Starting phenix.real_space_refine on Sun Aug 9 09:58:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sbs_54737/08_2026/9sbs_54737.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sbs_54737/08_2026/9sbs_54737.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sbs_54737/08_2026/9sbs_54737.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sbs_54737/08_2026/9sbs_54737.map" model { file = "/net/cci-nas-00/data/ceres_data/9sbs_54737/08_2026/9sbs_54737.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sbs_54737/08_2026/9sbs_54737.cif" } resolution = 3.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.021 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 96 5.49 5 Mg 2 5.21 5 S 182 5.16 5 C 20497 2.51 5 N 5747 2.21 5 O 6433 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s 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: 32965 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 10904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1384, 10904 Classifications: {'peptide': 1384} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1321} 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: "D" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1327 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 164} Chain breaks: 2 Chain: "E" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1744 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1340 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1077 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Chain: "I" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 909 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 904 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "N" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 825 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain breaks: 1 Chain: "R" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 197 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna3p': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 886 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 35 Unusual residues: {' MG': 2, ' ZN': 2, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 457 SG CYS A 67 107.025 69.833 94.976 1.00225.74 S ATOM 479 SG CYS A 70 106.281 66.417 93.450 1.00225.72 S ATOM 532 SG CYS A 77 103.897 69.266 92.896 1.00221.81 S ATOM 762 SG CYS A 107 81.555 75.362 135.405 1.00264.44 S ATOM 786 SG CYS A 110 82.950 71.943 136.071 1.00258.41 S ATOM 1091 SG CYS A 148 79.748 73.064 137.836 1.00276.08 S ATOM 1105 SG CYS A 167 83.101 74.684 138.745 1.00274.30 S ATOM 19565 SG CYS B1163 98.653 57.188 104.975 1.00222.17 S ATOM 19583 SG CYS B1166 97.140 60.579 105.154 1.00229.66 S ATOM 19708 SG CYS B1182 100.954 60.136 104.623 1.00226.99 S ATOM 19727 SG CYS B1185 99.265 59.504 108.019 1.00235.98 S ATOM 20715 SG CYS C 86 93.245 74.698 26.451 1.00276.81 S ATOM 20732 SG CYS C 88 95.374 76.879 28.486 1.00293.47 S ATOM 20765 SG CYS C 92 94.373 78.122 25.112 1.00254.17 S ATOM 20788 SG CYS C 95 91.820 77.936 28.034 1.00259.85 S ATOM 28373 SG CYS I 7 38.275 126.097 126.794 1.00442.50 S ATOM 28398 SG CYS I 10 42.072 125.570 126.543 1.00430.81 S ATOM 28564 SG CYS I 29 40.051 122.936 128.310 1.00446.63 S ATOM 28588 SG CYS I 32 40.375 126.382 129.844 1.00452.74 S ATOM 28915 SG CYS I 75 16.257 118.657 87.717 1.00512.03 S ATOM 28937 SG CYS I 78 16.169 122.156 86.450 1.00515.47 S ATOM 29153 SG CYS I 103 19.486 120.315 86.349 1.00492.77 S ATOM 29173 SG CYS I 106 18.020 121.353 89.704 1.00498.59 S ATOM 29275 SG CYS J 7 64.124 90.448 38.081 1.00173.88 S ATOM 29298 SG CYS J 10 64.005 88.277 34.988 1.00189.88 S ATOM 29578 SG CYS J 45 60.726 89.152 36.661 1.00190.42 S ATOM 29584 SG CYS J 46 62.820 91.465 34.489 1.00214.01 S ATOM 30707 SG CYS L 31 97.506 114.111 54.692 1.00349.05 S ATOM 30727 SG CYS L 34 98.922 115.466 51.423 1.00345.05 S ATOM 30831 SG CYS L 48 101.220 114.715 54.361 1.00355.21 S ATOM 30854 SG CYS L 51 98.938 117.680 54.534 1.00352.29 S Time building chain proxies: 5.26, per 1000 atoms: 0.16 Number of scatterers: 32965 At special positions: 0 Unit cell: (152.329, 155.593, 183.883, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 182 16.00 P 96 15.00 Mg 2 11.99 O 6433 8.00 N 5747 7.00 C 20497 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: 1.91 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1804 " pdb="ZN ZN A1804 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 67 " pdb=" ZN A1805 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 148 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " 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 C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " Number of angles added : 45 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7330 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 47 sheets defined 38.9% alpha, 19.0% beta 41 base pairs and 73 stacking pairs defined. Time for finding SS restraints: 3.38 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 105 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 212 Processing helix chain 'A' and resid 215 through 222 Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.537A pdb=" N ILE A 235 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 283 removed outlier: 3.689A 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: 3.763A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 524 through 535 removed outlier: 3.722A pdb=" N LEU A 528 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.698A pdb=" N VAL A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) 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 659 Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 672 through 699 Processing helix chain 'A' and resid 710 through 737 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 removed outlier: 3.589A pdb=" N ILE A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 798 Processing helix chain 'A' and resid 809 through 845 removed outlier: 3.658A pdb=" N GLU A 822 " --> pdb=" O MET A 818 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 824 " --> pdb=" O GLY A 820 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N THR A 831 " --> pdb=" O THR A 827 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 3.862A 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 removed outlier: 4.012A pdb=" N LEU A 920 " --> pdb=" O GLY A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 959 through 972 Processing helix chain 'A' and resid 982 through 995 removed outlier: 3.729A pdb=" N GLN A 994 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 3.694A 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 1056 removed outlier: 3.641A pdb=" N VAL A1045 " --> pdb=" O ALA A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1082 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1083 through 1085 No H-bonds generated for 'chain 'A' and resid 1083 through 1085' Processing helix chain 'A' and resid 1093 through 1106 removed outlier: 3.883A pdb=" N VAL A1098 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Proline residue: A1099 - end of helix Processing helix chain 'A' and resid 1130 through 1139 Processing helix chain 'A' and resid 1142 through 1145 Processing helix chain 'A' and resid 1166 through 1173 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 1270 Processing helix chain 'A' and resid 1312 through 1317 removed outlier: 3.511A pdb=" N MET A1317 " --> pdb=" O LEU A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1340 Processing helix chain 'A' and resid 1340 through 1357 Processing helix chain 'A' and resid 1364 through 1376 removed outlier: 3.991A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1401 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1431 Processing helix chain 'A' and resid 1447 through 1452 removed outlier: 3.630A pdb=" N LYS A1452 " --> pdb=" O GLU A1448 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 37 removed outlier: 4.185A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 65 removed outlier: 3.561A pdb=" N LEU B 48 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 179 through 183 removed outlier: 4.071A pdb=" N GLU B 183 " --> pdb=" O TYR B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 289 Processing helix chain 'B' and resid 293 through 302 removed outlier: 3.674A pdb=" N ILE B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 322 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 344 through 359 removed outlier: 3.506A pdb=" N ARG B 348 " --> pdb=" O LYS B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 390 Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 438 removed outlier: 3.605A pdb=" N LEU B 412 " --> pdb=" O LEU B 408 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU B 438 " --> pdb=" O ARG B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.775A pdb=" N THR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.620A pdb=" N ARG B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 565 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 701 removed outlier: 3.732A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 removed outlier: 3.539A pdb=" N LEU B 710 " --> pdb=" O PRO B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 Processing helix chain 'B' and resid 752 through 756 Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'B' and resid 763 through 775 removed outlier: 3.968A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 787 removed outlier: 3.607A pdb=" N TYR B 785 " --> pdb=" O LEU B 782 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ASN B 786 " --> pdb=" O THR B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 811 removed outlier: 3.636A 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 1015 through 1021 removed outlier: 4.547A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.700A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1061 removed outlier: 3.856A pdb=" N GLU B1061 " --> pdb=" O LYS B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1153 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 40 removed outlier: 3.546A pdb=" N ALA C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 removed outlier: 3.640A pdb=" N LEU C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 80 removed outlier: 3.611A pdb=" N ILE C 77 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLU C 78 " --> pdb=" O MET C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 206 through 210 Processing helix chain 'C' and resid 239 through 266 removed outlier: 3.604A pdb=" N ASP C 266 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 73 Processing helix chain 'D' and resid 118 through 132 Processing helix chain 'D' and resid 138 through 151 removed outlier: 3.643A pdb=" N LYS D 142 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 171 removed outlier: 3.519A pdb=" N VAL D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY D 171 " --> pdb=" O LEU D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 196 through 199 removed outlier: 3.679A pdb=" N ASN D 199 " --> pdb=" O PRO D 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 196 through 199' Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'E' and resid 