Starting phenix.real_space_refine on Sun Aug 9 09:58:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/24qp_69770/08_2026/24qp_69770_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/24qp_69770/08_2026/24qp_69770.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/24qp_69770/08_2026/24qp_69770.map" default_real_map = "/net/cci-nas-00/data/ceres_data/24qp_69770/08_2026/24qp_69770.map" model { file = "/net/cci-nas-00/data/ceres_data/24qp_69770/08_2026/24qp_69770_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/24qp_69770/08_2026/24qp_69770_neut.cif" } resolution = 2.73 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= 0.002 sd= 0.027 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: 8 Type Number sf(0) Gaussians Pt 1 10.81 5 Zn 9 6.06 5 P 49 5.49 5 Mg 1 5.21 5 S 186 5.16 5 C 20842 2.51 5 N 5806 2.21 5 O 6414 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s 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: 33308 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 11205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1424, 11205 Classifications: {'peptide': 1424} Link IDs: {'PCIS': 3, 'PTRANS': 63, 'TRANS': 1357} Chain breaks: 3 Chain: "B" Number of atoms: 9453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1187, 9453 Classifications: {'peptide': 1187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1134} Chain breaks: 3 Chain: "C" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2086 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain: "D" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1326 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 2, 'TRANS': 162} Chain breaks: 1 Chain: "E" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1752 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain: "F" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 705 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain: "G" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1339 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1113 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 134} Chain breaks: 1 Chain: "I" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 944 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 924 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} 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: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 385 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "P" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 135 Classifications: {'RNA': 6} Modifications used: {'rna3p_pur': 6} Link IDs: {'rna3p': 5} Chain: "Q" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 505 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "T" Number of atoms: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 489 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {' PT': 1, 'DNH': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 820 SG CYS A 107 94.425 76.946 128.255 1.00 57.01 S ATOM 844 SG CYS A 110 95.762 73.522 128.853 1.00 52.36 S ATOM 1149 SG CYS A 148 92.698 74.742 130.879 1.00 55.58 S ATOM 1287 SG CYS A 167 96.138 76.089 131.538 1.00 53.20 S ATOM 515 SG CYS A 67 111.663 69.643 84.810 1.00 55.30 S ATOM 537 SG CYS A 70 110.151 66.335 83.537 1.00 54.92 S ATOM 590 SG CYS A 77 107.945 69.386 83.758 1.00 50.94 S ATOM 20164 SG CYS B1163 103.555 58.275 96.389 1.00 48.00 S ATOM 20182 SG CYS B1166 102.280 61.749 97.114 1.00 46.91 S ATOM 20307 SG CYS B1182 105.845 61.236 95.855 1.00 40.34 S ATOM 20326 SG CYS B1185 104.826 60.299 99.436 1.00 50.89 S ATOM 21305 SG CYS C 86 87.453 77.886 21.102 1.00 59.39 S ATOM 21322 SG CYS C 88 89.847 79.886 23.244 1.00 58.35 S ATOM 21355 SG CYS C 92 89.042 80.931 19.635 1.00 54.66 S ATOM 21378 SG CYS C 95 86.489 81.311 22.522 1.00 61.25 S ATOM 29032 SG CYS I 7 56.432 132.276 127.235 1.00 77.83 S ATOM 29057 SG CYS I 10 60.222 130.947 126.249 1.00104.19 S ATOM 29223 SG CYS I 29 57.776 129.035 128.494 1.00 91.27 S ATOM 29247 SG CYS I 32 59.715 132.167 129.384 1.00 99.62 S ATOM 29574 SG CYS I 75 28.678 126.854 92.508 1.00 79.87 S ATOM 29596 SG CYS I 78 28.050 130.284 90.843 1.00 76.60 S ATOM 29812 SG CYS I 103 31.300 128.558 90.399 1.00 71.43 S ATOM 29832 SG CYS I 106 30.404 130.038 93.798 1.00 68.07 S ATOM 29977 SG CYS J 7 62.949 95.476 37.156 1.00 61.39 S ATOM 30000 SG CYS J 10 61.573 93.567 34.023 1.00 44.74 S ATOM 30280 SG CYS J 45 59.334 94.958 36.804 1.00 49.30 S ATOM 30286 SG CYS J 46 61.040 97.196 34.213 1.00 53.40 S ATOM 31466 SG CYS L 31 100.392 115.396 47.333 1.00 82.67 S ATOM 31486 SG CYS L 34 100.948 118.545 44.981 1.00 84.06 S ATOM 31590 SG CYS L 48 103.797 116.587 46.626 1.00 90.57 S ATOM 31613 SG CYS L 51 101.357 118.894 48.568 1.00 92.52 S ATOM 32385 SG CYS Q 25 91.429 109.698 134.141 1.00143.32 S ATOM 32410 SG CYS Q 28 94.121 107.091 134.258 1.00137.44 S ATOM 32565 SG CYS Q 49 90.489 106.107 134.918 1.00150.61 S ATOM 32588 SG CYS Q 52 92.321 108.152 137.509 1.00145.73 S Time building chain proxies: 6.75, per 1000 atoms: 0.20 Number of scatterers: 33308 At special positions: 0 Unit cell: (154.38, 154.38, 155.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Pt 1 77.96 Zn 9 29.99 S 186 16.00 P 49 15.00 Mg 1 11.99 O 6414 8.00 N 5806 7.00 C 20842 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.74 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " 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 95 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " 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 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb=" ZN Q 101 " pdb="ZN ZN Q 101 " - pdb=" SG CYS Q 25 " pdb="ZN ZN Q 101 " - pdb=" SG CYS Q 49 " pdb="ZN ZN Q 101 " - pdb=" SG CYS Q 52 " pdb="ZN ZN Q 101 " - pdb=" SG CYS Q 28 " Number of angles added : 51 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7636 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 51 sheets defined 37.5% alpha, 19.8% beta 22 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 4.47 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 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 214 Processing helix chain 'A' and resid 215 through 222 Processing helix chain 'A' and resid 230 through 233 Processing helix chain 'A' and resid 260 through 283 Processing helix chain 'A' and resid 285 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: 3.613A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 524 through 535 Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 574 through 582 removed outlier: 3.656A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 659 Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 672 through 699 Processing helix chain 'A' and resid 709 through 737 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 809 through 846 removed outlier: 3.861A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 874 through 878 Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 909 through 913 removed outlier: 3.664A pdb=" N LEU A 913 " --> pdb=" O PRO A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 959 through 972 Processing helix chain 'A' and resid 982 through 997 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 1033 Processing helix chain 'A' and resid 1038 through 1056 Processing helix chain 'A' and resid 1063 through 1079 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1097 through 1107 Processing helix chain 'A' and resid 1127 through 1139 removed outlier: 3.827A pdb=" N ALA A1131 " --> pdb=" O ASP A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1165 No H-bonds generated for 'chain 'A' and resid 1163 through 1165' Processing helix chain 'A' and resid 1166 through 1176 removed outlier: 3.578A pdb=" N ILE A1170 " --> pdb=" O ASP A1166 " (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 1249 through 1270 removed outlier: 7.125A pdb=" N ASP A1257 " --> pdb=" O GLU A1253 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N HIS A1258 " --> pdb=" O ALA A1254 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A1269 " --> pdb=" O ASN A1265 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1318 removed outlier: 3.854A pdb=" N THR A1318 " --> pdb=" O SER A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1339 Processing helix chain 'A' and resid 1340 through 1358 Processing helix chain 'A' and resid 1364 through 1376 removed outlier: 3.915A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1401 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1431 removed outlier: 3.833A pdb=" N ASN A1427 " --> pdb=" O GLY A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1439 Processing helix chain 'A' and resid 1446 through 1454 Processing helix chain 'B' and resid 28 through 41 removed outlier: 3.746A pdb=" N ALA B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 65 removed outlier: 4.491A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 82 removed outlier: 3.534A pdb=" N ASP B 82 " --> pdb=" O THR B 79 " (cutoff:3.500A) No H-bonds generated for '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 302 Processing helix chain 'B' and resid 307 through 322 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 337 Processing helix chain 'B' and resid 344 through 358 Processing helix chain 'B' and resid 370 through 390 removed outlier: 3.614A 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 437 Processing helix chain 'B' and resid 443 through 448 removed outlier: 3.635A pdb=" N ALA B 447 " --> pdb=" O ASN B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 