Starting phenix.real_space_refine on Sat Aug 8 23:36:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/30ep_57673/08_2026/30ep_57673.cif Found real_map, /net/cci-nas-00/data/ceres_data/30ep_57673/08_2026/30ep_57673.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/30ep_57673/08_2026/30ep_57673.cif" } default_model = "/net/cci-nas-00/data/ceres_data/30ep_57673/08_2026/30ep_57673.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/30ep_57673/08_2026/30ep_57673.map" default_real_map = "/net/cci-nas-00/data/ceres_data/30ep_57673/08_2026/30ep_57673.map" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 101 5.49 5 Mg 2 5.21 5 S 171 5.16 5 C 18827 2.51 5 N 5297 2.21 5 O 5941 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 30347 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 10853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1378, 10853 Classifications: {'peptide': 1378} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1315} Chain breaks: 9 Chain: "B" Number of atoms: 9155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1150, 9155 Classifications: {'peptide': 1150} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 1100} Chain breaks: 6 Chain: "C" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2095 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain: "E" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1744 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "H" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1077 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Chain: "I" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 909 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 904 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "N" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 825 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain breaks: 2 Chain: "R" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 297 Classifications: {'RNA': 14} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 7} Link IDs: {'rna3p': 13} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 886 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 2, ' ZN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: "T" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 457 SG CYS A 67 18.828 91.539 95.701 1.00 71.07 S ATOM 479 SG CYS A 70 18.078 88.437 97.877 1.00 68.18 S ATOM 532 SG CYS A 77 21.685 89.551 97.312 1.00 57.13 S ATOM 762 SG CYS A 107 33.320 80.626 51.581 1.00 87.57 S ATOM 786 SG CYS A 110 30.257 78.460 51.696 1.00 92.91 S ATOM 1091 SG CYS A 148 33.305 77.428 49.573 1.00 92.65 S ATOM 1105 SG CYS A 167 31.220 80.458 48.520 1.00 97.78 S ATOM 19514 SG CYS B1163 17.954 75.779 87.126 1.00 58.33 S ATOM 19532 SG CYS B1166 20.655 77.990 85.717 1.00 62.53 S ATOM 19657 SG CYS B1182 17.352 79.411 87.251 1.00 67.71 S ATOM 19676 SG CYS B1185 17.383 77.733 83.836 1.00 69.38 S ATOM 20664 SG CYS C 86 50.177 94.771 158.454 1.00 84.03 S ATOM 20681 SG CYS C 88 48.816 97.505 156.367 1.00 94.39 S ATOM 20714 SG CYS C 92 51.098 98.333 159.307 1.00 69.82 S ATOM 20737 SG CYS C 95 52.529 96.767 156.111 1.00 68.36 S ATOM 25655 SG CYS I 7 97.111 103.714 42.151 1.00112.82 S ATOM 25680 SG CYS I 10 93.645 104.959 42.936 1.00131.39 S ATOM 25846 SG CYS I 29 94.044 101.538 41.192 1.00122.88 S ATOM 25870 SG CYS I 32 94.791 104.623 39.300 1.00132.72 S ATOM 26197 SG CYS I 75 120.877 89.626 77.931 1.00 95.98 S ATOM 26219 SG CYS I 78 123.043 92.706 78.382 1.00108.61 S ATOM 26435 SG CYS I 103 119.381 92.788 79.407 1.00 98.74 S ATOM 26455 SG CYS I 106 120.318 92.645 75.725 1.00 94.24 S ATOM 26557 SG CYS J 7 79.158 92.463 139.079 1.00 32.41 S ATOM 26580 SG CYS J 10 79.296 90.714 142.543 1.00 39.05 S ATOM 26860 SG CYS J 45 81.687 89.982 139.588 1.00 42.89 S ATOM 26866 SG CYS J 46 81.943 93.201 141.673 1.00 48.06 S ATOM 27989 SG CYS L 31 58.243 127.968 124.235 1.00102.58 S ATOM 28009 SG CYS L 34 59.141 130.116 127.143 1.00 95.31 S ATOM 28113 SG CYS L 48 55.690 130.448 125.289 1.00 91.06 S ATOM 28136 SG CYS L 51 58.845 131.742 123.710 1.00114.20 S Time building chain proxies: 5.45, per 1000 atoms: 0.18 Number of scatterers: 30347 At special positions: 0 Unit cell: (134.208, 158.44, 178.012, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 171 16.00 P 101 15.00 Mg 2 11.99 O 5941 8.00 N 5297 7.00 C 18827 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: 2.75 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 67 " pdb=" ZN A1804 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 110 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " Number of angles added : 45 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6684 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 42 sheets defined 38.7% alpha, 19.1% beta 43 base pairs and 80 stacking pairs defined. Time for finding SS restraints: 3.88 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 203 through 213 removed outlier: 3.648A pdb=" N HIS A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 221 Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 259 through 283 removed outlier: 3.924A pdb=" N THR A 263 " --> pdb=" O GLU A 259 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE A 264 " --> pdb=" O ASP A 260 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 305 Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.712A 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 536 removed outlier: 3.525A pdb=" N LEU A 528 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 574 through 579 Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 661 removed outlier: 3.507A pdb=" N HIS A 659 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 removed outlier: 3.507A pdb=" N ILE A 670 " --> pdb=" O GLY A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 699 Processing helix chain 'A' and resid 710 through 737 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 removed outlier: 3.537A pdb=" N ILE A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 845 removed outlier: 3.955A pdb=" N GLU A 822 " --> pdb=" O MET A 818 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 824 " --> pdb=" O GLY A 820 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR A 831 " --> pdb=" O THR A 827 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU A 833 " --> pdb=" O VAL A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 874 through 876 No H-bonds generated for 'chain 'A' and resid 874 through 876' Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 909 through 913 Processing helix chain 'A' and resid 915 through 920 Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 959 through 972 Processing helix chain 'A' and resid 982 through 995 removed outlier: 3.618A pdb=" N GLN A 994 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU A 995 " --> pdb=" O LYS A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1015 Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1038 through 1057 removed outlier: 3.616A pdb=" N VAL A1057 " --> pdb=" O PHE A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1079 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1096 through 1107 Processing helix chain 'A' and resid 1130 through 1139 Processing helix chain 'A' and resid 1142 through 1145 Processing helix chain 'A' and resid 1166 through 1174 removed outlier: 3.791A pdb=" N PHE A1174 " --> pdb=" O ILE A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1205 Processing helix chain 'A' and resid 1208 through 1221 Processing helix chain 'A' and resid 1257 through 1271 removed outlier: 3.732A pdb=" N ILE A1271 " --> pdb=" O MET A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1317 removed outlier: 3.513A pdb=" N MET A1317 " --> pdb=" O LEU A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1340 Processing helix chain 'A' and resid 1340 through 1357 Processing helix chain 'A' and resid 1364 through 1375 removed outlier: 3.943A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1401 removed outlier: 3.505A pdb=" N SER A1401 " --> pdb=" O LEU A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1431 removed outlier: 3.712A pdb=" N ASN A1427 " --> pdb=" O GLY A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1452 Processing helix chain 'B' and resid 29 through 37 removed outlier: 3.958A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 66 removed outlier: 4.617A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ASP B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 293 through 303 removed outlier: 3.812A pdb=" N TYR B 303 " --> pdb=" O GLU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 370 through 390 Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 438 Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.580A pdb=" N THR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 473 removed outlier: 3.547A pdb=" N ALA B 472 " --> pdb=" O GLN B 469 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N MET B 473 " --> pdb=" O LYS B 470 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 469 through 473' Processing helix chain 'B' and resid 487 through 495 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 592 through 607 Processing helix chain 'B' and resid 654 through 667 Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 696 