4 through 27 removed outlier: 3.712A pdb=" N ASN E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 47 Processing helix chain 'E' and resid 54 through 59 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 91 through 104 removed outlier: 3.950A pdb=" N THR E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 124 Processing helix chain 'E' and resid 138 through 141 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.507A pdb=" N GLU G 32 " --> pdb=" O THR G 28 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'H' and resid 131 through 135 removed outlier: 4.510A pdb=" N ASN H 134 " --> pdb=" O ASN H 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 65 removed outlier: 3.851A pdb=" N GLY I 63 " --> pdb=" O GLN I 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.795A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 removed outlier: 3.523A pdb=" N PHE J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 53 removed outlier: 3.798A pdb=" N ASN K 44 " --> pdb=" O HIS K 40 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU K 49 " --> pdb=" O LEU K 45 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP K 53 " --> pdb=" O GLU K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 111 removed outlier: 3.731A 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 84 through 90 removed outlier: 11.308A pdb=" N LYS A 88 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N CYS A 238 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 177 removed outlier: 4.807A pdb=" N LEU A 181 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 250 through 252 removed outlier: 3.553A pdb=" N PHE A 252 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 344 Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.695A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS A 490 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N MET A 456 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N PHE A 468 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL A 352 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N LEU A 470 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N SER A 354 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.716A pdb=" N ARG A 434 " --> pdb=" O TYR A 376 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 512 through 513 Processing sheet with id=AA9, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AB1, first strand: chain 'A' and resid 588 through 590 removed outlier: 7.091A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AB3, first strand: chain 'A' and resid 849 through 850 removed outlier: 6.609A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 878 through 882 Processing sheet with id=AB5, first strand: chain 'A' and resid 1282 through 1292 Processing sheet with id=AB6, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.155A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU A1192 " --> pdb=" O ILE A1152 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE A1152 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ARG A1194 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER A1150 " --> pdb=" O ARG A1194 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLU A1196 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR I 44 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 48 through 50 removed outlier: 4.565A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 143 through 147 removed outlier: 5.265A pdb=" N VAL A1443 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY G 59 " --> pdb=" O ILE A1445 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 69 through 73 removed outlier: 5.103A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR B 136 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ALA B 153 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N GLU B 138 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LEU B 151 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 69 through 73 removed outlier: 5.103A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AC3, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC4, first strand: chain 'B' and resid 404 through 407 removed outlier: 5.986A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 224 through 227 removed outlier: 4.123A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC7, first strand: chain 'B' and resid 585 through 590 removed outlier: 5.072A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 640 through 641 removed outlier: 3.541A pdb=" N GLU B 650 " --> pdb=" O GLU B 641 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 703 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.821A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.821A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD4, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 7.113A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N LEU B1010 " --> pdb=" O ASN B 822 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE B 824 " --> pdb=" O LEU B1010 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ILE B1012 " --> pdb=" O ILE B 824 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA B 826 " --> pdb=" O ILE B1012 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 873 through 874 removed outlier: 3.666A pdb=" N THR B 873 " --> pdb=" O THR B 915 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.750A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD8, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD9, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.119A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN C 231 " --> pdb=" O GLU C 177 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.864A pdb=" N GLU C 152 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N THR C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N LYS C 154 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N VAL C 51 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR C 156 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N VAL C 49 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL C 158 " --> pdb=" O ASP C 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 111 through 114 removed outlier: 3.621A pdb=" N CYS C 145 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AE4, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.464A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.725A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 169 through 170 removed outlier: 6.300A pdb=" N ILE G 160 " --> pdb=" O GLU G 148 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N CYS G 150 " --> pdb=" O HIS G 158 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N HIS G 158 " --> pdb=" O CYS G 150 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS G 107 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE G 99 " --> pdb=" O VAL G 110 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR G 90 " --> pdb=" O GLN G 102 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL G 145 " --> pdb=" O VAL G 87 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.511A pdb=" N SER G 129 " --> pdb=" O ASN G 122 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.692A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 15 through 19 removed outlier: 3.502A pdb=" N GLU I 36 " --> pdb=" O PHE I 27 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 70 through 71 removed outlier: 3.529A pdb=" N SER I 71 " --> pdb=" O ASN I 83 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 19 through 23 1332 hydrogen bonds defined for protein. 3651 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 107 hydrogen bonds 214 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 73 stacking parallelities Total time for adding SS restraints: 7.56 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 5424 1.31 - 1.44: 8900 1.44 - 1.56: 18938 1.56 - 1.69: 187 1.69 - 1.81: 292 Bond restraints: 33741 Sorted by residual: bond pdb=" C4 ATP A1801 " pdb=" N9 ATP A1801 " ideal model delta sigma weight residual 1.374 1.188 0.186 1.00e-02 1.00e+04 3.45e+02 bond pdb=" C8 ATP A1801 " pdb=" N9 ATP A1801 " 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 A1801 " pdb=" N6 ATP A1801 " ideal model delta sigma weight residual 1.337 1.449 -0.112 1.10e-02 8.26e+03 1.04e+02 bond pdb=" C5 ATP A1801 " pdb=" C6 ATP A1801 " ideal model delta sigma weight residual 1.409 1.339 0.070 1.00e-02 1.00e+04 4.83e+01 bond pdb=" C5 ATP A1801 " pdb=" N7 ATP A1801 " ideal model delta sigma weight residual 1.387 1.455 -0.068 1.00e-02 1.00e+04 4.69e+01 ... (remaining 33736 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.65: 45807 3.65 - 7.30: 136 7.30 - 10.95: 5 10.95 - 14.60: 1 14.60 - 18.26: 1 Bond angle restraints: 45950 Sorted by residual: angle pdb=" PB ATP A1801 " pdb=" O3B ATP A1801 " pdb=" PG ATP A1801 " ideal model delta sigma weight residual 139.87 121.61 18.26 1.00e+00 1.00e+00 3.33e+02 angle pdb=" C4 ATP A1801 " pdb=" N9 ATP A1801 " pdb=" C8 ATP A1801 " ideal model delta sigma weight residual 105.72 119.25 -13.53 1.00e+00 1.00e+00 1.83e+02 angle pdb=" PA ATP A1801 " pdb=" O3A ATP A1801 " pdb=" PB ATP A1801 " ideal model delta sigma weight residual 136.83 126.08 10.75 1.00e+00 1.00e+00 1.16e+02 angle pdb=" N1 ATP A1801 " pdb=" C2 ATP A1801 " pdb=" N3 ATP A1801 " ideal model delta sigma weight residual 128.69 120.12 8.57 1.00e+00 1.00e+00 7.35e+01 angle pdb=" N3 ATP A1801 " pdb=" C4 ATP A1801 " pdb=" N9 ATP A1801 " ideal model delta sigma weight residual 127.04 133.38 -6.34 1.15e+00 7.59e-01 3.05e+01 ... (remaining 45945 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.54: 19502 27.54 - 55.09: 714 55.09 - 82.63: 171 82.63 - 110.18: 7 110.18 - 137.72: 3 Dihedral angle restraints: 20397 sinusoidal: 9081 harmonic: 11316 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 180.00 154.99 25.01 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA GLU A 398 " pdb=" C GLU A 398 " pdb=" N HIS A 399 " pdb=" CA HIS A 399 " ideal model delta harmonic sigma weight residual -180.00 -159.83 -20.17 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA HIS A1173 " pdb=" C HIS A1173 " pdb=" N PHE A1174 " pdb=" CA PHE A1174 " ideal model delta harmonic sigma weight residual 180.00 161.46 18.54 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 20394 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3563 0.036 - 0.073: 1087 0.073 - 0.109: 409 0.109 - 0.145: 104 0.145 - 0.182: 5 Chirality restraints: 5168 Sorted by residual: chirality pdb=" CB VAL A 474 " pdb=" CA VAL A 474 " pdb=" CG1 VAL A 474 " pdb=" CG2 VAL A 474 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.25e-01 chirality pdb=" C2' G R 9 " pdb=" C3' G R 9 " pdb=" O2' G R 9 " pdb=" C1' G R 9 " both_signs ideal model delta sigma weight residual False -2.62 -2.79 0.17 2.00e-01 2.50e+01 7.14e-01 chirality pdb=" CA ASN A 253 " pdb=" N ASN A 253 " pdb=" C ASN A 253 " pdb=" CB ASN A 253 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.86e-01 ... (remaining 5165 not shown) Planarity restraints: 5616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 710 " -0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C LEU A 710 " 0.059 2.00e-02 2.50e+03 