463 removed outlier: 4.287A pdb=" N ILE B 453 " --> pdb=" O ASN B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 550 through 562 removed outlier: 4.672A pdb=" N ILE B 554 " --> pdb=" O ASP B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 592 through 606 removed outlier: 3.748A pdb=" N LEU B 596 " --> pdb=" O ASN B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 668 Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 695 through 699 removed outlier: 3.600A pdb=" N GLU B 699 " --> pdb=" O ALA B 695 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 695 through 699' Processing helix chain 'B' and resid 706 through 711 removed outlier: 3.622A pdb=" N GLU B 711 " --> pdb=" O PRO B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 Processing helix chain 'B' and resid 752 through 756 Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'B' and resid 763 through 774 Processing helix chain 'B' and resid 775 through 777 No H-bonds generated for 'chain 'B' and resid 775 through 777' Processing helix chain 'B' and resid 806 through 811 removed outlier: 3.582A pdb=" N GLU B 810 " --> pdb=" O ARG B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.619A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.729A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1152 Processing helix chain 'B' and resid 1175 through 1178 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 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: 4.051A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU C 210 " --> pdb=" O CYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 267 Processing helix chain 'D' and resid 30 through 34 removed outlier: 3.549A pdb=" N GLN D 34 " --> pdb=" O GLN D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 72 Processing helix chain 'D' and resid 118 through 134 removed outlier: 3.582A pdb=" N GLU D 122 " --> pdb=" O THR D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 151 Processing helix chain 'D' and resid 156 through 170 removed outlier: 3.594A 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 193 removed outlier: 3.839A pdb=" N THR D 193 " --> pdb=" O ASP D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 219 removed outlier: 3.885A pdb=" N LEU D 207 " --> pdb=" O SER D 203 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 26 Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 47 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 104 Processing helix chain 'E' and resid 117 through 122 Processing helix chain 'E' and resid 138 through 141 removed outlier: 3.660A pdb=" N VAL E 141 " --> pdb=" O ALA E 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 138 through 141' Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 168 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 75 through 79 removed outlier: 3.561A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 31 Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'H' and resid 129 through 133 Processing helix chain 'I' and resid 61 through 65 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 52 Processing helix chain 'J' and resid 56 through 62 Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 52 removed outlier: 3.545A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 111 Processing helix chain 'Q' and resid 65 through 78 removed outlier: 3.616A pdb=" N GLU Q 78 " --> pdb=" O PHE Q 74 " (cutoff:3.500A) 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 91 removed outlier: 6.866A pdb=" N THR A 237 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 11.001A pdb=" N LYS A 88 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 10.508A pdb=" N ILE A 235 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA4, first strand: chain 'A' and resid 173 through 177 removed outlier: 4.759A pdb=" N LEU A 181 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 250 through 251 removed outlier: 3.602A pdb=" N GLY A 258 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 345 Processing sheet with id=AA7, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.670A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 375 through 379 removed outlier: 6.413A pdb=" N LYS A 431 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VAL A 405 " --> pdb=" O LYS A 431 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLU A 433 " --> pdb=" O LYS A 403 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.624A pdb=" N LYS A 518 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 567 removed outlier: 6.352A pdb=" N VAL H 96 " --> pdb=" O ILE A 566 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 588 through 590 removed outlier: 6.842A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AB5, first strand: chain 'A' and resid 849 through 850 Processing sheet with id=AB6, first strand: chain 'A' and resid 879 through 882 Processing sheet with id=AB7, first strand: chain 'A' and resid 1282 through 1287 Processing sheet with id=AB8, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 3.773A pdb=" N ARG A1239 " --> pdb=" O ILE A1227 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N VAL A1242 " --> pdb=" O TRP A1191 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TRP A1191 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA A1149 " --> pdb=" O GLU A1196 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR I 44 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1290 through 1292 removed outlier: 3.579A pdb=" N VAL A1299 " --> pdb=" O VAL A1291 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1441 through 1445 Processing sheet with id=AC2, first strand: chain 'B' and resid 69 through 73 removed outlier: 5.697A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLY B 127 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N SER B 125 " --> pdb=" O PRO B 100 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU B 138 " --> pdb=" O GLU B 150 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 109 through 111 removed outlier: 3.639A pdb=" N HIS B 110 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLY B 127 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N SER B 125 " --> pdb=" O PRO B 100 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC5, first strand: chain 'B' and resid 404 through 407 removed outlier: 6.355A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 224 through 227 removed outlier: 3.713A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR B 268 " --> pdb=" O TYR B 259 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC8, first strand: chain 'B' and resid 650 through 651 Processing sheet with id=AC9, first strand: chain 'B' and resid 564 through 565 removed outlier: 7.072A pdb=" N VAL B 580 " --> pdb=" O HIS B 587 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL B 589 " --> pdb=" O THR B 578 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N THR B 578 " --> pdb=" O VAL B 589 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ARG B 579 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ILE B 626 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE B 581 " --> pdb=" O ILE B 626 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 793 through 796 removed outlier: 6.789A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 793 through 796 removed outlier: 6.789A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU L 27 " --> pdb=" O LEU L 40 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD4, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 6.851A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 873 through 874 Processing sheet with id=AD6, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.711A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD8, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD9, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AE1, first strand: chain 'C' and resid 7 through 13 removed outlier: 5.590A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 43 through 54 removed outlier: 6.782A pdb=" N VAL C 158 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N VAL C 49 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR C 156 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N VAL C 51 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LYS C 154 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N THR C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N GLU C 152 " --> pdb=" O THR C 53 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 72 through 74 removed outlier: 4.907A pdb=" N HIS C 131 " --> pdb=" O GLN C 73 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 111 through 114 removed outlier: 3.518A pdb=" N CYS C 145 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AE6, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.663A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.646A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 2 through 13 removed outlier: 3.666A pdb=" N ALA G 76 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE G 11 " --> pdb=" O PHE G 70 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER G 37 " --> pdb=" O ILE G 45 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 2 through 13 removed outlier: 3.666A pdb=" N ALA G 76 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE G 11 " --> pdb=" O PHE G 70 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 85 through 93 removed outlier: 3.700A pdb=" N VAL G 92 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ALA G 159 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY G 161 " --> pdb=" O PHE G 109 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N HIS G 158 " --> pdb=" O CYS G 150 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N CYS G 150 " --> pdb=" O HIS G 158 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE G 160 " --> pdb=" O GLU G 148 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU G 85 " --> pdb=" O ILE G 147 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.577A pdb=" N THR G 120 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN G 131 " --> pdb=" O THR G 120 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER G 129 " --> pdb=" O ASN G 122 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR G 130 " --> pdb=" O ILE G 137 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 14 through 18 removed outlier: 3.730A pdb=" N PHE I 27 " --> pdb=" O GLU I 36 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU I 36 " --> pdb=" O PHE I 27 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 83 through 87 Processing sheet with id=AF5, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF6, first strand: chain 'Q' and resid 17 through 21 removed outlier: 3.762A pdb=" N THR Q 21 " --> pdb=" O VAL Q 34 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL Q 34 " --> pdb=" O THR Q 21 " (cutoff:3.500A) 1405 hydrogen bonds defined for protein. 