through 700 Processing helix chain 'B' and resid 706 through 710 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 removed outlier: 3.509A pdb=" N ASN B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 775 removed outlier: 4.187A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 788 Processing helix chain 'B' and resid 806 through 811 removed outlier: 3.634A pdb=" N GLU B 810 " --> pdb=" O ARG B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 849 Processing helix chain 'B' and resid 1016 through 1021 removed outlier: 4.081A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.922A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1061 Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1153 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 76 through 80 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: 4.061A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU C 210 " --> pdb=" O CYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 266 Processing helix chain 'E' and resid 4 through 27 removed outlier: 3.519A pdb=" N GLY E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 47 removed outlier: 3.720A pdb=" N CYS E 47 " --> pdb=" O LYS E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 91 through 103 removed outlier: 3.878A pdb=" N THR E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS E 103 " --> pdb=" O HIS E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 124 Processing helix chain 'E' and resid 138 through 141 Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.629A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'I' and resid 59 through 65 removed outlier: 4.039A pdb=" N GLY I 63 " --> pdb=" O GLN I 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 52 Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 53 removed outlier: 3.750A pdb=" N ASN K 44 " --> pdb=" O HIS K 40 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP K 53 " --> pdb=" O GLU K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 111 removed outlier: 3.594A pdb=" N LEU K 111 " --> pdb=" O THR K 107 " (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 90 removed outlier: 10.001A pdb=" N LEU A 86 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 11.266A pdb=" N LYS A 88 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N CYS A 238 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 173 through 177 removed outlier: 4.765A pdb=" N LEU A 181 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 343 through 345 removed outlier: 3.535A pdb=" N LEU B1128 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.526A pdb=" N MET A 456 " --> pdb=" O PHE A 444 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.818A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.580A pdb=" N LYS A 518 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AA9, first strand: chain 'A' and resid 588 through 590 removed outlier: 6.948A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AB2, first strand: chain 'A' and resid 849 through 850 removed outlier: 6.702A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 878 through 882 Processing sheet with id=AB4, first strand: chain 'A' and resid 1282 through 1292 removed outlier: 3.761A pdb=" N LEU A1116 " --> pdb=" O THR A1308 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.311A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR I 44 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1441 through 1445 Processing sheet with id=AB7, first strand: chain 'B' and resid 69 through 73 removed outlier: 5.369A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N VAL B 132 " --> pdb=" O SER B 156 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N SER B 156 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LYS B 134 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N GLU B 154 " --> pdb=" O LYS B 134 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N THR B 136 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE B 152 " --> pdb=" O THR B 136 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 69 through 73 removed outlier: 5.369A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AC1, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC2, first strand: chain 'B' and resid 404 through 407 removed outlier: 6.085A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 224 through 227 removed outlier: 3.815A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC5, first strand: chain 'B' and resid 650 through 651 Processing sheet with id=AC6, first strand: chain 'B' and resid 564 through 565 removed outlier: 5.439A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ARG B 579 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ILE B 626 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE B 581 " --> pdb=" O ILE B 626 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 792 through 796 removed outlier: 6.995A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 792 through 796 removed outlier: 6.995A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD1, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 7.089A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 873 through 874 Processing sheet with id=AD3, first strand: chain 'B' and resid 910 through 912 Processing sheet with id=AD4, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD5, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD6, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD7, first strand: chain 'C' and resid 7 through 13 removed outlier: 5.408A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.870A pdb=" N GLU C 152 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASN C 54 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LYS C 154 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 111 through 114 removed outlier: 6.293A pdb=" N THR C 111 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LYS C 146 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL C 113 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.333A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.706A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.639A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 15 through 19 removed outlier: 3.584A pdb=" N ARG I 24 " --> pdb=" O ASP I 19 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 70 through 71 removed outlier: 4.158A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 19 through 23 1226 hydrogen bonds defined for protein. 3369 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 112 hydrogen bonds 224 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 80 stacking parallelities Total time for adding SS restraints: 9.79 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4939 1.31 - 1.43: 8303 1.43 - 1.56: 17380 1.56 - 1.69: 196 1.69 - 1.82: 275 Bond restraints: 31093 Sorted by residual: bond pdb=" C4 ATP T 101 " pdb=" N9 ATP T 101 " ideal model delta sigma weight residual 1.374 1.180 0.194 1.00e-02 1.00e+04 3.76e+02 bond pdb=" C8 ATP T 101 " pdb=" N9 ATP T 101 " ideal model delta sigma weight residual 1.370 1.214 0.156 1.20e-02 6.94e+03 1.69e+02 bond pdb=" C6 ATP T 101 " pdb=" N6 ATP T 101 " ideal model delta sigma weight residual 1.337 1.450 -0.113 1.10e-02 8.26e+03 1.06e+02 bond pdb=" C5 ATP T 101 " pdb=" C6 ATP T 101 " ideal model delta sigma weight residual 1.409 1.336 0.073 1.00e-02 1.00e+04 5.31e+01 bond pdb=" C5 ATP T 101 " pdb=" N7 ATP T 101 " ideal model delta sigma weight residual 1.387 1.456 -0.069 1.00e-02 1.00e+04 4.78e+01 ... (remaining 31088 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 42134 2.82 - 5.65: 241 5.65 - 8.47: 19 8.47 - 11.30: 3 11.30 - 14.12: 4 Bond angle restraints: 42401 Sorted by residual: angle pdb=" C4 ATP T 101 " pdb=" N9 ATP T 101 " pdb=" C8 ATP T 101 " ideal model delta sigma weight residual 105.72 119.84 -14.12 1.00e+00 1.00e+00 1.99e+02 angle pdb=" PB ATP T 101 " pdb=" O3B ATP T 101 " pdb=" PG ATP T 101 " ideal model delta sigma weight residual 139.87 126.52 13.35 1.00e+00 1.00e+00 1.78e+02 angle pdb=" PA ATP T 101 " pdb=" O3A ATP T 101 " pdb=" PB ATP T 101 " ideal model delta sigma weight residual 136.83 124.21 12.62 1.00e+00 1.00e+00 1.59e+02 angle pdb=" N1 ATP T 101 " pdb=" C2 ATP T 101 " pdb=" N3 ATP T 101 " ideal model delta sigma weight residual 128.69 119.88 8.81 1.00e+00 1.00e+00 7.75e+01 angle pdb=" C1' C R 10 " pdb=" N1 C R 10 " pdb=" C2 C R 10 " ideal model delta sigma weight residual 118.80 125.87 -7.07 1.10e+00 8.26e-01 4.13e+01 ... (remaining 42396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.81: 17769 24.81 - 49.61: 808 49.61 - 74.42: 188 74.42 - 99.23: 21 99.23 - 124.03: 1 Dihedral angle restraints: 18787 sinusoidal: 8465 harmonic: 10322 Sorted by residual: dihedral pdb=" CA THR A 69 " pdb=" C THR A 69 " pdb=" N CYS A 70 " pdb=" CA CYS A 70 " ideal model delta harmonic sigma weight residual 180.00 154.30 25.70 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA ALA B 36 " pdb=" C ALA B 36 " pdb=" N PHE B 37 " pdb=" CA PHE B 37 " ideal model delta harmonic sigma weight residual 180.00 160.25 19.75 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA ALA C 39 " pdb=" C ALA C 39 " pdb=" N GLU C 40 " pdb=" CA GLU C 40 " ideal model delta harmonic sigma weight