Starting phenix.real_space_refine on Sun Aug 9 10:30:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sbv_54740/08_2026/9sbv_54740.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sbv_54740/08_2026/9sbv_54740.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9sbv_54740/08_2026/9sbv_54740.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sbv_54740/08_2026/9sbv_54740.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9sbv_54740/08_2026/9sbv_54740.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sbv_54740/08_2026/9sbv_54740.map" } resolution = 3.73 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= 0.023 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 100 5.49 5 Mg 2 5.21 5 S 182 5.16 5 C 20561 2.51 5 N 5765 2.21 5 O 6465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33083 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 10942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1390, 10942 Classifications: {'peptide': 1390} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1327} Chain breaks: 6 Chain: "B" Number of atoms: 9155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1150, 9155 Classifications: {'peptide': 1150} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 1100} Chain breaks: 6 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: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 909 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} 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: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 905 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "R" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 197 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna3p': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 886 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 35 Unusual residues: {' MG': 2, ' ZN': 2, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 457 SG CYS A 67 106.756 70.149 95.061 1.00206.43 S ATOM 479 SG CYS A 70 106.377 66.715 93.330 1.00216.65 S ATOM 532 SG CYS A 77 103.579 69.291 93.166 1.00193.62 S ATOM 762 SG CYS A 107 81.555 75.892 135.291 1.00246.15 S ATOM 786 SG CYS A 110 82.876 72.478 136.128 1.00235.38 S ATOM 1091 SG CYS A 148 79.489 73.556 137.476 1.00257.55 S ATOM 1105 SG CYS A 167 82.640 75.275 138.811 1.00254.04 S ATOM 19603 SG CYS B1163 98.630 57.774 104.959 1.00209.47 S ATOM 19621 SG CYS B1166 97.006 61.072 105.409 1.00217.99 S ATOM 19746 SG CYS B1182 100.815 60.773 104.855 1.00215.77 S ATOM 19765 SG CYS B1185 99.208 59.819 108.216 1.00214.13 S ATOM 20753 SG CYS C 86 93.207 74.923 26.246 1.00253.40 S ATOM 20770 SG CYS C 88 95.571 77.149 28.031 1.00263.75 S ATOM 20803 SG CYS C 92 94.353 78.210 24.677 1.00233.01 S ATOM 20826 SG CYS C 95 91.927 78.271 27.649 1.00230.51 S ATOM 28411 SG CYS I 7 39.773 125.843 127.305 1.00386.50 S ATOM 28436 SG CYS I 10 43.579 125.592 127.312 1.00379.88 S ATOM 28602 SG CYS I 29 41.487 122.824 128.982 1.00384.86 S ATOM 28626 SG CYS I 32 41.702 126.216 130.534 1.00392.35 S ATOM 28953 SG CYS I 75 16.879 116.668 88.988 1.00448.94 S ATOM 28975 SG CYS I 78 16.508 120.264 87.862 1.00451.00 S ATOM 29191 SG CYS I 103 19.891 118.628 87.663 1.00428.83 S ATOM 29211 SG CYS I 106 18.481 119.494 91.045 1.00439.03 S ATOM 29313 SG CYS J 7 64.113 90.520 37.889 1.00176.44 S ATOM 29336 SG CYS J 10 63.778 88.126 34.858 1.00180.17 S ATOM 29616 SG CYS J 45 60.716 89.093 36.805 1.00183.69 S ATOM 29622 SG CYS J 46 62.520 91.378 34.395 1.00192.09 S ATOM 30745 SG CYS L 31 97.421 113.947 54.248 1.00313.99 S ATOM 30765 SG CYS L 34 98.726 115.812 51.217 1.00314.84 S ATOM 30869 SG CYS L 48 101.085 114.668 54.005 1.00319.51 S ATOM 30892 SG CYS L 51 98.741 117.556 54.616 1.00329.41 S Time building chain proxies: 7.17, per 1000 atoms: 0.22 Number of scatterers: 33083 At special positions: 0 Unit cell: (152.329, 155.593, 183.883, 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 100 15.00 Mg 2 11.99 O 6465 8.00 N 5765 7.00 C 20561 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.24 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1804 " pdb="ZN ZN A1804 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 67 " pdb=" ZN A1805 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 167 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " 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 J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " 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 " Number of angles added : 45 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7340 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 47 sheets defined 39.1% alpha, 19.9% beta 41 base pairs and 77 stacking pairs defined. Time for finding SS restraints: 4.27 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 106 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: 3.669A pdb=" N HIS A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 222 Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.825A 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: 3.850A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 525 through 536 removed outlier: 3.592A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 574 through 579 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: 3.517A pdb=" N HIS A 659 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 672 through 699 removed outlier: 3.598A pdb=" N ALA A 699 " --> pdb=" O LYS A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 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 Processing helix chain 'A' and resid 809 through 829 removed outlier: 3.854A pdb=" N GLU A 822 " --> pdb=" O MET A 818 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLY A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 824 " --> pdb=" O GLY A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 845 removed outlier: 4.223A pdb=" N GLU A 833 " --> pdb=" O VAL A 829 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR A 834 " --> pdb=" O LYS A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 874 through 876 No H-bonds generated for 'chain 'A' and resid 874 through 876' Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 909 through 913 Processing helix chain 'A' and resid 915 through 920 removed outlier: 3.631A pdb=" N LEU A 920 " --> pdb=" O GLY A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 959 through 972 removed outlier: 3.503A pdb=" N ILE A 963 " --> pdb=" O ASN A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 removed outlier: 3.661A pdb=" N GLN A 994 " --> pdb=" O VAL A 990 " (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 1056 Processing helix chain 'A' and resid 1063 through 1083 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1084 through 1087 Processing helix chain 'A' and resid 1091 through 1107 removed outlier: 3.600A pdb=" N THR A1095 " --> pdb=" O SER A1091 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N VAL A1098 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Proline residue: A1099 - end of helix Processing helix chain 'A' and resid 1130 through 1139 Processing helix chain 'A' and resid 1142 through 1146 removed outlier: 3.857A pdb=" N VAL A1146 " --> pdb=" O THR A1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1142 through 1146' Processing helix chain 'A' and resid 1166 through 1174 removed outlier: 4.063A pdb=" N PHE A1174 " --> pdb=" O ILE A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1205 Processing helix chain 'A' and resid 1208 through 1220 Processing helix chain 'A' and resid 1257 through 1270 Processing helix chain 'A' and resid 1312 through 1317 removed outlier: 3.653A 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 1364 through 1376 removed outlier: 4.002A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1401 Processing helix chain 'A' and resid 1404 through 1415 Processing helix chain 'A' and resid 1423 through 1431 removed outlier: 3.518A 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: 4.148A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 65 removed outlier: 4.668A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.581A 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 185 through 192 Processing helix chain 'B' and resid 282 through 289 Processing helix chain 'B' and resid 293 through 303 removed outlier: 3.556A pdb=" N ILE B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU B 299 " --> pdb=" O GLY B 295 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR B 303 " --> pdb=" O GLU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 322 Proline residue: B 316 - end of helix removed outlier: 3.573A pdb=" N GLU B 319 " --> pdb=" O LYS B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 370 through 390 removed outlier: 3.665A 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 439 Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.780A pdb=" N THR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.710A pdb=" N ARG B 496 " --> pdb=" O LEU B 492 " (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 Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.754A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.574A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 756 Processing helix chain 'B' and resid 758 through 762 removed outlier: 3.902A pdb=" N ASN B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 775 removed outlier: 3.969A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 788 removed outlier: 3.625A pdb=" N ARG B 788 " --> pdb=" O TYR B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 813 Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.236A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.867A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1061 removed outlier: 3.750A 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: 3.613A 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 Processing helix chain 'C' and resid 204 through 210 removed outlier: 4.118A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU C 210 " --> pdb=" O CYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 