Starting phenix.real_space_refine on Sun Aug 9 10:27:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sc4_54749/08_2026/9sc4_54749.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sc4_54749/08_2026/9sc4_54749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9sc4_54749/08_2026/9sc4_54749.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sc4_54749/08_2026/9sc4_54749.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9sc4_54749/08_2026/9sc4_54749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sc4_54749/08_2026/9sc4_54749.map" } resolution = 3.76 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= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 100 5.49 5 Mg 2 5.21 5 S 182 5.16 5 C 20561 2.51 5 N 5765 2.21 5 O 6465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33083 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 10942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1390, 10942 Classifications: {'peptide': 1390} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1327} Chain breaks: 6 Chain: "B" Number of atoms: 9155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1150, 9155 Classifications: {'peptide': 1150} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 1100} Chain breaks: 6 Chain: "C" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2095 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain: "D" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1327 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 164} Chain breaks: 2 Chain: "E" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1744 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1340 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1077 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Chain: "I" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 909 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 904 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "N" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 905 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "R" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 197 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna3p': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 886 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 2, ' ZN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 457 SG CYS A 67 105.373 69.679 95.237 1.00198.77 S ATOM 479 SG CYS A 70 104.821 66.292 93.649 1.00198.63 S ATOM 532 SG CYS A 77 102.436 69.244 92.908 1.00197.88 S ATOM 762 SG CYS A 107 80.242 76.200 135.208 1.00229.08 S ATOM 786 SG CYS A 110 81.551 72.691 135.666 1.00217.05 S ATOM 1091 SG CYS A 148 78.215 73.649 137.207 1.00252.49 S ATOM 1105 SG CYS A 167 81.437 75.208 138.590 1.00230.09 S ATOM 19603 SG CYS B1163 97.504 57.562 105.036 1.00190.66 S ATOM 19621 SG CYS B1166 95.834 60.850 105.352 1.00200.81 S ATOM 19746 SG CYS B1182 99.650 60.626 104.903 1.00194.91 S ATOM 19765 SG CYS B1185 97.920 59.624 108.249 1.00205.72 S ATOM 20753 SG CYS C 86 91.645 74.027 25.829 1.00230.79 S ATOM 20770 SG CYS C 88 93.724 76.183 28.021 1.00244.97 S ATOM 20803 SG CYS C 92 93.083 77.308 24.466 1.00223.33 S ATOM 20826 SG CYS C 95 90.284 77.381 27.109 1.00215.50 S ATOM 28411 SG CYS I 7 40.795 124.074 128.664 1.00294.68 S ATOM 28436 SG CYS I 10 44.465 123.391 128.431 1.00295.55 S ATOM 28602 SG CYS I 29 42.181 120.715 130.025 1.00310.24 S ATOM 28626 SG CYS I 32 42.807 124.002 131.801 1.00296.68 S ATOM 28953 SG CYS I 75 15.882 114.702 90.259 1.00309.39 S ATOM 28975 SG CYS I 78 15.637 118.209 88.899 1.00315.67 S ATOM 29191 SG CYS I 103 18.865 116.293 88.409 1.00306.83 S ATOM 29211 SG CYS I 106 17.870 117.427 91.905 1.00305.87 S ATOM 29313 SG CYS J 7 62.688 89.355 37.684 1.00175.99 S ATOM 29336 SG CYS J 10 62.582 87.376 34.426 1.00183.03 S ATOM 29616 SG CYS J 45 59.319 88.165 36.419 1.00182.94 S ATOM 29622 SG CYS J 46 61.084 90.664 34.325 1.00178.60 S ATOM 30745 SG CYS L 31 96.076 112.978 53.608 1.00284.85 S ATOM 30765 SG CYS L 34 97.364 114.646 50.492 1.00278.74 S ATOM 30869 SG CYS L 48 99.625 113.765 53.568 1.00287.07 S ATOM 30892 SG CYS L 51 97.310 116.722 53.646 1.00308.62 S Time building chain proxies: 5.90, per 1000 atoms: 0.18 Number of scatterers: 33083 At special positions: 0 Unit cell: (151.241, 154.505, 183.883, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 182 16.00 P 100 15.00 Mg 2 11.99 O 6465 8.00 N 5765 7.00 C 20561 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 77 " pdb=" ZN A1804 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 148 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " Number of angles added : 45 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7340 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 48 sheets defined 38.9% alpha, 19.1% beta 41 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 4.17 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 203 through 213 Processing helix chain 'A' and resid 215 through 222 Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 260 through 283 removed outlier: 3.520A pdb=" N PHE A 264 " --> pdb=" O ASP A 260 " (cutoff:3.500A) removed outlier: 3.633A 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: 3.749A 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 506 through 510 Processing helix chain 'A' and resid 524 through 536 removed outlier: 3.728A pdb=" N LEU A 528 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.608A 