residual -180.00 -160.36 -19.64 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 18784 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 3322 0.041 - 0.082: 1031 0.082 - 0.122: 349 0.122 - 0.163: 55 0.163 - 0.204: 6 Chirality restraints: 4763 Sorted by residual: chirality pdb=" CA MET B1021 " pdb=" N MET B1021 " pdb=" C MET B1021 " pdb=" CB MET B1021 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" C2' ATP T 101 " pdb=" C1' ATP T 101 " pdb=" C3' ATP T 101 " pdb=" O2' ATP T 101 " both_signs ideal model delta sigma weight residual False -2.68 -2.48 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" C3' ATP T 101 " pdb=" C2' ATP T 101 " pdb=" C4' ATP T 101 " pdb=" O3' ATP T 101 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.32e-01 ... (remaining 4760 not shown) Planarity restraints: 5140 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 710 " 0.018 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C LEU A 710 " -0.062 2.00e-02 2.50e+03 pdb=" O LEU A 710 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG A 711 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 480 " -0.017 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C ALA A 480 " 0.062 2.00e-02 2.50e+03 pdb=" O ALA A 480 " -0.023 2.00e-02 2.50e+03 pdb=" N ASP A 481 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 797 " 0.014 2.00e-02 2.50e+03 1.39e-02 3.89e+00 pdb=" CG TYR B 797 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR B 797 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR B 797 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B 797 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 797 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 797 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 797 " 0.001 2.00e-02 2.50e+03 ... (remaining 5137 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 255 2.58 - 3.16: 24764 3.16 - 3.74: 48701 3.74 - 4.32: 68388 4.32 - 4.90: 111842 Nonbonded interactions: 253950 Sorted by model distance: nonbonded pdb="MG MG A1801 " pdb=" O1B ATP T 101 " model vdw 1.997 2.170 nonbonded pdb=" OD1 ASP A 483 " pdb="MG MG A1802 " model vdw 2.014 2.170 nonbonded pdb=" OD2 ASP A 481 " pdb="MG MG A1801 " model vdw 2.020 2.170 nonbonded pdb=" OD1 ASP A 481 " pdb="MG MG A1802 " model vdw 2.039 2.170 nonbonded pdb="MG MG A1801 " pdb=" O1G ATP T 101 " model vdw 2.073 2.170 ... (remaining 253945 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: 5.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 36.810 Find NCS groups from input model: 0.160 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:9.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.194 31125 Z= 0.303 Angle : 0.632 14.122 42446 Z= 0.416 Chirality : 0.045 0.204 4763 Planarity : 0.004 0.045 5140 Dihedral : 14.479 124.033 12103 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.54 % Favored : 96.32 % Rotamer: Outliers : 0.13 % Allowed : 0.22 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.14), residues: 3506 helix: 1.29 (0.15), residues: 1213 sheet: 0.37 (0.22), residues: 546 loop : -0.38 (0.15), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1366 TYR 0.034 0.002 TYR B 797 PHE 0.028 0.002 PHE A 219 TRP 0.029 0.002 TRP C 170 HIS 0.008 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.30 (31093) covalent geometry : angle 0.62536 / 0.42 (42401) hydrogen bonds : bond 0.17340 / 11.15 ( 1312) hydrogen bonds : angle 6.53538 / 4.67 ( 3593) metal coordination : bond 0.00389 / 0.26 ( 32) metal coordination : angle 2.77365 / 1.77 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 696 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LEU cc_start: 0.9184 (mt) cc_final: 0.8873 (mp) REVERT: A 175 ARG cc_start: 0.8435 (ttp80) cc_final: 0.8224 (ptt-90) REVERT: A 293 GLU cc_start: 0.8153 (tt0) cc_final: 0.7679 (tp30) REVERT: A 731 ARG cc_start: 0.8601 (mmt180) cc_final: 0.8242 (mtp180) REVERT: A 1079 MET cc_start: 0.7110 (ttp) cc_final: 0.6702 (mtm) REVERT: A 1185 PHE cc_start: 0.6904 (m-10) cc_final: 0.6576 (m-10) REVERT: A 1204 ASP cc_start: 0.8839 (t70) cc_final: 0.8628 (t0) REVERT: A 1281 ARG cc_start: 0.7052 (ttt180) cc_final: 0.6747 (ptp-110) REVERT: B 255 GLN cc_start: 0.8962 (pt0) cc_final: 0.8731 (pt0) REVERT: B 621 GLU cc_start: 0.8454 (tp30) cc_final: 0.8234 (mm-30) REVERT: B 730 ARG cc_start: 0.8269 (mtm-85) cc_final: 0.7916 (mtt90) REVERT: B 837 ASP cc_start: 0.8387 (m-30) cc_final: 0.8023 (m-30) REVERT: B 864 LYS cc_start: 0.8207 (mtmt) cc_final: 0.7473 (pptt) REVERT: B 1124 ARG cc_start: 0.8386 (mtm-85) cc_final: 0.8095 (mtp-110) REVERT: B 1169 MET cc_start: 0.9171 (mtm) cc_final: 0.8971 (mtm) REVERT: E 3 GLN cc_start: 0.7631 (mt0) cc_final: 0.7273 (tp-100) REVERT: E 50 MET cc_start: 0.8711 (ptm) cc_final: 0.8263 (pmm) REVERT: F 109 VAL cc_start: 0.9036 (t) cc_final: 0.8673 (p) REVERT: F 128 LYS cc_start: 0.9063 (mmtp) cc_final: 0.8810 (mmtm) REVERT: H 88 SER cc_start: 0.8860 (t) cc_final: 0.8043 (p) REVERT: H 91 ASP cc_start: 0.8699 (m-30) cc_final: 0.8405 (m-30) REVERT: H 128 ASN cc_start: 0.8925 (t0) cc_final: 0.8704 (t0) REVERT: K 22 ASP cc_start: 0.8272 (m-30) cc_final: 0.8054 (m-30) REVERT: K 78 THR cc_start: 0.8993 (m) cc_final: 0.8776 (p) REVERT: L 41 SER cc_start: 0.9235 (p) cc_final: 0.8858 (p) REVERT: L 44 ASP cc_start: 0.8138 (t70) cc_final: 0.7877 (m-30) outliers start: 4 outliers final: 3 residues processed: 700 average time/residue: 0.8116 time to fit residues: 651.7653 Evaluate side-chains 392 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 389 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 615 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 445 ASN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1258 HIS A1278 ASN B 278 GLN B 957 ASN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1062 HIS B1117 GLN C 79 GLN E 104 ASN J 23 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.116714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.075942 restraints weight = 43700.954| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.17 r_work: 0.2871 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 31125 Z= 0.189 Angle : 0.610 8.967 42446 Z= 0.326 Chirality : 0.046 0.272 4763 Planarity : 0.005 0.047 5140 Dihedral : 16.827 117.882 5009 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.31 % Favored : 96.58 % Rotamer: Outliers : 2.02 % Allowed : 10.76 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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 (0.14), residues: 3506 helix: 1.21 (0.15), residues: 1251 sheet: 0.19 (0.22), residues: 525 loop : -0.40 (0.15), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 620 TYR 0.024 0.002 TYR J 63 PHE 0.031 0.002 PHE A 219 TRP 0.014 0.001 TRP C 170 HIS 0.012 0.002 HIS B 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (31093) covalent geometry : angle 0.60179 / 0.33 (42401) hydrogen bonds : bond 0.04936 / 3.30 ( 1312) hydrogen bonds : angle 4.99374 / 3.56 ( 3593) metal coordination : bond 0.00593 / 0.38 ( 32) metal coordination : angle 3.08900 / 2.01 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 407 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 ARG cc_start: 0.8317 (ttp80) cc_final: 0.7993 (ttp80) REVERT: A 250 ILE cc_start: 0.7604 (mt) cc_final: 0.7379 (mt) REVERT: A 252 PHE cc_start: 0.7018 (OUTLIER) cc_final: 0.6668 (t80) REVERT: A 257 ARG cc_start: 0.7244 (mmp-170) cc_final: 0.6428 (mmp-170) REVERT: A 280 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7921 (tm-30) REVERT: A 293 GLU cc_start: 0.8133 (tt0) cc_final: 0.7695 (mt-10) REVERT: A 304 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8283 (mmm) REVERT: A 618 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7329 (pm20) REVERT: A 731 ARG cc_start: 0.7878 (mmt180) cc_final: 0.7335 (mtp180) REVERT: A 839 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8258 (ttt-90) REVERT: A 1079 MET cc_start: 0.7302 (ttp) cc_final: 0.6454 (mtm) REVERT: A 1211 GLN cc_start: 0.8728 (mt0) cc_final: 0.8447 (mt0) REVERT: A 1214 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8335 (pt0) REVERT: A 1281 ARG cc_start: 0.6793 (ttt180) cc_final: 0.6155 (ptp-110) REVERT: A 1336 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8729 (tmm) REVERT: B 621 GLU cc_start: 0.8627 (tp30) cc_final: 0.8154 (mm-30) REVERT: B 730 ARG cc_start: 0.8117 (mtm-85) cc_final: 0.7379 (mtt90) REVERT: B 864 LYS cc_start: 0.8097 (mtmt) cc_final: 0.7105 (pptt) REVERT: B 865 LYS cc_start: 0.6313 (OUTLIER) cc_final: 0.6029 (tmtp) REVERT: B 875 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7725 (pm20) REVERT: B 1124 ARG cc_start: 0.8210 (mtm-85) cc_final: 0.7513 (mtp180) REVERT: C 50 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7638 (mp0) REVERT: C 208 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8309 (mm-30) REVERT: E 3 GLN cc_start: 0.7854 (mt0) cc_final: 0.7252 (mm-40) REVERT: E 6 GLU cc_start: 0.7794 (mp0) cc_final: 0.7399 (mp0) REVERT: E 48 ASP cc_start: 0.8255 (m-30) cc_final: 0.7738 (m-30) REVERT: E 50 MET cc_start: 0.8704 (ptm) cc_final: 0.8249 (pmm) REVERT: F 109 VAL cc_start: 0.8757 (t) cc_final: 0.8349 (p) REVERT: F 128 LYS cc_start: 0.8403 (mmtp) cc_final: 0.8045 (mmtm) REVERT: H 78 SER cc_start: 0.9041 (OUTLIER) cc_final: 