266 Processing helix chain 'D' and resid 23 through 27 Processing helix chain 'D' and resid 30 through 34 removed outlier: 3.872A pdb=" N GLN D 34 " --> pdb=" O GLN D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 73 Processing helix chain 'D' and resid 118 through 132 Processing helix chain 'D' and resid 138 through 152 Processing helix chain 'D' and resid 156 through 171 removed outlier: 3.735A pdb=" N VAL D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 196 through 199 Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'E' and resid 4 through 27 removed outlier: 3.770A pdb=" N ASN E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 44 Processing helix chain 'E' and resid 54 through 59 removed outlier: 3.763A pdb=" N SER E 59 " --> pdb=" O LYS E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 91 through 104 removed outlier: 3.784A pdb=" N THR E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) removed outlier: 3.525A 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 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.685A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 188 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 128 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.707A pdb=" N GLU G 32 " --> pdb=" O THR G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 45 through 47 No H-bonds generated for 'chain 'H' and resid 45 through 47' Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'H' and resid 129 through 133 Processing helix chain 'I' and resid 59 through 65 removed outlier: 3.538A pdb=" N GLY I 63 " --> pdb=" O GLN I 60 " (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 removed outlier: 3.886A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 removed outlier: 3.501A pdb=" N LEU J 61 " --> pdb=" O ILE J 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 53 removed outlier: 3.585A pdb=" N ASN K 44 " --> pdb=" O HIS K 40 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) removed outlier: 3.574A 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: 9.899A pdb=" N LEU A 86 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 11.308A pdb=" N LYS A 88 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N CYS A 238 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 177 Processing sheet with id=AA4, first strand: chain 'A' and resid 250 through 252 Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 344 removed outlier: 3.596A pdb=" N LYS A 343 " --> pdb=" O PHE B1130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.590A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS A 490 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET A 456 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N PHE A 468 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL A 352 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N LEU A 470 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N SER A 354 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.752A pdb=" N ARG A 434 " --> pdb=" O TYR A 376 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.506A pdb=" N LYS A 518 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AB1, first strand: chain 'A' and resid 588 through 590 removed outlier: 7.111A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AB3, first strand: chain 'A' and resid 849 through 850 removed outlier: 6.661A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 878 through 882 Processing sheet with id=AB5, first strand: chain 'A' and resid 1282 through 1292 Processing sheet with id=AB6, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.336A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL A1242 " --> pdb=" O TRP A1191 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N TRP A1191 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU A1192 " --> pdb=" O ILE A1152 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE A1152 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ARG A1194 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER A1150 " --> pdb=" O ARG A1194 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLU A1196 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N TYR I 44 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 48 through 50 removed outlier: 4.676A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE G 4 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY G 59 " --> pdb=" O ILE A1445 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N VAL A1443 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 48 through 50 removed outlier: 4.676A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE G 4 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 71 through 73 removed outlier: 4.545A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL B 132 " --> pdb=" O SER B 156 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N SER B 156 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS B 134 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLU B 154 " --> pdb=" O LYS B 134 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N THR B 136 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE B 152 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B 138 " --> pdb=" O GLU B 150 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 71 through 73 removed outlier: 4.545A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AC3, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC4, first strand: chain 'B' and resid 404 through 407 removed outlier: 6.103A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 224 through 227 removed outlier: 4.183A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC7, first strand: chain 'B' and resid 650 through 651 removed outlier: 3.914A pdb=" N GLU B 650 " --> pdb=" O GLU B 641 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N CYS B 741 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 564 through 565 removed outlier: 5.353A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.577A pdb=" N ILE B 795 " --> pdb=" O LEU B 854 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.577A pdb=" N ILE B 795 " --> pdb=" O LEU B 854 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD3, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 7.003A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE B1012 " --> pdb=" O ALA B 826 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 873 through 874 Processing sheet with id=AD5, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.514A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD7, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD8, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD9, first strand: chain 'C' and resid 7 through 13 removed outlier: 6.893A pdb=" N ASP C 19 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ALA C 13 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASN C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ASN C 231 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE C 176 " --> pdb=" O ASN C 231 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLU C 233 " --> pdb=" O ALA C 174 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.738A pdb=" N GLU C 152 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASN C 54 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LYS C 154 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 111 through 114 removed outlier: 3.590A pdb=" N CYS C 145 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AE4, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.555A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.976A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 169 through 170 removed outlier: 3.526A pdb=" N LYS G 146 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE G 160 " --> pdb=" O GLU G 148 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N CYS G 150 " --> pdb=" O HIS G 158 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N HIS G 158 " --> pdb=" O CYS G 150 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS G 107 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA G 159 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N THR G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.628A pdb=" N TYR G 130 " --> pdb=" O ILE G 137 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE G 137 " --> pdb=" O TYR G 130 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 4 through 16 removed outlier: 5.648A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 15 through 19 Processing sheet with id=AF1, first strand: chain 'I' and resid 70 through 71 removed outlier: 3.552A pdb=" N SER I 71 " --> pdb=" O ASN I 83 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 19 through 23 1363 hydrogen bonds defined for protein. 3738 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 107 hydrogen bonds 214 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 77 stacking parallelities Total time for adding SS restraints: 10.87 Time building geometry restraints manager: 4.