3885 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 9.72 Time building geometry restraints manager: 3.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6320 1.33 - 1.45: 8159 1.45 - 1.57: 19130 1.57 - 1.70: 95 1.70 - 1.82: 295 Bond restraints: 33999 Sorted by residual: bond pdb=" CA GLY B1121 " pdb=" C GLY B1121 " ideal model delta sigma weight residual 1.516 1.483 0.033 6.90e-03 2.10e+04 2.33e+01 bond pdb=" N ASN B 499 " pdb=" CA ASN B 499 " ideal model delta sigma weight residual 1.455 1.503 -0.048 1.25e-02 6.40e+03 1.46e+01 bond pdb=" CA GLY B 503 " pdb=" C GLY B 503 " ideal model delta sigma weight residual 1.514 1.485 0.029 8.60e-03 1.35e+04 1.12e+01 bond pdb=" N LYS B 813 " pdb=" CA LYS B 813 " ideal model delta sigma weight residual 1.462 1.508 -0.046 1.54e-02 4.22e+03 8.94e+00 bond pdb=" CA SER B1123 " pdb=" CB SER B1123 " ideal model delta sigma weight residual 1.528 1.484 0.044 1.56e-02 4.11e+03 8.04e+00 ... (remaining 33994 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.04: 45599 3.04 - 6.07: 428 6.07 - 9.11: 76 9.11 - 12.14: 5 12.14 - 15.18: 2 Bond angle restraints: 46110 Sorted by residual: angle pdb=" CB GLU B1132 " pdb=" CG GLU B1132 " pdb=" CD GLU B1132 " ideal model delta sigma weight residual 112.60 97.42 15.18 1.70e+00 3.46e-01 7.97e+01 angle pdb=" C ILE B 502 " pdb=" N GLY B 503 " pdb=" CA GLY B 503 " ideal model delta sigma weight residual 121.61 115.75 5.86 7.70e-01 1.69e+00 5.80e+01 angle pdb=" N PHE B1130 " pdb=" CA PHE B1130 " pdb=" CB PHE B1130 " ideal model delta sigma weight residual 110.24 120.39 -10.15 1.45e+00 4.76e-01 4.90e+01 angle pdb=" CA PHE B1130 " pdb=" CB PHE B1130 " pdb=" CG PHE B1130 " ideal model delta sigma weight residual 113.80 120.14 -6.34 1.00e+00 1.00e+00 4.02e+01 angle pdb=" C PRO B 501 " pdb=" CA PRO B 501 " pdb=" CB PRO B 501 " ideal model delta sigma weight residual 111.71 119.58 -7.87 1.30e+00 5.92e-01 3.67e+01 ... (remaining 46105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 20282 35.88 - 71.76: 410 71.76 - 107.65: 23 107.65 - 143.53: 0 143.53 - 179.41: 3 Dihedral angle restraints: 20718 sinusoidal: 8926 harmonic: 11792 Sorted by residual: dihedral pdb=" C ASP B1125 " pdb=" N ASP B1125 " pdb=" CA ASP B1125 " pdb=" CB ASP B1125 " ideal model delta harmonic sigma weight residual -122.60 -135.82 13.22 0 2.50e+00 1.60e-01 2.79e+01 dihedral pdb=" C GLU B 810 " pdb=" N GLU B 810 " pdb=" CA GLU B 810 " pdb=" CB GLU B 810 " ideal model delta harmonic sigma weight residual -122.60 -111.28 -11.32 0 2.50e+00 1.60e-01 2.05e+01 dihedral pdb=" CA PHE A 22 " pdb=" C PHE A 22 " pdb=" N SER A 23 " pdb=" CA SER A 23 " ideal model delta harmonic sigma weight residual 180.00 159.21 20.79 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 20715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 5080 0.126 - 0.253: 62 0.253 - 0.379: 7 0.379 - 0.506: 18 0.506 - 0.632: 16 Chirality restraints: 5183 Sorted by residual: chirality pdb=" P DG N 1 " pdb=" OP1 DG N 1 " pdb=" OP2 DG N 1 " pdb=" O5' DG N 1 " both_signs ideal model delta sigma weight residual True 2.34 2.97 -0.63 2.00e-01 2.50e+01 9.99e+00 chirality pdb=" P DC T 2 " pdb=" OP1 DC T 2 " pdb=" OP2 DC T 2 " pdb=" O5' DC T 2 " both_signs ideal model delta sigma weight residual True 2.34 -2.97 -0.63 2.00e-01 2.50e+01 9.97e+00 chirality pdb=" P DT T 3 " pdb=" OP1 DT T 3 " pdb=" OP2 DT T 3 " pdb=" O5' DT T 3 " both_signs ideal model delta sigma weight residual True 2.34 -2.95 -0.61 2.00e-01 2.50e+01 9.43e+00 ... (remaining 5180 not shown) Planarity restraints: 5810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 504 " 0.468 9.50e-02 1.11e+02 2.10e-01 2.69e+01 pdb=" NE ARG B 504 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG B 504 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 504 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 504 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 512 " -0.356 9.50e-02 1.11e+02 1.60e-01 1.58e+01 pdb=" NE ARG B 512 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 512 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 512 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 512 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 532 " -0.300 9.50e-02 1.11e+02 1.34e-01 1.11e+01 pdb=" NE ARG A 532 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 532 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 532 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 532 " -0.009 2.00e-02 2.50e+03 ... (remaining 5807 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 32 2.57 - 3.15: 27043 3.15 - 3.74: 53920 3.74 - 4.32: 76778 4.32 - 4.90: 124645 Nonbonded interactions: 282418 Sorted by model distance: nonbonded pdb=" N7 DG N 5 " pdb="PT PT N 102 " model vdw 1.989 2.230 nonbonded pdb=" N7 DG T 13 " pdb="PT PT N 102 " model vdw 1.999 2.230 nonbonded pdb=" N1 DNH N 101 " pdb="PT PT N 102 " model vdw 2.028 2.230 nonbonded pdb=" N2 DNH N 101 " pdb="PT PT N 102 " model vdw 2.041 2.230 nonbonded pdb=" OD1 ASP A 483 " pdb="MG MG A1803 " model vdw 2.070 2.170 ... (remaining 282413 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 39.920 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 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 0.052 34035 Z= 0.215 Angle : 0.746 15.837 46161 Z= 0.424 Chirality : 0.062 0.632 5183 Planarity : 0.006 0.210 5810 Dihedral : 14.702 179.410 13082 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.86 % Favored : 97.06 % Rotamer: Outliers : 0.17 % Allowed : 0.20 % Favored : 99.64 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.89 % 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 (0.13), residues: 4019 helix: 0.82 (0.14), residues: 1372 sheet: -0.30 (0.20), residues: 676 loop : -0.20 (0.14), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 39 TYR 0.020 0.001 TYR B 797 PHE 0.033 0.001 PHE B1130 TRP 0.036 0.001 TRP C 170 HIS 0.005 0.001 HIS B1195 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.21 (33999) covalent geometry : angle 0.73390 / 0.42 (46110) hydrogen bonds : bond 0.16376 / 10.87 ( 1428) hydrogen bonds : angle 7.22425 / 5.17 ( 3993) metal coordination : bond 0.00700 / 0.35 ( 36) metal coordination : angle 4.13956 / 2.53 ( 51) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 638 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 818 MET cc_start: 0.8996 (mtp) cc_final: 0.8653 (mtp) REVERT: B 510 LYS cc_start: 0.8417 (mtmm) cc_final: 0.8186 (mmmt) REVERT: B 887 HIS cc_start: 0.7937 (t-90) cc_final: 0.7702 (t-90) REVERT: D 119 ARG cc_start: 0.2804 (mmt180) cc_final: 0.2261 (tpt170) REVERT: D 121 LYS cc_start: 0.3895 (pptt) cc_final: 0.3616 (pptt) REVERT: D 144 THR cc_start: 0.7082 (m) cc_final: 0.6675 (p) REVERT: E 57 MET cc_start: 0.6940 (pmm) cc_final: 0.6522 (ptp) REVERT: I 90 GLN cc_start: 0.8148 (mt0) cc_final: 0.7905 (mt0) outliers start: 6 outliers final: 3 residues processed: 644 average time/residue: 0.8384 time to fit residues: 631.4597 Evaluate side-chains 381 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 378 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1124 ARG Chi-restraints excluded: chain C residue 217 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.0670 chunk 401 optimal weight: 20.0000 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 0.0670 overall best weight: 1.