dihedral : 11.737 123.977 4877 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.15 % Favored : 96.75 % Rotamer: Outliers : 1.39 % Allowed : 11.42 % Favored : 87.19 % 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: 0.21 (0.13), residues: 3878 helix: 1.41 (0.14), residues: 1353 sheet: -0.20 (0.21), residues: 569 loop : -0.62 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 730 TYR 0.020 0.001 TYR B 666 PHE 0.081 0.002 PHE D 70 TRP 0.013 0.001 TRP A1044 HIS 0.005 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.01212 / 0.46 (33054) covalent geometry : angle 0.53631 / 0.29 (44859) hydrogen bonds : bond 0.03873 / 2.61 ( 1295) hydrogen bonds : angle 4.36403 / 3.10 ( 3618) metal coordination : bond 0.00395 / 0.27 ( 32) metal coordination : angle 2.83663 / 1.90 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 417 time to evaluate : 1.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.7901 (tt0) cc_final: 0.7478 (tt0) REVERT: A 307 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.8346 (t0) REVERT: A 317 LYS cc_start: 0.7371 (mttm) cc_final: 0.6902 (mttt) REVERT: A 479 ASN cc_start: 0.8950 (t0) cc_final: 0.8556 (t0) REVERT: A 486 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8275 (mt-10) REVERT: A 806 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8794 (mtt-85) REVERT: A 1109 LYS cc_start: 0.8850 (mptt) cc_final: 0.8185 (mmmt) REVERT: B 228 LYS cc_start: 0.8373 (mmmm) cc_final: 0.7907 (mmmt) REVERT: B 303 TYR cc_start: 0.7546 (m-80) cc_final: 0.6937 (m-80) REVERT: B 606 LYS cc_start: 0.8700 (ttpp) cc_final: 0.8454 (ttpp) REVERT: B 622 LYS cc_start: 0.8865 (mttt) cc_final: 0.8430 (mtmm) REVERT: B 1124 ARG cc_start: 0.8270 (mtm-85) cc_final: 0.8034 (mtm180) REVERT: B 1125 ASP cc_start: 0.8306 (t0) cc_final: 0.7746 (t0) REVERT: C 16 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.8018 (t0) REVERT: H 19 ARG cc_start: 0.7691 (mmp80) cc_final: 0.7152 (mtt180) REVERT: H 22 LYS cc_start: 0.8623 (mttp) cc_final: 0.8286 (mttt) REVERT: H 27 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7840 (mt-10) REVERT: H 138 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7954 (mt-10) REVERT: I 49 ILE cc_start: 0.7554 (OUTLIER) cc_final: 0.7206 (mt) REVERT: L 36 SER cc_start: 0.8712 (m) cc_final: 0.8378 (p) REVERT: L 47 ARG cc_start: 0.7948 (ttp80) cc_final: 0.7639 (ttp80) outliers start: 48 outliers final: 34 residues processed: 452 average time/residue: 0.2365 time to fit residues: 165.1256 Evaluate side-chains 435 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 397 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 806 ARG Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1005 GLU Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1138 ILE Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 648 HIS Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 963 PHE Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1019 SER Chi-restraints excluded: chain B residue 1153 GLU Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 105 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 172 optimal weight: 1.9990 chunk 3 optimal weight: 0.0030 chunk 214 optimal weight: 5.9990 chunk 364 optimal weight: 8.9990 chunk 149 optimal weight: 6.9990 chunk 201 optimal weight: 0.0970 chunk 225 optimal weight: 6.9990 chunk 349 optimal weight: 3.9990 chunk 74 optimal weight: 0.2980 chunk 138 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 838 GLN ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN H 33 GLN K 96 ASN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.156539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.113271 restraints weight = 40206.909| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.97 r_work: 0.3087 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.027 33086 Z= 0.451 Angle : 0.522 24.200 44904 Z= 0.282 Chirality : 0.043 0.789 5046 Planarity : 0.004 0.052 5622 Dihedral : 11.672 125.323 4877 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.86 % Favored : 97.03 % Rotamer: Outliers : 1.30 % Allowed : 11.71 % Favored : 86.99 % 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: 3878 helix: 1.52 (0.14), residues: 1353 sheet: -0.09 (0.21), residues: 566 loop : -0.57 (0.14), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 730 TYR 0.018 0.001 TYR B 666 PHE 0.081 0.001 PHE D 70 TRP 0.014 0.001 TRP A1044 HIS 0.004 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.01195 / 0.45 (33054) covalent geometry : angle 0.51595 / 0.28 (44859) hydrogen bonds : bond 0.03610 / 2.44 ( 1295) hydrogen bonds : angle 4.23033 / 3.00 ( 3618) metal coordination : bond 0.00342 / 0.23 ( 32) metal coordination : angle 2.61866 / 1.73 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 417 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 ASP cc_start: 0.8549 (OUTLIER) cc_final: 0.8324 (t0) REVERT: A 317 LYS cc_start: 0.7418 (mttm) cc_final: 0.6938 (mttt) REVERT: A 479 ASN cc_start: 0.8916 (t0) cc_final: 0.8544 (t0) REVERT: A 486 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8192 (mt-10) REVERT: A 1109 LYS cc_start: 0.8823 (mptt) cc_final: 0.8149 (mmmt) REVERT: A 1209 MET cc_start: 0.8302 (mmm) cc_final: 0.8101 (mmm) REVERT: A 1225 PHE cc_start: 0.8154 (t80) cc_final: 0.7598 (t80) REVERT: B 228 LYS cc_start: 0.8338 (mmmm) cc_final: 0.7900 (mmmt) REVERT: B 303 TYR cc_start: 0.7501 (m-80) cc_final: 0.6825 (m-80) REVERT: B 622 LYS cc_start: 0.8862 (mttt) cc_final: 0.8440 (mtmm) REVERT: B 1124 ARG cc_start: 0.8198 (mtm-85) cc_final: 0.7968 (mtm180) REVERT: B 1125 ASP cc_start: 0.8246 (t0) cc_final: 0.7712 (t0) REVERT: C 16 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.8024 (t0) REVERT: E 57 MET cc_start: 0.7948 (ttp) cc_final: 0.7681 (ttt) REVERT: H 19 ARG cc_start: 0.7618 (mmp80) cc_final: 0.7082 (mtt180) REVERT: H 22 LYS cc_start: 0.8617 (mttp) cc_final: 0.8281 (mttt) REVERT: H 27 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7836 (mt-10) REVERT: H 138 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7924 (mt-10) REVERT: L 36 SER cc_start: 0.8633 (m) cc_final: 0.8380 (p) REVERT: L 47 ARG cc_start: 0.7892 (ttp80) cc_final: 0.7575 (ttp80) outliers start: 45 outliers final: 32 residues processed: 450 average time/residue: 0.2283 time to fit residues: 159.0407 Evaluate side-chains 432 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 398 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1005 GLU Chi-restraints excluded: chain A residue 1033 GLN Chi-restraints excluded: chain A residue 1138 ILE Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 648 HIS Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 963 PHE Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1019 SER Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain I residue 105 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 177 optimal weight: 5.9990 chunk 131 optimal weight: 0.6980 chunk 123 optimal weight: 6.9990 chunk 321 optimal weight: 5.9990 chunk 229 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 205 optimal weight: 0.7980 chunk 324 optimal weight: 2.9990 chunk 370 optimal weight: 2.9990 chunk 295 optimal weight: 5.9990 chunk 386 optimal weight: 0.8980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 838 GLN ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 GLN F 104 ASN H 33 GLN K 96 ASN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.157229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.113205 restraints weight = 40483.131| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.97 r_work: 0.3096 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.026 33086 Z= 0.455 Angle : 0.534 24.187 44904 Z= 0.285 Chirality : 0.043 0.793 5046 Planarity : 0.004 0.054 5622 Dihedral : 11.635 126.613 4877 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.07 % Favored : 96.83 % Rotamer: Outliers : 1.62 % Allowed : 11.80 % Favored : 86.58 % 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: 0.31 (0.13), residues: 3878 helix: 1.51 (0.14), residues: 1355 sheet: -0.11 (0.21), residues: 579 loop : -0.60 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 348 TYR 0.022 0.001 TYR B 666 PHE 0.081 0.001 PHE D 70 TRP 0.013 0.001 TRP A1044 HIS 0.005 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.01205 / 0.46 (33054) covalent geometry : angle 0.52704 / 0.29 (44859) hydrogen bonds : bond 0.03669 / 2.48 ( 1295) hydrogen bonds : angle 4.19759 / 2.98 ( 3618) metal coordination : bond 0.00372 / 0.26 ( 32) metal coordination : angle 2.67850 / 1.79 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 410 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8244 (mp0) cc_final: 0.7945 (mp0) REVERT: A 116 ASP cc_start: 0.8008 (t0) cc_final: 0.7753 (t0) REVERT: A 307 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.8263 (t0) REVERT: A 317 LYS cc_start: 0.7502 (mttm) cc_final: 0.6993 (mttt) REVERT: A 479 ASN cc_start: 0.8909 (t0) cc_final: 0.8562 (t0) REVERT: A 486 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8157 (mt-10) REVERT: A 487 MET cc_start: 0.9190 (mtp) cc_final: 0.8868 (mtp) REVERT: A 806 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8779 (mtt-85) REVERT: A 1109 LYS cc_start: 0.8836 (mptt) cc_final: 0.8204 (mmmt) REVERT: A 1225 PHE cc_start: 0.8173 (t80) cc_final: 0.7630 (t80) REVERT: A 1228 TRP cc_start: 0.8115 (m-10) cc_final: 0.7760 (m-10) REVERT: B 228 LYS cc_start: 0.8330 (mmmm) cc_final: 0.7929 (mmmt) REVERT: B 303 TYR cc_start: 0.7527 (m-80) cc_final: 0.6850 (m-80) REVERT: B 622 LYS cc_start: 0.8810 (mttt) cc_final: 0.8358 (mtmm) REVERT: B 1124 ARG cc_start: 0.8346 (mtm-85) cc_final: 0.8038 (mtm180) REVERT: B 1125 ASP cc_start: 0.8272 (t0) cc_final: 0.7768 (t0) REVERT: E 57 MET cc_start: 0.8057 (ttp) cc_final: 0.7750 (ttt) REVERT: H 19 ARG cc_start: 0.7661 (mmp80) cc_final: 0.7119 (mtt180) REVERT: H 22 LYS cc_start: 0.8583 (mttp) cc_final: 0.8232 (mttt) REVERT: H 27 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7907 (mt-10) REVERT: H 138 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7950 (mt-10) REVERT: I 49 ILE cc_start: 0.7455 (OUTLIER) cc_final: 0.7122 (mt) REVERT: L 36 SER cc_start: 0.8656 (m) cc_final: 0.8432 (p) REVERT: L 47 ARG cc_start: 0.7933 (ttp80) cc_final: 0.7634 (ttp80) REVERT: L 54 ARG cc_start: 0.8297 (ptp-170) cc_final: 0.8005 (ptp-170) outliers start: 56 outliers final: 36 residues processed: 450 average time/residue: 0.2131 time to fit residues: 149.5786 Evaluate side-chains 441 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 402 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 806 ARG Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1005 GLU Chi-restraints excluded: chain A residue 1033 GLN Chi-restraints excluded: chain A residue 1138 ILE Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1361 SER Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 650 GLU Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 963 PHE Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1019 SER Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 105 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 249 optimal weight: 0.9980 chunk 254 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 357 optimal weight: 8.9990 chunk 384 optimal weight: 8.9990 chunk 130 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 101 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 838 GLN A 959 ASN ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN H 33 GLN K 96 ASN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.158045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.114800 restraints weight = 40526.770| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.07 r_work: 0.3093 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.026 33086 Z= 0.451 Angle : 0.522 24.191 44904 Z= 0.280 Chirality : 0.043 0.791 5046 Planarity : 0.004 0.055 5622 Dihedral : 11.565 127.105 4877 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.68 % Favored : 97.22 % Rotamer: Outliers : 1.36 % Allowed : 12.23 % Favored : 86.41 % 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: 0.40 (0.14), residues: 3878 helix: 1.59 (0.14), residues: 1356 sheet: -0.01 (0.21), residues: 575 loop : -0.57 (0.14), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG B 348 TYR 0.020 0.001 TYR B 666 PHE 0.081 0.001 PHE D 70 TRP 0.015 0.001 TRP A1044 HIS 0.003 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.01194 / 0.45 (33054) covalent geometry : angle 0.51563 / 0.28 (44859) hydrogen bonds : bond 0.03491 / 2.36 ( 1295) hydrogen bonds : angle 4.12632 / 2.93 ( 3618) metal coordination : bond 0.00318 / 0.22 ( 32) metal coordination : angle 2.51874 / 1.67 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 418 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8257 (mp0) cc_final: 0.7946 (mp0) REVERT: A 116 ASP cc_start: 0.8062 (t0) cc_final: 0.7785 (t0) REVERT: A 307 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.8296 (t0) REVERT: A 317 LYS cc_start: 0.7580 (mttm) cc_final: 0.7009 (mttt) REVERT: A 479 ASN cc_start: 0.8908 (t0) cc_final: 0.8600 (t0) REVERT: A 486 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8205 (mt-10) REVERT: A 806 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8771 (mtt-85) REVERT: A 1109 LYS cc_start: 0.8833 (mptt) cc_final: 0.8159 (mmmt) REVERT: A 1225 PHE cc_start: 0.8154 (t80) cc_final: 0.7583 (t80) REVERT: A 1228 TRP cc_start: 0.8102 (m-10) cc_final: 0.7734 (m-10) REVERT: B 303 TYR cc_start: 0.7389 (m-80) cc_final: 0.6659 (m-80) REVERT: B 622 LYS cc_start: 0.8849 (mttt) cc_final: 0.8420 (mtmm) REVERT: B 864 LYS cc_start: 0.7267 (mtmt) cc_final: 0.6621 (tttm) REVERT: B 1124 ARG cc_start: 0.8275 (mtm-85) cc_final: 0.7959 (mtm180) REVERT: B 1125 ASP cc_start: 0.8260 (t0) cc_final: 0.7725 (t0) REVERT: C 249 ASP cc_start: 0.8483 (t70) cc_final: 0.7908 (t0) REVERT: E 50 MET cc_start: 0.5575 (pmm) cc_final: 0.5199 (pmm) REVERT: H 19 ARG cc_start: 0.7598 (mmp80) cc_final: 0.7100 (mtt180) REVERT: H 22 LYS cc_start: 0.8588 (mttp) cc_final: 0.8215 (mttt) REVERT: H 27 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7867 (mt-10) REVERT: H 138 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7925 (mt-10) REVERT: I 49 ILE cc_start: 0.7334 (OUTLIER) cc_final: 0.6999 (mt) REVERT: L 36 SER cc_start: 0.8632 (m) cc_final: 0.8417 (p) REVERT: L 47 ARG cc_start: 0.7895 (ttp80) cc_final: 0.7581 (ttp80) REVERT: L 54 ARG cc_start: 0.8307 (ptp-170) cc_final: 0.7972 (ptp-170) outliers start: 47 outliers final: 35 residues processed: 455 average time/residue: 0.2388 time to fit residues: 168.8436 Evaluate side-chains 437 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 399 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 806 ARG Chi-restraints excluded: chain A residue 1005 GLU Chi-restraints excluded: chain A residue 1033 GLN Chi-restraints excluded: chain A residue 1138 ILE Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1361 SER Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 648 HIS Chi-restraints excluded: chain B residue 650 GLU Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 963 PHE Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1019 SER Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 105 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 74 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 283 optimal weight: 0.9980 chunk 284 optimal weight: 20.0000 chunk 267 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 838 GLN ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN H 33 GLN K 96 ASN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.154763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.110504 restraints weight = 40172.526| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.00 r_work: 0.3061 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.023 33086 Z= 0.468 Angle : 0.567 24.172 44904 Z= 0.300 Chirality : 0.044 0.798 5046 Planarity : 0.004 0.055 5622 Dihedral : 11.546 127.464 4877 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.33 % Favored : 96.57 % Rotamer: Outliers : 1.45 % Allowed : 12.26 % Favored : 86.29 % 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: 0.30 (0.13), residues: 3878 helix: 1.49 (0.14), residues: 1355 sheet: -0.15 (0.21), residues: 587 loop : -0.58 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 348 TYR 0.021 0.001 TYR B 666 PHE 0.081 0.002 PHE D 70 TRP 0.012 0.001 TRP A1044 HIS 0.006 0.001 HIS C 188 Details of bonding type rmsd/Z covalent geometry : bond 0.01235 / 0.47 (33054) covalent geometry : angle 0.56027 / 0.30 (44859) hydrogen bonds : bond 0.03884 / 2.62 ( 1295) hydrogen bonds : angle 4.23047 / 3.00 ( 3618) metal coordination : bond 0.00445 / 0.31 ( 32) metal coordination : angle 2.88545 / 1.94 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 400 