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5410 1.31 - 1.43: 8965 1.43 - 1.56: 19010 1.56 - 1.69: 196 1.69 - 1.81: 292 Bond restraints: 33873 Sorted by residual: bond pdb=" C4 ATP A1801 " pdb=" N9 ATP A1801 " ideal model delta sigma weight residual 1.374 1.182 0.192 1.00e-02 1.00e+04 3.69e+02 bond pdb=" C8 ATP A1801 " pdb=" N9 ATP A1801 " ideal model delta sigma weight residual 1.370 1.212 0.158 1.20e-02 6.94e+03 1.74e+02 bond pdb=" C6 ATP A1801 " pdb=" N6 ATP A1801 " ideal model delta sigma weight residual 1.337 1.449 -0.112 1.10e-02 8.26e+03 1.04e+02 bond pdb=" C5 ATP A1801 " pdb=" C6 ATP A1801 " ideal model delta sigma weight residual 1.409 1.335 0.074 1.00e-02 1.00e+04 5.43e+01 bond pdb=" C5 ATP A1801 " pdb=" N7 ATP A1801 " ideal model delta sigma weight residual 1.387 1.453 -0.066 1.00e-02 1.00e+04 4.42e+01 ... (remaining 33868 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.83: 46023 3.83 - 7.66: 124 7.66 - 11.49: 3 11.49 - 15.33: 2 15.33 - 19.16: 1 Bond angle restraints: 46153 Sorted by residual: angle pdb=" PB ATP A1801 " pdb=" O3B ATP A1801 " pdb=" PG ATP A1801 " ideal model delta sigma weight residual 139.87 120.71 19.16 1.00e+00 1.00e+00 3.67e+02 angle pdb=" C4 ATP A1801 " pdb=" N9 ATP A1801 " pdb=" C8 ATP A1801 " ideal model delta sigma weight residual 105.72 119.69 -13.97 1.00e+00 1.00e+00 1.95e+02 angle pdb=" PA ATP A1801 " pdb=" O3A ATP A1801 " pdb=" PB ATP A1801 " ideal model delta sigma weight residual 136.83 123.60 13.23 1.00e+00 1.00e+00 1.75e+02 angle pdb=" N1 ATP A1801 " pdb=" C2 ATP A1801 " pdb=" N3 ATP A1801 " ideal model delta sigma weight residual 128.69 120.22 8.47 1.00e+00 1.00e+00 7.17e+01 angle pdb=" N3 ATP A1801 " pdb=" C4 ATP A1801 " pdb=" N9 ATP A1801 " ideal model delta sigma weight residual 127.04 133.26 -6.22 1.15e+00 7.59e-01 2.94e+01 ... (remaining 46148 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.54: 19838 33.54 - 67.09: 583 67.09 - 100.63: 42 100.63 - 134.17: 2 134.17 - 167.72: 2 Dihedral angle restraints: 20467 sinusoidal: 9132 harmonic: 11335 Sorted by residual: dihedral pdb=" CA THR A 69 " pdb=" C THR A 69 " pdb=" N CYS A 70 " pdb=" CA CYS A 70 " ideal model delta harmonic sigma weight residual 180.00 156.84 23.16 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA GLN A 68 " pdb=" C GLN A 68 " pdb=" N THR A 69 " pdb=" CA THR A 69 " ideal model delta harmonic sigma weight residual 180.00 158.90 21.10 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA HIS A1173 " pdb=" C HIS A1173 " pdb=" N PHE A1174 " pdb=" CA PHE A1174 " ideal model delta harmonic sigma weight residual 180.00 159.95 20.05 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 20464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 3418 0.033 - 0.066: 1138 0.066 - 0.098: 403 0.098 - 0.131: 212 0.131 - 0.164: 19 Chirality restraints: 5190 Sorted by residual: chirality pdb=" C2' G R 9 " pdb=" C3' G R 9 " pdb=" O2' G R 9 " pdb=" C1' G R 9 " both_signs ideal model delta sigma weight residual False -2.62 -2.78 0.16 2.00e-01 2.50e+01 6.72e-01 chirality pdb=" CB VAL A 474 " pdb=" CA VAL A 474 " pdb=" CG1 VAL A 474 " pdb=" CG2 VAL A 474 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.41e-01 chirality pdb=" C2' ATP A1801 " pdb=" C1' ATP A1801 " pdb=" C3' ATP A1801 " pdb=" O2' ATP A1801 " both_signs ideal model delta sigma weight residual False -2.68 -2.52 -0.16 2.00e-01 2.50e+01 6.33e-01 ... (remaining 5187 not shown) Planarity restraints: 5630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 710 " -0.015 2.00e-02 2.50e+03 3.07e-02 9.44e+00 pdb=" C LEU A 710 " 0.053 2.00e-02 2.50e+03 pdb=" O LEU A 710 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG A 711 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A1098 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.76e+00 pdb=" N PRO A1099 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A1099 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A1099 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 244 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.49e+00 pdb=" N PRO A 245 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 245 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 245 " -0.022 5.00e-02 4.00e+02 ... (remaining 5627 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.27: 23 2.27 - 2.93: 13924 2.93 - 3.59: 48746 3.59 - 4.24: 77570 4.24 - 4.90: 129946 Nonbonded interactions: 270209 Sorted by model distance: nonbonded pdb=" O2A ATP A1801 " pdb="MG MG A1802 " model vdw 1.617 2.170 nonbonded pdb=" O1G ATP A1801 " pdb="MG MG A1802 " model vdw 1.701 2.170 nonbonded pdb=" OD2 ASP A 481 " pdb="MG MG A1802 " model vdw 1.720 2.170 nonbonded pdb=" OD2 ASP A 483 " pdb="MG MG A1802 " model vdw 2.051 2.170 nonbonded pdb=" OH TYR B 259 " pdb=" OD2 ASP B 279 " model vdw 2.176 3.040 ... (remaining 270204 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 group one per residue 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: 2.070 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: 0.030 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 42.950 Find NCS groups from input model: 0.170 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: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.192 33905 Z= 0.309 Angle : 0.607 19.157 46198 Z= 0.409 Chirality : 0.042 0.164 5190 Planarity : 0.003 0.055 5630 Dihedral : 14.668 167.717 13127 Min Nonbonded Distance : 1.617 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.37 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.70 (0.14), residues: 3854 helix: 1.84 (0.15), residues: 1310 sheet: -0.10 (0.21), residues: 628 loop : -0.25 (0.15), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1366 TYR 0.024 0.001 TYR B 797 PHE 0.020 0.001 PHE B 37 TRP 0.014 0.001 TRP B 681 HIS 0.009 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.31 (33873) covalent geometry : angle 0.60096 / 0.41 (46153) hydrogen bonds : bond 0.18663 / 12.57 ( 1426) hydrogen bonds : angle 6.81477 / 4.79 ( 3952) metal coordination : bond 0.00500 / 0.33 ( 32) metal coordination : angle 2.70993 / 1.65 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 613 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.9222 (ptt90) cc_final: 0.8961 (tmm-80) REVERT: A 74 MET cc_start: 0.8283 (mtt) cc_final: 0.7837 (mtt) REVERT: A 277 GLU cc_start: 0.9046 (tt0) cc_final: 0.8718 (pt0) REVERT: A 293 GLU cc_start: 0.8862 (tt0) cc_final: 0.8475 (tm-30) REVERT: A 453 MET cc_start: 0.9160 (mpp) cc_final: 0.8595 (mpp) REVERT: A 456 MET cc_start: 0.9063 (mtm) cc_final: 0.8851 (mtp) REVERT: A 618 GLU cc_start: 0.8157 (pm20) cc_final: 0.7949 (pm20) REVERT: A 698 GLN cc_start: 0.8396 (tt0) cc_final: 0.8099 (tp40) REVERT: A 873 MET cc_start: 0.9127 (mmp) cc_final: 0.7923 (mmp) REVERT: A 1062 GLU cc_start: 0.8875 (tp30) cc_final: 0.8662 (mm-30) REVERT: A 1110 ASN cc_start: 0.9591 (m-40) cc_final: 0.9373 (m-40) REVERT: A 1209 MET cc_start: 0.7907 (mmp) cc_final: 0.7441 (mmm) REVERT: A 1218 GLN cc_start: 0.8952 (mm-40) cc_final: 0.8599 (tm-30) REVERT: A 1220 PHE cc_start: 0.8472 (m-10) cc_final: 0.8157 (m-80) REVERT: A 1239 ARG cc_start: 0.7927 (mtp-110) cc_final: 0.7541 (mmm-85) REVERT: A 1315 GLU cc_start: 0.9207 (tt0) cc_final: 0.8800 (tm-30) REVERT: A 1444 MET cc_start: 0.8914 (mmm) cc_final: 0.8561 (mmm) REVERT: B 101 MET cc_start: 0.8759 (mtt) cc_final: 0.8483 (mtp) REVERT: B 216 GLU cc_start: 0.9164 (tt0) cc_final: 0.8084 (mt-10) REVERT: B 244 LEU cc_start: 0.7744 (mp) cc_final: 0.7475 (tp) REVERT: B 310 MET cc_start: 0.9180 (mtp) cc_final: 0.8921 (mtp) REVERT: B 313 MET cc_start: 0.9220 (tpp) cc_final: 0.8971 (mmm) REVERT: B 378 LEU cc_start: 0.9102 (tp) cc_final: 0.8880 (tp) REVERT: B 620 ARG cc_start: 0.9233 (ptp-170) cc_final: 0.8878 (mtm110) REVERT: B 705 MET cc_start: 0.8901 (tpt) cc_final: 0.8575 (tpp) REVERT: B 837 ASP cc_start: 0.9045 (m-30) cc_final: 0.8558 (m-30) REVERT: B 842 ASN cc_start: 0.8944 (t0) cc_final: 0.8723 (t0) REVERT: B 873 THR cc_start: 0.8529 (m) cc_final: 0.8260 (p) REVERT: B 894 ASP cc_start: 0.7325 (m-30) cc_final: 0.7043 (p0) REVERT: B 939 THR cc_start: 0.8430 (m) cc_final: 0.8118 (p) REVERT: B 1090 THR cc_start: 0.8711 (m) cc_final: 0.8077 (p) REVERT: B 1152 MET cc_start: 0.7868 (mmm) cc_final: 0.7428 (mmm) REVERT: B 1190 ASP cc_start: 0.8668 (m-30) cc_final: 0.8371 (t0) REVERT: C 15 LYS cc_start: 0.8953 (ptpt) cc_final: 0.8680 (pttm) REVERT: C 29 MET cc_start: 0.8453 (ttm) cc_final: 0.8134 (ttm) REVERT: C 37 MET cc_start: 0.8879 (mtm) cc_final: 0.8511 (mtm) REVERT: C 89 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8367 (pm20) REVERT: D 50 LEU cc_start: 0.8075 (mt) cc_final: 0.7870 (mp) REVERT: D 56 ARG cc_start: 0.8044 (ttp80) cc_final: 0.7661 (ttp80) REVERT: D 139 LYS cc_start: 0.7882 (tttt) cc_final: 0.7504 (mptt) REVERT: D 141 LEU cc_start: 0.8341 (tp) cc_final: 0.7937 (tp) REVERT: D 186 ASP cc_start: 0.5474 (m-30) cc_final: 0.5267 (m-30) REVERT: E 25 ASP cc_start: 0.8772 (m-30) cc_final: 0.8536 (m-30) REVERT: E 32 GLN cc_start: 0.8850 (tt0) cc_final: 0.8488 (tp-100) REVERT: E 36 GLU cc_start: 0.9275 (mt-10) cc_final: 0.8488 (mt-10) REVERT: E 48 ASP cc_start: 0.9187 (t70) cc_final: 0.8278 (t0) REVERT: E 57 MET cc_start: 0.9245 (mtm) cc_final: 0.9005 (tpp) REVERT: E 101 GLN cc_start: 0.8946 (mt0) cc_final: 0.8680 (mt0) REVERT: E 180 ARG cc_start: 0.8836 (mtt180) cc_final: 0.8555 (mtp85) REVERT: E 192 ARG cc_start: 0.9402 (ttt180) cc_final: 0.9061 (mtp-110) REVERT: E 201 LYS cc_start: 0.8974 (mtmt) cc_final: 0.8531 (mmmt) REVERT: F 116 ASP cc_start: 0.8769 (t0) cc_final: 0.8355 (t0) REVERT: F 127 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8570 (tt0) REVERT: G 23 LYS cc_start: 0.8618 (tttt) cc_final: 0.8386 (tppt) REVERT: G 24 GLN cc_start: 0.8448 (mt0) cc_final: 0.7975 (tm-30) REVERT: G 29 LYS cc_start: 0.8164 (tppt) cc_final: 0.7920 (ttmt) REVERT: G 49 LEU cc_start: 0.7415 (mt) cc_final: 0.7037 (mp) REVERT: G 51 TYR cc_start: 0.7208 (t80) cc_final: 0.6689 (t80) REVERT: G 52 ASP cc_start: 0.8862 (t0) cc_final: 0.8411 (t0) REVERT: G 53 ASN cc_start: 0.8958 (m-40) cc_final: 0.8678 (t0) REVERT: G 57 GLN cc_start: 0.8158 (mt0) cc_final: 0.7951 (mm-40) REVERT: G 69 GLU cc_start: 0.8190 (tt0) cc_final: 0.7902 (tm-30) REVERT: G 115 MET cc_start: 0.4960 (mtp) cc_final: 0.4581 (ttp) REVERT: G 119 LEU cc_start: 0.2906 (mp) cc_final: 0.2689 (mm) REVERT: G 164 LYS cc_start: 0.5942 (mttt) cc_final: 0.5708 (mmtt) REVERT: H 7 ASP cc_start: 0.8859 (t0) cc_final: 0.8467 (t0) REVERT: H 16 ASP cc_start: 0.8843 (t0) cc_final: 0.8624 (t0) REVERT: H 24 CYS cc_start: 0.9394 (m) cc_final: 0.9053 (m) REVERT: H 80 ARG cc_start: 0.9207 (mtp85) cc_final: 0.8950 (ttm110) REVERT: H 86 ASP cc_start: 0.7889 (m-30) cc_final: 0.7584 (m-30) REVERT: H 87 ARG cc_start: 0.8848 (mmm-85) cc_final: 0.8581 (tpp80) REVERT: H 105 GLU cc_start: 0.7702 (tt0) cc_final: 0.7330 (tm-30) REVERT: H 107 VAL cc_start: 0.8838 (t) cc_final: 0.8364 (t) REVERT: J 19 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8726 (pt0) REVERT: K 17 SER cc_start: 0.9176 (m) cc_final: 0.8826 (t) REVERT: K 22 ASP cc_start: 0.8998 (m-30) cc_final: 0.8613 (m-30) REVERT: K 39 ASP cc_start: 0.9074 (p0) cc_final: 0.8820 (p0) REVERT: K 54 ARG cc_start: 0.9308 (mtm180) cc_final: 0.8903 (mmm160) REVERT: K 79 GLU cc_start: 0.9561 (tt0) cc_final: 0.9177 (tm-30) outliers start: 0 outliers final: 0 residues processed: 613 average time/residue: 0.2439 time to fit residues: 235.5131 Evaluate side-chains 361 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 197 optimal weight: 0.0020 chunk 388 optimal weight: 50.0000 chunk 215 optimal weight: 0.1980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 6.9990 overall best weight: 2.