0.8777 (t) REVERT: H 87 ARG cc_start: 0.7923 (mmm-85) cc_final: 0.7688 (mmm-85) REVERT: H 88 SER cc_start: 0.8520 (t) cc_final: 0.8026 (p) REVERT: H 128 ASN cc_start: 0.8650 (t0) cc_final: 0.8246 (t0) REVERT: H 138 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7780 (pp20) REVERT: I 8 ARG cc_start: 0.8701 (tmm160) cc_final: 0.8337 (ptm-80) REVERT: K 78 THR cc_start: 0.8611 (m) cc_final: 0.8246 (p) REVERT: L 41 SER cc_start: 0.9160 (p) cc_final: 0.8814 (p) REVERT: L 44 ASP cc_start: 0.8266 (t70) cc_final: 0.7516 (m-30) REVERT: L 66 GLN cc_start: 0.8340 (tt0) cc_final: 0.7740 (mm-40) outliers start: 63 outliers final: 19 residues processed: 441 average time/residue: 0.7607 time to fit residues: 386.9514 Evaluate side-chains 387 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 358 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 734 GLU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 839 ARG Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1138 ILE Chi-restraints excluded: chain A residue 1336 MET Chi-restraints excluded: chain A residue 1454 MET Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 865 LYS Chi-restraints excluded: chain B residue 875 GLU Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain H residue 3 ASN Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 138 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 9 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 326 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 316 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 327 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 130 optimal weight: 0.0770 overall best weight: 1.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 451 HIS A1278 ASN B 957 ASN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.116547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.075932 restraints weight = 43598.504| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.16 r_work: 0.2869 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 31125 Z= 0.142 Angle : 0.552 8.695 42446 Z= 0.295 Chirality : 0.043 0.272 4763 Planarity : 0.004 0.048 5140 Dihedral : 16.793 117.274 5007 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.11 % Favored : 96.78 % Rotamer: Outliers : 1.98 % Allowed : 12.00 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.38 (0.14), residues: 3506 helix: 1.29 (0.15), residues: 1254 sheet: 0.08 (0.22), residues: 527 loop : -0.40 (0.15), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 30 TYR 0.021 0.001 TYR J 63 PHE 0.027 0.002 PHE A 219 TRP 0.009 0.001 TRP C 170 HIS 0.011 0.001 HIS B 440 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (31093) covalent geometry : angle 0.54503 / 0.29 (42401) hydrogen bonds : bond 0.04314 / 2.89 ( 1312) hydrogen bonds : angle 4.67318 / 3.33 ( 3593) metal coordination : bond 0.00403 / 0.26 ( 32) metal coordination : angle 2.80950 / 1.85 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 392 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.8876 (mmm) cc_final: 0.8675 (mmm) REVERT: A 175 ARG cc_start: 0.8276 (ttp80) cc_final: 0.7885 (ttp80) REVERT: A 280 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7908 (tm-30) REVERT: A 293 GLU cc_start: 0.8110 (tt0) cc_final: 0.7667 (mt-10) REVERT: A 304 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8274 (mmm) REVERT: A 330 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8414 (pttm) REVERT: A 685 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7779 (mt-10) REVERT: A 731 ARG cc_start: 0.7865 (mmt180) cc_final: 0.7321 (mtp180) REVERT: A 1079 MET cc_start: 0.7275 (ttp) cc_final: 0.6458 (mtm) REVERT: A 1112 LYS cc_start: 0.9014 (mmtp) cc_final: 0.8628 (mmpt) REVERT: A 1127 ASP cc_start: 0.7672 (OUTLIER) cc_final: 0.6759 (p0) REVERT: A 1214 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8315 (pt0) REVERT: A 1259 MET cc_start: 0.8688 (mmm) cc_final: 0.8145 (mmm) REVERT: A 1281 ARG cc_start: 0.6825 (ttt180) cc_final: 0.6104 (ptp-110) REVERT: B 88 TYR cc_start: 0.7716 (m-10) cc_final: 0.7436 (m-10) REVERT: B 216 GLU cc_start: 0.8871 (tt0) cc_final: 0.8602 (tt0) REVERT: B 241 ARG cc_start: 0.8457 (mmm-85) cc_final: 0.8131 (mmm-85) REVERT: B 621 GLU cc_start: 0.8615 (tp30) cc_final: 0.8205 (mm-30) REVERT: B 730 ARG cc_start: 0.8139 (mtm-85) cc_final: 0.7420 (mtt90) REVERT: B 864 LYS cc_start: 0.7998 (mtmt) cc_final: 0.7044 (pptt) REVERT: B 865 LYS cc_start: 0.6256 (OUTLIER) cc_final: 0.5963 (tmtp) REVERT: B 1021 MET cc_start: 0.9417 (OUTLIER) cc_final: 0.9193 (mtp) REVERT: B 1124 ARG cc_start: 0.8255 (mtm-85) cc_final: 0.7529 (mtp180) REVERT: C 50 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7696 (mp0) REVERT: E 3 GLN cc_start: 0.7830 (mt0) cc_final: 0.7213 (mm-40) REVERT: E 6 GLU cc_start: 0.7822 (mp0) cc_final: 0.7528 (mp0) REVERT: E 48 ASP cc_start: 0.8338 (m-30) cc_final: 0.8036 (m-30) REVERT: E 50 MET cc_start: 0.8709 (ptm) cc_final: 0.8225 (pmm) REVERT: F 109 VAL cc_start: 0.8765 (t) cc_final: 0.8380 (p) REVERT: F 128 LYS cc_start: 0.8439 (mmtp) cc_final: 0.8146 (mmtm) REVERT: H 88 SER cc_start: 0.8541 (t) cc_final: 0.8124 (p) REVERT: H 128 ASN cc_start: 0.8595 (t0) cc_final: 0.8234 (t0) REVERT: H 138 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.7756 (pp20) REVERT: I 90 GLN cc_start: 0.8582 (tp40) cc_final: 0.8306 (tt0) REVERT: K 78 THR cc_start: 0.8568 (m) cc_final: 0.8189 (p) REVERT: L 36 SER cc_start: 0.8081 (OUTLIER) cc_final: 0.7736 (p) REVERT: L 66 GLN cc_start: 0.8332 (tt0) cc_final: 0.7763 (mm-40) outliers start: 62 outliers final: 17 residues processed: 426 average time/residue: 0.7464 time to fit residues: 366.8160 Evaluate side-chains 390 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 365 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1138 ILE Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 865 LYS Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain H residue 3 ASN Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 138 GLU Chi-restraints excluded: chain I residue 109 ILE Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain L residue 36 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 39 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 223 optimal weight: 5.9990 chunk 245 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 186 optimal weight: 1.9990 chunk 279 optimal weight: 5.9990 chunk 307 optimal weight: 5.9990 chunk 52 optimal weight: 0.0980 chunk 336 optimal weight: 0.9980 chunk 281 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1258 HIS B 306 ASN B 740 HIS B 957 ASN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 ASN E 104 ASN I 12 ASN J 23 ASN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.117178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.076558 restraints weight = 43405.197| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.16 r_work: 0.2883 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 31125 Z= 0.118 Angle : 0.531 8.919 42446 Z= 0.283 Chirality : 0.042 0.276 4763 Planarity : 0.004 0.050 5140 Dihedral : 16.686 116.486 5002 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.17 % Favored : 96.72 % Rotamer: Outliers : 2.11 % Allowed : 13.09 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.14), residues: 3506 helix: 1.42 (0.15), residues: 1243 sheet: 0.10 (0.21), residues: 535 loop : -0.35 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 24 TYR 0.019 0.001 TYR E 112 PHE 0.025 0.001 PHE A 219 TRP 0.008 0.001 TRP B 561 HIS 0.009 0.001 HIS A1258 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (31093) covalent geometry : angle 0.52473 / 0.28 (42401) hydrogen bonds : bond 0.03846 / 2.58 ( 1312) hydrogen bonds : angle 4.45795 / 3.18 ( 3593) metal coordination : bond 0.00339 / 0.21 ( 32) metal coordination : angle 2.62229 / 1.76 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 387 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.8857 (mmm) cc_final: 0.8650 (mmm) REVERT: A 175 ARG cc_start: 0.8237 (ttp80) cc_final: 0.7856 (ttp80) REVERT: A 293 GLU cc_start: 0.8103 (tt0) cc_final: 0.7648 (mt-10) REVERT: A 330 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8368 (pttm) REVERT: A 685 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7788 (mt-10) REVERT: A 731 ARG cc_start: 0.7734 (mmt180) cc_final: 0.7304 (mtp180) REVERT: A 901 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7575 (pp) REVERT: A 1079 MET cc_start: 0.7199 (ttp) cc_final: 0.6445 (mtm) REVERT: A 1112 LYS cc_start: 0.8987 (mmtp) cc_final: 0.8592 (mmpt) REVERT: A 1127 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.6817 (p0) REVERT: A 1173 HIS cc_start: 0.8301 (t-90) cc_final: 0.7879 (t-90) REVERT: A 1281 ARG cc_start: 0.6751 (ttt180) cc_final: 0.6290 (ptp-170) REVERT: B 88 TYR cc_start: 0.7663 (m-10) cc_final: 0.7410 (m-10) REVERT: B 216 GLU cc_start: 0.8865 (tt0) cc_final: 0.8590 (tt0) REVERT: B 228 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8200 (mmmm) REVERT: B 241 ARG cc_start: 0.8362 (mmm-85) cc_final: 0.7961 (mmt90) REVERT: B 259 TYR cc_start: 0.8338 (m-80) cc_final: 0.8120 (m-80) REVERT: B 326 ASP cc_start: 0.7936 (t0) cc_final: 0.7391 (t70) REVERT: B 621 GLU cc_start: 0.8570 (tp30) cc_final: 0.8225 (mm-30) REVERT: B 730 ARG cc_start: 0.8140 (mtm-85) cc_final: 0.7415 (mtt90) REVERT: B 864 LYS cc_start: 0.7933 (mtmt) cc_final: 0.7039 (pptt) REVERT: B 875 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7548 (pm20) REVERT: B 1021 MET cc_start: 0.9403 (OUTLIER) cc_final: 0.9137 (mtp) REVERT: B 1124 ARG cc_start: 0.8242 (mtm-85) cc_final: 0.7554 (mtp180) REVERT: C 50 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7690 (mp0) REVERT: E 3 GLN cc_start: 0.7744 (mt0) cc_final: 0.7121 (mm-40) REVERT: E 6 GLU cc_start: 0.7786 (mp0) cc_final: 0.7540 (mp0) REVERT: E 48 ASP cc_start: 0.8362 (m-30) cc_final: 0.8063 (m-30) REVERT: E 50 MET cc_start: 0.8659 (ptm) cc_final: 0.8249 (pmm) REVERT: E 107 THR cc_start: 0.8399 (m) cc_final: 0.8136 (p) REVERT: E 121 MET cc_start: 0.8894 (mmt) cc_final: 0.8594 (mmm) REVERT: F 128 LYS cc_start: 0.8438 (mmtp) cc_final: 0.8145 (mmtm) REVERT: H 88 SER cc_start: 0.8437 (t) cc_final: 0.8028 (p) REVERT: H 128 ASN cc_start: 0.8551 (t0) cc_final: 0.8218 (t0) REVERT: H 138 GLU cc_start: 0.8476 (pt0) cc_final: 0.7706 (pp20) REVERT: I 8 ARG cc_start: 0.8647 (tmm-80) cc_final: 0.7819 (tmm-80) REVERT: I 30 ARG cc_start: 0.8784 (mpt-90) cc_final: 0.8469 (mpt-90) REVERT: I 90 GLN cc_start: 0.8617 (tp40) cc_final: 0.8318 (tt0) REVERT: J 19 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8233 (mt-10) REVERT: K 78 THR cc_start: 0.8540 (m) cc_final: 0.8183 (p) REVERT: L 36 SER cc_start: 0.8093 (t) cc_final: 0.7788 (p) REVERT: L 38 LEU cc_start: 0.8365 (mp) cc_final: 0.8015 (mm) REVERT: L 44 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.7227 (m-30) REVERT: L 66 GLN cc_start: 0.8347 (tt0) cc_final: 0.7726 (mm-40) outliers start: 66 outliers final: 22 residues processed: 421 average time/residue: 0.7273 time to fit residues: 354.3883 Evaluate side-chains 389 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 358 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 228 LYS Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 875 GLU Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain H residue 3 ASN Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain L residue 44 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 240 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 127 optimal weight: 3.9990 chunk 330 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 327 optimal weight: 0.9990 chunk 291 optimal weight: 3.9990 chunk 305 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 171 optimal weight: 0.4980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 278 GLN B 306 ASN B 395 GLN B 957 ASN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN J 23 ASN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.116595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.075884 restraints weight = 43666.323| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.17 r_work: 0.2870 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 31125 Z= 0.136 Angle : 0.539 11.770 42446 Z= 0.285 Chirality : 0.043 0.279 4763 Planarity : 0.004 0.050 5140 Dihedral : 16.626 115.666 5002 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.22 % Favored : 96.66 % Rotamer: Outliers : 1.98 % Allowed : 13.19 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.48 (0.14), residues: 3506 helix: 1.41 (0.15), residues: 1250 sheet: 0.15 (0.21), residues: 539 loop : -0.38 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 24 TYR 0.020 0.001 TYR J 63 PHE 0.026 0.001 PHE A 219 TRP 0.007 0.001 TRP B 561 HIS 0.009 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (31093) covalent geometry : angle 0.53200 / 0.28 (42401) hydrogen bonds : bond 0.03872 / 2.60 ( 1312) hydrogen bonds : angle 4.39620 / 3.14 ( 3593) metal coordination : bond 0.00387 / 0.24 ( 32) metal coordination : angle 2.66141 / 1.78 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 365 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.8135 (tt0) REVERT: A 108 MET cc_start: 0.8903 (mmm) cc_final: 0.8686 (mmm) REVERT: A 175 ARG cc_start: 0.8230 (ttp80) cc_final: 0.7861 (ttp80) REVERT: A 293 GLU cc_start: 0.8116 (tt0) cc_final: 0.7657 (mt-10) REVERT: A 330 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8343 (pttm) REVERT: A 455 MET cc_start: 0.9258 (ttm) cc_final: 0.8924 (mtp) REVERT: A 685 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7809 (mt-10) REVERT: A 731 ARG cc_start: 0.7764 (mmt180) cc_final: 0.7345 (mtp180) REVERT: A 901 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7557 (pp) REVERT: A 1079 MET cc_start: 0.7180 (ttp) cc_final: 0.6501 (mtm) REVERT: A 1112 LYS cc_start: 0.8995 (mmtp) cc_final: 0.8604 (mmpt) REVERT: A 1127 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.6852 (p0) REVERT: A 1173 HIS cc_start: 0.8289 (t-90) cc_final: 0.7854 (t-90) REVERT: A 1196 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7076 (tm-30) REVERT: A 1281 ARG cc_start: 0.6762 (ttt180) cc_final: 0.6005 (ptp-110) REVERT: A 1444 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7710 (mmm) REVERT: B 88 TYR cc_start: 0.7644 (m-10) cc_final: 0.7360 (m-10) REVERT: B 216 GLU cc_start: 0.8876 (tt0) cc_final: 0.8607 (tt0) REVERT: B 259 TYR cc_start: 0.8336 (m-80) cc_final: 0.8127 (m-80) REVERT: B 326 ASP cc_start: 0.8006 (t0) cc_final: 0.7490 (t70) REVERT: B 621 GLU cc_start: 0.8583 (tp30) cc_final: 0.8235 (mm-30) REVERT: B 637 LEU cc_start: 0.8530 (pp) cc_final: 0.8292 (pp) REVERT: B 730 ARG cc_start: 0.8191 (mtm-85) cc_final: 0.7430 (mtt90) REVERT: B 864 LYS cc_start: 0.7918 (mtmt) cc_final: 0.7051 (pptt) REVERT: B 875 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7574 (pm20) REVERT: B 1021 MET cc_start: 0.9390 (OUTLIER) cc_final: 0.9143 (mtp) REVERT: B 1124 ARG cc_start: 0.8259 (mtm-85) cc_final: 0.7579 (mtp180) REVERT: C 50 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7814 (mp0) REVERT: E 3 GLN cc_start: 0.7763 (mt0) cc_final: 0.7294 (mm-40) REVERT: E 50 MET cc_start: 0.8689 (ptm) cc_final: 0.8242 (pmm) REVERT: E 121 MET cc_start: 0.8851 (mmt) cc_final: 0.8527 (mmm) REVERT: F 128 LYS cc_start: 0.8432 (mmtp) cc_final: 0.8163 (mmtm) REVERT: H 33 GLN cc_start: 0.8181 (mm110) cc_final: 0.7977 (mm110) REVERT: H 88 SER cc_start: 0.8447 (t) cc_final: 0.8032 (p) REVERT: H 128 ASN cc_start: 0.8547 (t0) cc_final: 0.8216 (t0) REVERT: H 138 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7746 (pp20) REVERT: I 9 ASP cc_start: 0.9035 (m-30) cc_final: 0.8448 (m-30) REVERT: I 90 GLN cc_start: 0.8621 (tp40) cc_final: 0.8332 (tt0) REVERT: J 58 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8601 (mm-30) REVERT: K 78 THR cc_start: 0.8536 (m) cc_final: 0.8206 (p) REVERT: L 36 SER cc_start: 0.8108 (t) cc_final: 0.7796 (p) REVERT: L 66 GLN cc_start: 0.8345 (tt0) cc_final: 0.7818 (mm-40) outliers start: 62 outliers final: 32 residues processed: 405 average time/residue: 0.7141 time to fit residues: 334.7364 Evaluate side-chains 389 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 348 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain A residue 1454 MET Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 875 GLU Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain H residue 3 ASN Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 138 GLU Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain K residue 17 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 187 optimal weight: 0.6980 chunk 257 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 chunk 4 optimal weight: 0.2980 chunk 47 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 120 optimal weight: 7.9990 chunk 199 optimal weight: 0.8980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 957 ASN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN E 104 ASN F 78 GLN J 23 ASN L 53 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.114907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.074143 restraints weight = 43360.685| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.15 r_work: 0.2831 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 31125 Z= 0.177 Angle : 0.567 11.290 42446 Z= 0.299 Chirality : 0.044 0.280 4763 Planarity : 0.004 0.050 5140 Dihedral : 16.591 114.526 5002 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.37 % Favored : 96.52 % Rotamer: Outliers : 2.34 % Allowed : 13.57 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.46 (0.14), residues: 3506 helix: 1.35 (0.15), residues: 1249 sheet: 0.18 (0.22), residues: 539 loop : -0.38 (0.15), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 24 TYR 0.025 0.002 TYR J 63 PHE 0.028 0.002 PHE A 219 TRP 0.012 0.001 TRP A1228 HIS 0.011 0.002 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (31093) covalent geometry : angle 0.55961 / 0.30 (42401) hydrogen bonds : bond 0.04100 / 2.74 ( 1312) hydrogen bonds : angle 4.40358 / 3.15 ( 3593) metal coordination : bond 0.00510 / 0.32 ( 32) metal coordination : angle 2.88143 / 1.91 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 361 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.8929 (mmm) cc_final: 0.8717 (mmm) REVERT: A 175 ARG cc_start: 0.8317 (ttp80) cc_final: 0.7941 (ttp80) REVERT: A 206 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8402 (pt0) REVERT: A 257 ARG cc_start: 0.7215 (mmp-170) cc_final: 0.6557 (mmp-170) REVERT: A 293 GLU cc_start: 0.8108 (tt0) cc_final: 