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 removed outlier: 3.583A pdb=" N ALA A 699 " --> pdb=" O LYS A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 737 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 793 through 797 Processing helix chain 'A' and resid 809 through 829 removed outlier: 3.670A pdb=" N GLU A 822 " --> pdb=" O MET A 818 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLY A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A 824 " --> pdb=" O GLY A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 845 removed outlier: 4.150A pdb=" N THR A 834 " --> pdb=" O LYS A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 874 through 876 No H-bonds generated for 'chain 'A' and resid 874 through 876' Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 909 through 913 Processing helix chain 'A' and resid 915 through 920 removed outlier: 3.576A 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 994 removed outlier: 3.608A pdb=" N GLN A 994 " --> pdb=" O VAL A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1015 Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1038 through 1056 removed outlier: 3.642A pdb=" N VAL A1045 " --> pdb=" O ALA A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1083 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1084 through 1087 Processing helix chain 'A' and resid 1091 through 1107 removed outlier: 4.465A 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 1174 removed outlier: 4.759A pdb=" N PHE A1174 " --> pdb=" O ILE A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1205 Processing helix chain 'A' and resid 1208 through 1221 removed outlier: 3.506A pdb=" N VAL A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE A1220 " --> pdb=" O ILE A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1270 Processing helix chain 'A' and resid 1312 through 1317 removed outlier: 3.530A pdb=" N MET A1317 " --> pdb=" O LEU A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1339 Processing helix chain 'A' and resid 1340 through 1357 Processing helix chain 'A' and resid 1364 through 1376 removed outlier: 4.069A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1401 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1431 removed outlier: 3.528A pdb=" N ASN A1427 " --> pdb=" O GLY A1423 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 37 removed outlier: 4.074A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 65 removed outlier: 4.675A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.398A 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 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 293 through 303 removed outlier: 3.664A pdb=" N ILE B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR B 303 " --> pdb=" O GLU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Proline residue: B 316 - end of helix removed outlier: 3.533A pdb=" N GLU B 319 " --> pdb=" O LYS B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 370 through 390 Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 439 Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.714A pdb=" N THR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.560A pdb=" N ARG B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 592 through 607 Processing helix chain 'B' and resid 654 through 667 removed outlier: 3.505A pdb=" N ILE B 658 " --> pdb=" O ARG B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.656A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 removed outlier: 3.596A 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 removed outlier: 3.704A pdb=" N ASN B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 775 removed outlier: 3.786A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 788 removed outlier: 3.825A pdb=" N TYR B 785 " --> pdb=" O LEU B 782 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASN B 786 " --> pdb=" O THR B 783 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG B 788 " --> pdb=" O TYR B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 813 removed outlier: 3.533A pdb=" N GLU B 810 " --> pdb=" O ARG B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 3.983A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.833A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1061 removed outlier: 3.507A pdb=" N GLU B1061 " --> pdb=" O LYS B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1153 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 69 removed outlier: 3.610A pdb=" N LEU C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 196 through 201 removed outlier: 3.595A pdb=" N TRP C 201 " --> pdb=" O SER C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 210 removed outlier: 4.170A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 266 Processing helix chain 'D' and resid 30 through 34 removed outlier: 3.690A pdb=" N GLN D 34 " --> pdb=" O GLN D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 73 Processing helix chain 'D' and resid 118 through 134 removed outlier: 3.605A pdb=" N LEU D 129 " --> pdb=" O SER D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 151 Processing helix chain 'D' and resid 156 through 169 removed outlier: 3.803A pdb=" N VAL D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 removed outlier: 3.666A pdb=" N GLY D 181 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 196 through 199 removed outlier: 3.527A 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 Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 44 Processing helix chain 'E' and resid 54 through 59 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 91 through 104 Processing helix chain 'E' and resid 117 through 124 Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 171 through 175 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 19 through 20 No H-bonds generated for 'chain 'G' and resid 19 through 20' Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.506A pdb=" N LEU G 31 " --> pdb=" O LYS G 27 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU G 32 " --> pdb=" O THR G 28 " (cutoff:3.500A) removed outlier: 3.619A 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 'I' and resid 59 through 65 removed outlier: 3.682A 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 51 removed outlier: 3.871A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 removed outlier: 3.503A pdb=" N PHE J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU J 61 " --> pdb=" O ILE J 57 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 56 through 62' Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 53 removed outlier: 3.595A pdb=" N GLY K 43 " --> pdb=" O ASP K 39 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN K 44 " --> pdb=" O HIS K 40 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU K 49 " --> pdb=" O LEU K 45 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 111 removed outlier: 3.755A pdb=" N LEU K 111 " --> pdb=" O THR K 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 90 removed outlier: 9.950A pdb=" N LEU A 86 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 11.127A pdb=" N LYS A 88 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 7.317A 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: 4.632A pdb=" N LEU A 181 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 249 through 252 Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 344 removed outlier: 3.715A pdb=" N LYS A 343 " --> pdb=" O PHE B1130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 353 through 355 removed outlier: 3.544A pdb=" N LEU A 470 " --> pdb=" O SER A 354 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG A 469 " --> pdb=" O GLY A 365 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N MET A 456 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 348 " --> pdb=" O ARG B1106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.622A pdb=" N ARG A 434 " --> pdb=" O TYR A 376 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.674A 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 587 through 590 removed outlier: 7.067A 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: 6.765A 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: 4.324A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ARG A1194 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N SER A1150 " --> pdb=" O ARG A1194 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLU A1196 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 4.084A 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: 4.287A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE G 4 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ARG G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N VAL G 48 " --> pdb=" O ARG G 75 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N VAL G 77 " --> pdb=" O LEU G 46 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 143 through 147 removed outlier: 5.519A pdb=" N VAL A1443 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY G 59 " --> pdb=" O ILE A1445 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 68 through 73 removed outlier: 4.792A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LYS B 99 " --> pdb=" O SER B 125 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N SER B 125 " --> pdb=" O LYS B 99 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N THR B 136 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA B 153 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLU B 138 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LEU B 151 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 109 through 111 removed outlier: 4.792A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LYS B 99 " --> pdb=" O SER B 125 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N SER B 125 " --> pdb=" O LYS B 99 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC3, first strand: chain 'B' and resid 404 through 407 removed outlier: 5.882A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 224 through 227 removed outlier: 4.032A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC6, first strand: chain 'B' and resid 564 through 565 removed outlier: 7.353A pdb=" N VAL B 580 " --> pdb=" O HIS B 587 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL B 589 " --> pdb=" O THR B 578 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N THR B 578 " --> pdb=" O VAL B 589 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 640 through 641 removed outlier: 3.603A pdb=" N GLU B 650 " --> pdb=" O GLU B 641 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 703 through 704 Processing sheet with id=AC9, first strand: chain 'B' and resid 792 through 793 removed outlier: 6.970A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 792 through 793 removed outlier: 6.970A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD3, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 