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 GLN A 358 ASN ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1378 GLN B 110 HIS B 357 GLN B 862 GLN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 GLN ** I 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.093339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.062005 restraints weight = 85625.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.064080 restraints weight = 42483.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.065413 restraints weight = 27740.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.066208 restraints weight = 21527.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.066733 restraints weight = 18609.610| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 33905 Z= 0.201 Angle : 0.647 13.579 46198 Z= 0.338 Chirality : 0.046 0.292 5190 Planarity : 0.005 0.054 5630 Dihedral : 16.976 166.361 5346 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.26 % Favored : 95.64 % Rotamer: Outliers : 1.25 % Allowed : 6.55 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.45 (0.14), residues: 3854 helix: 1.55 (0.15), residues: 1334 sheet: -0.17 (0.21), residues: 592 loop : -0.38 (0.15), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1199 TYR 0.026 0.001 TYR D 147 PHE 0.022 0.002 PHE K 7 TRP 0.008 0.001 TRP B 31 HIS 0.007 0.001 HIS D 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.20 (33873) covalent geometry : angle 0.63694 / 0.34 (46153) hydrogen bonds : bond 0.04819 / 3.24 ( 1426) hydrogen bonds : angle 5.31760 / 3.74 ( 3952) metal coordination : bond 0.00744 / 0.46 ( 32) metal coordination : angle 3.63542 / 2.23 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 384 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8289 (mtt) cc_final: 0.7943 (mtt) REVERT: A 122 MET cc_start: 0.9130 (tpp) cc_final: 0.8690 (tpp) REVERT: A 133 LYS cc_start: 0.9544 (mttm) cc_final: 0.9210 (mtpp) REVERT: A 453 MET cc_start: 0.8715 (mpp) cc_final: 0.8495 (mpp) REVERT: A 698 GLN cc_start: 0.8301 (tt0) cc_final: 0.7955 (tp40) REVERT: A 708 MET cc_start: 0.5622 (OUTLIER) cc_final: 0.4619 (mtm) REVERT: A 873 MET cc_start: 0.9407 (mmp) cc_final: 0.8318 (mmp) REVERT: A 1209 MET cc_start: 0.7994 (mmp) cc_final: 0.7560 (mmm) REVERT: A 1239 ARG cc_start: 0.7687 (mtp-110) cc_final: 0.7417 (mtm180) REVERT: A 1444 MET cc_start: 0.9127 (mmm) cc_final: 0.8468 (mmm) REVERT: B 173 MET cc_start: 0.9110 (ttm) cc_final: 0.8771 (ttp) REVERT: B 378 LEU cc_start: 0.9409 (tp) cc_final: 0.9164 (tp) REVERT: B 470 LYS cc_start: 0.8909 (mppt) cc_final: 0.8701 (mmtt) REVERT: B 563 MET cc_start: 0.9135 (tmm) cc_final: 0.8905 (tmm) REVERT: B 837 ASP cc_start: 0.8656 (m-30) cc_final: 0.8212 (m-30) REVERT: B 860 MET cc_start: 0.8256 (tmm) cc_final: 0.7837 (tmm) REVERT: B 873 THR cc_start: 0.9157 (m) cc_final: 0.8615 (p) REVERT: B 939 THR cc_start: 0.9181 (m) cc_final: 0.8921 (p) REVERT: B 1152 MET cc_start: 0.8587 (mmm) cc_final: 0.8160 (mmm) REVERT: C 37 MET cc_start: 0.8770 (mtm) cc_final: 0.8567 (mtm) REVERT: D 1 MET cc_start: 0.0396 (tmm) cc_final: -0.0031 (tmm) REVERT: D 147 TYR cc_start: 0.7379 (t80) cc_final: 0.6481 (t80) REVERT: D 186 ASP cc_start: 0.4971 (m-30) cc_final: 0.4755 (m-30) REVERT: F 84 TYR cc_start: 0.8939 (m-80) cc_final: 0.8696 (m-10) REVERT: F 114 GLU cc_start: 0.8438 (tt0) cc_final: 0.8201 (tt0) REVERT: F 116 ASP cc_start: 0.8895 (t0) cc_final: 0.8592 (t70) REVERT: G 24 GLN cc_start: 0.8522 (mt0) cc_final: 0.8227 (tm-30) REVERT: G 53 ASN cc_start: 0.9151 (m-40) cc_final: 0.8668 (t0) REVERT: G 115 MET cc_start: 0.4679 (mtp) cc_final: 0.4388 (ttp) REVERT: H 107 VAL cc_start: 0.9505 (t) cc_final: 0.8936 (t) REVERT: K 49 GLU cc_start: 0.8222 (tp30) cc_final: 0.7955 (tp30) REVERT: L 30 ILE cc_start: 0.9137 (mp) cc_final: 0.8833 (mp) REVERT: L 33 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7290 (mt-10) REVERT: L 47 ARG cc_start: 0.7361 (mtp180) cc_final: 0.7078 (mtp180) REVERT: L 54 ARG cc_start: 0.7255 (mtt-85) cc_final: 0.7000 (mpt180) outliers start: 43 outliers final: 25 residues processed: 411 average time/residue: 0.2374 time to fit residues: 156.4019 Evaluate side-chains 349 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 323 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 HIS Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 1071 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain A residue 1420 ASP Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain K residue 77 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 242 optimal weight: 8.9990 chunk 191 optimal weight: 3.9990 chunk 5 optimal weight: 0.3980 chunk 373 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 333 optimal weight: 10.0000 chunk 304 optimal weight: 9.9990 chunk 239 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 249 optimal weight: 5.9990 chunk 222 optimal weight: 4.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN D 138 ASN I 11 ASN I 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.092199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.060855 restraints weight = 86354.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.062896 restraints weight = 43446.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.064211 restraints weight = 28578.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.065025 restraints weight = 22195.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.065520 restraints weight = 19180.328| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 33905 Z= 0.261 Angle : 0.647 14.639 46198 Z= 0.336 Chirality : 0.046 0.288 5190 Planarity : 0.004 0.060 5630 Dihedral : 16.952 167.464 5346 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.36 % Favored : 95.54 % Rotamer: Outliers : 1.60 % Allowed : 8.77 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.24 (0.14), residues: 3854 helix: 1.38 (0.14), residues: 1343 sheet: -0.36 (0.21), residues: 606 loop : -0.49 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1199 TYR 0.018 0.002 TYR D 147 PHE 0.023 0.002 PHE A 219 TRP 0.008 0.001 TRP B 31 HIS 0.008 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.26 (33873) covalent geometry : angle 0.63721 / 0.34 (46153) hydrogen bonds : bond 0.04366 / 2.92 ( 1426) hydrogen bonds : angle 5.12126 / 3.59 ( 3952) metal coordination : bond 0.00962 / 0.60 ( 32) metal coordination : angle 3.68805 / 2.22 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 339 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8315 (mtt) cc_final: 0.7950 (mtt) REVERT: A 133 LYS cc_start: 0.9536 (mttm) cc_final: 0.9201 (mtpp) REVERT: A 304 MET cc_start: 0.8680 (mtt) cc_final: 0.8260 (mtt) REVERT: A 698 GLN cc_start: 0.8308 (tt0) cc_final: 0.7961 (tp40) REVERT: A 708 MET cc_start: 0.5675 (OUTLIER) cc_final: 0.4690 (mtm) REVERT: A 739 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7691 (t0) REVERT: A 873 MET cc_start: 0.9442 (mmp) cc_final: 0.8395 (mmp) REVERT: A 1209 MET cc_start: 0.8143 (mmp) cc_final: 0.7815 (mmm) REVERT: A 1220 PHE cc_start: 0.8486 (m-80) cc_final: 0.8280 (m-80) REVERT: A 1239 ARG cc_start: 0.7645 (mtp-110) cc_final: 0.7346 (mtm180) REVERT: A 1285 MET cc_start: 0.7909 (mtp) cc_final: 0.7552 (mtp) REVERT: B 173 MET cc_start: 0.9110 (ttm) cc_final: 0.8888 (ttp) REVERT: B 378 LEU cc_start: 0.9449 (tp) cc_final: 0.9222 (tp) REVERT: B 393 LYS cc_start: 0.9235 (mtpp) cc_final: 0.9014 (ttmm) REVERT: B 563 MET cc_start: 0.9174 (tmm) cc_final: 0.8923 (tmm) REVERT: B 773 MET cc_start: 0.8792 (mtm) cc_final: 0.8541 (mtm) REVERT: B 835 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8300 (mt0) REVERT: B 837 ASP cc_start: 0.8665 (m-30) cc_final: 0.8191 (m-30) REVERT: B 873 THR cc_start: 0.9132 (m) cc_final: 0.8595 (p) REVERT: B 939 THR cc_start: 0.9163 (m) cc_final: 0.8849 (p) REVERT: B 1152 MET cc_start: 0.8555 (mmm) cc_final: 0.8088 (mmm) REVERT: C 37 MET cc_start: 0.8799 (mtm) cc_final: 0.8595 (mtm) REVERT: D 1 MET cc_start: 0.0187 (tmm) cc_final: -0.0240 (tmm) REVERT: D 186 ASP cc_start: 0.4832 (m-30) cc_final: 0.4627 (m-30) REVERT: E 48 ASP cc_start: 0.8274 (t0) cc_final: 0.7395 (t0) REVERT: E 58 MET cc_start: 0.8877 (mtm) cc_final: 0.8610 (mtm) REVERT: F 77 ASP cc_start: 0.8389 (t0) cc_final: 0.8145 (t0) REVERT: F 78 GLN cc_start: 0.9207 (mp10) cc_final: 0.8938 (pm20) REVERT: F 116 ASP cc_start: 0.8933 (t0) cc_final: 0.8632 (t70) REVERT: G 24 GLN cc_start: 0.8593 (mt0) cc_final: 0.8245 (tm-30) REVERT: G 50 ASP cc_start: 0.7802 (t0) cc_final: 0.7490 (t0) REVERT: G 53 ASN cc_start: 0.9064 (m-40) cc_final: 0.8666 (t0) REVERT: G 69 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7339 (tm-30) REVERT: G 115 MET cc_start: 0.4690 (mtp) cc_final: 0.4434 (ttp) REVERT: G 165 GLU cc_start: 0.6095 (mp0) cc_final: 0.5742 (mp0) REVERT: H 105 GLU cc_start: 0.7100 (tm-30) cc_final: 0.6832 (tm-30) REVERT: H 107 VAL cc_start: 0.9324 (t) cc_final: 0.9079 (t) REVERT: L 54 ARG cc_start: 0.7435 (mtt-85) cc_final: 0.7145 (mtt180) outliers start: 55 outliers final: 32 residues processed: 373 average time/residue: 0.2184 time to fit residues: 132.7984 Evaluate side-chains 352 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 317 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 281 HIS Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 1071 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1148 ILE Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain A residue 1420 ASP Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 835 GLN Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 167 TYR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain K residue 77 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 0 optimal weight: 9.9990 chunk 345 optimal weight: 0.0980 chunk 138 optimal weight: 7.9990 chunk 183 optimal weight: 4.9990 chunk 169 optimal weight: 10.0000 chunk 216 optimal weight: 0.9990 chunk 286 optimal weight: 20.0000 chunk 108 optimal weight: 0.6980 chunk 251 optimal weight: 4.9990 chunk 308 optimal weight: 6.9990 chunk 352 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 316 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN A 838 GLN ** A1173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN K 65 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.093420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.061906 restraints weight = 85546.