0.7662 (mt-10) REVERT: A 455 MET cc_start: 0.9246 (ttm) cc_final: 0.8939 (mtp) REVERT: A 708 MET cc_start: 0.6222 (mmt) cc_final: 0.5031 (mtm) REVERT: A 731 ARG cc_start: 0.7859 (mmt180) cc_final: 0.7340 (mtp180) REVERT: A 901 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7844 (pp) REVERT: A 919 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7586 (tp) REVERT: A 1079 MET cc_start: 0.7248 (ttp) cc_final: 0.6522 (mtm) REVERT: A 1112 LYS cc_start: 0.8981 (mmtp) cc_final: 0.8592 (mmpt) REVERT: A 1127 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.6901 (p0) REVERT: A 1173 HIS cc_start: 0.8358 (t-90) cc_final: 0.7962 (t-90) REVERT: A 1196 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7181 (tm-30) REVERT: A 1274 ARG cc_start: 0.6995 (OUTLIER) cc_final: 0.6698 (ppt90) REVERT: A 1281 ARG cc_start: 0.6866 (ttt180) cc_final: 0.6193 (ptt180) REVERT: A 1444 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7736 (mmm) REVERT: B 216 GLU cc_start: 0.8891 (tt0) cc_final: 0.8613 (tt0) REVERT: B 241 ARG cc_start: 0.8428 (mmm-85) cc_final: 0.8125 (mmm-85) REVERT: B 259 TYR cc_start: 0.8345 (m-80) cc_final: 0.8120 (m-80) REVERT: B 326 ASP cc_start: 0.7972 (t0) cc_final: 0.7474 (t70) REVERT: B 621 GLU cc_start: 0.8592 (tp30) cc_final: 0.8243 (mm-30) REVERT: B 730 ARG cc_start: 0.8182 (mtm-85) cc_final: 0.7392 (mtt90) REVERT: B 864 LYS cc_start: 0.7952 (mtmt) cc_final: 0.7064 (pptt) REVERT: B 875 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7600 (pm20) REVERT: B 1021 MET cc_start: 0.9389 (OUTLIER) cc_final: 0.9161 (mtp) REVERT: B 1124 ARG cc_start: 0.8290 (mtm-85) cc_final: 0.7581 (mtp180) REVERT: C 50 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7818 (mp0) REVERT: E 3 GLN cc_start: 0.7823 (mt0) cc_final: 0.6583 (mt0) REVERT: E 6 GLU cc_start: 0.7623 (mp0) cc_final: 0.7353 (pm20) REVERT: E 50 MET cc_start: 0.8674 (ptm) cc_final: 0.8189 (pmm) REVERT: E 54 GLN cc_start: 0.8037 (mm-40) cc_final: 0.7792 (mm110) REVERT: E 121 MET cc_start: 0.8890 (mmt) cc_final: 0.8556 (mmm) REVERT: F 128 LYS cc_start: 0.8444 (mmtp) cc_final: 0.8187 (mmtm) REVERT: H 88 SER cc_start: 0.8460 (t) cc_final: 0.8102 (p) REVERT: H 128 ASN cc_start: 0.8594 (t0) cc_final: 0.8236 (t0) REVERT: H 138 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7733 (pp20) REVERT: I 8 ARG cc_start: 0.8536 (tmm-80) cc_final: 0.8306 (tmm-80) REVERT: I 9 ASP cc_start: 0.9099 (m-30) cc_final: 0.8747 (m-30) REVERT: I 22 ASN cc_start: 0.7951 (t0) cc_final: 0.7395 (t0) REVERT: I 90 GLN cc_start: 0.8570 (tp40) cc_final: 0.8359 (tt0) REVERT: K 78 THR cc_start: 0.8538 (m) cc_final: 0.8207 (p) REVERT: L 36 SER cc_start: 0.8167 (t) cc_final: 0.7855 (p) REVERT: L 38 LEU cc_start: 0.8479 (mp) cc_final: 0.8122 (mm) REVERT: L 44 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.7173 (m-30) REVERT: L 66 GLN cc_start: 0.8363 (tt0) cc_final: 0.7822 (mm-40) outliers start: 73 outliers final: 33 residues processed: 410 average time/residue: 0.8084 time to fit residues: 383.0868 Evaluate side-chains 391 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 348 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1274 ARG Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain A residue 1454 MET Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 875 GLU Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain H residue 3 ASN Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 138 GLU Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain L residue 44 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 295 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 72.1949 > 50:) chunk 33 optimal weight: 0.9990 chunk 147 optimal weight: 0.6980 chunk 205 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 chunk 292 optimal weight: 4.9990 chunk 272 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 262 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 742 ASN A 786 HIS A1258 HIS B 278 GLN B 957 ASN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN F 78 GLN J 23 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.114193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.073350 restraints weight = 43419.580| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.14 r_work: 0.2818 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 31125 Z= 0.187 Angle : 0.576 11.211 42446 Z= 0.302 Chirality : 0.044 0.276 4763 Planarity : 0.004 0.050 5140 Dihedral : 16.551 113.540 5002 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.45 % Favored : 96.43 % Rotamer: Outliers : 2.37 % Allowed : 13.86 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.14), residues: 3506 helix: 1.27 (0.15), residues: 1250 sheet: 0.20 (0.21), residues: 549 loop : -0.42 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 24 TYR 0.020 0.002 TYR J 63 PHE 0.027 0.002 PHE A 219 TRP 0.011 0.001 TRP A1228 HIS 0.009 0.002 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 (31093) covalent geometry : angle 0.56767 / 0.30 (42401) hydrogen bonds : bond 0.04139 / 2.78 ( 1312) hydrogen bonds : angle 4.41475 / 3.16 ( 3593) metal coordination : bond 0.00548 / 0.34 ( 32) metal coordination : angle 2.98462 / 1.98 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 353 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7928 (tt0) REVERT: A 108 MET cc_start: 0.8935 (mmm) cc_final: 0.8716 (mmm) REVERT: A 123 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.8109 (mtm180) REVERT: A 175 ARG cc_start: 0.8322 (ttp80) cc_final: 0.7957 (ttp80) REVERT: A 206 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8408 (pt0) REVERT: A 293 GLU cc_start: 0.8078 (tt0) cc_final: 0.7663 (mt-10) REVERT: A 455 MET cc_start: 0.9225 (ttm) cc_final: 0.8983 (mtp) REVERT: A 688 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8063 (ttmm) REVERT: A 708 MET cc_start: 0.6380 (mmt) cc_final: 0.5116 (mtm) REVERT: A 731 ARG cc_start: 0.7860 (mmt180) cc_final: 0.7338 (mtp180) REVERT: A 901 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7856 (pp) REVERT: A 919 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7593 (tp) REVERT: A 1079 MET cc_start: 0.7295 (ttp) cc_final: 0.6615 (mtm) REVERT: A 1112 LYS cc_start: 0.8970 (mmtp) cc_final: 0.8614 (mmpt) REVERT: A 1127 ASP cc_start: 0.7679 (OUTLIER) cc_final: 0.6858 (p0) REVERT: A 1196 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7256 (tm-30) REVERT: A 1274 ARG cc_start: 0.7055 (OUTLIER) cc_final: 0.6650 (ppt170) REVERT: A 1281 ARG cc_start: 0.6938 (ttt180) cc_final: 0.6172 (ptt180) REVERT: A 1444 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7683 (mmm) REVERT: B 216 GLU cc_start: 0.8898 (tt0) cc_final: 0.8632 (tt0) REVERT: B 259 TYR cc_start: 0.8344 (m-80) cc_final: 0.8061 (m-80) REVERT: B 326 ASP cc_start: 0.8021 (t0) cc_final: 0.7530 (t70) REVERT: B 621 GLU cc_start: 0.8619 (tp30) cc_final: 0.8272 (mm-30) REVERT: B 730 ARG cc_start: 0.8160 (mtm-85) cc_final: 0.7403 (mtt90) REVERT: B 864 LYS cc_start: 0.7944 (mtmt) cc_final: 0.7006 (pptt) REVERT: B 875 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7577 (pm20) REVERT: B 1021 MET cc_start: 0.9387 (OUTLIER) cc_final: 0.9162 (mtp) REVERT: B 1124 ARG cc_start: 0.8265 (mtm-85) cc_final: 0.7515 (mtp180) REVERT: C 50 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7865 (mp0) REVERT: E 3 GLN cc_start: 0.7779 (mt0) cc_final: 0.6871 (mm-40) REVERT: E 6 GLU cc_start: 0.7635 (mp0) cc_final: 0.7251 (pm20) REVERT: E 50 MET cc_start: 0.8618 (ptm) cc_final: 0.8217 (pmm) REVERT: E 54 GLN cc_start: 0.8242 (mm-40) cc_final: 0.7891 (mm110) REVERT: E 121 MET cc_start: 0.8834 (mmt) cc_final: 0.8488 (mmm) REVERT: F 122 MET cc_start: 0.8723 (mtm) cc_final: 0.8485 (mtp) REVERT: F 128 LYS cc_start: 0.8468 (mmtp) cc_final: 0.8207 (mmtm) REVERT: H 88 SER cc_start: 0.8471 (t) cc_final: 0.8147 (p) REVERT: H 138 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7745 (pp20) REVERT: I 8 ARG cc_start: 0.8551 (tmm-80) cc_final: 0.8330 (tmm-80) REVERT: I 9 ASP cc_start: 0.9154 (m-30) cc_final: 0.8725 (m-30) REVERT: I 22 ASN cc_start: 0.7816 (t0) cc_final: 0.7509 (t0) REVERT: I 90 GLN cc_start: 0.8560 (tp40) cc_final: 0.8313 (tt0) REVERT: K 78 THR cc_start: 0.8539 (m) cc_final: 0.8232 (p) REVERT: L 38 LEU cc_start: 0.8466 (mp) cc_final: 0.8187 (mm) REVERT: L 66 GLN cc_start: 0.8381 (tt0) cc_final: 0.7843 (mm-40) outliers start: 74 outliers final: 32 residues processed: 403 average time/residue: 0.8173 time to fit residues: 380.4093 Evaluate side-chains 384 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 340 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 688 LYS Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1274 ARG Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain A residue 1454 MET Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 875 GLU Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain H residue 3 ASN Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 138 GLU Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain L residue 68 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 35 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 223 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 251 optimal weight: 3.9990 chunk 258 optimal weight: 0.9980 chunk 250 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 174 optimal weight: 7.