pdb=" O LEU A 710 " -0.022 2.00e-02 2.50e+03 pdb=" N ARG A 711 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A1074 " -0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO A1075 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A1075 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1075 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 244 " -0.028 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO A 245 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 245 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 245 " -0.024 5.00e-02 4.00e+02 ... (remaining 5613 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.38: 122 2.38 - 3.01: 19275 3.01 - 3.64: 50636 3.64 - 4.27: 75514 4.27 - 4.90: 125083 Nonbonded interactions: 270630 Sorted by model distance: nonbonded pdb=" O2G ATP A1801 " pdb="MG MG A1802 " model vdw 1.756 2.170 nonbonded pdb=" OD2 ASP A 481 " pdb="MG MG A1802 " model vdw 1.801 2.170 nonbonded pdb=" O2A ATP A1801 " pdb="MG MG A1802 " model vdw 1.881 2.170 nonbonded pdb=" OD2 ASP A 483 " pdb="MG MG A1802 " model vdw 2.048 2.170 nonbonded pdb=" O2A ATP A1801 " pdb="MG MG A1803 " model vdw 2.071 2.170 ... (remaining 270625 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 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: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 31.210 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.186 33773 Z= 0.316 Angle : 0.624 18.256 45995 Z= 0.416 Chirality : 0.042 0.182 5168 Planarity : 0.003 0.042 5616 Dihedral : 14.467 137.719 13067 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.09 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 0.03 % Favored : 99.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.14), residues: 3842 helix: 1.84 (0.15), residues: 1312 sheet: -0.00 (0.22), residues: 580 loop : -0.28 (0.15), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 30 TYR 0.029 0.001 TYR B 797 PHE 0.016 0.001 PHE K 105 TRP 0.013 0.001 TRP A 552 HIS 0.009 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.32 (33741) covalent geometry : angle 0.61593 / 0.42 (45950) hydrogen bonds : bond 0.18098 / 11.92 ( 1411) hydrogen bonds : angle 6.90479 / 5.00 ( 3865) metal coordination : bond 0.00641 / 0.44 ( 32) metal coordination : angle 3.26680 / 1.98 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 628 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8802 (mtt) cc_final: 0.8226 (mtt) REVERT: A 122 MET cc_start: 0.9464 (tpp) cc_final: 0.9092 (tpp) REVERT: A 456 MET cc_start: 0.9108 (mtm) cc_final: 0.8637 (mtp) REVERT: A 486 GLU cc_start: 0.8921 (tt0) cc_final: 0.8718 (mp0) REVERT: A 496 GLU cc_start: 0.8975 (tt0) cc_final: 0.8595 (tm-30) REVERT: A 605 MET cc_start: 0.9232 (tpp) cc_final: 0.8972 (tpp) REVERT: A 830 LYS cc_start: 0.9018 (mptt) cc_final: 0.8673 (mmtm) REVERT: A 838 GLN cc_start: 0.9218 (tp40) cc_final: 0.8774 (tp40) REVERT: A 873 MET cc_start: 0.9525 (mmp) cc_final: 0.8793 (mmp) REVERT: A 1005 GLU cc_start: 0.9332 (mm-30) cc_final: 0.8712 (tp30) REVERT: A 1063 MET cc_start: 0.9433 (mmm) cc_final: 0.9060 (mmt) REVERT: A 1257 ASP cc_start: 0.7355 (m-30) cc_final: 0.6858 (p0) REVERT: A 1267 MET cc_start: 0.8835 (mtm) cc_final: 0.8473 (ptm) REVERT: A 1276 VAL cc_start: 0.9090 (t) cc_final: 0.8889 (t) REVERT: A 1315 GLU cc_start: 0.9153 (tt0) cc_final: 0.8794 (tm-30) REVERT: A 1404 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8486 (mt-10) REVERT: B 101 MET cc_start: 0.8864 (mtt) cc_final: 0.8334 (mmm) REVERT: B 137 TYR cc_start: 0.8010 (m-80) cc_final: 0.7563 (m-80) REVERT: B 173 MET cc_start: 0.9163 (ttm) cc_final: 0.8830 (ttm) REVERT: B 224 GLN cc_start: 0.8380 (mt0) cc_final: 0.7389 (mt0) REVERT: B 239 GLU cc_start: 0.8671 (pt0) cc_final: 0.8158 (pm20) REVERT: B 313 MET cc_start: 0.9356 (tpp) cc_final: 0.9009 (tpt) REVERT: B 388 CYS cc_start: 0.9212 (t) cc_final: 0.8979 (t) REVERT: B 444 MET cc_start: 0.9022 (mmp) cc_final: 0.8331 (pmm) REVERT: B 470 LYS cc_start: 0.8823 (mtmm) cc_final: 0.8131 (mmtt) REVERT: B 513 GLN cc_start: 0.9156 (mm-40) cc_final: 0.8433 (mp10) REVERT: B 563 MET cc_start: 0.9203 (ttp) cc_final: 0.8194 (tmm) REVERT: B 615 MET cc_start: 0.8815 (mtm) cc_final: 0.8439 (mtm) REVERT: B 620 ARG cc_start: 0.9249 (ptp-170) cc_final: 0.8833 (ttp80) REVERT: B 629 ASP cc_start: 0.9322 (t0) cc_final: 0.8905 (p0) REVERT: B 699 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8615 (tp30) REVERT: B 775 LYS cc_start: 0.9587 (mtmt) cc_final: 0.9353 (mtmm) REVERT: B 809 MET cc_start: 0.8943 (mtt) cc_final: 0.8564 (mtp) REVERT: B 1072 MET cc_start: 0.9217 (mmm) cc_final: 0.8561 (mmm) REVERT: B 1090 THR cc_start: 0.8826 (m) cc_final: 0.8149 (p) REVERT: B 1095 LEU cc_start: 0.9714 (mt) cc_final: 0.9402 (mm) REVERT: B 1111 MET cc_start: 0.8759 (mmm) cc_final: 0.8419 (mmm) REVERT: B 1202 LEU cc_start: 0.8987 (tp) cc_final: 0.8461 (tp) REVERT: B 1206 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8328 (mt-10) REVERT: C 75 MET cc_start: 0.9163 (mmm) cc_final: 0.8707 (tpp) REVERT: C 125 MET cc_start: 0.9314 (mtp) cc_final: 0.9051 (mtt) REVERT: C 190 ASP cc_start: 0.8836 (t0) cc_final: 0.8614 (t0) REVERT: D 50 LEU cc_start: 0.8884 (mt) cc_final: 0.8127 (mp) REVERT: D 120 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7429 (mm-30) REVERT: D 134 THR cc_start: 0.4594 (t) cc_final: 0.3696 (p) REVERT: D 150 ASN cc_start: 0.7160 (m-40) cc_final: 0.6953 (m-40) REVERT: E 121 MET cc_start: 0.9544 (mtm) cc_final: 0.9153 (mpp) REVERT: E 179 GLN cc_start: 0.8800 (mt0) cc_final: 0.8514 (mm-40) REVERT: E 182 ASP cc_start: 0.8963 (t0) cc_final: 0.8717 (t0) REVERT: F 109 VAL cc_start: 0.8427 (t) cc_final: 0.7909 (m) REVERT: F 110 ASP cc_start: 0.8699 (m-30) cc_final: 0.8220 (t0) REVERT: F 114 GLU cc_start: 0.9049 (mt-10) cc_final: 0.7947 (mp0) REVERT: F 115 THR cc_start: 0.9322 (p) cc_final: 0.8875 (t) REVERT: F 116 ASP cc_start: 0.8937 (t0) cc_final: 0.8490 (t0) REVERT: F 124 GLU cc_start: 0.9515 (mt-10) cc_final: 0.9019 (tp30) REVERT: F 129 LYS cc_start: 0.9088 (mmtm) cc_final: 0.8571 (mmtm) REVERT: F 130 ILE cc_start: 0.9419 (mt) cc_final: 0.9215 (mt) REVERT: F 144 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8284 (tt0) REVERT: G 3 PHE cc_start: 0.7699 (m-80) cc_final: 0.7197 (m-80) REVERT: G 46 LEU cc_start: 0.9433 (mt) cc_final: 0.9159 (mm) REVERT: G 50 ASP cc_start: 0.8032 (t0) cc_final: 0.7420 (t70) REVERT: G 55 ASP cc_start: 0.8635 (t0) cc_final: 0.8288 (t0) REVERT: G 57 GLN cc_start: 0.7268 (mt0) cc_final: 0.6854 (mt0) REVERT: G 69 GLU cc_start: 0.7758 (tt0) cc_final: 0.7451 (tm-30) REVERT: G 71 ASN cc_start: 0.7585 (t0) cc_final: 0.7152 (t0) REVERT: H 14 GLU cc_start: 0.8773 (tt0) cc_final: 0.8072 (tm-30) REVERT: H 16 ASP cc_start: 0.9366 (t0) cc_final: 0.8942 (t0) REVERT: H 52 GLN cc_start: 0.9289 (mt0) cc_final: 0.9030 (mp10) REVERT: H 112 ILE cc_start: 0.7553 (tt) cc_final: 0.6619 (tt) REVERT: H 116 TYR cc_start: 0.9376 (m-80) cc_final: 0.9048 (m-80) REVERT: H 126 GLU cc_start: 0.8860 (tt0) cc_final: 0.8541 (tp30) REVERT: H 136 LYS cc_start: 0.9069 (mmtp) cc_final: 0.8689 (mmtt) REVERT: J 29 GLU cc_start: 0.9350 (mt-10) cc_final: 0.9017 (tp30) REVERT: K 6 ARG cc_start: 0.7821 (mmm-85) cc_final: 0.7490 (mmm160) REVERT: K 11 LEU cc_start: 0.7837 (mt) cc_final: 0.7451 (mt) REVERT: K 22 ASP cc_start: 0.8930 (m-30) cc_final: 0.8675 (p0) REVERT: K 38 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8852 (mm-30) REVERT: K 39 ASP cc_start: 0.9302 (p0) cc_final: 0.8743 (p0) REVERT: K 41 THR cc_start: 0.9329 (m) cc_final: 0.8758 (p) REVERT: K 54 ARG cc_start: 0.9404 (mtm180) cc_final: 0.9128 (mmm160) REVERT: K 108 GLU cc_start: 0.9277 (mm-30) cc_final: 0.8625 (tp30) REVERT: L 27 LEU cc_start: 0.6532 (mm) cc_final: 0.6189 (mm) REVERT: L 47 ARG cc_start: 0.7866 (ptm160) cc_final: 0.7549 (mtp85) REVERT: L 66 GLN cc_start: 0.8954 (tt0) cc_final: 0.8349 (tm-30) outliers start: 0 outliers final: 0 residues processed: 628 average time/residue: 0.2067 time to fit residues: 204.4770 Evaluate side-chains 392 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 392 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.0980 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 20.0000 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 742 ASN ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1218 GLN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 HIS ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 862 GLN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 2 ASN D 216 ASN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.079980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.054560 restraints weight = 109377.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.056197 restraints weight = 56140.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.057289 restraints weight = 37297.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.057970 restraints weight = 28916.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.058379 restraints weight = 24813.434| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 33773 Z= 0.155 Angle : 0.640 17.947 45995 Z= 0.334 Chirality : 0.046 0.251 5168 Planarity : 0.004 0.044 5616 Dihedral : 16.487 137.409 5290 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.72 % Favored : 96.15 % Rotamer: Outliers : 1.05 % Allowed : 7.14 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.14), residues: 3842 helix: 1.59 (0.15), residues: 1337 sheet: -0.08 (0.21), residues: 608 loop : -0.42 (0.15), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 52 TYR 0.023 0.001 TYR H 95 PHE 0.022 0.002 PHE A 219 TRP 0.022 0.001 TRP B 308 HIS 0.008 0.001 HIS B 440 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (33741) covalent geometry : angle 0.62727 / 0.33 (45950) hydrogen bonds : bond 0.04634 / 3.04 ( 1411) hydrogen bonds : angle 5.26803 / 3.80 ( 3865) metal coordination : bond 0.00668 / 0.47 ( 32) metal coordination : angle 4.12888 / 2.31 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 431 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8273 (mtt) cc_final: 0.7973 (mtt) REVERT: A 122 MET cc_start: 0.9072 (tpp) cc_final: 0.8871 (tpt) REVERT: A 341 MET cc_start: 0.8891 (mmm) cc_final: 0.7981 (mmm) REVERT: A 445 ASN cc_start: 0.8302 (t0) cc_final: 0.7321 (t0) REVERT: A 453 MET cc_start: 0.9050 (mpp) cc_final: 0.8503 (mpp) REVERT: A 456 MET cc_start: 0.9035 (mtm) cc_final: 0.8617 (mtp) REVERT: A 818 MET cc_start: 0.9341 (mtp) cc_final: 0.9102 (mtp) REVERT: A 830 LYS cc_start: 0.9406 (mptt) cc_final: 0.9164 (mmtm) REVERT: A 838 GLN cc_start: 0.9396 (tp40) cc_final: 0.9000 (tp40) REVERT: A 873 MET cc_start: 0.9165 (mmp) cc_final: 0.8807 (mmp) REVERT: A 923 LEU cc_start: 0.9183 (pt) cc_final: 0.8967 (mm) REVERT: A 1111 MET cc_start: 0.8099 (ttm) cc_final: 0.7861 (ttm) REVERT: A 1257 ASP cc_start: 0.7479 (m-30) cc_final: 0.6929 (p0) REVERT: A 1285 MET cc_start: 0.7951 (mmm) cc_final: 0.7739 (tmm) REVERT: A 1315 GLU cc_start: 0.8711 (tt0) cc_final: 0.8358 (tp30) REVERT: B 137 TYR cc_start: 0.8056 (m-80) cc_final: 0.7509 (m-80) REVERT: B 173 MET cc_start: 0.9116 (ttm) cc_final: 0.8767 (ttm) REVERT: B 308 TRP cc_start: 0.8872 (p-90) cc_final: 0.8425 (p-90) REVERT: B 313 MET cc_start: 0.9175 (tpp) cc_final: 0.8763 (tpt) REVERT: B 388 CYS cc_start: 0.8678 (t) cc_final: 0.8456 (t) REVERT: B 444 MET cc_start: 0.8656 (mmp) cc_final: 0.8335 (pmm) REVERT: B 470 LYS cc_start: 0.8690 (mtmm) cc_final: 0.8107 (mmtt) REVERT: B 513 GLN cc_start: 0.8917 (mm-40) cc_final: 0.8428 (mp10) REVERT: B 563 MET cc_start: 0.8977 (ttp) cc_final: 0.8423 (tmm) REVERT: B 597 MET cc_start: 0.9134 (tpt) cc_final: 0.8820 (tpt) REVERT: B 615 MET cc_start: 0.8067 (mtm) cc_final: 0.7680 (mtm) REVERT: B 747 MET cc_start: 0.9249 (mmp) cc_final: 0.8950 (mmm) REVERT: B 775 LYS cc_start: 0.9651 (mtmt) cc_final: 0.9392 (mtmm) REVERT: B 809 MET cc_start: 0.9029 (mtt) cc_final: 0.8787 (mtp) REVERT: B 862 GLN cc_start: 0.8626 (mt0) cc_final: 0.8390 (pm20) REVERT: B 898 LEU cc_start: 0.8545 (mp) cc_final: 0.8274 (mp) REVERT: B 986 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8369 (mp10) REVERT: B 1072 MET cc_start: 0.8662 (mmm) cc_final: 0.8386 (mmm) REVERT: B 1090 THR cc_start: 0.9104 (m) cc_final: 0.8596 (p) REVERT: B 1111 MET cc_start: 0.8829 (mmm) cc_final: 0.8401 (mmm) REVERT: B 1152 MET cc_start: 0.8460 (tpp) cc_final: 0.7893 (tpp) REVERT: B 1202 LEU cc_start: 0.9356 (tp) cc_final: 0.8629 (tp) REVERT: B 1206 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8116 (mt-10) REVERT: C 190 ASP cc_start: 0.8365 (t0) cc_final: 0.8144 (t0) REVERT: D 120 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7481 (mm-30) REVERT: D 147 TYR cc_start: 0.6588 (t80) cc_final: 0.6092 (t80) REVERT: D 151 PHE cc_start: 0.4100 (m-80) cc_final: 0.3596 (m-80) REVERT: D 214 LEU cc_start: 0.7922 (pp) cc_final: 0.7722 (tt) REVERT: E 112 TYR cc_start: 0.9108 (p90) cc_final: 0.7940 (p90) REVERT: E 198 ILE cc_start: 0.9585 (mp) cc_final: 0.9297 (tp) REVERT: F 115 THR cc_start: 0.9241 (p) cc_final: 0.8987 (t) REVERT: F 116 ASP cc_start: 0.8943 (t0) cc_final: 0.8660 (t0) REVERT: F 129 LYS cc_start: 0.9093 (mmtm) cc_final: 0.8843 (mmtt) REVERT: G 3 PHE cc_start: 0.7483 (m-80) cc_final: 0.7077 (m-80) REVERT: G 24 GLN cc_start: 0.8375 (tm-30) cc_final: 0.8013 (tm-30) REVERT: G 49 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8591 (pp) REVERT: G 50 ASP cc_start: 0.8291 (t0) cc_final: 0.7824 (t0) REVERT: G 53 ASN cc_start: 0.9195 (t0) cc_final: 0.8861 (t0) REVERT: G 55 ASP cc_start: 0.8976 (t0) cc_final: 0.8564 (t0) REVERT: G 57 GLN cc_start: 0.7641 (mt0) cc_final: 0.7177 (mt0) REVERT: G 65 ASP cc_start: 0.8785 (p0) cc_final: 0.8543 (p0) REVERT: G 71 ASN cc_start: 0.8761 (t0) cc_final: 0.8111 (t0) REVERT: G 75 ARG cc_start: 0.8829 (ttm170) cc_final: 0.8365 (mtp180) REVERT: H 14 GLU cc_start: 0.8734 (tt0) cc_final: 0.8522 (tm-30) REVERT: H 112 ILE cc_start: 0.8230 (tt) cc_final: 0.7213 (tt) REVERT: H 116 TYR cc_start: 0.9166 (m-80) cc_final: 0.8931 (m-10) REVERT: H 136 LYS cc_start: 0.9055 (mmtp) cc_final: 0.8837 (mmtt) REVERT: I 1 MET cc_start: 0.7092 (tpt) cc_final: 0.5726 (mtm) REVERT: K 5 ASP cc_start: 0.8379 (m-30) cc_final: 0.8131 (t0) REVERT: K 75 ILE cc_start: 0.9538 (mt) cc_final: 0.9188 (pt) REVERT: K 89 ASN cc_start: 0.8967 (m-40) cc_final: 0.8715 (t0) REVERT: K 108 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8492 (tp30) REVERT: L 47 ARG cc_start: 0.8328 (ptm160) cc_final: 0.8045 (mtp85) REVERT: L 67 PHE cc_start: 0.8052 (m-10) cc_final: 0.7748 (m-10) outliers start: 36 outliers final: 18 residues processed: 453 average time/residue: 0.1948 time to fit residues: 143.4923 Evaluate side-chains 382 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 362 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 932 GLU Chi-restraints excluded: chain A residue 1433 MET Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 986 GLN Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 167 TYR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 46 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 116 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 310 optimal weight: 0.0770 chunk 250 optimal weight: 3.9990 chunk 223 optimal weight: 0.0770 chunk 374 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 258 optimal weight: 6.9990 chunk 226 optimal weight: 0.8980 overall best weight: 1.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 HIS ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN I 87 GLN K 76 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.079946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.054401 restraints weight = 108994.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.056034 restraints weight = 56993.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.057108 restraints weight = 38147.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.057741 restraints weight = 29763.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.058195 restraints weight = 25701.899| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33773 Z= 0.152 Angle : 0.592 16.149 45995 Z= 0.309 Chirality : 0.044 0.212 5168 Planarity : 0.004 0.045 5616 Dihedral : 16.388 137.064 5290 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.54 % Favored : 96.30 % Rotamer: Outliers : 1.52 % Allowed : 8.95 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.14), residues: 3842 helix: 1.54 (0.14), residues: 1351 sheet: -0.17 (0.21), residues: 628 loop : -0.44 (0.15), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 47 TYR 0.015 0.001 TYR B 797 PHE 0.025 0.001 PHE K 7 TRP 0.011 0.001 TRP B 308 HIS 0.006 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (33741) covalent geometry : angle 0.58083 / 0.31 (45950) hydrogen bonds : bond 0.04001 / 2.59 ( 1411) hydrogen bonds : angle 4.92109 / 3.55 ( 3865) metal coordination : bond 0.00668 / 0.46 ( 32) metal coordination : angle 3.75943 / 2.11 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 389 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8214 (mtt) cc_final: 0.7949 (mtt) REVERT: A 445 ASN cc_start: 0.8283 (t0) cc_final: 0.7399 (t0) REVERT: A 453 MET cc_start: 0.9038 (mpp) cc_final: 0.8473 (mpp) REVERT: A 487 MET cc_start: 0.8947 (mtp) cc_final: 0.8544 (mtp) REVERT: A 526 ASP cc_start: 0.8372 (m-30) cc_final: 0.7715 (m-30) REVERT: A 826 ASP cc_start: 0.9176 (m-30) cc_final: 0.8901 (m-30) REVERT: A 830 LYS cc_start: 0.9432 (mptt) cc_final: 0.9038 (mmtm) REVERT: A 873 MET cc_start: 0.9146 (mmp) cc_final: 0.8762 (mmp) REVERT: A 919 ILE cc_start: 0.9083 (tp) cc_final: 0.8867 (tp) REVERT: A 923 LEU cc_start: 0.9162 (pt) cc_final: 0.8948 (mm) REVERT: A 1257 ASP cc_start: 0.7465 (m-30) cc_final: 0.6922 (p0) REVERT: A 1315 GLU cc_start: 0.8736 (tt0) cc_final: 0.8403 (tp30) REVERT: A 1368 MET cc_start: 0.8918 (mtp) cc_final: 0.8545 (mtm) REVERT: B 101 MET cc_start: 0.8630 (mmm) cc_final: 0.8229 (mmm) REVERT: B 137 TYR cc_start: 0.8072 (m-80) cc_final: 0.6869 (m-80) REVERT: B 173 MET cc_start: 0.9165 (ttm) cc_final: 0.8819 (ttm) REVERT: B 246 LYS cc_start: 0.9035 (mmtm) cc_final: 0.8575 (mmtm) REVERT: B 308 TRP cc_start: 0.8710 (p-90) cc_final: 0.8499 (p-90) REVERT: B 313 MET cc_start: 0.9186 (tpp) cc_final: 0.8979 (tpt) REVERT: B 388 CYS cc_start: 0.8799 (t) cc_final: 0.8587 (t) REVERT: B 444 MET cc_start: 0.8647 (mmp) cc_final: 0.8311 (pmm) REVERT: B 470 LYS cc_start: 0.8677 (mtmm) cc_final: 0.8125 (mmtt) REVERT: B 513 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8426 (mp10) REVERT: B 542 MET cc_start: 0.8346 (mtp) cc_final: 0.8078 (mmm) REVERT: B 563 MET cc_start: 0.9012 (ttp) cc_final: 0.8405 (tmm) REVERT: B 597 MET cc_start: 0.9128 (tpt) cc_final: 0.8840 (tpt) REVERT: B 615 MET cc_start: 0.8085 (mtm) cc_final: 0.7873 (mpp) REVERT: B 775 LYS cc_start: 0.9626 (mtmt) cc_final: 0.9279 (mttp) REVERT: B 809 MET cc_start: 0.9016 (mtt) cc_final: 0.8816 (mtp) REVERT: B 898 LEU cc_start: 0.8536 (mp) cc_final: 0.8250 (mp) REVERT: B 1072 MET cc_start: 0.8603 (mmm) cc_final: 0.8311 (mmm) REVERT: B 1090 THR cc_start: 0.9101 (m) cc_final: 0.8603 (p) REVERT: B 1111 MET cc_start: 0.8812 (mmm) cc_final: 0.8379 (mmm) REVERT: B 1152 MET cc_start: 0.8481 (tpp) cc_final: 0.7911 (tpp) REVERT: B 1202 LEU cc_start: 0.9358 (tp) cc_final: 0.8626 (tp) REVERT: B 1206 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8106 (mt-10) REVERT: C 190 ASP cc_start: 0.8153 (t0) cc_final: 0.7888 (p0) REVERT: D 120 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7446 (mm-30) REVERT: D 147 TYR cc_start: 0.6693 (t80) cc_final: 0.6159 (t80) REVERT: D 214 LEU cc_start: 0.7914 (pp) cc_final: 0.7706 (tt) REVERT: E 93 MET cc_start: 0.8199 (mmm) cc_final: 0.7634 (tmm) REVERT: E 112 TYR cc_start: 0.9092 (p90) cc_final: 0.8790 (p90) REVERT: E 121 MET cc_start: 0.9116 (mtm) cc_final: 0.8814 (mtt) REVERT: E 179 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8356 (mm-40) REVERT: F 116 ASP cc_start: 0.8888 (t0) cc_final: 0.8461 (t0) REVERT: F 123 LYS cc_start: 0.9727 (OUTLIER) cc_final: 0.9518 (ttmm) REVERT: G 3 PHE cc_start: 0.7188 (m-80) cc_final: 0.6808 (m-80) REVERT: G 21 ARG cc_start: 0.8173 (ptm160) cc_final: 0.7898 (ptm160) REVERT: G 42 PHE cc_start: 0.7908 (m-80) cc_final: 0.7528 (m-10) REVERT: G 50 ASP cc_start: 0.8289 (t0) cc_final: 0.7729 (t0) REVERT: G 53 ASN cc_start: 0.9255 (t0) cc_final: 0.8887 (t0) REVERT: G 55 ASP cc_start: 0.8917 (t0) cc_final: 0.8533 (t0) REVERT: G 57 GLN cc_start: 0.7820 (mt0) cc_final: 0.7461 (mt0) REVERT: G 71 ASN cc_start: 0.8754 (t0) cc_final: 0.8027 (t0) REVERT: G 100 GLU cc_start: 0.6560 (mm-30) cc_final: 0.6192 (mm-30) REVERT: H 52 GLN cc_start: 0.8170 (mp10) cc_final: 0.7862 (mp10) REVERT: H 123 MET cc_start: 0.9107 (tmm) cc_final: 0.8321 (tmm) REVERT: H 136 LYS cc_start: 0.9044 (mmtp) cc_final: 0.8822 (mmtt) REVERT: I 1 MET cc_start: 0.7055 (tpt) cc_final: 0.5853 (mtm) REVERT: I 97 MET cc_start: 0.8010 (mtp) cc_final: 0.7654 (tpp) REVERT: K 6 ARG cc_start: 0.8119 (mmm-85) cc_final: 0.7547 (mmm160) REVERT: K 11 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8684 (mp) REVERT: K 38 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8378 (mm-30) REVERT: K 39 ASP cc_start: 0.9148 (p0) cc_final: 0.8898 (p0) REVERT: K 41 THR cc_start: 0.9384 (OUTLIER) cc_final: 0.9090 (p) REVERT: K 75 ILE cc_start: 0.9535 (mt) cc_final: 0.9182 (pt) REVERT: K 89 ASN cc_start: 0.8945 (m-40) cc_final: 0.8685 (t0) REVERT: K 108 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8460 (tp30) REVERT: L 47 ARG cc_start: 0.8328 (ptm160) cc_final: 0.8098 (mtp85) outliers start: 52 outliers final: 28 residues processed: 422 average time/residue: 0.2151 time to fit residues: 146.3820 Evaluate side-chains 383 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 352 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 681 GLU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 932 GLU Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain A residue 1433 MET Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 620 ARG Chi-restraints excluded: chain B residue 1100 ASP Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 123 LYS Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 121 PHE Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 77 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 138 optimal weight: 2.9990 chunk 259 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 224 optimal weight: 30.0000 chunk 84 optimal weight: 10.0000 chunk 239 optimal weight: 0.9990 chunk 339 optimal weight: 40.0000 chunk 347 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 349 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.079880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.054345 restraints weight = 111494.