7.347A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE B1012 " --> pdb=" O ALA B 826 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 873 through 874 Processing sheet with id=AD5, first strand: chain 'B' and resid 910 through 912 Processing sheet with id=AD6, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD7, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD8, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD9, first strand: chain 'C' and resid 7 through 13 removed outlier: 5.567A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN C 231 " --> pdb=" O GLU C 177 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.753A pdb=" N GLU C 152 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N THR C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LYS C 154 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N VAL C 51 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N THR C 156 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL C 49 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL C 158 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA C 45 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 111 through 114 Processing sheet with id=AE3, first strand: chain 'D' and resid 36 through 38 removed outlier: 3.542A pdb=" N GLN D 37 " --> pdb=" O GLU D 45 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.420A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.447A 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: 3.726A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 86 through 87 removed outlier: 6.178A pdb=" N ILE G 160 " --> pdb=" O GLU G 148 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N CYS G 150 " --> pdb=" O HIS G 158 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N HIS G 158 " --> pdb=" O CYS G 150 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N LYS G 107 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N GLY G 161 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHE G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE G 99 " --> pdb=" O VAL G 110 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER G 93 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLN G 102 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N VAL G 91 " --> pdb=" O GLN G 102 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 86 through 87 Processing sheet with id=AE8, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.544A pdb=" N TYR G 130 " --> pdb=" O ILE G 137 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.780A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU H 121 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 15 through 19 removed outlier: 3.582A pdb=" N ARG I 24 " --> pdb=" O ASP I 19 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 83 through 86 removed outlier: 3.665A pdb=" N HIS I 108 " --> pdb=" O CYS I 103 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 19 through 23 removed outlier: 6.561A pdb=" N LYS K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TYR K 61 " --> pdb=" O LYS K 72 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLN K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) 1337 hydrogen bonds defined for protein. 3654 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 107 hydrogen bonds 214 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 10.30 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5406 1.31 - 1.43: 8964 1.43 - 1.56: 19015 1.56 - 1.69: 196 1.69 - 1.82: 292 Bond restraints: 33873 Sorted by residual: bond pdb=" C4 ATP T 101 " pdb=" N9 ATP T 101 " ideal model delta sigma weight residual 1.374 1.180 0.194 1.00e-02 1.00e+04 3.75e+02 bond pdb=" C8 ATP T 101 " pdb=" N9 ATP T 101 " ideal model delta sigma weight residual 1.370 1.210 0.160 1.20e-02 6.94e+03 1.78e+02 bond pdb=" C6 ATP T 101 " pdb=" N6 ATP T 101 " ideal model delta sigma weight residual 1.337 1.448 -0.111 1.10e-02 8.26e+03 1.01e+02 bond pdb=" C5 ATP T 101 " pdb=" C6 ATP T 101 " ideal model delta sigma weight residual 1.409 1.335 0.074 1.00e-02 1.00e+04 5.49e+01 bond pdb=" C5 ATP T 101 " pdb=" N7 ATP T 101 " ideal model delta sigma weight residual 1.387 1.453 -0.066 1.00e-02 1.00e+04 4.31e+01 ... (remaining 33868 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.24: 46039 4.24 - 8.47: 109 8.47 - 12.71: 2 12.71 - 16.95: 2 16.95 - 21.19: 1 Bond angle restraints: 46153 Sorted by residual: angle pdb=" PB ATP T 101 " pdb=" O3B ATP T 101 " pdb=" PG ATP T 101 " ideal model delta sigma weight residual 139.87 118.68 21.19 1.00e+00 1.00e+00 4.49e+02 angle pdb=" PA ATP T 101 " pdb=" O3A ATP T 101 " pdb=" PB ATP T 101 " ideal model delta sigma weight residual 136.83 121.11 15.72 1.00e+00 1.00e+00 2.47e+02 angle pdb=" C4 ATP T 101 " pdb=" N9 ATP T 101 " pdb=" C8 ATP T 101 " ideal model delta sigma weight residual 105.72 119.60 -13.88 1.00e+00 1.00e+00 1.93e+02 angle pdb=" N1 ATP T 101 " pdb=" C2 ATP T 101 " pdb=" N3 ATP T 101 " ideal model delta sigma weight residual 128.69 120.32 8.37 1.00e+00 1.00e+00 7.00e+01 angle pdb=" N3 ATP T 101 " pdb=" C4 ATP T 101 " pdb=" N9 ATP T 101 " ideal model delta sigma weight residual 127.04 133.05 -6.01 1.15e+00 7.59e-01 2.74e+01 ... (remaining 46148 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.22: 19850 34.22 - 68.45: 584 68.45 - 102.67: 29 102.67 - 136.90: 3 136.90 - 171.12: 1 Dihedral angle restraints: 20467 sinusoidal: 