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 957 ASN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 23 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.115016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.074290 restraints weight = 43174.283| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.14 r_work: 0.2834 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 31125 Z= 0.146 Angle : 0.555 13.112 42446 Z= 0.292 Chirality : 0.043 0.274 4763 Planarity : 0.004 0.050 5140 Dihedral : 16.482 113.100 5002 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.28 % Favored : 96.61 % Rotamer: Outliers : 1.76 % Allowed : 14.66 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.14), residues: 3506 helix: 1.40 (0.15), residues: 1238 sheet: 0.21 (0.21), residues: 550 loop : -0.38 (0.15), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 54 TYR 0.021 0.001 TYR E 112 PHE 0.026 0.001 PHE A1225 TRP 0.011 0.001 TRP A1228 HIS 0.007 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (31093) covalent geometry : angle 0.54755 / 0.29 (42401) hydrogen bonds : bond 0.03868 / 2.60 ( 1312) hydrogen bonds : angle 4.33439 / 3.10 ( 3593) metal coordination : bond 0.00433 / 0.26 ( 32) metal coordination : angle 2.89653 / 1.93 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 349 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8321 (pt0) REVERT: A 108 MET cc_start: 0.8933 (mmm) cc_final: 0.8716 (mmm) REVERT: A 175 ARG cc_start: 0.8320 (ttp80) cc_final: 0.7952 (ttp80) REVERT: A 206 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8405 (pt0) REVERT: A 293 GLU cc_start: 0.8077 (tt0) cc_final: 0.7665 (mt-10) REVERT: A 455 MET cc_start: 0.9182 (ttm) cc_final: 0.8889 (mtp) REVERT: A 688 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.8044 (ttmm) REVERT: A 708 MET cc_start: 0.6386 (mmt) cc_final: 0.5062 (mtm) REVERT: A 731 ARG cc_start: 0.7842 (mmt180) cc_final: 0.7314 (mtp180) REVERT: A 901 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7845 (pp) REVERT: A 919 ILE cc_start: 0.7897 (OUTLIER) cc_final: 0.7584 (tp) REVERT: A 1079 MET cc_start: 0.7296 (ttp) cc_final: 0.6558 (mtm) REVERT: A 1112 LYS cc_start: 0.9024 (mmtp) cc_final: 0.8634 (mmpt) REVERT: A 1127 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.6957 (p0) REVERT: A 1173 HIS cc_start: 0.8312 (t-90) cc_final: 0.7904 (t-90) REVERT: A 1196 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7249 (tm-30) REVERT: A 1274 ARG cc_start: 0.6958 (OUTLIER) cc_final: 0.6713 (ppt90) REVERT: A 1281 ARG cc_start: 0.6919 (ttt180) cc_final: 0.6201 (ptt180) REVERT: B 216 GLU cc_start: 0.8891 (tt0) cc_final: 0.8613 (tt0) REVERT: B 241 ARG cc_start: 0.8392 (mmm-85) cc_final: 0.8164 (mmt90) REVERT: B 259 TYR cc_start: 0.8358 (m-80) cc_final: 0.8090 (m-80) REVERT: B 326 ASP cc_start: 0.8019 (t0) cc_final: 0.7580 (t70) REVERT: B 621 GLU cc_start: 0.8567 (tp30) cc_final: 0.8241 (mm-30) REVERT: B 730 ARG cc_start: 0.8135 (mtm-85) cc_final: 0.7307 (mtt90) REVERT: B 864 LYS cc_start: 0.7908 (mtmt) cc_final: 0.7022 (pptt) REVERT: B 875 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7566 (pm20) REVERT: B 1021 MET cc_start: 0.9375 (OUTLIER) cc_final: 0.9163 (mtp) REVERT: B 1124 ARG cc_start: 0.8247 (mtm-85) cc_final: 0.7506 (mtp180) REVERT: C 50 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7905 (mp0) REVERT: E 3 GLN cc_start: 0.7795 (mt0) cc_final: 0.7234 (tt0) REVERT: E 6 GLU cc_start: 0.7593 (mp0) cc_final: 0.7266 (pm20) REVERT: E 50 MET cc_start: 0.8607 (ptm) cc_final: 0.8179 (pmm) REVERT: E 54 GLN cc_start: 0.8219 (mm-40) cc_final: 0.7819 (mm110) REVERT: E 121 MET cc_start: 0.8805 (mmt) cc_final: 0.8471 (mmm) REVERT: F 128 LYS cc_start: 0.8467 (mmtp) cc_final: 0.8212 (mmtm) REVERT: H 88 SER cc_start: 0.8439 (t) cc_final: 0.8105 (p) REVERT: H 138 GLU cc_start: 0.8506 (pt0) cc_final: 0.7754 (pp20) REVERT: I 8 ARG cc_start: 0.8550 (tmm-80) cc_final: 0.8325 (tmm-80) REVERT: I 9 ASP cc_start: 0.9182 (m-30) cc_final: 0.8687 (m-30) REVERT: I 22 ASN cc_start: 0.7854 (t0) cc_final: 0.7542 (t0) REVERT: I 90 GLN cc_start: 0.8556 (tp40) cc_final: 0.8301 (tt0) REVERT: K 54 ARG cc_start: 0.8641 (mmm160) cc_final: 0.8319 (mmm160) REVERT: K 78 THR cc_start: 0.8528 (m) cc_final: 0.8232 (p) REVERT: L 38 LEU cc_start: 0.8448 (mp) cc_final: 0.8178 (mm) REVERT: L 44 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.7181 (m-30) REVERT: L 66 GLN cc_start: 0.8345 (tt0) cc_final: 0.7802 (mm-40) outliers start: 55 outliers final: 32 residues processed: 388 average time/residue: 0.8377 time to fit residues: 375.7875 Evaluate side-chains 383 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 341 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 688 LYS Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1274 ARG Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1454 MET Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 875 GLU Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain H residue 3 ASN Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain L residue 44 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 213 optimal weight: 0.8980 chunk 154 optimal weight: 0.4980 chunk 114 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 253 optimal weight: 1.9990 chunk 187 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 285 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 290 optimal weight: 0.0070 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 957 ASN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN H 35 GLN J 23 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.115709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.075075 restraints weight = 43146.847| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.14 r_work: 0.2849 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 31125 Z= 0.127 Angle : 0.543 12.104 42446 Z= 0.285 Chirality : 0.042 0.275 4763 Planarity : 0.004 0.055 5140 Dihedral : 16.417 112.690 5002 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.22 % Favored : 96.66 % Rotamer: Outliers : 1.73 % Allowed : 14.85 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.55 (0.14), residues: 3506 helix: 1.46 (0.15), residues: 1238 sheet: 0.24 (0.21), residues: 550 loop : -0.35 (0.15), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 119 TYR 0.021 0.001 TYR E 112 PHE 0.023 0.001 PHE A 219 TRP 0.009 0.001 TRP C 192 HIS 0.008 0.001 HIS A1258 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (31093) covalent geometry : angle 0.53579 / 0.28 (42401) hydrogen bonds : bond 0.03682 / 2.48 ( 1312) hydrogen bonds : angle 4.25864 / 3.05 ( 3593) metal coordination : bond 0.00374 / 0.22 ( 32) metal coordination : angle 2.77075 / 1.87 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 356 time to evaluate : 1.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7898 (tt0) REVERT: A 68 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8299 (pt0) REVERT: A 108 MET cc_start: 0.8953 (mmm) cc_final: 0.8751 (mmm) REVERT: A 175 ARG cc_start: 0.8315 (ttp80) cc_final: 0.7946 (ttp80) REVERT: A 206 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8422 (pt0) REVERT: A 286 HIS cc_start: 0.7717 (OUTLIER) cc_final: 0.7048 (t70) REVERT: A 293 GLU cc_start: 0.8070 (tt0) cc_final: 0.7652 (mt-10) REVERT: A 455 MET cc_start: 0.9147 (ttm) cc_final: 0.8918 (mtp) REVERT: A 688 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.8034 (ttmm) REVERT: A 708 MET cc_start: 0.6400 (mmt) cc_final: 0.4896 (mtm) REVERT: A 731 ARG cc_start: 0.7834 (mmt180) cc_final: 0.7315 (mtp180) REVERT: A 901 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7846 (pp) REVERT: A 919 ILE cc_start: 0.7880 (OUTLIER) cc_final: 0.7561 (tp) REVERT: A 1079 MET cc_start: 0.7258 (ttp) cc_final: 0.6582 (mtm) REVERT: A 1112 LYS cc_start: 0.9023 (mmtp) cc_final: 0.8619 (mmpt) REVERT: A 1127 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.6990 (p0) REVERT: A 1173 HIS cc_start: 0.8298 (t-90) cc_final: 0.7887 (t-90) REVERT: A 1196 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7229 (tm-30) REVERT: A 1274 ARG cc_start: 0.6852 (OUTLIER) cc_final: 0.6650 (ppt-90) REVERT: A 1281 ARG cc_start: 0.6920 (ttt180) cc_final: 0.6229 (ptt180) REVERT: A 1444 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7661 (mmm) REVERT: B 216 GLU cc_start: 0.8886 (tt0) cc_final: 0.8610 (tt0) REVERT: B 259 TYR cc_start: 0.8364 (m-80) cc_final: 0.8107 (m-80) REVERT: B 326 ASP cc_start: 0.7963 (t0) cc_final: 0.7514 (t70) REVERT: B 621 GLU cc_start: 0.8557 (tp30) cc_final: 0.8237 (mm-30) REVERT: B 730 ARG cc_start: 0.8165 (mtm-85) cc_final: 0.7353 (mtt90) REVERT: B 864 LYS cc_start: 0.7913 (mtmt) cc_final: 0.7039 (pptt) REVERT: B 875 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7522 (pm20) REVERT: B 1021 MET cc_start: 0.9362 (OUTLIER) cc_final: 0.9160 (mtp) REVERT: B 1124 ARG cc_start: 0.8245 (mtm-85) cc_final: 0.7501 (mtp180) REVERT: C 19 ASP cc_start: 0.8042 (t0) cc_final: 0.7792 (t0) REVERT: C 50 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7805 (mp0) REVERT: E 3 GLN cc_start: 0.7858 (mt0) cc_final: 0.7343 (tt0) REVERT: E 6 GLU cc_start: 0.7592 (mp0) cc_final: 0.7254 (pm20) REVERT: E 50 MET cc_start: 0.8594 (ptm) cc_final: 0.8176 (pmm) REVERT: E 54 GLN cc_start: 0.8321 (mm-40) cc_final: 0.7925 (mm110) REVERT: E 113 GLN cc_start: 0.7268 (OUTLIER) cc_final: 0.6691 (mp10) REVERT: E 121 MET cc_start: 0.8788 (mmt) cc_final: 0.8454 (mmm) REVERT: F 128 LYS cc_start: 0.8446 (mmtp) cc_final: 0.8155 (mmtm) REVERT: H 88 SER cc_start: 0.8430 (t) cc_final: 0.8080 (p) REVERT: H 138 GLU cc_start: 0.8511 (pt0) cc_final: 0.7772 (pp20) REVERT: I 1 MET cc_start: 0.6801 (ppp) cc_final: 0.6173 (tpt) REVERT: I 9 ASP cc_start: 0.9211 (m-30) cc_final: 0.8694 (m-30) REVERT: I 22 ASN cc_start: 0.7852 (t0) cc_final: 0.7591 (t0) REVERT: I 90 GLN cc_start: 0.8547 (tp40) cc_final: 0.8292 (tt0) REVERT: K 54 ARG cc_start: 0.8633 (mmm160) cc_final: 0.8312 (mmm160) REVERT: K 78 THR cc_start: 0.8521 (m) cc_final: 0.8237 (p) REVERT: L 28 LYS cc_start: 0.8716 (mmpt) cc_final: 0.8406 (mmpt) REVERT: L 38 LEU cc_start: 0.8484 (mp) cc_final: 0.8164 (mm) REVERT: L 44 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.7219 (m-30) REVERT: L 66 GLN cc_start: 0.8345 (tt0) cc_final: 0.7697 (mm-40) outliers start: 54 outliers final: 32 residues processed: 391 average time/residue: 0.8389 time to fit residues: 379.5249 Evaluate side-chains 390 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 344 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 286 HIS Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 688 LYS Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1274 ARG Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain A residue 1454 MET Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 875 GLU Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 1021 MET Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain H residue 3 ASN Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain L residue 44 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 311 optimal weight: 0.6980 chunk 219 optimal weight: 0.8980 chunk 275 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 297 optimal weight: 0.6980 chunk 259 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 203 optimal weight: 0.0170 chunk 187 optimal weight: 0.0980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 357 GLN B 957 ASN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN H 35 GLN J 23 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.117028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.076662 restraints weight = 42987.297| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.14 r_work: 0.2873 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.110 31125 Z= 0.107 Angle : 0.535 12.449 42446 Z= 0.281 Chirality : 0.041 0.274 4763 Planarity : 0.004 0.051 5140 Dihedral : 16.326 112.335 5002 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.08 % Favored : 96.83 % Rotamer: Outliers : 1.57 % Allowed : 15.08 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.63 (0.14), residues: 3506 helix: 1.55 (0.15), residues: 1236 sheet: 0.29 (0.22), residues: 549 loop : -0.32 (0.15), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 87 TYR 0.020 0.001 TYR E 112 PHE 0.028 0.001 PHE A1225 TRP 0.012 0.001 TRP A1228 HIS 0.009 0.001 HIS A1258 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (31093) covalent geometry : angle 0.52840 / 0.28 (42401) hydrogen bonds : bond 0.03446 / 2.33 ( 1312) hydrogen bonds : angle 4.15802 / 2.97 ( 3593) metal coordination : bond 0.00370 / 0.21 ( 32) metal coordination : angle 2.68143 / 1.83 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 369 time to evaluate : 1.155 Fit side-chains revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8214 (pt0) REVERT: A 175 ARG cc_start: 0.8252 (ttp80) cc_final: 0.7887 (ttp80) REVERT: A 293 GLU cc_start: 0.8042 (tt0) cc_final: 0.7628 (mt-10) REVERT: A 455 MET cc_start: 0.9097 (ttm) cc_final: 0.8848 (mtp) REVERT: A 688 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.8009 (ttmm) REVERT: A 708 MET cc_start: 0.6209 (mmt) cc_final: 0.5115 (mtm) REVERT: A 731 ARG cc_start: 0.7715 (mmt180) cc_final: 0.7271 (mtp180) REVERT: A 901 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7842 (pp) REVERT: A 919 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7586 (tp) REVERT: A 1079 MET cc_start: 0.6959 (ttp) cc_final: 0.6487 (mtm) REVERT: A 1112 LYS cc_start: 0.9026 (mmtp) cc_final: 0.8615 (mmpt) REVERT: A 1127 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7009 (p0) REVERT: A 1173 HIS cc_start: 0.8293 (t-90) cc_final: 0.7938 (t-90) REVERT: A 1196 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7152 (tm-30) REVERT: A 1214 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8391 (pt0) REVERT: A 1258 HIS cc_start: 0.7676 (p-80) cc_final: 0.7457 (p90) REVERT: A 1281 ARG cc_start: 0.6869 (ttt180) cc_final: 0.6168 (ptt180) REVERT: A 1444 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7638 (mmm) REVERT: B 216 GLU cc_start: 0.8862 (tt0) cc_final: 0.8582 (tt0) REVERT: B 259 TYR cc_start: 0.8304 (m-80) cc_final: 0.8080 (m-80) REVERT: B 326 ASP cc_start: 0.7953 (t0) cc_final: 0.7447 (t70) REVERT: B 621 GLU cc_start: 0.8543 (tp30) cc_final: 0.8218 (mm-30) REVERT: B 730 ARG cc_start: 0.8106 (mtm-85) cc_final: 0.7256 (mtt90) REVERT: B 864 LYS cc_start: 0.7848 (mtmt) cc_final: 0.6972 (pptt) REVERT: B 875 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7488 (pm20) REVERT: B 1124 ARG cc_start: 0.8213 (mtm-85) cc_final: 0.7460 (mtp180) REVERT: C 50 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7710 (mp0) REVERT: E 3 GLN cc_start: 0.7866 (mt0) cc_final: 0.7359 (tt0) REVERT: E 6 GLU cc_start: 0.7597 (mp0) cc_final: 0.7266 (pm20) REVERT: E 50 MET cc_start: 0.8586 (ptm) cc_final: 0.8196 (pmm) REVERT: E 54 GLN cc_start: 0.8196 (mm-40) cc_final: 0.7806 (mm110) REVERT: E 113 GLN cc_start: 0.7207 (mt0) cc_final: 0.6761 (mp10) REVERT: E 121 MET cc_start: 0.8726 (mmt) cc_final: 0.8385 (mmm) REVERT: F 128 LYS cc_start: 0.8404 (mmtp) cc_final: 0.8132 (mmtm) REVERT: H 88 SER cc_start: 0.8414 (t) cc_final: 0.8037 (p) REVERT: H 138 GLU cc_start: 0.8507 (pt0) cc_final: 0.7718 (pp20) REVERT: I 1 MET cc_start: 0.6905 (ppp) cc_final: 0.6343 (tpp) REVERT: I 9 ASP cc_start: 0.9158 (m-30) cc_final: 0.8906 (m-30) REVERT: I 22 ASN cc_start: 0.7873 (t0) cc_final: 0.7615 (t0) REVERT: I 90 GLN cc_start: 0.8533 (tp40) cc_final: 0.8093 (tt0) REVERT: I 94 ASP cc_start: 0.8913 (p0) cc_final: 0.8548 (p0) REVERT: J 49 MET cc_start: 0.9020 (tpp) cc_final: 0.8489 (mmm) REVERT: K 22 ASP cc_start: 0.8591 (m-30) cc_final: 0.8233 (m-30) REVERT: K 54 ARG cc_start: 0.8668 (mmm160) cc_final: 0.8361 (mmm160) REVERT: K 78 THR cc_start: 0.8490 (m) cc_final: 0.8217 (p) REVERT: L 28 LYS cc_start: 0.8640 (mmpt) cc_final: 0.8349 (mmpt) REVERT: L 36 SER cc_start: 0.8079 (t) cc_final: 0.7743 (p) REVERT: L 38 LEU cc_start: 0.8413 (mp) cc_final: 0.7913 (mm) REVERT: L 44 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.7058 (m-30) REVERT: L 46 VAL cc_start: 0.8256 (p) cc_final: 0.8023 (m) REVERT: L 66 GLN cc_start: 0.8341 (tt0) cc_final: 0.7692 (mm-40) outliers start: 49 outliers final: 25 residues processed: 400 average time/residue: 0.8153 time to fit residues: 376.8239 Evaluate side-chains 383 residues out of total 3124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 350 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 688 LYS Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1109 LYS Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain A residue 1454 MET Chi-restraints excluded: chain B residue 77 HIS Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 875 GLU Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain L residue 44 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 192 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 200 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 318 optimal weight: 5.9990 chunk 57 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 335 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 GLN B 862 GLN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN H 35 GLN J 23 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.115926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.075324 restraints weight = 43522.912| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.15 r_work: 0.2852 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31125 Z= 0.138 Angle : 0.546 11.799 42446 Z= 0.287 Chirality : 0.042 0.277 4763 Planarity : 0.004 0.052 5140 Dihedral : 16.318 111.602 5002 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.22 % Favored : 96.66 % Rotamer: Outliers : 1.31 % Allowed : 15.62 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.14), residues: 3506 helix: 1.52 (0.15), residues: 1237 sheet: 0.30 (0.22), residues: 550 loop : -0.33 (0.15), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 87 TYR 0.022 0.001 TYR E 112 PHE 0.024 0.001 PHE A 219 TRP 0.016 0.001 TRP B 561 HIS 0.007 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (31093) covalent geometry : angle 0.53841 / 0.29 (42401) hydrogen bonds : bond 0.03633 / 2.45 ( 1312) hydrogen bonds : angle 4.18367 / 2.99 ( 3593) metal coordination : bond 0.00426 / 0.25 ( 32) metal coordination : angle 2.84720 / 1.95 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13887.92 seconds wall clock time: 236 minutes 22.88 seconds (14182.88 seconds total)