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.056019 restraints weight = 57896.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.057099 restraints weight = 38499.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.057797 restraints weight = 30023.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.058210 restraints weight = 25806.654| |-----------------------------------------------------------------------------| r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 33773 Z= 0.214 Angle : 0.620 18.016 45995 Z= 0.319 Chirality : 0.044 0.221 5168 Planarity : 0.004 0.050 5616 Dihedral : 16.413 137.454 5290 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.93 % Favored : 95.91 % Rotamer: Outliers : 1.81 % Allowed : 10.08 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.14), residues: 3842 helix: 1.48 (0.15), residues: 1345 sheet: -0.20 (0.21), residues: 606 loop : -0.53 (0.15), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 320 TYR 0.018 0.001 TYR G 167 PHE 0.024 0.002 PHE A1220 TRP 0.008 0.001 TRP A 556 HIS 0.006 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.21 (33741) covalent geometry : angle 0.60806 / 0.32 (45950) hydrogen bonds : bond 0.03839 / 2.48 ( 1411) hydrogen bonds : angle 4.82221 / 3.48 ( 3865) metal coordination : bond 0.00869 / 0.59 ( 32) metal coordination : angle 3.94494 / 2.18 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 355 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8239 (mtt) cc_final: 0.7981 (mtt) REVERT: A 122 MET cc_start: 0.9065 (tpt) cc_final: 0.8747 (tpp) REVERT: A 445 ASN cc_start: 0.8446 (t0) cc_final: 0.7901 (t0) REVERT: A 453 MET cc_start: 0.9089 (mpp) cc_final: 0.8834 (mpp) REVERT: A 455 MET cc_start: 0.8550 (tpp) cc_final: 0.8060 (tpp) REVERT: A 487 MET cc_start: 0.8988 (mtp) cc_final: 0.8709 (mtp) REVERT: A 605 MET cc_start: 0.9117 (tpp) cc_final: 0.8410 (tpp) REVERT: A 830 LYS cc_start: 0.9429 (mptt) cc_final: 0.9212 (mmtm) REVERT: A 873 MET cc_start: 0.9167 (mmp) cc_final: 0.8590 (mmp) REVERT: A 919 ILE cc_start: 0.9150 (tp) cc_final: 0.8900 (tp) REVERT: A 923 LEU cc_start: 0.9171 (pt) cc_final: 0.8948 (mm) REVERT: A 1257 ASP cc_start: 0.7517 (m-30) cc_final: 0.6920 (p0) REVERT: A 1285 MET cc_start: 0.7999 (mmm) cc_final: 0.7797 (tmm) REVERT: A 1315 GLU cc_start: 0.8736 (tt0) cc_final: 0.8419 (tp30) REVERT: A 1368 MET cc_start: 0.8941 (mtp) cc_final: 0.8466 (mtp) REVERT: B 101 MET cc_start: 0.8655 (mmm) cc_final: 0.8220 (mmm) REVERT: B 137 TYR cc_start: 0.7677 (m-80) cc_final: 0.7038 (m-80) REVERT: B 173 MET cc_start: 0.9160 (ttm) cc_final: 0.8815 (ttm) REVERT: B 308 TRP cc_start: 0.8668 (p-90) cc_final: 0.8352 (p-90) REVERT: B 388 CYS cc_start: 0.8824 (t) cc_final: 0.8621 (t) REVERT: B 470 LYS cc_start: 0.8721 (mtmm) cc_final: 0.8194 (mmtt) REVERT: B 513 GLN cc_start: 0.8895 (mm-40) cc_final: 0.8436 (mp10) REVERT: B 597 MET cc_start: 0.9100 (tpt) cc_final: 0.8773 (tpt) REVERT: B 615 MET cc_start: 0.8099 (mtm) cc_final: 0.7798 (mtm) REVERT: B 747 MET cc_start: 0.9275 (mmp) cc_final: 0.8989 (mmm) REVERT: B 775 LYS cc_start: 0.9623 (mtmt) cc_final: 0.9371 (mttm) REVERT: B 809 MET cc_start: 0.9050 (mtt) cc_final: 0.8821 (mtp) REVERT: B 898 LEU cc_start: 0.8539 (mp) cc_final: 0.8274 (mp) REVERT: B 1090 THR cc_start: 0.9128 (m) cc_final: 0.8668 (p) REVERT: B 1111 MET cc_start: 0.8831 (mmm) cc_final: 0.8408 (mmm) REVERT: B 1152 MET cc_start: 0.8498 (tpp) cc_final: 0.7930 (tpp) REVERT: B 1202 LEU cc_start: 0.9377 (tp) cc_final: 0.8658 (tp) REVERT: B 1206 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8189 (mt-10) REVERT: D 120 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7444 (mm-30) REVERT: D 147 TYR cc_start: 0.6798 (t80) cc_final: 0.6431 (t80) REVERT: E 93 MET cc_start: 0.8268 (mmm) cc_final: 0.7664 (tmm) REVERT: E 112 TYR cc_start: 0.9057 (p90) cc_final: 0.7846 (p90) REVERT: E 121 MET cc_start: 0.9084 (mtm) cc_final: 0.8782 (mtt) REVERT: E 215 MET cc_start: 0.7206 (ptt) cc_final: 0.6955 (ptt) REVERT: F 116 ASP cc_start: 0.8856 (t0) cc_final: 0.8551 (t70) REVERT: G 3 PHE cc_start: 0.7269 (m-80) cc_final: 0.6942 (m-80) REVERT: G 42 PHE cc_start: 0.8006 (m-80) cc_final: 0.7535 (m-80) REVERT: G 49 LEU cc_start: 0.8975 (mp) cc_final: 0.8596 (pp) REVERT: G 50 ASP cc_start: 0.8222 (t0) cc_final: 0.7641 (t0) REVERT: G 53 ASN cc_start: 0.9307 (t0) cc_final: 0.8957 (t0) REVERT: G 57 GLN cc_start: 0.7730 (mt0) cc_final: 0.7401 (mt0) REVERT: G 71 ASN cc_start: 0.8813 (t0) cc_final: 0.8177 (t0) REVERT: G 100 GLU cc_start: 0.6575 (mm-30) cc_final: 0.6235 (mm-30) REVERT: H 52 GLN cc_start: 0.8342 (mp10) cc_final: 0.8001 (mp10) REVERT: H 116 TYR cc_start: 0.9006 (m-10) cc_final: 0.8804 (m-10) REVERT: H 136 LYS cc_start: 0.9054 (mmtp) cc_final: 0.8848 (mmtt) REVERT: I 1 MET cc_start: 0.7292 (tpt) cc_final: 0.6144 (mtm) REVERT: K 5 ASP cc_start: 0.8381 (t0) cc_final: 0.8063 (t0) REVERT: K 6 ARG cc_start: 0.8396 (mmm-85) cc_final: 0.7707 (mmm160) REVERT: K 39 ASP cc_start: 0.9148 (p0) cc_final: 0.8838 (p0) REVERT: K 41 THR cc_start: 0.9381 (OUTLIER) cc_final: 0.9025 (p) REVERT: K 75 ILE cc_start: 0.9532 (mt) cc_final: 0.9166 (pt) REVERT: K 89 ASN cc_start: 0.8918 (m-40) cc_final: 0.8646 (t0) REVERT: K 108 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8493 (tp30) REVERT: L 47 ARG cc_start: 0.8387 (ptm160) cc_final: 0.8086 (mtp85) outliers start: 62 outliers final: 37 residues processed: 396 average time/residue: 0.1932 time to fit residues: 126.0489 Evaluate side-chains 367 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 329 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 932 GLU Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1100 ASP Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 121 PHE Chi-restraints excluded: chain G residue 167 TYR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 53 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 34 optimal weight: 0.9990 chunk 83 optimal weight: 8.9990 chunk 3 optimal weight: 0.0870 chunk 119 optimal weight: 10.0000 chunk 349 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 190 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 257 optimal weight: 0.9980 chunk 265 optimal weight: 5.9990 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1218 GLN B 110 HIS ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 HIS ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.080980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.055455 restraints weight = 109956.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.057188 restraints weight = 56836.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.058305 restraints weight = 37438.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.058989 restraints weight = 29098.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.059396 restraints weight = 25034.830| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33773 Z= 0.128 Angle : 0.567 16.247 45995 Z= 0.294 Chirality : 0.043 0.212 5168 Planarity : 0.004 0.057 5616 Dihedral : 16.368 137.172 5290 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.54 % Favored : 96.33 % Rotamer: Outliers : 1.14 % Allowed : 11.45 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.14), residues: 3842 helix: 1.57 (0.15), residues: 1343 sheet: -0.23 (0.21), residues: 607 loop : -0.47 (0.15), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 135 TYR 0.024 0.001 TYR G 167 PHE 0.026 0.001 PHE A1220 TRP 0.009 0.001 TRP C 201 HIS 0.005 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (33741) covalent geometry : angle 0.55660 / 0.29 (45950) hydrogen bonds : bond 0.03480 / 2.24 ( 1411) hydrogen bonds : angle 4.63379 / 3.34 ( 3865) metal coordination : bond 0.00606 / 0.43 ( 32) metal coordination : angle 3.49706 / 1.95 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 357 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8239 (mtt) cc_final: 0.7968 (mtt) REVERT: A 453 MET cc_start: 0.9092 (mpp) cc_final: 0.8815 (mpp) REVERT: A 455 MET cc_start: 0.8587 (tpp) cc_final: 0.8334 (tpp) REVERT: A 487 MET cc_start: 0.8940 (mtp) cc_final: 0.8670 (mtp) REVERT: A 526 ASP cc_start: 0.8312 (m-30) cc_final: 0.7638 (m-30) REVERT: A 605 MET cc_start: 0.9141 (tpp) cc_final: 0.8479 (tpp) REVERT: A 826 ASP cc_start: 0.9171 (m-30) cc_final: 0.8912 (m-30) REVERT: A 830 LYS cc_start: 0.9429 (mptt) cc_final: 0.9109 (mmtm) REVERT: A 873 MET cc_start: 0.9107 (mmp) cc_final: 0.8758 (mmp) REVERT: A 919 ILE cc_start: 0.9129 (tp) cc_final: 0.8890 (tp) REVERT: A 1062 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8064 (mm-30) REVERT: A 1257 ASP cc_start: 0.7567 (m-30) cc_final: 0.6980 (p0) REVERT: A 1315 GLU cc_start: 0.8698 (tt0) cc_final: 0.8401 (tp30) REVERT: B 101 MET cc_start: 0.8637 (mmm) cc_final: 0.8178 (mmm) REVERT: B 137 TYR cc_start: 0.7622 (m-80) cc_final: 0.7001 (m-80) REVERT: B 173 MET cc_start: 0.9168 (ttm) cc_final: 0.8818 (ttm) REVERT: B 308 TRP cc_start: 0.8664 (p-90) cc_final: 0.8393 (p-90) REVERT: B 470 LYS cc_start: 0.8698 (mtmm) cc_final: 0.8144 (mmtt) REVERT: B 513 GLN cc_start: 0.8817 (mm-40) cc_final: 0.8375 (mp10) REVERT: B 597 MET cc_start: 0.9097 (tpt) cc_final: 0.8826 (tpt) REVERT: B 615 MET cc_start: 0.7973 (mtm) cc_final: 0.7647 (mtm) REVERT: B 775 LYS cc_start: 0.9587 (mtmt) cc_final: 0.9345 (mttm) REVERT: B 898 LEU cc_start: 0.8574 (mp) cc_final: 0.8320 (mp) REVERT: B 1072 MET cc_start: 0.8659 (mmm) cc_final: 0.8440 (mmm) REVERT: B 1090 THR cc_start: 0.9120 (m) cc_final: 0.8658 (p) REVERT: B 1111 MET cc_start: 0.8792 (mmm) cc_final: 0.8484 (mpp) REVERT: B 1202 LEU cc_start: 0.9362 (tp) cc_final: 0.8632 (tp) REVERT: B 1206 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8098 (mt-10) REVERT: D 120 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7344 (tp30) REVERT: D 147 TYR cc_start: 0.6716 (t80) cc_final: 0.6307 (t80) REVERT: D 214 LEU cc_start: 0.8165 (tt) cc_final: 0.7903 (pp) REVERT: E 93 MET cc_start: 0.8296 (mmm) cc_final: 0.7735 (tmm) REVERT: E 112 TYR cc_start: 0.9010 (p90) cc_final: 0.7751 (p90) REVERT: F 116 ASP cc_start: 0.8832 (t0) cc_final: 0.8560 (t70) REVERT: G 3 PHE cc_start: 0.7308 (m-80) cc_final: 0.6607 (m-80) REVERT: G 42 PHE cc_start: 0.7972 (m-80) cc_final: 0.7441 (m-80) REVERT: G 49 LEU cc_start: 0.8993 (mp) cc_final: 0.8630 (pp) REVERT: G 50 ASP cc_start: 0.8231 (t0) cc_final: 0.7590 (t0) REVERT: G 53 ASN cc_start: 0.9318 (t0) cc_final: 0.8970 (t0) REVERT: G 57 GLN cc_start: 0.7805 (mt0) cc_final: 0.7511 (mt0) REVERT: G 71 ASN cc_start: 0.8721 (t0) cc_final: 0.8182 (t0) REVERT: G 100 GLU cc_start: 0.6522 (mm-30) cc_final: 0.6152 (mm-30) REVERT: H 52 GLN cc_start: 0.8328 (mp10) cc_final: 0.7992 (mp10) REVERT: I 1 MET cc_start: 0.7097 (tpt) cc_final: 0.6008 (mtm) REVERT: I 19 ASP cc_start: 0.6176 (t0) cc_final: 0.5965 (t0) REVERT: I 97 MET cc_start: 0.7836 (mtp) cc_final: 0.7324 (tpp) REVERT: K 5 ASP cc_start: 0.8335 (t0) cc_final: 0.8097 (t0) REVERT: K 6 ARG cc_start: 0.8381 (mmm-85) cc_final: 0.7644 (mmm160) REVERT: K 38 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8412 (mm-30) REVERT: K 89 ASN cc_start: 0.8924 (m-40) cc_final: 0.8696 (t0) REVERT: K 108 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8482 (tp30) REVERT: L 47 ARG cc_start: 0.8401 (ptm160) cc_final: 0.8118 (mtp85) outliers start: 39 outliers final: 28 residues processed: 384 average time/residue: 0.1974 time to fit residues: 123.8956 Evaluate side-chains 364 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 336 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 932 GLU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 1099 VAL Chi-restraints excluded: chain B residue 1100 ASP Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 121 PHE Chi-restraints excluded: chain G residue 167 TYR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain L residue 53 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 359 optimal weight: 7.9990 chunk 272 optimal weight: 5.9990 chunk 213 optimal weight: 7.9990 chunk 298 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 212 optimal weight: 3.9990 chunk 295 optimal weight: 10.0000 chunk 128 optimal weight: 0.9980 chunk 345 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 173 optimal weight: 7.