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 316 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 GLN A 996 ASN A1033 GLN A1140 HIS A1387 HIS A1393 ASN ** B 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN B 415 GLN B 440 HIS ** B 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 975 GLN C 123 ASN C 231 ASN ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 ASN ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 57 GLN ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.131779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.091965 restraints weight = 44673.261| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.21 r_work: 0.3207 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 34035 Z= 0.166 Angle : 0.624 14.376 46161 Z= 0.323 Chirality : 0.045 0.329 5183 Planarity : 0.004 0.054 5810 Dihedral : 12.052 179.320 4972 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.65 % Allowed : 9.59 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.13), residues: 4019 helix: 0.94 (0.14), residues: 1388 sheet: -0.20 (0.20), residues: 673 loop : -0.07 (0.14), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 155 TYR 0.021 0.001 TYR B 797 PHE 0.034 0.002 PHE E 96 TRP 0.022 0.002 TRP C 170 HIS 0.005 0.001 HIS A 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (33999) covalent geometry : angle 0.60909 / 0.32 (46110) hydrogen bonds : bond 0.04923 / 3.36 ( 1428) hydrogen bonds : angle 5.64744 / 4.05 ( 3993) metal coordination : bond 0.00669 / 0.32 ( 36) metal coordination : angle 4.08848 / 2.56 ( 51) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 405 time to evaluate : 1.312 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 304 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8228 (mtt) REVERT: A 705 LYS cc_start: 0.8078 (ptpp) cc_final: 0.7782 (pttt) REVERT: A 818 MET cc_start: 0.8883 (mtp) cc_final: 0.8605 (mtp) REVERT: A 849 MET cc_start: 0.9240 (ttm) cc_final: 0.8916 (ttp) REVERT: A 903 ASN cc_start: 0.8024 (OUTLIER) cc_final: 0.7655 (p0) REVERT: A 1228 TRP cc_start: 0.8152 (p90) cc_final: 0.7884 (p90) REVERT: A 1270 ASN cc_start: 0.7959 (m110) cc_final: 0.7694 (m110) REVERT: A 1444 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8589 (mtm) REVERT: B 101 MET cc_start: 0.8872 (mmm) cc_final: 0.7918 (mmm) REVERT: B 135 ARG cc_start: 0.7860 (mtp85) cc_final: 0.7559 (mmm160) REVERT: B 434 ARG cc_start: 0.7685 (mtm110) cc_final: 0.6908 (mtm110) REVERT: B 510 LYS cc_start: 0.8743 (mtmm) cc_final: 0.7698 (mmmt) REVERT: B 792 MET cc_start: 0.8431 (mtp) cc_final: 0.8165 (mtm) REVERT: B 887 HIS cc_start: 0.8631 (t-90) cc_final: 0.8030 (t-90) REVERT: B 944 THR cc_start: 0.8289 (p) cc_final: 0.7976 (t) REVERT: B 1153 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8237 (mt-10) REVERT: C 119 VAL cc_start: 0.8383 (t) cc_final: 0.8097 (m) REVERT: D 65 GLU cc_start: 0.9066 (pt0) cc_final: 0.8865 (pp20) REVERT: D 138 ASN cc_start: 0.7430 (m-40) cc_final: 0.7111 (m-40) REVERT: D 144 THR cc_start: 0.6488 (m) cc_final: 0.6216 (p) REVERT: E 32 GLN cc_start: 0.8272 (mm110) cc_final: 0.7910 (mm110) REVERT: E 60 PHE cc_start: 0.8136 (p90) cc_final: 0.7586 (p90) REVERT: F 71 GLU cc_start: 0.6459 (pm20) cc_final: 0.6240 (pm20) REVERT: F 76 LYS cc_start: 0.8308 (ttpp) cc_final: 0.8001 (tttp) REVERT: G 33 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7377 (tt0) REVERT: G 57 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8381 (mp10) REVERT: G 106 MET cc_start: 0.1729 (mmm) cc_final: 0.1497 (mmm) REVERT: H 66 GLU cc_start: 0.7943 (mp0) cc_final: 0.7543 (mm-30) REVERT: H 129 TYR cc_start: 0.8307 (p90) cc_final: 0.7994 (p90) REVERT: I 45 ARG cc_start: 0.7475 (ttt-90) cc_final: 0.7172 (ttt-90) REVERT: I 90 GLN cc_start: 0.7969 (mt0) cc_final: 0.7583 (mt0) REVERT: K 106 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7480 (mt-10) outliers start: 59 outliers final: 20 residues processed: 433 average time/residue: 0.8323 time to fit residues: 423.3384 Evaluate side-chains 392 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 367 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain A residue 1048 ASN Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1124 ARG Chi-restraints excluded: chain B residue 1153 GLU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain G residue 57 GLN Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain Q residue 67 VAL Chi-restraints excluded: chain Q residue 69 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 105 optimal weight: 0.9980 chunk 326 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 chunk 212 optimal weight: 0.8980 chunk 190 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 298 optimal weight: 6.9990 chunk 287 optimal weight: 9.9990 chunk 230 optimal weight: 0.7980 chunk 3 optimal weight: 0.1980 chunk 384 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 969 GLN A1033 GLN ** B 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 592 ASN ** B 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN F 104 ASN G 57 GLN G 131 GLN H 83 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.131470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.091580 restraints weight = 44560.461| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.21 r_work: 0.3219 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34035 Z= 0.146 Angle : 0.585 12.115 46161 Z= 0.302 Chirality : 0.044 0.322 5183 Planarity : 0.004 0.061 5810 Dihedral : 12.024 176.008 4970 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.48 % Allowed : 11.69 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % 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: 0.36 (0.13), residues: 4019 helix: 1.08 (0.14), residues: 1386 sheet: -0.18 (0.20), residues: 663 loop : -0.11 (0.14), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 24 TYR 0.023 0.001 TYR I 15 PHE 0.027 0.001 PHE A 444 TRP 0.017 0.001 TRP C 170 HIS 0.005 0.001 HIS A 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (33999) covalent geometry : angle 0.57113 / 0.30 (46110) hydrogen bonds : bond 0.04130 / 2.81 ( 1428) hydrogen bonds : angle 5.23240 / 3.75 ( 3993) metal coordination : bond 0.00535 / 0.27 ( 36) metal coordination : angle 3.86886 / 2.45 ( 51) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 388 time to evaluate : 1.298 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: 0.7916 (mtm) cc_final: 0.7681 (mtt) REVERT: A 705 LYS cc_start: 0.8156 (ptpp) cc_final: 0.7785 (ptmt) REVERT: A 818 MET cc_start: 0.8857 (mtp) cc_final: 0.8522 (mtp) REVERT: A 849 MET cc_start: 0.9264 (ttm) cc_final: 0.8933 (ttp) REVERT: A 1214 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8481 (mp0) REVERT: A 1228 TRP cc_start: 0.8163 (p90) cc_final: 0.7893 (p90) REVERT: A 1268 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6766 (mt) REVERT: B 101 MET cc_start: 0.8879 (mmm) cc_final: 0.7951 (mmm) REVERT: B 348 ARG cc_start: 0.7687 (mtm180) cc_final: 0.6852 (mtm-85) REVERT: B 434 ARG cc_start: 0.7743 (mtm110) cc_final: 0.7035 (mtm110) REVERT: B 444 MET cc_start: 0.8094 (mmm) cc_final: 0.7808 (tpt) REVERT: B 510 LYS cc_start: 0.8687 (mtmm) cc_final: 0.7623 (mmmt) REVERT: B 552 MET cc_start: 0.8091 (mmm) cc_final: 0.7402 (tpp) REVERT: B 887 HIS cc_start: 0.8649 (t-90) cc_final: 0.8018 (t-90) REVERT: C 119 VAL cc_start: 0.8366 (t) cc_final: 0.8092 (m) REVERT: D 34 GLN cc_start: 0.7692 (pp30) cc_final: 0.7424 (pp30) REVERT: D 65 GLU cc_start: 0.9044 (pt0) cc_final: 0.8657 (pp20) REVERT: D 138 ASN cc_start: 0.7891 (m-40) cc_final: 0.7543 (m-40) REVERT: D 144 THR cc_start: 0.6730 (m) cc_final: 0.6464 (p) REVERT: E 60 PHE cc_start: 0.8141 (p90) cc_final: 0.7657 (p90) REVERT: E 121 MET cc_start: 0.8536 (mmt) cc_final: 0.8291 (mmt) REVERT: F 71 GLU cc_start: 0.6415 (pm20) cc_final: 0.6188 (pm20) REVERT: F 76 LYS cc_start: 0.8364 (ttpp) cc_final: 0.8064 (tttp) REVERT: G 33 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7439 (tt0) REVERT: G 57 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8205 (mp10) REVERT: G 106 MET cc_start: 0.1749 (mmm) cc_final: 0.1396 (mmt) REVERT: H 66 GLU cc_start: 0.7985 (mp0) cc_final: 0.7555 (mm-30) REVERT: H 128 ASN cc_start: 0.8034 (m110) cc_final: 0.7675 (t0) REVERT: I 90 GLN cc_start: 0.8065 (mt0) cc_final: 0.7682 (mt0) REVERT: K 106 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7445 (mt-10) outliers start: 53 outliers final: 19 residues processed: 414 average time/residue: 0.7871 time to fit residues: 385.9499 Evaluate side-chains 385 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 363 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 1048 ASN Chi-restraints excluded: chain A residue 1214 GLU Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain G residue 57 GLN Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain Q residue 62 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 234 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 256 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 249 optimal weight: 2.9990 chunk 30 optimal weight: 0.0870 chunk 176 optimal weight: 10.0000 chunk 294 optimal weight: 30.0000 chunk 59 optimal weight: 7.9990 chunk 110 optimal weight: 0.0170 overall best weight: 2.