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.064007 restraints weight = 42756.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.065351 restraints weight = 28035.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.066192 restraints weight = 21740.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.066695 restraints weight = 18749.235| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 33905 Z= 0.162 Angle : 0.581 13.777 46198 Z= 0.304 Chirality : 0.044 0.285 5190 Planarity : 0.004 0.047 5630 Dihedral : 16.910 167.338 5346 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.81 % Favored : 96.08 % Rotamer: Outliers : 1.49 % Allowed : 9.87 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.27 (0.14), residues: 3854 helix: 1.45 (0.14), residues: 1344 sheet: -0.36 (0.21), residues: 613 loop : -0.51 (0.15), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 620 TYR 0.027 0.001 TYR D 147 PHE 0.024 0.001 PHE A 219 TRP 0.010 0.001 TRP B 681 HIS 0.005 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (33873) covalent geometry : angle 0.57231 / 0.30 (46153) hydrogen bonds : bond 0.03783 / 2.52 ( 1426) hydrogen bonds : angle 4.82345 / 3.38 ( 3952) metal coordination : bond 0.00692 / 0.43 ( 32) metal coordination : angle 3.32978 / 1.99 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 353 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8309 (mtt) cc_final: 0.8022 (mtt) REVERT: A 122 MET cc_start: 0.9076 (tpp) cc_final: 0.8687 (tpp) REVERT: A 133 LYS cc_start: 0.9549 (mttm) cc_final: 0.9211 (mtpp) REVERT: A 453 MET cc_start: 0.8606 (mpp) cc_final: 0.8054 (mtm) REVERT: A 698 GLN cc_start: 0.8244 (tt0) cc_final: 0.7823 (tp40) REVERT: A 708 MET cc_start: 0.5390 (OUTLIER) cc_final: 0.4534 (mtm) REVERT: A 739 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7662 (t0) REVERT: A 1079 MET cc_start: 0.7555 (tmm) cc_final: 0.7277 (tmm) REVERT: A 1153 TYR cc_start: 0.7826 (m-10) cc_final: 0.7616 (m-10) REVERT: A 1209 MET cc_start: 0.8133 (mmp) cc_final: 0.7824 (mmm) REVERT: A 1220 PHE cc_start: 0.8456 (m-80) cc_final: 0.8185 (m-80) REVERT: A 1239 ARG cc_start: 0.7625 (mtp-110) cc_final: 0.7292 (mtm180) REVERT: A 1268 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8452 (mm) REVERT: A 1285 MET cc_start: 0.7918 (mtp) cc_final: 0.7614 (mtp) REVERT: A 1444 MET cc_start: 0.9015 (mmm) cc_final: 0.8527 (mmm) REVERT: B 72 GLU cc_start: 0.8810 (pm20) cc_final: 0.8259 (tt0) REVERT: B 378 LEU cc_start: 0.9440 (tp) cc_final: 0.9178 (tp) REVERT: B 393 LYS cc_start: 0.9221 (mtpp) cc_final: 0.9006 (ttmm) REVERT: B 563 MET cc_start: 0.9172 (tmm) cc_final: 0.8903 (tmm) REVERT: B 705 MET cc_start: 0.9362 (tpp) cc_final: 0.8736 (tpp) REVERT: B 837 ASP cc_start: 0.8612 (m-30) cc_final: 0.8109 (m-30) REVERT: B 873 THR cc_start: 0.9107 (m) cc_final: 0.8580 (p) REVERT: B 939 THR cc_start: 0.9141 (m) cc_final: 0.8824 (p) REVERT: B 1152 MET cc_start: 0.8468 (mmm) cc_final: 0.8015 (mmm) REVERT: D 1 MET cc_start: -0.0019 (tmm) cc_final: -0.0464 (tmm) REVERT: D 186 ASP cc_start: 0.4859 (m-30) cc_final: 0.4648 (m-30) REVERT: E 32 GLN cc_start: 0.8545 (tp-100) cc_final: 0.7956 (tp-100) REVERT: E 48 ASP cc_start: 0.8492 (t0) cc_final: 0.8133 (t0) REVERT: E 58 MET cc_start: 0.8823 (mtm) cc_final: 0.8556 (mtm) REVERT: E 84 ASP cc_start: 0.9238 (t0) cc_final: 0.9008 (t0) REVERT: F 77 ASP cc_start: 0.8466 (t0) cc_final: 0.8005 (t0) REVERT: F 78 GLN cc_start: 0.9179 (mp10) cc_final: 0.8688 (pm20) REVERT: F 116 ASP cc_start: 0.8881 (t0) cc_final: 0.8564 (t70) REVERT: G 24 GLN cc_start: 0.8586 (mt0) cc_final: 0.8212 (tm-30) REVERT: G 50 ASP cc_start: 0.7774 (t0) cc_final: 0.7507 (t0) REVERT: G 53 ASN cc_start: 0.9000 (m-40) cc_final: 0.8693 (t0) REVERT: G 69 GLU cc_start: 0.8365 (tm-30) cc_final: 0.7482 (tm-30) REVERT: G 75 ARG cc_start: 0.8164 (mtm180) cc_final: 0.7724 (tpp80) REVERT: G 115 MET cc_start: 0.4498 (mtp) cc_final: 0.4253 (ttp) REVERT: H 105 GLU cc_start: 0.7142 (tm-30) cc_final: 0.6917 (tm-30) REVERT: H 107 VAL cc_start: 0.9393 (t) cc_final: 0.9108 (t) REVERT: I 1 MET cc_start: 0.7570 (mmt) cc_final: 0.4953 (tmm) REVERT: J 32 GLU cc_start: 0.8960 (mp0) cc_final: 0.8644 (mp0) REVERT: L 36 SER cc_start: 0.8049 (m) cc_final: 0.7667 (p) REVERT: L 54 ARG cc_start: 0.7499 (mtt-85) cc_final: 0.6969 (mtt180) REVERT: L 60 ARG cc_start: 0.8659 (ttm-80) cc_final: 0.8410 (ttt90) outliers start: 51 outliers final: 33 residues processed: 382 average time/residue: 0.2274 time to fit residues: 141.4525 Evaluate side-chains 364 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 328 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 HIS Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 1071 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1265 ASN Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain A residue 1420 ASP Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 167 TYR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 53 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 46 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 105 optimal weight: 0.0040 chunk 111 optimal weight: 30.0000 chunk 182 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 138 optimal weight: 0.4980 chunk 103 optimal weight: 6.9990 overall best weight: 2.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 GLN ** A1173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1270 ASN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN ** I 11 ASN ** 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 = 0.3515 r_free = 0.3515 target = 0.092985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.061701 restraints weight = 85595.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.063797 restraints weight = 42675.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.065139 restraints weight = 27892.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.065973 restraints weight = 21593.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.066429 restraints weight = 18602.630| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 33905 Z= 0.171 Angle : 0.575 12.887 46198 Z= 0.300 Chirality : 0.043 0.288 5190 Planarity : 0.004 0.087 5630 Dihedral : 16.889 168.806 5346 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.15 % Favored : 95.74 % Rotamer: Outliers : 1.72 % Allowed : 10.98 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.28 (0.14), residues: 3854 helix: 1.46 (0.14), residues: 1348 sheet: -0.36 (0.21), residues: 599 loop : -0.51 (0.15), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 54 TYR 0.026 0.001 TYR D 147 PHE 0.027 0.001 PHE K 7 TRP 0.008 0.001 TRP B 31 HIS 0.005 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (33873) covalent geometry : angle 0.56576 / 0.30 (46153) hydrogen bonds : bond 0.03605 / 2.40 ( 1426) hydrogen bonds : angle 4.70271 / 3.30 ( 3952) metal coordination : bond 0.00656 / 0.41 ( 32) metal coordination : angle 3.29028 / 2.00 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 345 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8331 (mtt) cc_final: 0.8007 (mtt) REVERT: A 133 LYS cc_start: 0.9554 (mttm) cc_final: 0.9219 (mtpp) REVERT: A 304 MET cc_start: 0.8643 (mtt) cc_final: 0.8332 (mtt) REVERT: A 453 MET cc_start: 0.8637 (mpp) cc_final: 0.8143 (mtm) REVERT: A 708 MET cc_start: 0.5280 (OUTLIER) cc_final: 0.4632 (mtm) REVERT: A 739 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7617 (t0) REVERT: A 1079 MET cc_start: 0.7603 (tmm) cc_final: 0.7268 (tmm) REVERT: A 1209 MET cc_start: 0.8206 (mmp) cc_final: 0.7904 (mmm) REVERT: A 1220 PHE cc_start: 0.8349 (m-80) cc_final: 0.8103 (m-80) REVERT: A 1239 ARG cc_start: 0.7681 (mtp-110) cc_final: 0.7301 (mtm180) REVERT: A 1285 MET cc_start: 0.7966 (mtp) cc_final: 0.7646 (mtp) REVERT: A 1444 MET cc_start: 0.9004 (mmm) cc_final: 0.8548 (mmm) REVERT: B 378 LEU cc_start: 0.9439 (tp) cc_final: 0.9178 (tp) REVERT: B 393 LYS cc_start: 0.9233 (mtpp) cc_final: 0.9015 (ttmm) REVERT: B 563 MET cc_start: 0.9226 (tmm) cc_final: 0.8940 (tmm) REVERT: B 773 MET cc_start: 0.8800 (mtm) cc_final: 0.8581 (mtm) REVERT: B 835 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8479 (mt0) REVERT: B 837 ASP cc_start: 0.8633 (m-30) cc_final: 0.8120 (m-30) REVERT: B 873 THR cc_start: 0.9089 (m) cc_final: 0.8579 (p) REVERT: B 939 THR cc_start: 0.9148 (m) cc_final: 0.8839 (p) REVERT: B 1152 MET cc_start: 0.8475 (mmm) cc_final: 0.7991 (mmm) REVERT: D 1 MET cc_start: 0.0239 (tmm) cc_final: -0.0230 (tmm) REVERT: D 46 GLU cc_start: 0.8163 (tp30) cc_final: 0.7501 (pm20) REVERT: D 186 ASP cc_start: 0.4666 (m-30) cc_final: 0.4436 (m-30) REVERT: E 32 GLN cc_start: 0.8673 (tp-100) cc_final: 0.8053 (tp-100) REVERT: E 58 MET cc_start: 0.8858 (mtp) cc_final: 0.8618 (mtm) REVERT: E 84 ASP cc_start: 0.9272 (t0) cc_final: 0.9031 (t0) REVERT: F 77 ASP cc_start: 0.8386 (t0) cc_final: 0.7871 (t0) REVERT: F 78 GLN cc_start: 0.9201 (mp10) cc_final: 0.8643 (pm20) REVERT: F 116 ASP cc_start: 0.8873 (t0) cc_final: 0.8543 (t70) REVERT: F 127 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8280 (tt0) REVERT: G 24 GLN cc_start: 0.8558 (mt0) cc_final: 0.8193 (tm-30) REVERT: G 50 ASP cc_start: 0.7770 (t0) cc_final: 0.7506 (t0) REVERT: G 69 GLU cc_start: 0.8437 (tm-30) cc_final: 0.7541 (tm-30) REVERT: G 75 ARG cc_start: 0.8191 (mtm180) cc_final: 0.7948 (tpp80) REVERT: G 119 LEU cc_start: 0.2417 (mm) cc_final: 0.1969 (mm) REVERT: G 168 LEU cc_start: 0.6797 (mp) cc_final: 0.6351 (mm) REVERT: H 105 GLU cc_start: 0.7179 (tm-30) cc_final: 0.6939 (tm-30) REVERT: H 107 VAL cc_start: 0.9408 (t) cc_final: 0.9110 (t) REVERT: I 1 MET cc_start: 0.7553 (mmt) cc_final: 0.4968 (tmm) REVERT: J 32 GLU cc_start: 0.8973 (mp0) cc_final: 0.8634 (mp0) REVERT: K 49 GLU cc_start: 0.8371 (tp30) cc_final: 0.8136 (tp30) REVERT: L 36 SER cc_start: 0.8081 (m) cc_final: 0.7771 (p) REVERT: L 54 ARG cc_start: 0.7647 (mtt-85) cc_final: 0.7092 (mtt180) REVERT: L 60 ARG cc_start: 0.8674 (ttm-80) cc_final: 0.8451 (ttt90) outliers start: 59 outliers final: 39 residues processed: 381 average time/residue: 0.2274 time to fit residues: 141.1403 Evaluate side-chains 360 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 318 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 HIS Chi-restraints excluded: chain A residue 281 HIS Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 1071 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1265 ASN Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain A residue 1420 ASP Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 835 GLN Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 167 TYR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 53 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 317 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 159 optimal weight: 0.0010 chunk 89 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 114 optimal weight: 20.0000 chunk 150 optimal weight: 2.9990 chunk 144 optimal weight: 0.0670 chunk 31 optimal weight: 3.9990 chunk 293 optimal weight: 30.0000 overall best weight: 1.6130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 HIS ** A1173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.093371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.062156 restraints weight = 85415.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.064249 restraints weight = 42379.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.065592 restraints weight = 27639.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.066421 restraints weight = 21378.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.066903 restraints weight = 18443.779| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33905 Z= 0.145 Angle : 0.565 11.555 46198 Z= 0.294 Chirality : 0.043 0.288 5190 Planarity : 0.004 0.066 5630 Dihedral : 16.873 169.089 5346 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.94 % Favored : 95.95 % Rotamer: Outliers : 1.25 % Allowed : 12.14 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.32 (0.14), residues: 3854 helix: 1.51 (0.14), residues: 1348 sheet: -0.38 (0.20), residues: 607 loop : -0.49 (0.15), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 54 TYR 0.021 0.001 TYR D 147 PHE 0.023 0.001 PHE A 219 TRP 0.008 0.001 TRP B 31 HIS 0.011 0.001 HIS B 440 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (33873) covalent geometry : angle 0.55747 / 0.29 (46153) hydrogen bonds : bond 0.03452 / 2.29 ( 1426) hydrogen bonds : angle 4.61173 / 3.24 ( 3952) metal coordination : bond 0.00586 / 0.36 ( 32) metal coordination : angle 3.03130 / 1.84 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 339 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8358 (mtt) cc_final: 0.8043 (mtt) REVERT: A 122 MET cc_start: 0.9050 (tpp) cc_final: 0.8683 (tpp) REVERT: A 133 LYS cc_start: 0.9553 (mttm) cc_final: 0.9207 (mtpp) REVERT: A 304 MET cc_start: 0.8627 (mtt) cc_final: 0.8222 (mtt) REVERT: A 453 MET cc_start: 0.8634 (mpp) cc_final: 0.8141 (mtm) REVERT: A 1079 MET cc_start: 0.7601 (tmm) cc_final: 0.7283 (tmm) REVERT: A 1209 MET cc_start: 0.8218 (mmp) cc_final: 0.7922 (mmm) REVERT: A 1220 PHE cc_start: 0.8421 (m-80) cc_final: 0.8114 (m-80) REVERT: A 1239 ARG cc_start: 0.7685 (mtp-110) cc_final: 0.7295 (mtm180) REVERT: A 1268 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8255 (mm) REVERT: A 1285 MET cc_start: 0.7975 (mtp) cc_final: 0.7662 (mtp) REVERT: A 1444 MET cc_start: 0.8999 (mmm) cc_final: 0.8564 (mmm) REVERT: B 378 LEU cc_start: 0.9436 (tp) cc_final: 0.9162 (tp) REVERT: B 393 LYS cc_start: 0.9215 (mtpp) cc_final: 0.8995 (ttmm) REVERT: B 563 MET cc_start: 0.9233 (tmm) cc_final: 0.8938 (tmm) REVERT: B 620 ARG cc_start: 0.8242 (mtp-110) cc_final: 0.7946 (mtm110) REVERT: B 837 ASP cc_start: 0.8617 (m-30) cc_final: 0.8076 (m-30) REVERT: B 873 THR cc_start: 0.9129 (m) cc_final: 0.8608 (p) REVERT: B 939 THR cc_start: 0.9152 (m) cc_final: 0.8856 (p) REVERT: B 1152 MET cc_start: 0.8459 (mmm) cc_final: 0.7990 (mmm) REVERT: D 1 MET cc_start: 0.0320 (tmm) cc_final: -0.0145 (tmm) REVERT: D 46 GLU cc_start: 0.8154 (tp30) cc_final: 0.7489 (pm20) REVERT: D 186 ASP cc_start: 0.4739 (m-30) cc_final: 0.4486 (m-30) REVERT: E 32 GLN cc_start: 0.8689 (tp-100) cc_final: 0.8065 (tp-100) REVERT: E 58 MET cc_start: 0.8918 (mtp) cc_final: 0.8717 (mtm) REVERT: F 77 ASP cc_start: 0.8459 (t0) cc_final: 0.7990 (t0) REVERT: F 78 GLN cc_start: 0.9195 (mp10) cc_final: 0.8610 (pm20) REVERT: F 85 MET cc_start: 0.8694 (ttt) cc_final: 0.8292 (ttt) REVERT: F 116 ASP cc_start: 0.8863 (t0) cc_final: 0.8529 (t70) REVERT: F 127 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8369 (tt0) REVERT: G 24 GLN cc_start: 0.8552 (mt0) cc_final: 0.8191 (tm-30) REVERT: G 50 ASP cc_start: 0.7737 (t0) cc_final: 0.7412 (t0) REVERT: G 69 GLU cc_start: 0.8442 (tm-30) cc_final: 0.7594 (tm-30) REVERT: G 166 ASP cc_start: 0.7720 (p0) cc_final: 0.7476 (p0) REVERT: G 168 LEU cc_start: 0.6522 (mp) cc_final: 0.6071 (mm) REVERT: I 1 MET cc_start: 0.7528 (mmt) cc_final: 0.5092 (tmm) REVERT: J 32 GLU cc_start: 0.8948 (mp0) cc_final: 0.8623 (mp0) REVERT: K 38 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8555 (mm-30) REVERT: K 49 GLU cc_start: 0.8447 (tp30) cc_final: 0.8164 (tp30) REVERT: L 36 SER cc_start: 0.8062 (m) cc_final: 0.7613 (p) REVERT: L 54 ARG cc_start: 0.7625 (mtt-85) cc_final: 0.7022 (mtt180) REVERT: L 60 ARG cc_start: 0.8678 (ttm-80) cc_final: 0.8467 (ttt90) outliers start: 43 outliers final: 35 residues processed: 363 average time/residue: 0.2278 time to fit residues: 135.1094 Evaluate side-chains 356 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 320 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 HIS Chi-restraints excluded: chain A residue 281 HIS Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 1071 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1202 MET Chi-restraints excluded: chain A residue 1265 ASN Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain A residue 1420 ASP Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 53 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 382 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 200 optimal weight: 0.8980 chunk 306 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 354 optimal weight: 7.9990 chunk 270 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 357 optimal weight: 10.0000 chunk 254 optimal weight: 4.9990 chunk 351 optimal weight: 4.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B 215 GLN B1117 GLN ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN G 113 HIS H 33 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.091306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.060595 restraints weight = 86743.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.062614 restraints weight = 43532.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.063906 restraints weight = 28507.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.064727 restraints weight = 22092.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.065208 restraints weight = 19014.701| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 33905 Z= 0.285 Angle : 0.660 14.564 46198 Z= 0.338 Chirality : 0.045 0.288 5190 Planarity : 0.004 0.064 5630 Dihedral : 16.958 171.203 5346 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.09 % Favored : 94.81 % Rotamer: Outliers : 1.60 % Allowed : 12.52 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.16 (0.14), residues: 3854 helix: 1.41 (0.14), residues: 1346 sheet: -0.46 (0.20), residues: 624 loop : -0.61 (0.15), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 54 TYR 0.018 0.002 TYR D 147 PHE 0.034 0.002 PHE K 7 TRP 0.008 0.001 TRP B 31 HIS 0.009 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00645 / 0.28 (33873) covalent geometry : angle 0.64920 / 0.34 (46153) hydrogen bonds : bond 0.03831 / 2.54 ( 1426) hydrogen bonds : angle 4.79205 / 3.37 ( 3952) metal coordination : bond 0.01076 / 0.67 ( 32) metal coordination : angle 3.91070 / 2.38 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 330 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8391 (mtt) cc_final: 0.8108 (mtt) REVERT: A 133 LYS cc_start: 0.9530 (mttm) cc_final: 0.9178 (mtpp) REVERT: A 304 MET cc_start: 0.8770 (mtt) cc_final: 0.8404 (mtt) REVERT: A 453 MET cc_start: 0.8666 (mpp) cc_final: 0.8159 (mtm) REVERT: A 739 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7617 (t0) REVERT: A 1079 MET cc_start: 0.7738 (tmm) cc_final: 0.7519 (tmm) REVERT: A 1209 MET cc_start: 0.8378 (mmp) cc_final: 0.8097 (mmm) REVERT: A 1220 PHE cc_start: 0.8468 (m-80) cc_final: 0.8169 (m-80) REVERT: A 1239 ARG cc_start: 0.7690 (mtp-110) cc_final: 0.7404 (mtm180) REVERT: A 1268 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8253 (mm) REVERT: A 1285 MET cc_start: 0.7946 (mtp) cc_final: 0.7614 (mtp) REVERT: B 378 LEU cc_start: 0.9448 (tp) cc_final: 0.9210 (tp) REVERT: B 393 LYS cc_start: 0.9241 (mtpp) cc_final: 0.9029 (ttmm) REVERT: B 563 MET cc_start: 0.9209 (tmm) cc_final: 0.8896 (tmm) REVERT: B 705 MET cc_start: 0.9366 (tpp) cc_final: 0.8659 (tpp) REVERT: B 835 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8466 (mt0) REVERT: B 837 ASP cc_start: 0.8697 (m-30) cc_final: 0.8354 (m-30) REVERT: B 873 THR cc_start: 0.9114 (m) cc_final: 