9132 harmonic: 11335 Sorted by residual: dihedral pdb=" CA THR A 69 " pdb=" C THR A 69 " pdb=" N CYS A 70 " pdb=" CA CYS A 70 " ideal model delta harmonic sigma weight residual 180.00 153.79 26.21 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA ILE C 38 " pdb=" C ILE C 38 " pdb=" N ALA C 39 " pdb=" CA ALA C 39 " ideal model delta harmonic sigma weight residual -180.00 -159.60 -20.40 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" C4' DC N 38 " pdb=" C3' DC N 38 " pdb=" O3' DC N 38 " pdb=" P DC N 39 " ideal model delta sinusoidal sigma weight residual -140.00 31.12 -171.12 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 20464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 4010 0.046 - 0.091: 849 0.091 - 0.137: 317 0.137 - 0.183: 11 0.183 - 0.228: 3 Chirality restraints: 5190 Sorted by residual: chirality pdb=" CB ILE A 336 " pdb=" CA ILE A 336 " pdb=" CG1 ILE A 336 " pdb=" CG2 ILE A 336 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CG LEU A 472 " pdb=" CB LEU A 472 " pdb=" CD1 LEU A 472 " pdb=" CD2 LEU A 472 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CB ILE A1152 " pdb=" CA ILE A1152 " pdb=" CG1 ILE A1152 " pdb=" CG2 ILE A1152 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.47e-01 ... (remaining 5187 not shown) Planarity restraints: 5630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 710 " -0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C LEU A 710 " 0.061 2.00e-02 2.50e+03 pdb=" O LEU A 710 " -0.023 2.00e-02 2.50e+03 pdb=" N ARG A 711 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC N 39 " 0.023 2.00e-02 2.50e+03 1.40e-02 4.39e+00 pdb=" N1 DC N 39 " -0.022 2.00e-02 2.50e+03 pdb=" C2 DC N 39 " 0.016 2.00e-02 2.50e+03 pdb=" O2 DC N 39 " -0.015 2.00e-02 2.50e+03 pdb=" N3 DC N 39 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DC N 39 " 0.012 2.00e-02 2.50e+03 pdb=" N4 DC N 39 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DC N 39 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DC N 39 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A1098 " 0.033 5.00e-02 4.00e+02 5.05e-02 4.07e+00 pdb=" N PRO A1099 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A1099 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1099 " 0.028 5.00e-02 4.00e+02 ... (remaining 5627 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 94 2.37 - 3.00: 17995 3.00 - 3.63: 50295 3.63 - 4.27: 76224 4.27 - 4.90: 125862 Nonbonded interactions: 270470 Sorted by model distance: nonbonded pdb="MG MG A1801 " pdb=" O2A ATP T 101 " model vdw 1.734 2.170 nonbonded pdb=" CB THR E 117 " pdb=" OP1 DA N 65 " model vdw 1.852 3.470 nonbonded pdb=" OD2 ASP A 481 " pdb="MG MG A1801 " model vdw 1.893 2.170 nonbonded pdb="MG MG A1801 " pdb=" O2B ATP T 101 " model vdw 1.897 2.170 nonbonded pdb="MG MG A1801 " pdb=" O1G ATP T 101 " model vdw 1.932 2.170 ... (remaining 270465 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 38.820 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 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 0.194 33905 Z= 0.302 Angle : 0.627 21.187 46198 Z= 0.418 Chirality : 0.042 0.228 5190 Planarity : 0.003 0.050 5630 Dihedral : 14.864 171.121 13127 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.74 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.14), residues: 3854 helix: 1.83 (0.15), residues: 1304 sheet: 0.18 (0.21), residues: 620 loop : -0.26 (0.15), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1366 TYR 0.025 0.001 TYR B 797 PHE 0.015 0.001 PHE A 444 TRP 0.015 0.001 TRP C 192 HIS 0.012 0.001 HIS A 706 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.30 (33873) covalent geometry : angle 0.62056 / 0.42 (46153) hydrogen bonds : bond 0.18985 / 12.82 ( 1420) hydrogen bonds : angle 7.02191 / 5.07 ( 3868) metal coordination : bond 0.00451 / 0.28 ( 32) metal coordination : angle 2.97898 / 2.13 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 777 time to evaluate : 1.431 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: A 122 MET cc_start: 0.9531 (tpp) cc_final: 0.9282 (tpp) REVERT: A 138 ILE cc_start: 0.9692 (mt) cc_final: 0.9483 (tp) REVERT: A 226 GLU cc_start: 0.9019 (tt0) cc_final: 0.8631 (mp0) REVERT: A 229 SER cc_start: 0.9320 (t) cc_final: 0.8968 (p) REVERT: A 415 LEU cc_start: 0.9292 (mt) cc_final: 0.8987 (mt) REVERT: A 542 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8398 (mp0) REVERT: A 605 MET cc_start: 0.9179 (tpt) cc_final: 0.8657 (tpp) REVERT: A 676 MET cc_start: 0.9230 (mmm) cc_final: 0.8606 (mmm) REVERT: A 695 LYS cc_start: 0.9552 (mmtm) cc_final: 0.9237 (ptpt) REVERT: A 746 MET cc_start: 0.9333 (mtm) cc_final: 0.9031 (mtt) REVERT: A 748 MET cc_start: 0.9093 (mtm) cc_final: 0.8602 (mmp) REVERT: A 789 LYS cc_start: 0.8951 (mttt) cc_final: 0.8650 (mtpp) REVERT: A 850 VAL cc_start: 0.9543 (t) cc_final: 0.9242 (p) REVERT: A 873 MET cc_start: 0.9306 (mmp) cc_final: 0.8957 (mmp) REVERT: A 939 ASP cc_start: 0.9063 (m-30) cc_final: 0.8837 (m-30) REVERT: A 965 GLN cc_start: 0.9192 (mt0) cc_final: 0.8873 (mp10) REVERT: A 985 ASP cc_start: 0.8990 (m-30) cc_final: 0.8704 (t0) REVERT: A 1109 LYS cc_start: 0.9240 (mttt) cc_final: 0.8953 (mtmm) REVERT: A 1110 ASN cc_start: 0.9263 (m-40) cc_final: 0.8329 (p0) REVERT: A 1166 ASP cc_start: 0.7062 (m-30) cc_final: 0.6575 (t0) REVERT: A 1196 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8202 (mm-30) REVERT: A 1199 ARG cc_start: 0.8540 (ttm110) cc_final: 