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 311 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 742 ASN A1218 GLN ** B 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 GLN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN H 35 GLN H 83 GLN Q 65 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.128562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.087977 restraints weight = 44085.750| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.18 r_work: 0.3155 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 34035 Z= 0.231 Angle : 0.625 12.952 46161 Z= 0.321 Chirality : 0.046 0.294 5183 Planarity : 0.004 0.045 5810 Dihedral : 12.051 175.638 4965 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.21 % Allowed : 12.92 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % 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: 0.23 (0.13), residues: 4019 helix: 0.96 (0.14), residues: 1391 sheet: -0.42 (0.19), residues: 687 loop : -0.10 (0.14), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 879 TYR 0.025 0.002 TYR B 797 PHE 0.028 0.002 PHE A 444 TRP 0.018 0.002 TRP B 308 HIS 0.007 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.23 (33999) covalent geometry : angle 0.60806 / 0.32 (46110) hydrogen bonds : bond 0.04320 / 2.95 ( 1428) hydrogen bonds : angle 5.16685 / 3.70 ( 3993) metal coordination : bond 0.00739 / 0.41 ( 36) metal coordination : angle 4.43353 / 2.74 ( 51) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 372 time to evaluate : 1.318 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 12 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8223 (mtm180) REVERT: A 146 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.7686 (mpt) REVERT: A 705 LYS cc_start: 0.8121 (ptpp) cc_final: 0.7780 (ptmt) REVERT: A 818 MET cc_start: 0.8859 (mtp) cc_final: 0.8624 (mtp) REVERT: A 849 MET cc_start: 0.9281 (ttm) cc_final: 0.8943 (ttp) REVERT: A 903 ASN cc_start: 0.7650 (OUTLIER) cc_final: 0.7311 (p0) REVERT: A 932 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6889 (tt0) REVERT: A 992 ASP cc_start: 0.6636 (OUTLIER) cc_final: 0.6394 (t70) REVERT: A 1218 GLN cc_start: 0.8813 (mt0) cc_final: 0.8530 (mt0) REVERT: A 1228 TRP cc_start: 0.8286 (p90) cc_final: 0.8051 (p90) REVERT: A 1268 LEU cc_start: 0.7026 (OUTLIER) cc_final: 0.6815 (mt) REVERT: A 1281 ARG cc_start: 0.6545 (ttp80) cc_final: 0.6275 (ttp80) REVERT: B 101 MET cc_start: 0.8906 (mmm) cc_final: 0.7960 (mmm) REVERT: B 134 LYS cc_start: 0.6293 (tptm) cc_final: 0.6033 (tptt) REVERT: B 135 ARG cc_start: 0.7990 (mtp85) cc_final: 0.7620 (mmm160) REVERT: B 344 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7719 (tmmm) REVERT: B 434 ARG cc_start: 0.7750 (mtm110) cc_final: 0.6992 (mtm110) REVERT: B 510 LYS cc_start: 0.8657 (mtmm) cc_final: 0.7642 (mmmt) REVERT: B 513 GLN cc_start: 0.8836 (mt0) cc_final: 0.8565 (mt0) REVERT: B 552 MET cc_start: 0.8190 (mmm) cc_final: 0.7551 (tpp) REVERT: B 887 HIS cc_start: 0.8639 (t-90) cc_final: 0.8003 (t-90) REVERT: B 1124 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7903 (mtt180) REVERT: B 1153 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8220 (mt-10) REVERT: C 119 VAL cc_start: 0.8435 (t) cc_final: 0.8151 (m) REVERT: D 58 VAL cc_start: 0.7720 (p) cc_final: 0.7504 (m) REVERT: D 65 GLU cc_start: 0.9003 (pt0) cc_final: 0.8530 (pp20) REVERT: D 138 ASN cc_start: 0.7908 (m-40) cc_final: 0.7555 (m-40) REVERT: D 144 THR cc_start: 0.6845 (m) cc_final: 0.6579 (p) REVERT: D 154 PHE cc_start: 0.7285 (m-10) cc_final: 0.6855 (m-10) REVERT: E 8 ASN cc_start: 0.8224 (m-40) cc_final: 0.7972 (m-40) REVERT: E 114 ASN cc_start: 0.8773 (m110) cc_final: 0.8246 (t0) REVERT: E 121 MET cc_start: 0.8687 (mmt) cc_final: 0.8405 (mmt) REVERT: F 71 GLU cc_start: 0.6450 (pm20) cc_final: 0.6174 (pm20) REVERT: F 76 LYS cc_start: 0.8428 (ttpp) cc_final: 0.8113 (tttp) REVERT: G 24 GLN cc_start: 0.7806 (mp10) cc_final: 0.7555 (mp10) REVERT: G 33 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7471 (tm-30) REVERT: G 106 MET cc_start: 0.1852 (mmm) cc_final: 0.1463 (mmt) REVERT: H 66 GLU cc_start: 0.8030 (mp0) cc_final: 0.7638 (mm-30) REVERT: H 100 THR cc_start: 0.9262 (t) cc_final: 0.8968 (p) REVERT: H 128 ASN cc_start: 0.8029 (m110) cc_final: 0.7763 (t0) REVERT: I 64 SER cc_start: 0.8487 (t) cc_final: 0.8273 (t) REVERT: I 90 GLN cc_start: 0.8216 (mt0) cc_final: 0.7797 (mt0) REVERT: K 21 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8848 (mp) REVERT: K 106 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7543 (mt-10) outliers start: 79 outliers final: 29 residues processed: 410 average time/residue: 0.7986 time to fit residues: 389.2964 Evaluate side-chains 384 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 345 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain A residue 932 GLU Chi-restraints excluded: chain A residue 992 ASP Chi-restraints excluded: chain A residue 1214 GLU Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 1124 ARG Chi-restraints excluded: chain B residue 1153 GLU Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain Q residue 67 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 333 optimal weight: 9.9990 chunk 110 optimal weight: 20.0000 chunk 386 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 196 optimal weight: 10.0000 chunk 325 optimal weight: 2.9990 chunk 236 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 311 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 GLN ** B 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN G 57 GLN Q 65 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.128993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.088176 restraints weight = 44179.051| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.20 r_work: 0.3163 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 34035 Z= 0.182 Angle : 0.594 12.269 46161 Z= 0.304 Chirality : 0.045 0.262 5183 Planarity : 0.004 0.046 5810 Dihedral : 12.033 175.541 4965 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.96 % Allowed : 14.01 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % 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: 0.25 (0.13), residues: 4019 helix: 1.02 (0.14), residues: 1385 sheet: -0.43 (0.20), residues: 674 loop : -0.12 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 68 TYR 0.020 0.001 TYR G 25 PHE 0.022 0.002 PHE A 219 TRP 0.018 0.001 TRP B 308 HIS 0.006 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (33999) covalent geometry : angle 0.57796 / 0.30 (46110) hydrogen bonds : bond 0.03997 / 2.72 ( 1428) hydrogen bonds : angle 5.05879 / 3.62 ( 3993) metal coordination : bond 0.00623 / 0.34 ( 36) metal coordination : angle 4.21190 / 2.62 ( 51) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 374 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8173 (mtm180) REVERT: A 146 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7666 (mpt) REVERT: A 705 LYS cc_start: 0.8113 (ptpp) cc_final: 0.7778 (ptmt) REVERT: A 818 MET cc_start: 0.8839 (mtp) cc_final: 0.8596 (mtp) REVERT: A 849 MET cc_start: 0.9277 (ttm) cc_final: 0.8926 (ttp) REVERT: A 903 ASN cc_start: 0.7562 (OUTLIER) cc_final: 0.7235 (p0) REVERT: A 932 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6862 (tt0) REVERT: A 992 ASP cc_start: 0.6583 (OUTLIER) cc_final: 0.6353 (t70) REVERT: A 1116 LEU cc_start: 0.8405 (tp) cc_final: 0.8078 (mt) REVERT: A 1218 GLN cc_start: 0.8803 (mt0) cc_final: 0.8514 (mt0) REVERT: A 1228 TRP cc_start: 0.8300 (p90) cc_final: 0.8078 (p90) REVERT: A 1268 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6784 (mt) REVERT: B 96 TYR cc_start: 0.8184 (m-80) cc_final: 0.7819 (m-80) REVERT: B 101 MET cc_start: 0.8901 (mmm) cc_final: 0.7940 (mmm) REVERT: B 135 ARG cc_start: 0.8081 (mtp85) cc_final: 0.7658 (mmm160) REVERT: B 344 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7709 (tmmm) REVERT: B 434 ARG cc_start: 0.7744 (mtm110) cc_final: 0.6975 (mtm110) REVERT: B 510 LYS cc_start: 0.8606 (mtmm) cc_final: 0.7617 (mmmt) REVERT: B 513 GLN cc_start: 0.8835 (mt0) cc_final: 0.8560 (mm110) REVERT: B 552 MET cc_start: 0.8137 (mmm) cc_final: 0.7615 (tpp) REVERT: B 887 HIS cc_start: 0.8655 (t-90) cc_final: 0.8026 (t-90) REVERT: B 1124 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7896 (mtt180) REVERT: C 119 VAL cc_start: 0.8414 (t) cc_final: 0.8126 (m) REVERT: D 34 GLN cc_start: 0.7492 (pp30) cc_final: 0.7275 (pp30) REVERT: D 65 GLU cc_start: 0.8931 (pt0) cc_final: 0.8544 (pp20) REVERT: D 138 ASN cc_start: 0.7914 (m-40) cc_final: 0.7513 (m110) REVERT: D 144 THR cc_start: 0.6862 (m) cc_final: 0.6620 (p) REVERT: E 8 ASN cc_start: 0.8217 (m-40) cc_final: 0.7948 (m-40) REVERT: E 114 ASN cc_start: 0.8810 (m110) cc_final: 0.8252 (t0) REVERT: E 121 MET cc_start: 0.8764 (mmt) cc_final: 0.8546 (mmt) REVERT: F 71 GLU cc_start: 0.6424 (pm20) cc_final: 0.6180 (pm20) REVERT: F 76 LYS cc_start: 0.8401 (ttpp) cc_final: 0.8110 (tttp) REVERT: G 24 GLN cc_start: 0.7688 (mp10) cc_final: 0.7339 (mp10) REVERT: G 33 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7425 (tm-30) REVERT: G 57 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8286 (mp10) REVERT: H 35 GLN cc_start: 0.7014 (pm20) cc_final: 0.6636 (tp40) REVERT: H 66 GLU cc_start: 0.8007 (mp0) cc_final: 0.7602 (mm-30) REVERT: H 100 THR cc_start: 0.9281 (t) cc_final: 0.9030 (p) REVERT: H 128 ASN cc_start: 0.8001 (m110) cc_final: 0.7692 (t0) REVERT: I 15 TYR cc_start: 0.7149 (t80) cc_final: 0.6794 (t80) REVERT: I 90 GLN cc_start: 0.8179 (mt0) cc_final: 0.7729 (mt0) REVERT: J 1 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.6928 (mpp) REVERT: K 21 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8818 (mp) REVERT: K 106 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7527 (mt-10) outliers start: 70 outliers final: 26 residues processed: 413 average time/residue: 0.7745 time to fit residues: 376.7513 Evaluate side-chains 389 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 352 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain A residue 932 GLU Chi-restraints excluded: chain A residue 992 ASP Chi-restraints excluded: chain A residue 1112 LYS Chi-restraints excluded: chain A residue 1214 GLU Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1124 ARG Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain G residue 57 GLN Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain L residue 53 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 285 optimal weight: 3.9990 chunk 379 optimal weight: 4.9990 chunk 335 optimal weight: 10.0000 chunk 213 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 318 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 238 optimal weight: 