0.8598 (p) REVERT: B 939 THR cc_start: 0.9165 (m) cc_final: 0.8847 (p) REVERT: B 1152 MET cc_start: 0.8524 (mmm) cc_final: 0.8012 (mmm) REVERT: C 230 MET cc_start: 0.8901 (mtp) cc_final: 0.8362 (mtm) REVERT: D 1 MET cc_start: 0.0473 (tmm) cc_final: -0.0017 (tmm) REVERT: D 186 ASP cc_start: 0.4844 (m-30) cc_final: 0.4573 (m-30) REVERT: E 32 GLN cc_start: 0.8851 (tp-100) cc_final: 0.8211 (tp-100) REVERT: E 58 MET cc_start: 0.8966 (mtp) cc_final: 0.8749 (mtm) REVERT: F 77 ASP cc_start: 0.8450 (t0) cc_final: 0.7995 (t0) REVERT: F 78 GLN cc_start: 0.9245 (mp10) cc_final: 0.8662 (pm20) REVERT: F 116 ASP cc_start: 0.8891 (t0) cc_final: 0.8547 (t70) REVERT: F 127 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8368 (tt0) REVERT: G 24 GLN cc_start: 0.8568 (mt0) cc_final: 0.8271 (tm-30) REVERT: G 50 ASP cc_start: 0.7820 (t0) cc_final: 0.7503 (t0) REVERT: G 69 GLU cc_start: 0.8495 (tm-30) cc_final: 0.7651 (tm-30) REVERT: G 166 ASP cc_start: 0.7747 (p0) cc_final: 0.7446 (p0) REVERT: G 168 LEU cc_start: 0.6551 (mp) cc_final: 0.6198 (mm) REVERT: H 105 GLU cc_start: 0.6897 (tm-30) cc_final: 0.6679 (tm-30) REVERT: I 1 MET cc_start: 0.7556 (mmt) cc_final: 0.5123 (tmm) REVERT: J 32 GLU cc_start: 0.9005 (mp0) cc_final: 0.8690 (mp0) REVERT: K 5 ASP cc_start: 0.8274 (t70) cc_final: 0.7974 (t0) REVERT: K 49 GLU cc_start: 0.8657 (tp30) cc_final: 0.8389 (tp30) REVERT: K 64 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7963 (mt-10) REVERT: L 36 SER cc_start: 0.8205 (m) cc_final: 0.7806 (p) REVERT: L 54 ARG cc_start: 0.7692 (mtt-85) cc_final: 0.7130 (mtt180) REVERT: L 65 VAL cc_start: 0.8400 (m) cc_final: 0.8178 (p) outliers start: 55 outliers final: 41 residues processed: 364 average time/residue: 0.2283 time to fit residues: 135.7716 Evaluate side-chains 363 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 318 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 HIS Chi-restraints excluded: chain A residue 281 HIS Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 932 GLU Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain A residue 1071 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1202 MET Chi-restraints excluded: chain A residue 1265 ASN Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain A residue 1420 ASP Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 835 GLN Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 53 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 20 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 chunk 363 optimal weight: 10.0000 chunk 243 optimal weight: 0.6980 chunk 331 optimal weight: 5.9990 chunk 139 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 126 optimal weight: 5.9990 chunk 275 optimal weight: 0.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.092943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.061703 restraints weight = 85484.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.063805 restraints weight = 42516.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.065152 restraints weight = 27730.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.065993 restraints weight = 21456.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.066461 restraints weight = 18473.871| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33905 Z= 0.145 Angle : 0.583 12.790 46198 Z= 0.303 Chirality : 0.043 0.285 5190 Planarity : 0.004 0.079 5630 Dihedral : 16.921 170.260 5346 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.81 % Favored : 96.08 % Rotamer: Outliers : 1.43 % Allowed : 13.22 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.26 (0.14), residues: 3854 helix: 1.49 (0.15), residues: 1349 sheet: -0.40 (0.20), residues: 604 loop : -0.55 (0.15), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 54 TYR 0.020 0.001 TYR D 147 PHE 0.036 0.001 PHE K 7 TRP 0.009 0.001 TRP C 201 HIS 0.006 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (33873) covalent geometry : angle 0.57411 / 0.30 (46153) hydrogen bonds : bond 0.03485 / 2.31 ( 1426) hydrogen bonds : angle 4.60362 / 3.23 ( 3952) metal coordination : bond 0.00603 / 0.38 ( 32) metal coordination : angle 3.31633 / 2.01 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 334 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8371 (mtt) cc_final: 0.8069 (mtt) REVERT: A 122 MET cc_start: 0.9040 (tpp) cc_final: 0.8703 (tpp) REVERT: A 133 LYS cc_start: 0.9542 (mttm) cc_final: 0.9172 (mtpp) REVERT: A 304 MET cc_start: 0.8717 (mtt) cc_final: 0.8388 (mtt) REVERT: A 453 MET cc_start: 0.8611 (mpp) cc_final: 0.8084 (mtm) REVERT: A 1079 MET cc_start: 0.7661 (tmm) cc_final: 0.7431 (tmm) REVERT: A 1209 MET cc_start: 0.8192 (mmp) cc_final: 0.7870 (mmm) REVERT: A 1220 PHE cc_start: 0.8478 (m-80) cc_final: 0.8227 (m-80) REVERT: A 1239 ARG cc_start: 0.7677 (mtp-110) cc_final: 0.7369 (mtm180) REVERT: A 1267 MET cc_start: 0.8519 (mtp) cc_final: 0.8140 (mtm) REVERT: A 1268 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8280 (mm) REVERT: A 1285 MET cc_start: 0.7972 (mtp) cc_final: 0.7666 (mtp) REVERT: B 378 LEU cc_start: 0.9433 (tp) cc_final: 0.9156 (tp) REVERT: B 393 LYS cc_start: 0.9223 (mtpp) cc_final: 0.9000 (ttmm) REVERT: B 563 MET cc_start: 0.9249 (tmm) cc_final: 0.8948 (tmm) REVERT: B 705 MET cc_start: 0.9310 (tpp) cc_final: 0.8729 (tpp) REVERT: B 835 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8475 (mt0) REVERT: B 837 ASP cc_start: 0.8657 (m-30) cc_final: 0.8187 (m-30) REVERT: B 873 THR cc_start: 0.9104 (m) cc_final: 0.8594 (p) REVERT: B 939 THR cc_start: 0.9160 (m) cc_final: 0.8850 (p) REVERT: B 1152 MET cc_start: 0.8439 (mmm) cc_final: 0.7939 (mmm) REVERT: D 1 MET cc_start: 0.0388 (tmm) cc_final: -0.0075 (tmm) REVERT: D 186 ASP cc_start: 0.4928 (m-30) cc_final: 0.4656 (m-30) REVERT: E 32 GLN cc_start: 0.8790 (tp-100) cc_final: 0.8102 (tp-100) REVERT: F 77 ASP cc_start: 0.8438 (t0) cc_final: 0.7961 (t0) REVERT: F 78 GLN cc_start: 0.9246 (mp10) cc_final: 0.8690 (pm20) REVERT: F 85 MET cc_start: 0.8829 (ttt) cc_final: 0.8370 (ttt) REVERT: F 116 ASP cc_start: 0.8851 (t0) cc_final: 0.8515 (t70) REVERT: F 127 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8346 (tt0) REVERT: G 24 GLN cc_start: 0.8501 (mt0) cc_final: 0.8196 (tm-30) REVERT: G 50 ASP cc_start: 0.7868 (t0) cc_final: 0.7535 (t0) REVERT: G 69 GLU cc_start: 0.8402 (tm-30) cc_final: 0.7585 (tm-30) REVERT: I 1 MET cc_start: 0.7522 (mmt) cc_final: 0.5121 (tmm) REVERT: J 32 GLU cc_start: 0.8983 (mp0) cc_final: 0.8675 (mp0) REVERT: K 5 ASP cc_start: 0.8144 (t70) cc_final: 0.7932 (t0) REVERT: K 38 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8449 (mm-30) REVERT: K 49 GLU cc_start: 0.8566 (tp30) cc_final: 0.8323 (tp30) REVERT: K 64 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7840 (mt-10) REVERT: L 36 SER cc_start: 0.8129 (m) cc_final: 0.7842 (p) REVERT: L 37 LYS cc_start: 0.8981 (mmmt) cc_final: 0.8737 (mmmt) REVERT: L 54 ARG cc_start: 0.7627 (mtt-85) cc_final: 0.7080 (mtt180) outliers start: 49 outliers final: 38 residues processed: 361 average time/residue: 0.2308 time to fit residues: 135.9712 Evaluate side-chains 355 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 314 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 HIS Chi-restraints excluded: chain A residue 281 HIS Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain A residue 1071 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1202 MET Chi-restraints excluded: chain A residue 1265 ASN Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1420 ASP Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain B residue 835 GLN Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 53 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 58 optimal weight: 5.9990 chunk 377 optimal weight: 6.9990 chunk 167 optimal weight: 8.9990 chunk 196 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 331 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 247 optimal weight: 10.0000 chunk 163 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 GLN ** A1173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN B 357 GLN E 5 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.090317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.059401 restraints weight = 87248.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.061356 restraints weight = 44514.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.062636 restraints weight = 29482.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.063414 restraints weight = 22959.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.063892 restraints weight = 19835.440| |-----------------------------------------------------------------------------| r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 33905 Z= 0.373 Angle : 0.756 17.185 46198 Z= 0.384 Chirality : 0.048 0.288 5190 Planarity : 0.005 0.066 5630 Dihedral : 17.067 173.048 5346 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.58 % Favored : 94.32 % Rotamer: Outliers : 1.69 % Allowed : 13.74 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: -0.07 (0.14), residues: 3854 helix: 1.19 (0.14), residues: 1347 sheet: -0.55 (0.20), residues: 620 loop : -0.73 (0.15), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 54 TYR 0.020 0.002 TYR B 830 PHE 0.033 0.002 PHE K 7 TRP 0.013 0.002 TRP B 561 HIS 0.011 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00842 / 0.37 (33873) covalent geometry : angle 0.74453 / 0.38 (46153) hydrogen bonds : bond 0.04178 / 2.77 ( 1426) hydrogen bonds : angle 4.96137 / 3.49 ( 3952) metal coordination : bond 0.01415 / 0.89 ( 32) metal coordination : angle 4.28533 / 2.55 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 305 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8394 (mtt) cc_final: 0.8091 (mtt) REVERT: A 109 HIS cc_start: 0.8455 (OUTLIER) cc_final: 0.8252 (t70) REVERT: A 133 LYS cc_start: 0.9490 (mttm) cc_final: 0.9137 (mtpp) REVERT: A 304 MET cc_start: 0.8858 (mtt) cc_final: 0.8561 (mtt) REVERT: A 453 MET cc_start: 0.8649 (mpp) cc_final: 0.7969 (mtm) REVERT: A 708 MET cc_start: 0.4487 (OUTLIER) cc_final: 