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8286 (mp0) cc_final: 0.7988 (mp0) REVERT: A 41 MET cc_start: 0.6892 (mmm) cc_final: 0.6104 (mmm) REVERT: A 116 ASP cc_start: 0.8081 (t0) cc_final: 0.7831 (t0) REVERT: A 311 GLN cc_start: 0.8595 (mm110) cc_final: 0.8247 (mp10) REVERT: A 317 LYS cc_start: 0.7557 (mttm) cc_final: 0.7046 (mttt) REVERT: A 479 ASN cc_start: 0.8935 (t0) cc_final: 0.8571 (t0) REVERT: A 486 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8144 (mt-10) REVERT: A 526 ASP cc_start: 0.8156 (m-30) cc_final: 0.7937 (m-30) REVERT: A 1109 LYS cc_start: 0.8865 (mptt) cc_final: 0.8228 (mmmt) REVERT: A 1225 PHE cc_start: 0.8182 (t80) cc_final: 0.7659 (t80) REVERT: A 1228 TRP cc_start: 0.8118 (m-10) cc_final: 0.7846 (m-10) REVERT: A 1272 THR cc_start: 0.8516 (m) cc_final: 0.8236 (t) REVERT: B 303 TYR cc_start: 0.7442 (m-80) cc_final: 0.6775 (m-80) REVERT: B 595 ARG cc_start: 0.7657 (ttp-110) cc_final: 0.7384 (ttm170) REVERT: B 622 LYS cc_start: 0.8908 (mttt) cc_final: 0.8466 (mtmm) REVERT: B 705 MET cc_start: 0.9199 (tpt) cc_final: 0.8945 (tpt) REVERT: B 730 ARG cc_start: 0.7970 (mtm-85) cc_final: 0.7671 (mtt90) REVERT: B 864 LYS cc_start: 0.7365 (mtmt) cc_final: 0.6772 (tttm) REVERT: B 1125 ASP cc_start: 0.8278 (t0) cc_final: 0.7767 (t0) REVERT: E 50 MET cc_start: 0.5811 (pmm) cc_final: 0.5340 (pmm) REVERT: H 19 ARG cc_start: 0.7837 (mmp80) cc_final: 0.7236 (mtt180) REVERT: H 22 LYS cc_start: 0.8624 (mttp) cc_final: 0.8263 (mttt) REVERT: H 138 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7958 (mt-10) REVERT: I 49 ILE cc_start: 0.7529 (OUTLIER) cc_final: 0.7166 (mt) REVERT: L 36 SER cc_start: 0.8658 (m) cc_final: 0.8440 (p) REVERT: L 47 ARG cc_start: 0.7923 (ttp80) cc_final: 0.7617 (ttp80) REVERT: L 54 ARG cc_start: 0.8375 (ptp-170) cc_final: 0.8028 (ptp-170) outliers start: 50 outliers final: 41 residues processed: 439 average time/residue: 0.2333 time to fit residues: 159.6675 Evaluate side-chains 436 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 394 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 1005 GLU Chi-restraints excluded: chain A residue 1033 GLN Chi-restraints excluded: chain A residue 1138 ILE Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1361 SER Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 650 GLU Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 963 PHE Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 105 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 135 optimal weight: 6.9990 chunk 367 optimal weight: 0.6980 chunk 311 optimal weight: 5.9990 chunk 139 optimal weight: 0.0370 chunk 188 optimal weight: 0.5980 chunk 275 optimal weight: 0.0070 chunk 95 optimal weight: 0.8980 chunk 223 optimal weight: 8.9990 chunk 117 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 208 optimal weight: 1.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 838 GLN ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN H 33 GLN K 96 ASN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.157587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.114370 restraints weight = 40517.481| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.07 r_work: 0.3097 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.025 33086 Z= 0.448 Angle : 0.522 24.183 44904 Z= 0.281 Chirality : 0.042 0.791 5046 Planarity : 0.004 0.053 5622 Dihedral : 11.454 127.773 4877 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.60 % Favored : 97.29 % Rotamer: Outliers : 1.04 % Allowed : 12.75 % Favored : 86.21 % 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: 3878 helix: 1.66 (0.15), residues: 1354 sheet: -0.00 (0.21), residues: 566 loop : -0.52 (0.14), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 348 TYR 0.019 0.001 TYR B 666 PHE 0.080 0.001 PHE D 70 TRP 0.017 0.001 TRP A1044 HIS 0.003 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.01187 / 0.45 (33054) covalent geometry : angle 0.51700 / 0.28 (44859) hydrogen bonds : bond 0.03351 / 2.27 ( 1295) hydrogen bonds : angle 4.06597 / 2.89 ( 3618) metal coordination : bond 0.00297 / 0.20 ( 32) metal coordination : angle 2.35959 / 1.55 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7756 Ramachandran restraints generated. 