0.8115 (mtp180) REVERT: A 1239 ARG cc_start: 0.8477 (mtp-110) cc_final: 0.8160 (mtm-85) REVERT: A 1259 MET cc_start: 0.9053 (mmp) cc_final: 0.8593 (mmm) REVERT: A 1276 VAL cc_start: 0.8713 (t) cc_final: 0.8201 (m) REVERT: A 1284 MET cc_start: 0.9155 (ttm) cc_final: 0.8920 (ttm) REVERT: A 1307 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8599 (mt-10) REVERT: A 1315 GLU cc_start: 0.9286 (tt0) cc_final: 0.8865 (tm-30) REVERT: A 1454 MET cc_start: 0.8049 (mtp) cc_final: 0.7727 (mtt) REVERT: B 89 GLU cc_start: 0.6980 (tm-30) cc_final: 0.6566 (tm-30) REVERT: B 101 MET cc_start: 0.9143 (mtt) cc_final: 0.8794 (mtp) REVERT: B 135 ARG cc_start: 0.8705 (mpt-90) cc_final: 0.8072 (mtm-85) REVERT: B 173 MET cc_start: 0.9396 (ttm) cc_final: 0.9160 (ttp) REVERT: B 213 ILE cc_start: 0.9596 (mm) cc_final: 0.9388 (tp) REVERT: B 216 GLU cc_start: 0.9083 (tt0) cc_final: 0.8757 (tt0) REVERT: B 239 GLU cc_start: 0.8899 (pt0) cc_final: 0.8231 (pm20) REVERT: B 269 ILE cc_start: 0.9693 (mt) cc_final: 0.9165 (tp) REVERT: B 415 GLN cc_start: 0.8747 (tt0) cc_final: 0.8493 (pp30) REVERT: B 616 ILE cc_start: 0.8992 (tt) cc_final: 0.8771 (mp) REVERT: B 620 ARG cc_start: 0.9237 (ptp-170) cc_final: 0.8942 (ptm-80) REVERT: B 665 GLU cc_start: 0.9079 (tt0) cc_final: 0.8756 (tp30) REVERT: B 783 THR cc_start: 0.9415 (m) cc_final: 0.8918 (p) REVERT: B 810 GLU cc_start: 0.9385 (tt0) cc_final: 0.8992 (tp30) REVERT: B 864 LYS cc_start: 0.8077 (mtmt) cc_final: 0.7216 (pptt) REVERT: B 872 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7684 (mm-30) REVERT: B 906 SER cc_start: 0.8249 (p) cc_final: 0.8024 (t) REVERT: B 978 ASP cc_start: 0.7977 (m-30) cc_final: 0.7307 (m-30) REVERT: B 1049 ASP cc_start: 0.8945 (m-30) cc_final: 0.8608 (p0) REVERT: B 1072 MET cc_start: 0.9487 (mtp) cc_final: 0.9251 (mtp) REVERT: B 1082 MET cc_start: 0.8776 (tpp) cc_final: 0.8287 (tpt) REVERT: B 1098 MET cc_start: 0.9199 (mtm) cc_final: 0.8972 (mtm) REVERT: B 1120 GLU cc_start: 0.8577 (tt0) cc_final: 0.8242 (tt0) REVERT: B 1152 MET cc_start: 0.8945 (mmm) cc_final: 0.8740 (mmt) REVERT: B 1206 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8548 (mt-10) REVERT: C 37 MET cc_start: 0.9109 (mtm) cc_final: 0.8650 (mtm) REVERT: C 125 MET cc_start: 0.9175 (mtp) cc_final: 0.8917 (mmt) REVERT: C 220 ASP cc_start: 0.9130 (t0) cc_final: 0.8718 (t0) REVERT: C 264 GLN cc_start: 0.8500 (tp-100) cc_final: 0.8230 (tm-30) REVERT: C 265 MET cc_start: 0.7952 (tpt) cc_final: 0.7613 (mmp) REVERT: D 23 ASN cc_start: 0.7393 (t0) cc_final: 0.7063 (t0) REVERT: D 28 GLN cc_start: 0.7720 (tt0) cc_final: 0.7405 (tt0) REVERT: D 39 ASN cc_start: 0.8142 (p0) cc_final: 0.7922 (p0) REVERT: D 56 ARG cc_start: 0.7930 (ttp80) cc_final: 0.7374 (ttp-110) REVERT: D 68 ARG cc_start: 0.8573 (mtt180) cc_final: 0.7860 (tpm170) REVERT: D 72 ARG cc_start: 0.4503 (mtt180) cc_final: 0.4123 (tpp80) REVERT: D 142 LYS cc_start: 0.8660 (tttt) cc_final: 0.8106 (pttt) REVERT: D 165 GLN cc_start: 0.8599 (tm-30) cc_final: 0.7922 (pt0) REVERT: D 213 GLU cc_start: 0.9056 (tt0) cc_final: 0.8803 (pt0) REVERT: D 214 LEU cc_start: 0.9312 (tt) cc_final: 0.9076 (pp) REVERT: E 33 GLU cc_start: 0.9420 (tt0) cc_final: 0.9080 (tm-30) REVERT: E 41 ASP cc_start: 0.9666 (m-30) cc_final: 0.9445 (m-30) REVERT: E 57 MET cc_start: 0.9365 (mtm) cc_final: 0.9162 (mtp) REVERT: E 93 MET cc_start: 0.9290 (tpp) cc_final: 0.8985 (tpt) REVERT: E 94 LYS cc_start: 0.9457 (mmmt) cc_final: 0.9227 (mtmt) REVERT: E 137 GLU cc_start: 0.9297 (tt0) cc_final: 0.8902 (mt-10) REVERT: E 182 ASP cc_start: 0.9051 (t0) cc_final: 0.8662 (t0) REVERT: E 192 ARG cc_start: 0.9066 (ttt180) cc_final: 0.8751 (tmm-80) REVERT: E 208 TYR cc_start: 0.9063 (t80) cc_final: 0.8846 (t80) REVERT: E 211 TYR cc_start: 0.9084 (m-80) cc_final: 0.8817 (m-80) REVERT: F 81 THR cc_start: 0.9559 (m) cc_final: 0.8798 (p) REVERT: F 89 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8645 (mt-10) REVERT: F 116 ASP cc_start: 0.9067 (t0) cc_final: 0.8434 (t0) REVERT: F 124 GLU cc_start: 0.9677 (mt-10) cc_final: 0.9429 (tt0) REVERT: F 129 LYS cc_start: 0.8839 (mmtm) cc_final: 0.8213 (mmmm) REVERT: F 144 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8466 (mt-10) REVERT: F 149 GLU cc_start: 0.9221 (tt0) cc_final: 0.8933 (tm-30) REVERT: G 1 MET cc_start: 0.7992 (mmm) cc_final: 0.7343 (tpt) REVERT: G 46 LEU cc_start: 0.9421 (mt) cc_final: 0.9175 (mm) REVERT: G 50 ASP cc_start: 0.8132 (t0) cc_final: 0.7612 (t0) REVERT: G 111 THR cc_start: 0.8326 (p) cc_final: 0.8036 (t) REVERT: G 115 MET cc_start: 0.7001 (mtp) cc_final: 0.6285 (ptm) REVERT: G 167 TYR cc_start: 0.7145 (m-80) cc_final: 0.6855 (m-80) REVERT: H 12 VAL cc_start: 0.9702 (t) cc_final: 0.9285 (p) REVERT: H 37 LYS cc_start: 0.8649 (ptpt) cc_final: 0.8332 (mptt) REVERT: H 40 LEU cc_start: 0.9072 (tp) cc_final: 0.8844 (tp) REVERT: H 58 THR cc_start: 0.8676 (m) cc_final: 0.8347 (p) REVERT: H 80 ARG cc_start: 0.9089 (mtp85) cc_final: 0.8843 (mtm110) REVERT: I 21 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7956 (tt0) REVERT: I 34 TYR cc_start: 0.7057 (t80) cc_final: 0.6673 (t80) REVERT: I 36 GLU cc_start: 0.8805 (pt0) cc_final: 0.8569 (pm20) REVERT: I 68 LEU cc_start: 0.8904 (mt) cc_final: 0.8480 (mt) REVERT: J 29 GLU cc_start: 0.9386 (mt-10) cc_final: 0.8697 (tm-30) REVERT: J 32 GLU cc_start: 0.9120 (mp0) cc_final: 0.8696 (mm-30) REVERT: J 58 GLU cc_start: 0.9230 (mm-30) cc_final: 0.8718 (tm-30) REVERT: K 39 ASP