0.4213 (mtp) REVERT: A 1079 MET cc_start: 0.7775 (tmm) cc_final: 0.7556 (tmm) REVERT: A 1209 MET cc_start: 0.8421 (mmp) cc_final: 0.8102 (mmm) REVERT: A 1220 PHE cc_start: 0.8522 (m-80) cc_final: 0.8282 (m-80) REVERT: A 1239 ARG cc_start: 0.7636 (mtp-110) cc_final: 0.7374 (mtm180) REVERT: A 1267 MET cc_start: 0.8571 (mtp) cc_final: 0.8179 (mtm) REVERT: A 1268 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8289 (mm) REVERT: A 1285 MET cc_start: 0.8015 (mtp) cc_final: 0.7645 (mtp) REVERT: B 393 LYS cc_start: 0.9248 (mtpp) cc_final: 0.9037 (ttmm) REVERT: B 563 MET cc_start: 0.9208 (tmm) cc_final: 0.8882 (tmm) REVERT: B 773 MET cc_start: 0.8958 (mtm) cc_final: 0.8705 (ptp) REVERT: B 835 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8512 (mt0) REVERT: B 873 THR cc_start: 0.9099 (m) cc_final: 0.8603 (p) REVERT: B 939 THR cc_start: 0.9152 (m) cc_final: 0.8795 (p) REVERT: D 1 MET cc_start: 0.0511 (tmm) cc_final: -0.0022 (tmm) REVERT: E 58 MET cc_start: 0.8883 (mtp) cc_final: 0.8639 (mtm) REVERT: F 77 ASP cc_start: 0.8428 (t0) cc_final: 0.7944 (t0) REVERT: F 78 GLN cc_start: 0.9284 (mp10) cc_final: 0.8779 (pm20) REVERT: F 116 ASP cc_start: 0.8909 (t0) cc_final: 0.8569 (t70) REVERT: F 127 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8414 (tt0) REVERT: G 24 GLN cc_start: 0.8623 (mt0) cc_final: 0.8306 (tm-30) REVERT: G 50 ASP cc_start: 0.7923 (t0) cc_final: 0.7613 (t0) REVERT: G 69 GLU cc_start: 0.8530 (tm-30) cc_final: 0.7707 (tm-30) REVERT: G 166 ASP cc_start: 0.7459 (p0) cc_final: 0.6839 (t0) REVERT: I 1 MET cc_start: 0.7448 (mmt) cc_final: 0.5102 (tmm) REVERT: J 32 GLU cc_start: 0.9068 (mp0) cc_final: 0.8738 (mp0) REVERT: K 49 GLU cc_start: 0.8754 (tp30) cc_final: 0.8477 (tp30) REVERT: K 64 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7895 (mt-10) REVERT: L 36 SER cc_start: 0.8021 (m) cc_final: 0.7667 (p) outliers start: 58 outliers final: 45 residues processed: 338 average time/residue: 0.2319 time to fit residues: 127.8551 Evaluate side-chains 353 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 303 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 109 HIS Chi-restraints excluded: chain A residue 281 HIS Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 932 GLU Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain A residue 1071 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1202 MET Chi-restraints excluded: chain A residue 1265 ASN Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1420 ASP Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 835 GLN Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 153 ARG Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 167 TYR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 53 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 308 optimal weight: 9.9990 chunk 268 optimal weight: 0.9980 chunk 200 optimal weight: 0.8980 chunk 176 optimal weight: 10.0000 chunk 232 optimal weight: 0.3980 chunk 49 optimal weight: 2.9990 chunk 314 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 164 optimal weight: 0.9990 chunk 321 optimal weight: 0.6980 chunk 241 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1173 HIS A1203 ASN B 215 GLN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.093341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.062215 restraints weight = 85366.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.064319 restraints weight = 42238.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.065677 restraints weight = 27476.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.066521 restraints weight = 21219.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.067032 restraints weight = 18248.849| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33905 Z= 0.120 Angle : 0.608 13.333 46198 Z= 0.314 Chirality : 0.044 0.279 5190 Planarity : 0.004 0.079 5630 Dihedral : 16.924 170.380 5346 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.35 % Favored : 96.55 % Rotamer: Outliers : 0.99 % Allowed : 14.56 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.14), residues: 3854 helix: 1.42 (0.15), residues: 1349 sheet: -0.37 (0.20), residues: 623 loop : -0.59 (0.15), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 54 TYR 0.022 0.001 TYR D 147 PHE 0.040 0.001 PHE K 7 TRP 0.015 0.001 TRP C 201 HIS 0.007 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (33873) covalent geometry : angle 0.60005 / 0.31 (46153) hydrogen bonds : bond 0.03508 / 2.30 ( 1426) hydrogen bonds : angle 4.57105 / 3.22 ( 3952) metal coordination : bond 0.00511 / 0.32 ( 32) metal coordination : angle 3.12665 / 1.91 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 337 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8323 (mtt) cc_final: 0.8042 (mtt) REVERT: A 133 LYS cc_start: 0.9517 (mttm) cc_final: 0.9153 (mtpp) REVERT: A 304 MET cc_start: 0.8796 (mtt) cc_final: 0.8457 (mtt) REVERT: A 453 MET cc_start: 0.8583 (mpp) cc_final: 0.8093 (mtm) REVERT: A 708 MET cc_start: 0.4249 (OUTLIER) cc_final: 0.4025 (mtp) REVERT: A 1079 MET cc_start: 0.7686 (tmm) cc_final: 0.7285 (tmm) REVERT: A 1209 MET cc_start: 0.8188 (mmp) cc_final: 0.7892 (mmm) REVERT: A 1220 PHE cc_start: 0.8510 (m-80) cc_final: 0.8242 (m-80) REVERT: A 1267 MET cc_start: 0.8527 (mtp) cc_final: 0.8151 (mtm) REVERT: A 1268 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8270 (mm) REVERT: A 1285 MET cc_start: 0.8048 (mtp) cc_final: 0.7754 (mtp) REVERT: B 393 LYS cc_start: 0.9203 (mtpp) cc_final: 0.8977 (ttmm) REVERT: B 563 MET cc_start: 0.9291 (tmm) cc_final: 0.9001 (tmm) REVERT: B 705 MET cc_start: 0.9220 (tpp) cc_final: 0.8608 (tpp) REVERT: B 835 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8450 (mt0) REVERT: B 837 ASP cc_start: 0.8827 (m-30) cc_final: 0.8521 (m-30) REVERT: B 873 THR cc_start: 0.9068 (m) cc_final: 0.8556 (p) REVERT: B 939 THR cc_start: 0.9122 (m) cc_final: 0.8776 (p) REVERT: B 1152 MET cc_start: 0.8415 (mmm) cc_final: 0.8210 (mmm) REVERT: C 61 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7881 (mp0) REVERT: D 1 MET cc_start: 0.0398 (tmm) cc_final: -0.0044 (tmm) REVERT: E 32 GLN cc_start: 0.8843 (tp-100) cc_final: 0.8388 (tp40) REVERT: E 58 MET cc_start: 0.8892 (mtp) cc_final: 0.8585 (mtm) REVERT: F 77 ASP cc_start: 0.8428 (t0) cc_final: 0.7926 (t0) REVERT: F 78 GLN cc_start: 0.9172 (mp10) cc_final: 0.8534 (pm20) REVERT: F 116 ASP cc_start: 0.8855 (t0) cc_final: 0.8522 (t70) REVERT: F 127 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8387 (tt0) REVERT: G 14 HIS cc_start: 0.8210 (t-90) cc_final: 0.7531 (t-90) REVERT: G 24 GLN cc_start: 0.8510 (mt0) cc_final: 0.8174 (tm-30) REVERT: G 50 ASP cc_start: 0.7827 (t0) cc_final: 0.7511 (t0) REVERT: G 69 GLU cc_start: 0.8458 (tm-30) cc_final: 0.7640 (tm-30) REVERT: H 45 GLU cc_start: 0.8608 (tp30) cc_final: 0.8395 (tp30) REVERT: I 1 MET cc_start: 0.7521 (mmt) cc_final: 0.5157 (tmm) REVERT: J 32 GLU cc_start: 0.9011 (mp0) cc_final: 0.8718 (mp0) REVERT: K 5 ASP cc_start: 0.8227 (t0) cc_final: 0.7928 (t0) REVERT: K 38 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8478 (mp0) REVERT: K 49 GLU cc_start: 0.8577 (tp30) cc_final: 0.8376 (tp30) REVERT: K 64 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7802 (mt-10) REVERT: L 36 SER cc_start: 0.7977 (m) cc_final: 0.7622 (p) REVERT: L 42 ARG cc_start: 0.6655 (ttm170) cc_final: 0.6213 (mpp-170) REVERT: L 47 ARG cc_start: 0.8089 (mtp180) cc_final: 0.7723 (mtp180) REVERT: L 54 ARG cc_start: 0.7803 (mtt90) cc_final: 0.6873 (mpt180) outliers start: 34 outliers final: 26 residues processed: 358 average time/residue: 0.2332 time to fit residues: 135.8320 Evaluate side-chains 347 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 316 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 HIS Chi-restraints excluded: chain A residue 281 HIS Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain A residue 1071 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1265 ASN Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1420 ASP Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain B residue 835 GLN Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 53 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 352 optimal weight: 4.9990 chunk 284 optimal weight: 9.9990 chunk 354 optimal weight: 0.9990 chunk 214 optimal weight: 2.9990 chunk 374 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 343 optimal weight: 9.9990 chunk 296 optimal weight: 8.9990 chunk 250 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.091517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.060929 restraints weight = 86146.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.062950 restraints weight = 43246.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.064243 restraints weight = 28325.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.065043 restraints weight = 21954.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.065529 restraints weight = 18939.906| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 33905 Z= 0.247 Angle : 0.657 13.465 46198 Z= 0.336 Chirality : 0.045 0.287 5190 Planarity : 0.004 0.078 5630 Dihedral : 16.935 172.539 5346 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.70 % Favored : 95.20 % Rotamer: Outliers : 0.99 % Allowed : 14.97 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % 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: 0.11 (0.14), residues: 3854 helix: 1.38 (0.15), residues: 1350 sheet: -0.46 (0.20), residues: 617 loop : -0.67 (0.15), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1366 TYR 0.036 0.002 TYR E 112 PHE 0.035 0.002 PHE C 219 TRP 0.008 0.001 TRP B 31 HIS 0.008 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.25 (33873) covalent geometry : angle 0.64881 / 0.34 (46153) hydrogen bonds : bond 0.03698 / 2.43 ( 1426) hydrogen bonds : angle 4.68458 / 3.30 ( 3952) metal coordination : bond 0.00959 / 0.60 ( 32) metal coordination : angle 3.40789 / 2.05 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6503.40 seconds wall clock time: 113 minutes 24.06 seconds (6804.06 seconds total)