0.0980 chunk 10 optimal weight: 0.4980 chunk 349 optimal weight: 5.9990 chunk 99 optimal weight: 0.1980 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 969 GLN B 121 ASN B 236 HIS ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN F 78 GLN F 104 ASN G 57 GLN Q 65 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.130720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.090605 restraints weight = 44828.139| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.19 r_work: 0.3173 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34035 Z= 0.115 Angle : 0.565 12.301 46161 Z= 0.288 Chirality : 0.043 0.249 5183 Planarity : 0.004 0.043 5810 Dihedral : 11.978 175.021 4965 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.85 % Allowed : 14.82 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % 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: 0.37 (0.13), residues: 4019 helix: 1.16 (0.14), residues: 1388 sheet: -0.32 (0.20), residues: 667 loop : -0.10 (0.14), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 68 TYR 0.021 0.001 TYR G 25 PHE 0.021 0.001 PHE A 219 TRP 0.018 0.001 TRP B 308 HIS 0.005 0.001 HIS A 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (33999) covalent geometry : angle 0.55096 / 0.29 (46110) hydrogen bonds : bond 0.03623 / 2.46 ( 1428) hydrogen bonds : angle 4.90997 / 3.51 ( 3993) metal coordination : bond 0.00467 / 0.24 ( 36) metal coordination : angle 3.76287 / 2.38 ( 51) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 378 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8017 (mtm180) REVERT: A 264 PHE cc_start: 0.8465 (m-10) cc_final: 0.8231 (m-80) REVERT: A 705 LYS cc_start: 0.8082 (ptpp) cc_final: 0.7723 (ptmt) REVERT: A 849 MET cc_start: 0.9282 (ttm) cc_final: 0.8968 (ttp) REVERT: A 903 ASN cc_start: 0.7501 (OUTLIER) cc_final: 0.7179 (p0) REVERT: A 932 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6902 (tt0) REVERT: A 992 ASP cc_start: 0.6604 (OUTLIER) cc_final: 0.6386 (t70) REVERT: A 1116 LEU cc_start: 0.8411 (tp) cc_final: 0.8052 (mt) REVERT: A 1218 GLN cc_start: 0.8795 (mt0) cc_final: 0.8425 (mt0) REVERT: A 1268 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6787 (mt) REVERT: A 1300 LYS cc_start: 0.8949 (mttt) cc_final: 0.8652 (mtmt) REVERT: B 96 TYR cc_start: 0.8157 (m-80) cc_final: 0.7770 (m-80) REVERT: B 101 MET cc_start: 0.8848 (mmm) cc_final: 0.7910 (mmm) REVERT: B 134 LYS cc_start: 0.6551 (tptt) cc_final: 0.5626 (tmtt) REVERT: B 135 ARG cc_start: 0.8138 (mtp85) cc_final: 0.7609 (mmm160) REVERT: B 344 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7427 (tmmm) REVERT: B 348 ARG cc_start: 0.7489 (mtm180) cc_final: 0.6478 (mtm-85) REVERT: B 434 ARG cc_start: 0.7814 (mtm110) cc_final: 0.7085 (mtm110) REVERT: B 552 MET cc_start: 0.8087 (mmm) cc_final: 0.7551 (tpp) REVERT: B 887 HIS cc_start: 0.8613 (t-90) cc_final: 0.7973 (t-90) REVERT: B 1124 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7872 (mtt180) REVERT: C 119 VAL cc_start: 0.8387 (t) cc_final: 0.8136 (m) REVERT: D 65 GLU cc_start: 0.8924 (pt0) cc_final: 0.8532 (pp20) REVERT: D 138 ASN cc_start: 0.7921 (m-40) cc_final: 0.7565 (m110) REVERT: D 144 THR cc_start: 0.6879 (m) cc_final: 0.6627 (p) REVERT: D 187 THR cc_start: 0.7991 (OUTLIER) cc_final: 0.7788 (p) REVERT: E 8 ASN cc_start: 0.8246 (m-40) cc_final: 0.7978 (m-40) REVERT: E 121 MET cc_start: 0.8696 (mmt) cc_final: 0.8472 (mmt) REVERT: F 71 GLU cc_start: 0.6445 (pm20) cc_final: 0.6205 (pm20) REVERT: G 22 MET cc_start: 0.7501 (ttm) cc_final: 0.7246 (ttm) REVERT: G 24 GLN cc_start: 0.7713 (mp10) cc_final: 0.7368 (mp10) REVERT: G 33 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7392 (tm-30) REVERT: G 57 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8279 (mp10) REVERT: G 71 ASN cc_start: 0.8548 (OUTLIER) cc_final: 0.7974 (m-40) REVERT: H 66 GLU cc_start: 0.8000 (mp0) cc_final: 0.7607 (mm-30) REVERT: H 100 THR cc_start: 0.9242 (t) cc_final: 0.9006 (p) REVERT: H 128 ASN cc_start: 0.7994 (m110) cc_final: 0.7761 (t0) REVERT: I 15 TYR cc_start: 0.7044 (t80) cc_final: 0.6656 (t80) REVERT: K 21 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8818 (mp) REVERT: K 36 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8124 (mp0) REVERT: K 106 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7541 (mt-10) outliers start: 66 outliers final: 23 residues processed: 416 average time/residue: 0.7988 time to fit residues: 393.1177 Evaluate side-chains 388 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 353 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain A residue 932 GLU Chi-restraints excluded: chain A residue 992 ASP Chi-restraints excluded: chain A residue 1112 LYS Chi-restraints excluded: chain A residue 1214 GLU Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 1124 ARG Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain G residue 57 GLN Chi-restraints excluded: chain G residue 71 ASN Chi-restraints excluded: chain G residue 131 GLN Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain L residue 53 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 72 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 223 optimal weight: 6.9990 chunk 237 optimal weight: 3.9990 chunk 319 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 136 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 236 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 313 optimal weight: 0.5980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 GLN B 309 GLN B 443 ASN ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1195 HIS ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN G 57 GLN Q 65 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.129193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.088748 restraints weight = 44953.098| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.18 r_work: 0.3145 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 34035 Z= 0.179 Angle : 0.594 13.063 46161 Z= 0.302 Chirality : 0.044 0.246 5183 Planarity : 0.004 0.048 5810 Dihedral : 11.980 174.915 4965 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.90 % Allowed : 15.49 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.13), residues: 4019 helix: 1.07 (0.14), residues: 1399 sheet: -0.35 (0.20), residues: 673 loop : -0.11 (0.14), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 68 TYR 0.021 0.001 TYR G 25 PHE 0.024 0.001 PHE A 219 TRP 0.030 0.002 TRP A1228 HIS 0.005 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (33999) covalent geometry : angle 0.57746 / 0.30 (46110) hydrogen bonds : bond 0.03838 / 2.61 ( 1428) hydrogen bonds : angle 4.91399 / 3.51 ( 3993) metal coordination : bond 0.00786 / 0.40 ( 36) metal coordination : angle 4.16665 / 2.58 ( 51) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 354 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8165 (mtm180) REVERT: A 146 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.7624 (mpt) REVERT: A 264 PHE cc_start: 0.8490 (m-10) cc_final: 0.8254 (m-80) REVERT: A 705 LYS cc_start: 0.8050 (ptpp) cc_final: 0.7678 (ptmt) REVERT: A 818 MET cc_start: 0.8900 (mtp) cc_final: 0.8657 (mtp) REVERT: A 849 MET cc_start: 0.9284 (ttm) cc_final: 0.8967 (ttp) REVERT: A 903 ASN cc_start: 0.7412 (OUTLIER) cc_final: 0.7092 (p0) REVERT: A 932 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6945 (tt0) REVERT: A 1268 LEU cc_start: 0.7039 (OUTLIER) cc_final: 0.6813 (mt) REVERT: A 1285 MET cc_start: 0.7701 (pmm) cc_final: 0.7384 (pmm) REVERT: A 1300 LYS cc_start: 0.8933 (mttt) cc_final: 0.8668 (mtmt) REVERT: A 1444 MET cc_start: 0.8542 (mmm) cc_final: 0.8300 (mtm) REVERT: B 96 TYR cc_start: 0.8191 (m-80) cc_final: 0.7810 (m-80) REVERT: B 101 MET cc_start: 0.8887 (mmm) cc_final: 0.7912 (mmm) REVERT: B 135 ARG cc_start: 0.8145 (mtp85) cc_final: 0.7661 (mmm160) REVERT: B 344 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7714 (tmmm) REVERT: B 434 ARG cc_start: 0.7814 (mtm110) cc_final: 0.7066 (mtm110) REVERT: B 552 MET cc_start: 0.8127 (mmm) cc_final: 0.7558 (tpp) REVERT: B 887 HIS cc_start: 0.8596 (t-90) cc_final: 0.7976 (t-90) REVERT: B 904 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.5422 (mpt180) REVERT: B 1124 ARG cc_start: 0.8158 (mtt-85) cc_final: 0.7874 (mtt180) REVERT: C 119 VAL cc_start: 0.8417 (t) cc_final: 0.8155 (m) REVERT: D 65 GLU cc_start: 0.8906 (pt0) cc_final: 0.8605 (pp20) REVERT: D 138 ASN cc_start: 0.7915 (m-40) cc_final: 0.7554 (m110) REVERT: D 187 THR cc_start: 0.7987 (OUTLIER) cc_final: 0.7762 (p) REVERT: E 8 ASN cc_start: 0.8243 (m-40) cc_final: 0.7964 (m-40) REVERT: E 91 LYS cc_start: 0.9204 (mttp) cc_final: 0.8960 (pmtt) REVERT: E 114 ASN cc_start: 0.8794 (m110) cc_final: 0.8205 (t0) REVERT: E 115 ASN cc_start: 0.8642 (p0) cc_final: 0.8386 (p0) REVERT: E 121 MET cc_start: 0.8754 (mmt) cc_final: 0.8543 (mmt) REVERT: E 215 MET cc_start: 0.6898 (OUTLIER) cc_final: 0.5295 (mmm) REVERT: F 71 GLU cc_start: 0.6512 (pm20) cc_final: 0.6215 (pm20) REVERT: G 24 GLN cc_start: 0.7774 (mp10) cc_final: 0.7518 (mp10) REVERT: G 33 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7462 (tm-30) REVERT: G 57 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8145 (mp-120) REVERT: H 27 GLU cc_start: 0.8451 (mp0) cc_final: 0.8115 (mp0) REVERT: H 35 GLN cc_start: 0.7001 (pm20) cc_final: 0.6645 (tp40) REVERT: H 66 GLU cc_start: 0.8013 (mp0) cc_final: 0.7621 (mm-30) REVERT: H 100 THR cc_start: 0.9255 (t) cc_final: 0.9031 (p) REVERT: H 128 ASN cc_start: 0.7976 (m110) cc_final: 0.7730 (t0) REVERT: I 15 TYR cc_start: 