3878 Oldfield, 0 Emsley, 3878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 423 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8292 (mp0) cc_final: 0.8019 (mp0) REVERT: A 41 MET cc_start: 0.6974 (mmm) cc_final: 0.6285 (mmm) REVERT: A 116 ASP cc_start: 0.8064 (t0) cc_final: 0.7820 (t0) REVERT: A 293 GLU cc_start: 0.7500 (tt0) cc_final: 0.7184 (mm-30) REVERT: A 311 GLN cc_start: 0.8554 (mm110) cc_final: 0.8212 (mp10) REVERT: A 317 LYS cc_start: 0.7556 (mttm) cc_final: 0.7041 (mttt) REVERT: A 479 ASN cc_start: 0.8925 (t0) cc_final: 0.8666 (t0) REVERT: A 486 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8191 (mt-10) REVERT: A 1003 LYS cc_start: 0.8000 (mppt) cc_final: 0.7780 (mppt) REVERT: A 1109 LYS cc_start: 0.8827 (mptt) cc_final: 0.8156 (mmmt) REVERT: A 1225 PHE cc_start: 0.8208 (t80) cc_final: 0.7704 (t80) REVERT: A 1228 TRP cc_start: 0.7990 (m-10) cc_final: 0.7603 (m-10) REVERT: A 1230 GLU cc_start: 0.5796 (mm-30) cc_final: 0.5413 (mm-30) REVERT: B 101 MET cc_start: 0.8735 (mtt) cc_final: 0.8417 (mmm) REVERT: B 303 TYR cc_start: 0.7332 (m-80) cc_final: 0.6533 (m-80) REVERT: B 622 LYS cc_start: 0.8872 (mttt) cc_final: 0.8507 (mtmm) REVERT: B 864 LYS cc_start: 0.7239 (mtmt) cc_final: 0.6658 (tttm) REVERT: B 1124 ARG cc_start: 0.8362 (mtm-85) cc_final: 0.8051 (mtm180) REVERT: B 1125 ASP cc_start: 0.8277 (t0) cc_final: 0.7780 (t0) REVERT: C 249 ASP cc_start: 0.8437 (t70) cc_final: 0.8029 (t0) REVERT: E 50 MET cc_start: 0.5821 (pmm) cc_final: 0.5388 (pmm) REVERT: H 19 ARG cc_start: 0.7676 (mmp80) cc_final: 0.7167 (mtt180) REVERT: H 22 LYS cc_start: 0.8629 (mttp) cc_final: 0.8268 (mttt) REVERT: H 27 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7643 (pt0) REVERT: H 138 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7983 (mt-10) REVERT: L 47 ARG cc_start: 0.7939 (ttp80) cc_final: 0.7642 (ttp80) REVERT: L 54 ARG cc_start: 0.8329 (ptp-170) cc_final: 0.7947 (ptp-170) outliers start: 36 outliers final: 32 residues processed: 450 average time/residue: 0.2275 time to fit residues: 159.3502 Evaluate side-chains 441 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 409 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 1005 GLU Chi-restraints excluded: chain A residue 1033 GLN Chi-restraints excluded: chain A residue 1138 ILE Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1361 SER Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 963 PHE Chi-restraints excluded: chain B residue 1019 SER Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain H residue 37 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 170 optimal weight: 7.9990 chunk 220 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 341 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 365 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN I 87 GLN K 96 ASN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.153662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.110677 restraints weight = 40359.657| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.13 r_work: 0.3043 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 1.021 33086 Z= 0.483 Angle : 0.597 24.143 44904 Z= 0.315 Chirality : 0.046 0.803 5046 Planarity : 0.005 0.055 5622 Dihedral : 11.503 127.795 4877 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.56 % Favored : 96.34 % Rotamer: Outliers : 1.13 % Allowed : 12.96 % Favored : 85.92 % 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: 0.30 (0.13), residues: 3878 helix: 1.46 (0.14), residues: 1351 sheet: -0.17 (0.21), residues: 567 loop : -0.54 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 348 TYR 0.021 0.001 TYR B 666 PHE 0.081 0.002 PHE D 70 TRP 0.010 0.001 TRP A1044 HIS 0.009 0.001 HIS C 188 Details of bonding type rmsd/Z covalent geometry : bond 0.01270 / 0.48 (33054) covalent geometry : angle 0.58891 / 0.31 (44859) hydrogen bonds : bond 0.04128 / 2.78 ( 1295) hydrogen bonds : angle 4.28180 / 3.05 ( 3618) metal coordination : bond 0.00553 / 0.38 ( 32) metal coordination : angle 3.10934 / 2.10 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10278.66 seconds wall clock time: 175 minutes 51.59 seconds (10551.59 seconds total)