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 996 ASN A1033 GLN ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.079650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.054025 restraints weight = 111926.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.055736 restraints weight = 57411.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.056846 restraints weight = 37958.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.057547 restraints weight = 29487.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.057978 restraints weight = 25305.230| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 33773 Z= 0.236 Angle : 0.629 16.967 45995 Z= 0.322 Chirality : 0.044 0.208 5168 Planarity : 0.004 0.044 5616 Dihedral : 16.403 137.523 5290 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.90 % Favored : 95.97 % Rotamer: Outliers : 1.52 % Allowed : 11.92 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.14), residues: 3842 helix: 1.51 (0.15), residues: 1337 sheet: -0.32 (0.21), residues: 618 loop : -0.53 (0.15), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 177 TYR 0.026 0.001 TYR G 167 PHE 0.023 0.001 PHE A 219 TRP 0.009 0.001 TRP A 556 HIS 0.006 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.24 (33741) covalent geometry : angle 0.61902 / 0.32 (45950) hydrogen bonds : bond 0.03689 / 2.37 ( 1411) hydrogen bonds : angle 4.68216 / 3.37 ( 3865) metal coordination : bond 0.00896 / 0.60 ( 32) metal coordination : angle 3.70914 / 2.06 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 335 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8303 (mtt) cc_final: 0.7962 (mtt) REVERT: A 453 MET cc_start: 0.9203 (mpp) cc_final: 0.8845 (mpp) REVERT: A 526 ASP cc_start: 0.8465 (m-30) cc_final: 0.7813 (m-30) REVERT: A 605 MET cc_start: 0.9167 (tpp) cc_final: 0.8632 (tpp) REVERT: A 830 LYS cc_start: 0.9437 (mptt) cc_final: 0.9224 (mmtm) REVERT: A 873 MET cc_start: 0.9195 (mmp) cc_final: 0.8619 (mmp) REVERT: A 919 ILE cc_start: 0.9176 (tp) cc_final: 0.8942 (tp) REVERT: A 1062 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8114 (mm-30) REVERT: A 1257 ASP cc_start: 0.7619 (m-30) cc_final: 0.7002 (p0) REVERT: B 101 MET cc_start: 0.8648 (mmm) cc_final: 0.8209 (mmm) REVERT: B 137 TYR cc_start: 0.7684 (m-80) cc_final: 0.7206 (m-80) REVERT: B 173 MET cc_start: 0.9205 (ttm) cc_final: 0.8786 (ttm) REVERT: B 246 LYS cc_start: 0.9011 (mmtm) cc_final: 0.8384 (mmtm) REVERT: B 308 TRP cc_start: 0.8721 (p-90) cc_final: 0.8424 (p-90) REVERT: B 513 GLN cc_start: 0.8952 (mm-40) cc_final: 0.8401 (mp10) REVERT: B 542 MET cc_start: 0.8529 (mmm) cc_final: 0.8184 (mmm) REVERT: B 563 MET cc_start: 0.9067 (tmm) cc_final: 0.7912 (tmm) REVERT: B 597 MET cc_start: 0.9132 (tpt) cc_final: 0.8868 (tpt) REVERT: B 615 MET cc_start: 0.8081 (mtm) cc_final: 0.7713 (mtm) REVERT: B 662 MET cc_start: 0.9058 (mtm) cc_final: 0.8770 (mtm) REVERT: B 775 LYS cc_start: 0.9645 (mtmt) cc_final: 0.9382 (mttm) REVERT: B 898 LEU cc_start: 0.8537 (mp) cc_final: 0.8292 (mp) REVERT: B 1072 MET cc_start: 0.8670 (mmm) cc_final: 0.8382 (mmm) REVERT: B 1090 THR cc_start: 0.9167 (m) cc_final: 0.8692 (p) REVERT: B 1111 MET cc_start: 0.8856 (mmm) cc_final: 0.8466 (mmm) REVERT: B 1202 LEU cc_start: 0.9365 (tp) cc_final: 0.8563 (tp) REVERT: B 1206 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8151 (mt-10) REVERT: D 120 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7326 (tp30) REVERT: D 147 TYR cc_start: 0.6728 (t80) cc_final: 0.6322 (t80) REVERT: D 214 LEU cc_start: 0.8099 (tt) cc_final: 0.7837 (pp) REVERT: E 93 MET cc_start: 0.8470 (mmm) cc_final: 0.7838 (tmm) REVERT: F 116 ASP cc_start: 0.8882 (t0) cc_final: 0.8577 (t70) REVERT: G 3 PHE cc_start: 0.7462 (m-80) cc_final: 0.7110 (m-80) REVERT: G 42 PHE cc_start: 0.7982 (m-80) cc_final: 0.7753 (m-10) REVERT: G 49 LEU cc_start: 0.8941 (mp) cc_final: 0.8602 (pp) REVERT: G 50 ASP cc_start: 0.8226 (t0) cc_final: 0.7604 (t0) REVERT: G 53 ASN cc_start: 0.9308 (t0) cc_final: 0.9014 (t0) REVERT: G 57 GLN cc_start: 0.7788 (mt0) cc_final: 0.7501 (mt0) REVERT: G 71 ASN cc_start: 0.8664 (t0) cc_final: 0.8185 (t0) REVERT: G 100 GLU cc_start: 0.6557 (mm-30) cc_final: 0.6214 (mm-30) REVERT: G 166 ASP cc_start: 0.8796 (p0) cc_final: 0.8112 (p0) REVERT: I 1 MET cc_start: 0.7331 (tpt) cc_final: 0.6290 (mtm) REVERT: I 97 MET cc_start: 0.7675 (mtp) cc_final: 0.7016 (tpp) REVERT: K 11 LEU cc_start: 0.9404 (tt) cc_final: 0.8925 (mt) REVERT: K 38 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8452 (mm-30) REVERT: K 39 ASP cc_start: 0.9230 (p0) cc_final: 0.8947 (p0) REVERT: K 41 THR cc_start: 0.9416 (OUTLIER) cc_final: 0.9171 (p) REVERT: K 89 ASN cc_start: 0.8986 (m-40) cc_final: 0.8698 (t0) REVERT: K 108 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8485 (tp30) REVERT: L 47 ARG cc_start: 0.8454 (ptm160) cc_final: 0.8055 (mtp85) outliers start: 52 outliers final: 35 residues processed: 374 average time/residue: 0.1998 time to fit residues: 122.2615 Evaluate side-chains 359 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 323 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 932 GLU Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1100 ASP Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 121 PHE Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 53 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 337 optimal weight: 30.0000 chunk 234 optimal weight: 4.9990 chunk 383 optimal weight: 0.0370 chunk 92 optimal weight: 0.8980 chunk 287 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 chunk 293 optimal weight: 0.5980 chunk 247 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 347 optimal weight: 5.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 443 ASN B 734 HIS ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.081440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.055868 restraints weight = 110585.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.057599 restraints weight = 57005.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.058725 restraints weight = 37780.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.059435 restraints weight = 29346.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.059865 restraints weight = 25200.649| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 33773 Z= 0.110 Angle : 0.574 13.689 45995 Z= 0.297 Chirality : 0.043 0.233 5168 Planarity : 0.004 0.081 5616 Dihedral : 16.337 137.081 5290 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.41 % Favored : 96.46 % Rotamer: Outliers : 1.34 % Allowed : 12.50 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.14), residues: 3842 helix: 1.56 (0.15), residues: 1335 sheet: -0.33 (0.21), residues: 624 loop : -0.45 (0.15), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 192 TYR 0.022 0.001 TYR G 25 PHE 0.028 0.001 PHE A1220 TRP 0.011 0.001 TRP A1228 HIS 0.007 0.001 HIS B 648 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (33741) covalent geometry : angle 0.56577 / 0.30 (45950) hydrogen bonds : bond 0.03369 / 2.17 ( 1411) hydrogen bonds : angle 4.51263 / 3.25 ( 3865) metal coordination : bond 0.00512 / 0.36 ( 32) metal coordination : angle 3.07545 / 1.77 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 369 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8235 (mtt) cc_final: 0.7954 (mtt) REVERT: A 453 MET cc_start: 0.9086 (mpp) cc_final: 0.8822 (mpp) REVERT: A 526 ASP cc_start: 0.8198 (m-30) cc_final: 0.7561 (m-30) REVERT: A 605 MET cc_start: 0.9140 (tpp) cc_final: 0.8695 (tpp) REVERT: A 826 ASP cc_start: 0.9146 (m-30) cc_final: 0.8897 (m-30) REVERT: A 830 LYS cc_start: 0.9421 (mptt) cc_final: 0.9105 (mmtm) REVERT: A 873 MET cc_start: 0.9021 (mmp) cc_final: 0.8520 (mmp) REVERT: A 1070 GLN cc_start: 0.9361 (mt0) cc_final: 0.9036 (mt0) REVERT: A 1257 ASP cc_start: 0.7599 (m-30) cc_final: 0.6981 (p0) REVERT: B 101 MET cc_start: 0.8613 (mmm) cc_final: 0.8179 (mmm) REVERT: B 137 TYR cc_start: 0.7573 (m-80) cc_final: 0.7038 (m-80) REVERT: B 173 MET cc_start: 0.9161 (ttm) cc_final: 0.8811 (ttm) REVERT: B 239 GLU cc_start: 0.6876 (tp30) cc_final: 0.6657 (tp30) REVERT: B 246 LYS cc_start: 0.8989 (mmtm) cc_final: 0.8349 (mmtm) REVERT: B 308 TRP cc_start: 0.8583 (p-90) cc_final: 0.8375 (p-90) REVERT: B 513 GLN cc_start: 0.8779 (mm-40) cc_final: 0.8323 (mp10) REVERT: B 563 MET cc_start: 0.9094 (tmm) cc_final: 0.8410 (tmm) REVERT: B 615 MET cc_start: 0.7946 (mtm) cc_final: 0.7615 (mtm) REVERT: B 775 LYS cc_start: 0.9565 (mtmt) cc_final: 0.9342 (mttm) REVERT: B 948 ILE cc_start: 0.9539 (mp) cc_final: 0.9336 (mm) REVERT: B 1072 MET cc_start: 0.8583 (mmm) cc_final: 0.8267 (mmm) REVERT: B 1111 MET cc_start: 0.8776 (mmm) cc_final: 0.8409 (mmm) REVERT: B 1133 MET cc_start: 0.8371 (mtm) cc_final: 0.7483 (mtm) REVERT: B 1152 MET cc_start: 0.8342 (tpp) cc_final: 0.7837 (tpp) REVERT: B 1202 LEU cc_start: 0.9345 (tp) cc_final: 0.8606 (tp) REVERT: B 1206 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8054 (mt-10) REVERT: D 9 GLN cc_start: 0.1092 (mt0) cc_final: 0.0870 (mt0) REVERT: D 31 GLN cc_start: 0.7750 (mt0) cc_final: 0.7524 (tt0) REVERT: D 34 GLN cc_start: 0.8549 (mt0) cc_final: 0.8033 (mt0) REVERT: D 35 LEU cc_start: 0.8432 (pp) cc_final: 0.8213 (pp) REVERT: D 37 GLN cc_start: 0.6180 (mm-40) cc_final: 0.5303 (mp-120) REVERT: D 120 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7277 (tp30) REVERT: D 132 GLN cc_start: 0.9138 (mt0) cc_final: 0.8916 (tt0) REVERT: D 147 TYR cc_start: 0.6686 (t80) cc_final: 0.6476 (t80) REVERT: D 157 GLN cc_start: 0.8335 (mm110) cc_final: 0.8125 (mm110) REVERT: D 214 LEU cc_start: 0.8155 (tt) cc_final: 0.7894 (pp) REVERT: E 93 MET cc_start: 0.8304 (mmm) cc_final: 0.7729 (tmm) REVERT: E 112 TYR cc_start: 0.8807 (p90) cc_final: 0.7832 (p90) REVERT: F 116 ASP cc_start: 0.8791 (t0) cc_final: 0.8519 (t70) REVERT: G 3 PHE cc_start: 0.7356 (m-80) cc_final: 0.7030 (m-80) REVERT: G 42 PHE cc_start: 0.7987 (m-80) cc_final: 0.7739 (m-10) REVERT: G 49 LEU cc_start: 0.8975 (mp) cc_final: 0.8626 (pp) REVERT: G 50 ASP cc_start: 0.8228 (t0) cc_final: 0.7514 (t0) REVERT: G 53 ASN cc_start: 0.9298 (t0) cc_final: 0.8986 (t0) REVERT: G 57 GLN cc_start: 0.7782 (mt0) cc_final: 0.7393 (mt0) REVERT: G 71 ASN cc_start: 0.8675 (t0) cc_final: 0.7927 (t0) REVERT: G 100 GLU cc_start: 0.6539 (mm-30) cc_final: 0.6182 (mm-30) REVERT: H 14 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7751 (tm-30) REVERT: H 27 GLU cc_start: 0.7852 (mp0) cc_final: 0.7319 (pm20) REVERT: I 1 MET cc_start: 0.7212 (tpt) cc_final: 0.6207 (mtm) REVERT: I 97 MET cc_start: 0.7671 (mtp) cc_final: 0.7080 (tpp) REVERT: K 5 ASP cc_start: 0.8187 (t0) cc_final: 0.7815 (t0) REVERT: K 6 ARG cc_start: 0.8470 (mmm-85) cc_final: 0.7752 (mmm160) REVERT: K 11 LEU cc_start: 0.9460 (tt) cc_final: 0.8901 (mt) REVERT: K 39 ASP cc_start: 0.9184 (p0) cc_final: 0.8903 (p0) REVERT: K 41 THR cc_start: 0.9386 (OUTLIER) cc_final: 0.9159 (p) REVERT: K 89 ASN cc_start: 0.8892 (m-40) cc_final: 0.8687 (t0) REVERT: K 108 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8431 (tp30) REVERT: L 47 ARG cc_start: 0.8399 (ptm160) cc_final: 0.8036 (mtp85) outliers start: 46 outliers final: 30 residues processed: 403 average time/residue: 0.1851 time to fit residues: 122.9286 Evaluate side-chains 370 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 339 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 932 GLU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 771 SER Chi-restraints excluded: chain B residue 1099 VAL Chi-restraints excluded: chain B residue 1100 ASP Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 121 PHE Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 53 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 79 optimal weight: 8.9990 chunk 137 optimal weight: 7.9990 chunk 366 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 327 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 353 optimal weight: 8.9990 chunk 88 optimal weight: 9.9990 chunk 220 optimal weight: 9.9990 chunk 227 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.079214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.053564 restraints weight = 112449.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.055219 restraints weight = 59335.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.056304 restraints weight = 39917.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.056976 restraints weight = 31258.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.057373 restraints weight = 27028.574| |-----------------------------------------------------------------------------| r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 33773 Z= 0.269 Angle : 0.664 16.476 45995 Z= 0.338 Chirality : 0.044 0.224 5168 Planarity : 0.004 0.048 5616 Dihedral : 16.383 137.558 5290 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.22 % Favored : 95.65 % Rotamer: Outliers : 1.40 % Allowed : 13.32 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.14), residues: 3842 helix: 1.45 (0.15), residues: 1343 sheet: -0.44 (0.21), residues: 617 loop : -0.59 (0.15), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 180 TYR 0.020 0.001 TYR G 25 PHE 0.023 0.002 PHE A 219 TRP 0.012 0.001 TRP B 308 HIS 0.009 0.001 HIS B 440 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.27 (33741) covalent geometry : angle 0.65455 / 0.34 (45950) hydrogen bonds : bond 0.03737 / 2.39 ( 1411) hydrogen bonds : angle 4.67728 / 3.37 ( 3865) metal coordination : bond 0.01027 / 0.68 ( 32) metal coordination : angle 3.55202 / 1.98 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 327 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8250 (mtt) cc_final: 0.7944 (mtt) REVERT: A 453 MET cc_start: 0.9151 (mpp) cc_final: 0.8860 (mpp) REVERT: A 526 ASP cc_start: 0.8301 (m-30) cc_final: 0.7775 (m-30) REVERT: A 605 MET cc_start: 0.9103 (tpp) cc_final: 0.8564 (tpp) REVERT: A 826 ASP cc_start: 0.9173 (m-30) cc_final: 0.8914 (m-30) REVERT: A 830 LYS cc_start: 0.9429 (mptt) cc_final: 0.9110 (mmtm) REVERT: A 873 MET cc_start: 0.9076 (mmp) cc_final: 0.8446 (mmp) REVERT: A 1062 GLU cc_start: 0.8481 (mm-30) cc_final: 0.7947 (mm-30) REVERT: A 1202 MET cc_start: 0.7889 (ttt) cc_final: 0.7631 (ttt) REVERT: A 1257 ASP cc_start: 0.7557 (m-30) cc_final: 0.6900 (p0) REVERT: A 1368 MET cc_start: 0.9096 (mtp) cc_final: 0.8690 (ttp) REVERT: A 1444 MET cc_start: 0.8471 (ptp) cc_final: 0.8208 (ptp) REVERT: B 101 MET cc_start: 0.8671 (mmm) cc_final: 0.8245 (mmm) REVERT: B 137 TYR cc_start: 0.7687 (m-80) cc_final: 0.7234 (m-80) REVERT: B 173 MET cc_start: 0.9186 (ttm) cc_final: 0.8788 (ttm) REVERT: B 308 TRP cc_start: 0.8629 (p-90) cc_final: 0.8310 (p-90) REVERT: B 513 GLN cc_start: 0.8915 (mm-40) cc_final: 0.8398 (mp10) REVERT: B 563 MET cc_start: 0.8984 (tmm) cc_final: 0.8563 (tmm) REVERT: B 615 MET cc_start: 0.8013 (mtm) cc_final: 0.7651 (mtm) REVERT: B 662 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8652 (mtm) REVERT: B 775 LYS cc_start: 0.9627 (mtmt) cc_final: 0.9389 (mttm) REVERT: B 1072 MET cc_start: 0.8639 (mmm) cc_final: 0.8308 (mmm) REVERT: B 1111 MET cc_start: 0.8830 (mmm) cc_final: 0.8456 (mmm) REVERT: B 1152 MET cc_start: 0.8465 (tpp) cc_final: 0.8031 (tpp) REVERT: B 1202 LEU cc_start: 0.9389 (tp) cc_final: 0.8638 (tp) REVERT: B 1206 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8103 (mt-10) REVERT: D 120 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7333 (tp30) REVERT: D 147 TYR cc_start: 0.6871 (t80) cc_final: 0.6440 (t80) REVERT: D 214 LEU cc_start: 0.8051 (tt) cc_final: 0.7822 (pp) REVERT: E 93 MET cc_start: 0.8353 (mmm) cc_final: 0.8140 (tmm) REVERT: F 116 ASP cc_start: 0.8848 (t0) cc_final: 0.8550 (t70) REVERT: G 3 PHE cc_start: 0.7468 (m-80) cc_final: 0.7142 (m-80) REVERT: G 42 PHE cc_start: 0.8022 (m-80) cc_final: 0.7741 (m-10) REVERT: G 49 LEU cc_start: 0.8978 (mp) cc_final: 0.8641 (pp) REVERT: G 50 ASP cc_start: 0.8262 (t0) cc_final: 0.7571 (t0) REVERT: G 53 ASN cc_start: 0.9292 (t0) cc_final: 0.9007 (t0) REVERT: G 57 GLN cc_start: 0.7829 (mt0) cc_final: 0.7545 (mt0) REVERT: G 71 ASN cc_start: 0.8750 (t0) cc_final: 0.8323 (t0) REVERT: G 100 GLU cc_start: 0.6549 (mm-30) cc_final: 0.6195 (mm-30) REVERT: H 14 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7612 (tm-30) REVERT: H 27 GLU cc_start: 0.7834 (mp0) cc_final: 0.6902 (mp0) REVERT: I 1 MET cc_start: 0.7370 (tpt) cc_final: 0.6254 (mtm) REVERT: I 97 MET cc_start: 0.7671 (mtp) cc_final: 0.7132 (tpp) REVERT: J 49 MET cc_start: 0.9236 (tpp) cc_final: 0.8925 (mmm) REVERT: K 6 ARG cc_start: 0.8552 (mmm-85) cc_final: 0.7880 (mmm-85) REVERT: K 11 LEU cc_start: 0.9486 (tt) cc_final: 0.8949 (mt) REVERT: K 39 ASP cc_start: 0.9210 (p0) cc_final: 0.8869 (p0) REVERT: K 41 THR cc_start: 0.9393 (OUTLIER) cc_final: 0.9084 (p) REVERT: K 89 ASN cc_start: 0.8920 (m-40) cc_final: 0.8665 (t0) REVERT: K 108 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8424 (tp30) REVERT: L 47 ARG cc_start: 0.8429 (ptm160) cc_final: 0.8040 (mtp85) outliers start: 48 outliers final: 35 residues processed: 362 average time/residue: 0.1864 time to fit residues: 110.8497 Evaluate side-chains 354 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 317 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 932 GLU Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1309 ASP Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1409 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 662 MET Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1099 VAL Chi-restraints excluded: chain B residue 1100 ASP Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 121 PHE Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain L residue 53 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 129 optimal weight: 0.5980 chunk 369 optimal weight: 1.9990 chunk 253 optimal weight: 2.9990 chunk 325 optimal weight: 0.9990 chunk 389 optimal weight: 50.0000 chunk 286 optimal weight: 0.9990 chunk 209 optimal weight: 0.7980 chunk 211 optimal weight: 3.9990 chunk 320 optimal weight: 0.9980 chunk 135 optimal weight: 6.9990 chunk 140 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1218 GLN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1093 GLN ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.081093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.055559 restraints weight = 109783.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.057287 restraints weight = 57203.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.058401 restraints weight = 38082.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.059085 restraints weight = 29672.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.059511 restraints weight = 25552.493| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33773 Z= 0.114 Angle : 0.583 13.692 45995 Z= 0.301 Chirality : 0.043 0.242 5168 Planarity : 0.003 0.045 5616 Dihedral : 16.319 137.239 5290 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.70 % Favored : 96.17 % Rotamer: Outliers : 1.11 % Allowed : 13.61 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.14), residues: 3842 helix: 1.54 (0.15), residues: 1341 sheet: -0.39 (0.21), residues: 626 loop : -0.50 (0.15), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1215 TYR 0.027 0.001 TYR G 25 PHE 0.027 0.001 PHE A1220 TRP 0.009 0.001 TRP C 201 HIS 0.005 0.001 HIS J 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (33741) covalent geometry : angle 0.57568 / 0.30 (45950) hydrogen bonds : bond 0.03337 / 2.14 ( 1411) hydrogen bonds : angle 4.49834 / 3.23 ( 3865) metal coordination : bond 0.00533 / 0.37 ( 32) metal coordination : angle 3.03694 / 1.74 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 343 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8222 (mtt) cc_final: 0.7899 (mtt) REVERT: A 453 MET cc_start: 0.9090 (mpp) cc_final: 0.8804 (mpp) REVERT: A 526 ASP cc_start: 0.8133 (m-30) cc_final: 0.7577 (m-30) REVERT: A 605 MET cc_start: 0.9117 (tpp) cc_final: 0.8551 (tpp) REVERT: A 826 ASP cc_start: 0.9152 (m-30) cc_final: 0.8950 (m-30) REVERT: A 830 LYS cc_start: 0.9423 (mptt) cc_final: 0.9143 (mmtm) REVERT: A 873 MET cc_start: 0.8997 (mmp) cc_final: 0.8489 (mmp) REVERT: A 1111 MET cc_start: 0.8285 (ttm) cc_final: 0.7977 (ttm) REVERT: A 1257 ASP cc_start: 0.7545 (m-30) cc_final: 0.6919 (p0) REVERT: A 1368 MET cc_start: 0.9039 (mtp) cc_final: 0.8675 (ttp) REVERT: A 1444 MET cc_start: 0.8405 (ptp) cc_final: 0.8161 (ptp) REVERT: B 101 MET cc_start: 0.8628 (mmm) cc_final: 0.8195 (mmm) REVERT: B 137 TYR cc_start: 0.7539 (m-80) cc_final: 0.7049 (m-80) REVERT: B 173 MET cc_start: 0.9182 (ttm) cc_final: 0.8818 (ttm) REVERT: B 246 LYS cc_start: 0.9006 (mmtm) cc_final: 0.8334 (mmtm) REVERT: B 513 GLN cc_start: 0.8789 (mm-40) cc_final: 0.8327 (mp10) REVERT: B 563 MET cc_start: 0.9062 (tmm) cc_final: 0.8378 (tmm) REVERT: B 597 MET cc_start: 0.9024 (tpt) cc_final: 0.8644 (tpt) REVERT: B 615 MET cc_start: 0.7932 (mtm) cc_final: 0.7555 (mtm) REVERT: B 775 LYS cc_start: 0.9567 (mtmt) cc_final: 