0.6965 (t80) cc_final: 0.6571 (t80) REVERT: K 21 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8815 (mp) REVERT: K 36 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7143 (mp0) REVERT: K 106 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7586 (mt-10) outliers start: 68 outliers final: 33 residues processed: 391 average time/residue: 0.7751 time to fit residues: 357.4031 Evaluate side-chains 392 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 347 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain A residue 932 GLU Chi-restraints excluded: chain A residue 1214 GLU Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 904 ARG Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 57 GLN Chi-restraints excluded: chain G residue 131 GLN Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain Q residue 67 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 34 optimal weight: 0.9990 chunk 309 optimal weight: 5.9990 chunk 302 optimal weight: 0.6980 chunk 72 optimal weight: 0.4980 chunk 274 optimal weight: 7.9990 chunk 285 optimal weight: 3.9990 chunk 260 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 138 optimal weight: 2.9990 chunk 222 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 969 GLN B 309 GLN ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN G 57 GLN Q 65 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.129917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.089590 restraints weight = 45138.160| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.19 r_work: 0.3160 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34035 Z= 0.140 Angle : 0.580 13.059 46161 Z= 0.295 Chirality : 0.043 0.250 5183 Planarity : 0.004 0.043 5810 Dihedral : 11.945 174.887 4965 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.65 % Allowed : 16.08 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % 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: 0.36 (0.13), residues: 4019 helix: 1.13 (0.14), residues: 1399 sheet: -0.32 (0.20), residues: 673 loop : -0.10 (0.14), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 77 TYR 0.021 0.001 TYR G 25 PHE 0.022 0.001 PHE A 219 TRP 0.031 0.001 TRP A1228 HIS 0.004 0.001 HIS A 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (33999) covalent geometry : angle 0.56426 / 0.29 (46110) hydrogen bonds : bond 0.03658 / 2.48 ( 1428) hydrogen bonds : angle 4.83722 / 3.46 ( 3993) metal coordination : bond 0.00528 / 0.28 ( 36) metal coordination : angle 4.01961 / 2.51 ( 51) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 360 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.8119 (mtm180) REVERT: A 264 PHE cc_start: 0.8495 (m-10) cc_final: 0.8240 (m-80) REVERT: A 705 LYS cc_start: 0.7994 (ptpp) cc_final: 0.7667 (ptmt) REVERT: A 818 MET cc_start: 0.8871 (mtp) cc_final: 0.8618 (mtp) REVERT: A 849 MET cc_start: 0.9289 (ttm) cc_final: 0.8970 (ttp) REVERT: A 903 ASN cc_start: 0.7339 (OUTLIER) cc_final: 0.7018 (p0) REVERT: A 932 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6889 (tt0) REVERT: A 1116 LEU cc_start: 0.8408 (tp) cc_final: 0.8093 (mt) REVERT: A 1268 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6902 (mt) REVERT: A 1288 ASP cc_start: 0.8485 (p0) cc_final: 0.8220 (m-30) REVERT: A 1300 LYS cc_start: 0.8932 (mttt) cc_final: 0.8647 (mtmt) REVERT: B 96 TYR cc_start: 0.8156 (m-80) cc_final: 0.7751 (m-80) REVERT: B 101 MET cc_start: 0.8884 (mmm) cc_final: 0.7914 (mmm) REVERT: B 135 ARG cc_start: 0.8204 (mtp85) cc_final: 0.7617 (mmm160) REVERT: B 241 ARG cc_start: 0.8119 (ttm-80) cc_final: 0.7540 (mtp85) REVERT: B 344 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7432 (tmmm) REVERT: B 348 ARG cc_start: 0.7386 (mtm180) cc_final: 0.6447 (mtm-85) REVERT: B 434 ARG cc_start: 0.7844 (mtm110) cc_final: 0.6995 (mtm110) REVERT: B 552 MET cc_start: 0.8119 (mmm) cc_final: 0.7648 (tpp) REVERT: B 792 MET cc_start: 0.8604 (mtm) cc_final: 0.8315 (mtp) REVERT: B 887 HIS cc_start: 0.8622 (t-90) cc_final: 0.7972 (t-90) REVERT: B 904 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.5431 (mpt180) REVERT: B 935 ARG cc_start: 0.7643 (ttm110) cc_final: 0.7119 (ptp90) REVERT: B 1124 ARG cc_start: 0.8145 (mtt-85) cc_final: 0.7849 (mtt180) REVERT: C 119 VAL cc_start: 0.8405 (t) cc_final: 0.8153 (m) REVERT: D 65 GLU cc_start: 0.8932 (pt0) cc_final: 0.8563 (pp20) REVERT: D 138 ASN cc_start: 0.7952 (m-40) cc_final: 0.7575 (m110) REVERT: D 154 PHE cc_start: 0.7019 (m-10) cc_final: 0.6436 (m-10) REVERT: E 8 ASN cc_start: 0.8264 (m-40) cc_final: 0.7995 (m-40) REVERT: E 91 LYS cc_start: 0.9210 (mttp) cc_final: 0.8981 (pmtt) REVERT: E 114 ASN cc_start: 0.8775 (m110) cc_final: 0.8183 (t0) REVERT: E 115 ASN cc_start: 0.8649 (p0) cc_final: 0.8432 (p0) REVERT: E 121 MET cc_start: 0.8781 (mmt) cc_final: 0.8580 (mmt) REVERT: F 71 GLU cc_start: 0.6522 (pm20) cc_final: 0.6273 (pm20) REVERT: F 76 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8098 (tttp) REVERT: F 89 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8789 (mt-10) REVERT: G 22 MET cc_start: 0.7807 (ttm) cc_final: 0.7441 (ttm) REVERT: G 24 GLN cc_start: 0.7752 (mp10) cc_final: 0.7404 (mp10) REVERT: G 33 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7280 (tm-30) REVERT: G 57 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8141 (mp10) REVERT: H 27 GLU cc_start: 0.8434 (mp0) cc_final: 0.8130 (mp0) REVERT: H 35 GLN cc_start: 0.7001 (pm20) cc_final: 0.6576 (tp40) REVERT: H 66 GLU cc_start: 0.8022 (mp0) cc_final: 0.7638 (mm-30) REVERT: H 128 ASN cc_start: 0.7920 (m110) cc_final: 0.7708 (t0) REVERT: I 15 TYR cc_start: 0.6956 (t80) cc_final: 0.6545 (t80) REVERT: K 21 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8803 (mp) REVERT: K 36 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8174 (mp0) REVERT: K 106 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7575 (mt-10) REVERT: L 37 LYS cc_start: 0.8705 (mtpt) cc_final: 0.8412 (mtpm) outliers start: 59 outliers final: 28 residues processed: 394 average time/residue: 0.7489 time to fit residues: 347.6305 Evaluate side-chains 388 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 350 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain A residue 932 GLU Chi-restraints excluded: chain A residue 1214 GLU Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 904 ARG Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 57 GLN Chi-restraints excluded: chain G residue 131 GLN Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain L residue 53 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 232 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 321 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 128 optimal weight: 0.7980 chunk 355 optimal weight: 10.0000 chunk 330 optimal weight: 3.9990 chunk 245 optimal weight: 4.9990 chunk 156 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 311 GLN A 969 GLN B 309 GLN ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN G 10 ASN Q 65 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.131310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.091586 restraints weight = 45967.092| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.24 r_work: 0.3188 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34035 Z= 0.140 Angle : 0.583 13.252 46161 Z= 0.297 Chirality : 0.043 0.252 5183 Planarity : 0.004 0.060 5810 Dihedral : 11.920 174.938 4965 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.37 % Allowed : 16.72 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % 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: 0.37 (0.13), residues: 4019 helix: 1.14 (0.14), residues: 1399 sheet: -0.31 (0.20), residues: 673 loop : -0.10 (0.14), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 879 TYR 0.021 0.001 TYR G 25 PHE 0.026 0.001 PHE D 154 TRP 0.024 0.001 TRP A1228 HIS 0.005 0.001 HIS A 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (33999) covalent geometry : angle 0.56769 / 0.30 (46110) hydrogen bonds : bond 0.03626 / 2.45 ( 1428) hydrogen bonds : angle 4.79752 / 3.43 ( 3993) metal coordination : bond 0.00524 / 0.27 ( 36) metal coordination : angle 3.98094 / 2.48 ( 51) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 361 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.8039 (mtm180) REVERT: A 264 PHE cc_start: 0.8603 (m-10) cc_final: 0.8333 (m-80) REVERT: A 705 LYS cc_start: 0.7984 (ptpp) cc_final: 0.7705 (ptmt) REVERT: A 849 MET cc_start: 0.9341 (ttm) cc_final: 0.9045 (ttp) REVERT: A 903 ASN cc_start: 0.7445 (OUTLIER) cc_final: 0.7134 (p0) REVERT: A 932 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6993 (tt0) REVERT: A 1116 LEU cc_start: 0.8504 (tp) cc_final: 0.8170 (mt) REVERT: A 1268 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.7036 (mt) REVERT: A 1300 LYS cc_start: 0.8919 (mttt) cc_final: 0.8661 (mtmt) REVERT: B 96 TYR cc_start: 0.8243 (m-80) cc_final: 0.7850 (m-80) REVERT: B 101 MET cc_start: 0.8894 (mmm) cc_final: 0.7982 (mmm) REVERT: B 135 ARG cc_start: 0.8209 (mtp85) cc_final: 0.7752 (mtp85) REVERT: B 241 ARG cc_start: 0.8220 (ttm-80) cc_final: 0.7670 (mtp85) REVERT: B 344 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7748 (tmmm) REVERT: B 434 ARG cc_start: 0.7888 (mtm110) cc_final: 0.7055 (mtm110) REVERT: B 552 MET cc_start: 0.8184 (mmm) cc_final: 0.7582 (tpp) REVERT: B 792 MET cc_start: 0.8587 (mtm) cc_final: 0.8328 (mtp) REVERT: B 887 HIS cc_start: 0.8611 (t-90) cc_final: 0.7986 (t-90) REVERT: B 904 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.5486 (mpt180) REVERT: B 1124 ARG cc_start: 0.8286 (mtt-85) cc_final: 0.7991 (mtt180) REVERT: C 119 VAL cc_start: 0.8423 (t) cc_final: 0.8213 (m) REVERT: D 65 GLU cc_start: 0.8967 (pt0) cc_final: 0.8542 (pp20) REVERT: D 138 ASN cc_start: 0.7836 (m-40) cc_final: 0.7456 (m110) REVERT: D 153 ARG cc_start: 0.6083 (ppt170) cc_final: 0.5474 (ppt170) REVERT: E 8 ASN cc_start: 0.8339 (m-40) cc_final: 0.8073 (m-40) REVERT: E 91 LYS cc_start: 0.9173 (mttp) cc_final: 0.8969 (pmtt) REVERT: E 114 ASN cc_start: 0.8782 (m110) cc_final: 0.8198 (t0) REVERT: F 71 GLU cc_start: 0.6597 (pm20) cc_final: 0.6283 (pm20) REVERT: F 76 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8205 (tttp) REVERT: F 89 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8771 (mt-10) REVERT: G 22 MET cc_start: 0.7883 (ttm) cc_final: 0.7529 (ttm) REVERT: G 24 GLN cc_start: 0.7825 (mp10) cc_final: 0.7499 (mp10) REVERT: G 33 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7318 (tm-30) REVERT: H 35 GLN cc_start: 0.6967 (pm20) cc_final: 0.6613 (tp40) REVERT: H 66 GLU cc_start: 0.8003 (mp0) cc_final: 0.7628 (mm-30) REVERT: I 15 TYR cc_start: 0.6910 (t80) cc_final: 0.6514 (t80) REVERT: I 54 GLU cc_start: 0.5515 (pt0) cc_final: 0.4918 (pm20) REVERT: K 21 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8832 (mp) REVERT: K 36 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8304 (mp0) REVERT: K 106 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7520 (mt-10) REVERT: L 37 LYS cc_start: 0.8713 (mtpt) cc_final: 0.8396 (mtpm) outliers start: 49 outliers final: 27 residues processed: 394 average time/residue: 0.7143 time to fit residues: 332.7830 Evaluate side-chains 384 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 348 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain A residue 932 GLU Chi-restraints excluded: chain A residue 1214 GLU Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 904 ARG Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 131 GLN Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain L residue 53 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 377 optimal weight: 0.7980 chunk 180 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 275 optimal weight: 1.9990 chunk 228 optimal weight: 0.8980 chunk 281 optimal weight: 0.8980 chunk 165 optimal weight: 7.9990 chunk 127 optimal weight: 0.8980 chunk 340 optimal weight: 6.9990 chunk 268 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 311 GLN A 969 GLN A1265 ASN B 309 GLN ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN G 57 GLN Q 65 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.131842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.092039 restraints weight = 46461.878| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.26 r_work: 0.3206 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 34035 Z= 0.128 Angle : 0.584 12.882 46161 Z= 0.296 Chirality : 0.043 0.254 5183 Planarity : 0.004 0.050 5810 Dihedral : 11.831 175.189 4965 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.15 % Allowed : 17.03 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % 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: 0.41 (0.13), residues: 4019 helix: 1.18 (0.14), residues: 1397 sheet: -0.27 (0.20), residues: 669 loop : -0.09 (0.14), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 879 TYR 0.017 0.001 TYR E 187 PHE 0.022 0.001 PHE A 219 TRP 0.020 0.001 TRP A1228 HIS 0.005 0.001 HIS A 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (33999) covalent geometry : angle 0.56981 / 0.30 (46110) hydrogen bonds : bond 0.03546 / 2.41 ( 1428) hydrogen bonds : angle 4.75932 / 3.40 ( 3993) metal coordination : bond 0.00497 / 0.25 ( 36) metal coordination : angle 3.83502 / 2.40 ( 51) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8038 Ramachandran restraints generated. 4019 Oldfield, 0 Emsley, 4019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 364 time to evaluate : 1.326 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 12 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7977 (mtm180) REVERT: A 264 PHE cc_start: 0.8583 (m-10) cc_final: 0.8301 (m-80) REVERT: A 705 LYS cc_start: 0.7937 (ptpp) cc_final: 0.7672 (ptmt) REVERT: A 849 MET cc_start: 0.9341 (ttm) cc_final: 0.9036 (ttp) REVERT: A 903 ASN cc_start: 0.7316 (OUTLIER) cc_final: 0.7019 (p0) REVERT: A 932 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6956 (tt0) REVERT: A 1116 LEU cc_start: 0.8529 (tp) cc_final: 0.8202 (mt) REVERT: A 1268 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.7018 (mt) REVERT: A 1300 LYS cc_start: 0.8952 (mttt) cc_final: 0.8652 (mtmt) REVERT: A 1444 MET cc_start: 0.8573 (mmm) cc_final: 0.8318 (mtm) REVERT: B 96 TYR cc_start: 0.8231 (m-80) cc_final: 0.7842 (m-80) REVERT: B 101 MET cc_start: 0.8891 (mmm) cc_final: 0.7987 (mmm) REVERT: B 135 ARG cc_start: 0.8217 (mtp85) cc_final: 0.7858 (mtp85) REVERT: B 344 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7686 (tmmm) REVERT: B 348 ARG cc_start: 0.7546 (mtm180) cc_final: 0.6706 (mtm-85) REVERT: B 434 ARG cc_start: 0.7880 (mtm110) cc_final: 0.7035 (mtm110) REVERT: B 792 MET cc_start: 0.8548 (mtm) cc_final: 0.8279 (mtp) REVERT: B 887 HIS cc_start: 0.8637 (t-90) cc_final: 0.8007 (t-90) REVERT: B 904 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.5466 (mpt180) REVERT: B 1124 ARG cc_start: 0.8262 (mtt-85) cc_final: 0.7891 (mtt180) REVERT: C 119 VAL cc_start: 0.8350 (t) cc_final: 0.8147 (m) REVERT: D 65 GLU cc_start: 0.8947 (pt0) cc_final: 0.8480 (pp20) REVERT: D 138 ASN cc_start: 0.7835 (m-40) cc_final: 0.7452 (m110) REVERT: D 153 ARG cc_start: 0.5974 (ppt170) cc_final: 0.5489 (ppt170) REVERT: E 8 ASN cc_start: 0.8327 (m-40) cc_final: 0.8069 (m-40) REVERT: E 84 ASP cc_start: 0.7809 (m-30) cc_final: 0.7288 (p0) REVERT: E 91 LYS cc_start: 0.9193 (mttp) cc_final: 0.8949 (pmtt) REVERT: E 114 ASN cc_start: 0.8748 (m110) cc_final: 0.8240 (t0) REVERT: F 71 GLU cc_start: 0.6566 (pm20) cc_final: 0.6253 (pm20) REVERT: F 76 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8209 (tttp) REVERT: F 89 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8736 (mt-10) REVERT: G 22 MET cc_start: 0.7862 (ttm) cc_final: 0.7542 (ttm) REVERT: G 24 GLN cc_start: 0.7830 (mp10) cc_final: 0.7614 (mp10) REVERT: G 33 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7351 (tm-30) REVERT: H 14 GLU cc_start: 0.8360 (tt0) cc_final: 0.8026 (pt0) REVERT: H 35 GLN cc_start: 0.6997 (pm20) cc_final: 0.6587 (tp40) REVERT: H 66 GLU cc_start: 0.8049 (mp0) cc_final: 0.7671 (mm-30) REVERT: H 106 GLU cc_start: 0.7750 (mp0) cc_final: 0.7524 (mt-10) REVERT: I 15 TYR cc_start: 0.6925 (t80) cc_final: 0.6503 (t80) REVERT: I 54 GLU cc_start: 0.5416 (pt0) cc_final: 0.4852 (pm20) REVERT: I 87 GLN cc_start: 0.8021 (pt0) cc_final: 0.7805 (mt0) REVERT: K 21 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8797 (mp) REVERT: K 36 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8255 (mp0) REVERT: K 106 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7608 (mt-10) REVERT: L 37 LYS cc_start: 0.8673 (mtpt) cc_final: 0.8362 (mtpm) outliers start: 41 outliers final: 28 residues processed: 388 average time/residue: 0.7459 time to fit residues: 341.4137 Evaluate side-chains 389 residues out of total 3576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 352 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 903 ASN Chi-restraints excluded: chain A residue 932 GLU Chi-restraints excluded: chain A residue 1214 GLU Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 344 LYS Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 904 ARG Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 154 PHE Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 131 GLN Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 62 ILE Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain L residue 53 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 84 optimal weight: 0.9980 chunk 307 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 108 optimal weight: 0.4980 chunk 36 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 295 optimal weight: 5.9990 chunk 258 optimal weight: 0.5980 chunk 129 optimal weight: 5.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 GLN B 309 GLN ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 65 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.131577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.091755 restraints weight = 46183.831| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.26 r_work: 0.3194 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34035 Z= 0.140 Angle : 0.594 15.501 46161 Z= 0.301 Chirality : 0.043 0.253 5183 Planarity : 0.004 0.043 5810 Dihedral : 11.774 175.722 4965 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.09 % Allowed : 17.09 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.13), residues: 4019 helix: 1.18 (0.14), residues: 1391 sheet: -0.26 (0.20), residues: 671 loop : -0.12 (0.14), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 879 TYR 0.048 0.001 TYR E 46 PHE 0.023 0.001 PHE A 219 TRP 0.017 0.001 TRP A1228 HIS 0.004 0.001 HIS A 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (33999) covalent geometry : angle 0.58051 / 0.30 (46110) hydrogen bonds : bond 0.03583 / 2.43 ( 1428) hydrogen bonds : angle 4.72985 / 3.38 ( 3993) metal coordination : bond 0.00518 / 0.27 ( 36) metal coordination : angle 3.84141 / 2.39 ( 51) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16129.27 seconds wall clock time: 274 minutes 18.17 seconds (16458.17 seconds total)