0.9342 (mttm) REVERT: B 1072 MET cc_start: 0.8553 (mmm) cc_final: 0.8245 (mmm) REVERT: B 1082 MET cc_start: 0.9041 (tpp) cc_final: 0.8681 (mmm) REVERT: B 1111 MET cc_start: 0.8784 (mmm) cc_final: 0.8406 (mmm) REVERT: B 1152 MET cc_start: 0.8294 (tpp) cc_final: 0.7902 (tpp) REVERT: B 1202 LEU cc_start: 0.9359 (tp) cc_final: 0.8596 (tp) REVERT: B 1206 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8073 (mt-10) REVERT: C 177 GLU cc_start: 0.8319 (mp0) cc_final: 0.8048 (mp0) REVERT: D 120 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7258 (tp30) REVERT: D 147 TYR cc_start: 0.6794 (t80) cc_final: 0.6394 (t80) REVERT: D 214 LEU cc_start: 0.8088 (tt) cc_final: 0.7805 (pp) REVERT: E 112 TYR cc_start: 0.8755 (p90) cc_final: 0.7756 (p90) REVERT: E 179 GLN cc_start: 0.8741 (mm-40) cc_final: 0.8509 (mm-40) REVERT: F 116 ASP cc_start: 0.8791 (t0) cc_final: 0.8501 (t70) REVERT: F 143 PHE cc_start: 0.9288 (p90) cc_final: 0.9015 (p90) REVERT: G 3 PHE cc_start: 0.7506 (m-80) cc_final: 0.7193 (m-80) REVERT: G 42 PHE cc_start: 0.8025 (m-80) cc_final: 0.7740 (m-10) REVERT: G 49 LEU cc_start: 0.8972 (mp) cc_final: 0.8627 (pp) REVERT: G 50 ASP cc_start: 0.8300 (t0) cc_final: 0.7552 (t0) REVERT: G 53 ASN cc_start: 0.9349 (t0) cc_final: 0.9070 (t0) REVERT: G 57 GLN cc_start: 0.7758 (mt0) cc_final: 0.7302 (mt0) REVERT: G 71 ASN cc_start: 0.8667 (t0) cc_final: 0.7705 (t0) REVERT: G 100 GLU cc_start: 0.6703 (mm-30) cc_final: 0.6340 (mm-30) REVERT: H 14 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7580 (tm-30) REVERT: H 27 GLU cc_start: 0.7818 (mp0) cc_final: 0.6848 (mp0) REVERT: I 1 MET cc_start: 0.7126 (tpt) cc_final: 0.6140 (mtm) REVERT: I 97 MET cc_start: 0.7582 (mtp) cc_final: 0.7096 (tpp) REVERT: K 5 ASP cc_start: 0.8040 (t0) cc_final: 0.7631 (t0) REVERT: K 6 ARG cc_start: 0.8494 (mmm-85) cc_final: 0.7750 (mmm160) REVERT: K 11 LEU cc_start: 0.9463 (tt) cc_final: 0.8898 (mt) REVERT: K 39 ASP cc_start: 0.9203 (p0) cc_final: 0.8854 (p0) REVERT: K 41 THR cc_start: 0.9380 (OUTLIER) cc_final: 0.9121 (p) REVERT: K 61 TYR cc_start: 0.9454 (p90) cc_final: 0.9252 (p90) REVERT: K 89 ASN cc_start: 0.8887 (m-40) cc_final: 0.8686 (t0) REVERT: K 108 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8380 (tp30) REVERT: L 47 ARG cc_start: 0.8429 (ptm160) cc_final: 0.8019 (mtp85) outliers start: 38 outliers final: 30 residues processed: 371 average time/residue: 0.2257 time to fit residues: 137.6231 Evaluate side-chains 360 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 329 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 932 GLU Chi-restraints excluded: chain A residue 1218 GLN Chi-restraints excluded: chain A residue 1309 ASP Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 1099 VAL Chi-restraints excluded: chain B residue 1100 ASP Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 121 PHE Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain L residue 53 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 162 optimal weight: 0.9990 chunk 281 optimal weight: 5.9990 chunk 388 optimal weight: 30.0000 chunk 43 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 359 optimal weight: 30.0000 chunk 204 optimal weight: 3.9990 chunk 250 optimal weight: 1.9990 chunk 350 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.080211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.054610 restraints weight = 112080.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.056287 restraints weight = 58825.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.057386 restraints weight = 39485.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.058067 restraints weight = 30900.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.058415 restraints weight = 26641.604| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 33773 Z= 0.172 Angle : 0.605 13.990 45995 Z= 0.310 Chirality : 0.043 0.243 5168 Planarity : 0.004 0.044 5616 Dihedral : 16.293 137.139 5290 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.83 % Favored : 96.04 % Rotamer: Outliers : 1.02 % Allowed : 13.82 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.14), residues: 3842 helix: 1.51 (0.15), residues: 1342 sheet: -0.41 (0.21), residues: 615 loop : -0.53 (0.15), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 192 TYR 0.027 0.001 TYR G 25 PHE 0.024 0.001 PHE A 219 TRP 0.073 0.001 TRP B 308 HIS 0.005 0.001 HIS J 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (33741) covalent geometry : angle 0.59781 / 0.31 (45950) hydrogen bonds : bond 0.03383 / 2.17 ( 1411) hydrogen bonds : angle 4.52628 / 3.25 ( 3865) metal coordination : bond 0.00631 / 0.42 ( 32) metal coordination : angle 3.06594 / 1.74 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 333 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8244 (mtt) cc_final: 0.7927 (mtt) REVERT: A 453 MET cc_start: 0.9089 (mpp) cc_final: 0.8815 (mpp) REVERT: A 487 MET cc_start: 0.9322 (mmm) cc_final: 0.8722 (mmm) REVERT: A 526 ASP cc_start: 0.8146 (m-30) cc_final: 0.7730 (m-30) REVERT: A 605 MET cc_start: 0.9108 (tpp) cc_final: 0.8554 (tpp) REVERT: A 826 ASP cc_start: 0.9143 (m-30) cc_final: 0.8942 (m-30) REVERT: A 830 LYS cc_start: 0.9425 (mptt) cc_final: 0.9146 (mmtm) REVERT: A 873 MET cc_start: 0.9017 (mmp) cc_final: 0.8434 (mmp) REVERT: A 1111 MET cc_start: 0.8328 (ttm) cc_final: 0.8014 (ttm) REVERT: A 1257 ASP cc_start: 0.7554 (m-30) cc_final: 0.6918 (p0) REVERT: A 1368 MET cc_start: 0.9014 (mtp) cc_final: 0.8685 (ttp) REVERT: A 1444 MET cc_start: 0.8394 (ptp) cc_final: 0.8137 (ptp) REVERT: B 101 MET cc_start: 0.8648 (mmm) cc_final: 0.8207 (mmm) REVERT: B 137 TYR cc_start: 0.7579 (m-80) cc_final: 0.7090 (m-80) REVERT: B 173 MET cc_start: 0.9192 (ttm) cc_final: 0.8811 (ttm) REVERT: B 239 GLU cc_start: 0.7596 (tp30) cc_final: 0.7351 (tp30) REVERT: B 246 LYS cc_start: 0.9016 (mmtm) cc_final: 0.8349 (mmtm) REVERT: B 513 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8331 (mp10) REVERT: B 563 MET cc_start: 0.9028 (tmm) cc_final: 0.8628 (tmm) REVERT: B 597 MET cc_start: 0.9033 (tpt) cc_final: 0.8666 (tpt) REVERT: B 615 MET cc_start: 0.7951 (mtm) cc_final: 0.7582 (mtm) REVERT: B 662 MET cc_start: 0.8929 (mtm) cc_final: 0.8503 (mtm) REVERT: B 775 LYS cc_start: 0.9577 (mtmt) cc_final: 0.9366 (mttm) REVERT: B 1072 MET cc_start: 0.8585 (mmm) cc_final: 0.8251 (mmm) REVERT: B 1082 MET cc_start: 0.9059 (tpp) cc_final: 0.8734 (mmm) REVERT: B 1111 MET cc_start: 0.8801 (mmm) cc_final: 0.8487 (mpp) REVERT: B 1202 LEU cc_start: 0.9387 (tp) cc_final: 0.8643 (tp) REVERT: B 1206 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8084 (mt-10) REVERT: C 177 GLU cc_start: 0.8338 (mp0) cc_final: 0.8070 (mp0) REVERT: D 120 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7250 (tp30) REVERT: D 147 TYR cc_start: 0.6944 (t80) cc_final: 0.6542 (t80) REVERT: D 214 LEU cc_start: 0.8084 (tt) cc_final: 0.7821 (pp) REVERT: E 93 MET cc_start: 0.8199 (tmm) cc_final: 0.7710 (tmm) REVERT: E 112 TYR cc_start: 0.8788 (p90) cc_final: 0.7764 (p90) REVERT: E 179 GLN cc_start: 0.8686 (mm-40) cc_final: 0.8455 (mm-40) REVERT: F 116 ASP cc_start: 0.8787 (t0) cc_final: 0.8501 (t70) REVERT: F 143 PHE cc_start: 0.9292 (p90) cc_final: 0.9035 (p90) REVERT: G 3 PHE cc_start: 0.7505 (m-80) cc_final: 0.7217 (m-80) REVERT: G 42 PHE cc_start: 0.8027 (m-80) cc_final: 0.7739 (m-10) REVERT: G 49 LEU cc_start: 0.8983 (mp) cc_final: 0.8657 (pp) REVERT: G 50 ASP cc_start: 0.8299 (t0) cc_final: 0.7564 (t0) REVERT: G 53 ASN cc_start: 0.9340 (t0) cc_final: 0.9062 (t0) REVERT: G 57 GLN cc_start: 0.7792 (mt0) cc_final: 0.7335 (mt0) REVERT: G 71 ASN cc_start: 0.8704 (t0) cc_final: 0.7718 (t0) REVERT: G 100 GLU cc_start: 0.6693 (mm-30) cc_final: 0.6344 (mm-30) REVERT: H 14 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7548 (tm-30) REVERT: H 27 GLU cc_start: 0.7814 (mp0) cc_final: 0.6828 (mp0) REVERT: I 1 MET cc_start: 0.6994 (tpt) cc_final: 0.6307 (mtp) REVERT: I 97 MET cc_start: 0.7577 (mtp) cc_final: 0.7124 (tpp) REVERT: K 5 ASP cc_start: 0.8065 (t0) cc_final: 0.7652 (t0) REVERT: K 6 ARG cc_start: 0.8532 (mmm-85) cc_final: 0.7705 (mmm160) REVERT: K 11 LEU cc_start: 0.9472 (tt) cc_final: 0.8921 (mt) REVERT: K 38 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8365 (mp0) REVERT: K 39 ASP cc_start: 0.9195 (p0) cc_final: 0.8878 (p0) REVERT: K 41 THR cc_start: 0.9428 (OUTLIER) cc_final: 0.9171 (p) REVERT: K 108 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8392 (tp30) REVERT: L 47 ARG cc_start: 0.8417 (ptm160) cc_final: 0.8038 (mtp85) outliers start: 35 outliers final: 30 residues processed: 359 average time/residue: 0.2263 time to fit residues: 133.6035 Evaluate side-chains 357 residues out of total 3431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 326 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 932 GLU Chi-restraints excluded: chain A residue 1309 ASP Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 1099 VAL Chi-restraints excluded: chain B residue 1100 ASP Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 121 PHE Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain L residue 53 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 176 optimal weight: 6.9990 chunk 386 optimal weight: 50.0000 chunk 334 optimal weight: 5.9990 chunk 246 optimal weight: 10.0000 chunk 298 optimal weight: 0.6980 chunk 183 optimal weight: 20.0000 chunk 94 optimal weight: 4.9990 chunk 292 optimal weight: 0.0270 chunk 216 optimal weight: 0.8980 chunk 389 optimal weight: 50.0000 chunk 245 optimal weight: 0.8980 overall best weight: 1.5040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1218 GLN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.080788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.055105 restraints weight = 111493.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.056808 restraints weight = 58494.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.057919 restraints weight = 39134.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.058613 restraints weight = 30608.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.059037 restraints weight = 26386.289| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33773 Z= 0.133 Angle : 0.591 13.584 45995 Z= 0.303 Chirality : 0.043 0.239 5168 Planarity : 0.004 0.045 5616 Dihedral : 16.254 137.017 5290 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.72 % Favored : 96.15 % Rotamer: Outliers : 1.11 % Allowed : 13.87 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.14), residues: 3842 helix: 1.49 (0.15), residues: 1349 sheet: -0.36 (0.21), residues: 607 loop : -0.54 (0.15), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 192 TYR 0.027 0.001 TYR G 25 PHE 0.025 0.001 PHE A 219 TRP 0.054 0.001 TRP B 308 HIS 0.005 0.001 HIS J 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (33741) covalent geometry : angle 0.58350 / 0.30 (45950) hydrogen bonds : bond 0.03329 / 2.14 ( 1411) hydrogen bonds : angle 4.48807 / 3.22 ( 3865) metal coordination : bond 0.00514 / 0.35 ( 32) metal coordination : angle 2.97246 / 1.70 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5633.93 seconds wall clock time: 98 minutes 24.23 seconds (5904.23 seconds total)