cc_start: 0.8581 (p0) cc_final: 0.8281 (p0) REVERT: K 76 GLN cc_start: 0.9110 (tt0) cc_final: 0.8790 (tt0) REVERT: K 85 ASP cc_start: 0.9319 (m-30) cc_final: 0.9083 (m-30) REVERT: L 54 ARG cc_start: 0.7757 (mtt-85) cc_final: 0.7367 (mtt-85) REVERT: L 58 LYS cc_start: 0.8447 (tttm) cc_final: 0.8124 (tttp) outliers start: 0 outliers final: 0 residues processed: 777 average time/residue: 0.2224 time to fit residues: 269.3036 Evaluate side-chains 497 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 497 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 40.0000 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 698 GLN ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 GLN B 481 GLN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 ASN D 179 GLN E 101 GLN H 11 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.081805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.058773 restraints weight = 95171.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.060723 restraints weight = 45291.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.062015 restraints weight = 27994.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.062835 restraints weight = 20502.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.063345 restraints weight = 16858.162| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 33905 Z= 0.163 Angle : 0.650 10.549 46198 Z= 0.338 Chirality : 0.046 0.251 5190 Planarity : 0.005 0.069 5630 Dihedral : 16.927 166.411 5346 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.58 % Favored : 96.29 % Rotamer: Outliers : 1.34 % Allowed : 8.27 % Favored : 90.39 % 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: 0.58 (0.14), residues: 3854 helix: 1.56 (0.15), residues: 1341 sheet: 0.07 (0.21), residues: 618 loop : -0.30 (0.15), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 326 TYR 0.018 0.001 TYR D 147 PHE 0.025 0.002 PHE A 444 TRP 0.009 0.001 TRP A 656 HIS 0.013 0.001 HIS D 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (33873) covalent geometry : angle 0.64113 / 0.34 (46153) hydrogen bonds : bond 0.04932 / 3.33 ( 1420) hydrogen bonds : angle 5.39660 / 3.88 ( 3868) metal coordination : bond 0.00771 / 0.47 ( 32) metal coordination : angle 3.50660 / 2.46 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 543 time to evaluate : 1.026 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: A 30 ILE cc_start: 0.9477 (OUTLIER) cc_final: 0.9250 (mm) REVERT: A 108 MET cc_start: 0.8664 (mmt) cc_final: 0.8026 (tpp) REVERT: A 122 MET cc_start: 0.9443 (tpp) cc_final: 0.9116 (tpp) REVERT: A 254 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8700 (mp0) REVERT: A 415 LEU cc_start: 0.9543 (mt) cc_final: 0.9315 (mt) REVERT: A 486 GLU cc_start: 0.8028 (tt0) cc_final: 0.7792 (tt0) REVERT: A 676 MET cc_start: 0.9372 (mmm) cc_final: 0.9067 (mmm) REVERT: A 708 MET cc_start: 0.8135 (ttm) cc_final: 0.7756 (ptm) REVERT: A 873 MET cc_start: 0.9158 (mmp) cc_final: 0.8893 (mmp) REVERT: A 884 ASP cc_start: 0.8089 (t0) cc_final: 0.7849 (t0) REVERT: A 939 ASP cc_start: 0.8669 (m-30) cc_final: 0.8460 (m-30) REVERT: A 965 GLN cc_start: 0.9037 (mt0) cc_final: 0.8819 (mp10) REVERT: A 1110 ASN cc_start: 0.8840 (m-40) cc_final: 0.8233 (p0) REVERT: A 1166 ASP cc_start: 0.7062 (m-30) cc_final: 0.6560 (t0) REVERT: A 1196 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8189 (mm-30) REVERT: A 1202 MET cc_start: 0.8081 (mtp) cc_final: 0.7702 (ttt) REVERT: A 1239 ARG cc_start: 0.8384 (mtp-110) cc_final: 0.8089 (mtm-85) REVERT: A 1259 MET cc_start: 0.9153 (mmp) cc_final: 0.8395 (mmm) REVERT: A 1276 VAL cc_start: 0.9378 (t) cc_final: 0.8720 (m) REVERT: B 101 MET cc_start: 0.9028 (mtt) cc_final: 0.8751 (mtp) REVERT: B 135 ARG cc_start: 0.8796 (mpt-90) cc_final: 0.8584 (mpp80) REVERT: B 173 MET cc_start: 0.9154 (ttm) cc_final: 0.8829 (ttp) REVERT: B 216 GLU cc_start: 0.8308 (tt0) cc_final: 0.8047 (tt0) REVERT: B 313 MET cc_start: 0.9635 (mmm) cc_final: 0.9376 (mmm) REVERT: B 665 GLU cc_start: 0.8622 (tt0) cc_final: 0.8402 (tp30) REVERT: B 864 LYS cc_start: 0.8743 (mtmt) cc_final: 0.7346 (pptt) REVERT: B 872 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7598 (mm-30) REVERT: B 906 SER cc_start: 0.8307 (p) cc_final: 0.8050 (t) REVERT: B 1072 MET cc_start: 0.8941 (mtp) cc_final: 0.8631 (mtp) REVERT: B 1082 MET cc_start: 0.9386 (tpp) cc_final: 0.8872 (tpt) REVERT: B 1152 MET cc_start: 0.8823 (mmm) cc_final: 0.8371 (mmm) REVERT: B 1206 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8322 (mt-10) REVERT: C 37 MET cc_start: 0.9110 (mtm) cc_final: 0.8766 (mtm) REVERT: C 60 ASP cc_start: 0.8463 (m-30) cc_final: 0.8215 (t70) REVERT: C 220 ASP cc_start: 0.8642 (t0) cc_final: 0.8266 (t0) REVERT: D 23 ASN cc_start: 0.7464 (t0) cc_final: 0.7229 (t0) REVERT: D 56 ARG cc_start: 0.7828 (ttp80) cc_final: 0.7138 (ttp80) REVERT: D 65 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8390 (mp0) REVERT: D 68 ARG cc_start: 0.8538 (mtt180) cc_final: 0.7943 (tpm170) REVERT: D 139 LYS cc_start: 0.7977 (mmtt) cc_final: 0.7529 (mttt) REVERT: D 142 LYS cc_start: 0.8738 (tttt) cc_final: 0.8240 (pttt) REVERT: D 156 ASP cc_start: 0.8170 (p0) cc_final: 0.7828 (p0) REVERT: E 22 MET cc_start: 0.9637 (ttp) cc_final: 0.9126 (tmm) REVERT: E 182 ASP cc_start: 0.9000 (t0) cc_final: 0.8735 (t0) REVERT: E 187 TYR cc_start: 0.9245 (t80) cc_final: 0.8762 (t80) REVERT: E 208 TYR cc_start: 0.9290 (t80) cc_final: 0.9083 (t80) REVERT: F 81 THR cc_start: 0.9539 (m) cc_final: 0.8816 (p) REVERT: F 116 ASP cc_start: 0.8959 (t0) cc_final: 0.8584 (t70) REVERT: F 129 LYS cc_start: 0.9271 (mmtm) cc_final: 0.8663 (mmmm) REVERT: F 136 ARG cc_start: 0.9006 (mtp85) cc_final: 0.8731 (mtt180) REVERT: F 144 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8143 (mt-10) REVERT: G 50 ASP cc_start: 0.8123 (t0) cc_final: 0.7907 (t0) REVERT: G 111 THR cc_start: 0.8507 (p) cc_final: 0.8125 (t) REVERT: G 115 MET cc_start: 0.7228 (mtp) cc_final: 0.6009 (ptm) REVERT: H 11 GLN cc_start: 0.8894 (tt0) cc_final: 0.8531 (tp40) REVERT: H 126 GLU cc_start: 0.8602 (pt0) cc_final: 0.8185 (pp20) REVERT: H 136 LYS cc_start: 0.8859 (mmmt) cc_final: 0.8260 (tttp) REVERT: I 4 PHE cc_start: 0.7707 (m-80) cc_final: 0.6210 (m-80) REVERT: I 30 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.8064 (mpt-90) REVERT: I 36 GLU cc_start: 0.9130 (pt0) cc_final: 0.8805 (pt0) REVERT: I 45 ARG cc_start: 0.8465 (ttt90) cc_final: 0.8062 (ttt90) REVERT: I 62 ILE cc_start: 0.8740 (tt) cc_final: 0.8437 (tt) REVERT: I 68 LEU cc_start: 0.9202 (mt) cc_final: 0.8867 (mt) REVERT: J 29 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8245 (tm-30) REVERT: J 49 MET cc_start: 0.9501 (tpp) cc_final: 0.8682 (mmm) REVERT: K 85 ASP cc_start: 0.9233 (m-30) cc_final: 0.9019 (m-30) REVERT: L 33 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7527 (mt-10) REVERT: L 47 ARG cc_start: 0.7751 (ttp-110) cc_final: 0.6969 (ttt90) outliers start: 46 outliers final: 26 residues processed: 567 average time/residue: 0.2129 time to fit residues: 193.5267 Evaluate side-chains 480 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 452 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1079 MET Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain L residue 64 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 242 optimal weight: 10.0000 chunk 191 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 373 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 333 optimal weight: 40.0000 chunk 304 optimal weight: 6.9990 chunk 239 optimal weight: 9.9990 chunk 7 optimal weight: 0.7980 chunk 249 optimal weight: 10.0000 chunk 222 optimal weight: 10.0000 overall best weight: 6.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 HIS A 171 GLN ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 ASN D 216 ASN E 115 ASN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN I 87 GLN J 23 ASN K 76 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.077706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.055230 restraints weight = 97810.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.057027 restraints weight = 50225.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.058180 restraints weight = 32238.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.058933 restraints weight = 24218.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.059406 restraints weight = 20181.272| |-----------------------------------------------------------------------------| r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.143 33905 Z= 0.400 Angle : 0.792 13.015 46198 Z= 0.402 Chirality : 0.049 0.298 5190 Planarity : 0.005 0.065 5630 Dihedral : 16.990 164.473 5346 Min Nonbonded Distance : 1.688 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.14 % Favored : 94.76 % Rotamer: Outliers : 2.21 % Allowed : 11.18 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.14), residues: 3854 helix: 1.14 (0.14), residues: 1333 sheet: -0.24 (0.21), residues: 605 loop : -0.55 (0.14), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 344 TYR 0.023 0.002 TYR G 44 PHE 0.029 0.002 PHE I 6 TRP 0.013 0.002 TRP B 561 HIS 0.012 0.002 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00881 / 0.40 (33873) covalent geometry : angle 0.77825 / 0.40 (46153) hydrogen bonds : bond 0.04822 / 3.21 ( 1420) hydrogen bonds : angle 5.40851 / 3.90 ( 3868) metal coordination : bond 0.01590 / 1.02 ( 32) metal coordination : angle 4.76078 / 3.45 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 423 time to evaluate : 1.253 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 504 LEU cc_start: 0.9524 (mp) cc_final: 0.9296 (mp) REVERT: A 708 MET cc_start: 0.8224 (ttm) cc_final: 0.7759 (ptm) REVERT: A 884 ASP cc_start: 0.8188 (t0) cc_final: 0.7726 (t0) REVERT: A 901 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8854 (pp) REVERT: A 1110 ASN cc_start: 0.8954 (m-40) cc_final: 0.8245 (p0) REVERT: A 1192 LEU cc_start: 0.8790 (tp) cc_final: 0.8534 (tp) REVERT: A 1196 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8227 (mm-30) REVERT: A 1199 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8289 (mtp180) REVERT: A 1239 ARG cc_start: 0.8471 (mtp-110) cc_final: 0.8153 (mtm-85) REVERT: A 1259 MET cc_start: 0.9100 (mmp) cc_final: 0.8616 (mmm) REVERT: A 1269 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8316 (mp0) REVERT: B 101 MET cc_start: 0.9078 (mtt) cc_final: 0.8806 (mtp) REVERT: B 216 GLU cc_start: 0.8365 (tt0) cc_final: 0.8152 (tt0) REVERT: B 563 MET cc_start: 0.8597 (ttp) cc_final: 0.8192 (ptm) REVERT: B 615 MET cc_start: 0.8180 (mtm) cc_final: 0.7786 (ptp) REVERT: B 816 GLU cc_start: 0.8581 (mp0) cc_final: 0.8165 (mp0) REVERT: B 864 LYS cc_start: 0.8712 (mtmt) cc_final: 0.8293 (pptt) REVERT: B 906 SER cc_start: 0.8462 (p) cc_final: 0.8156 (t) REVERT: B 1072 MET cc_start: 0.8995 (mtp) cc_final: 0.8604 (mtp) REVERT: B 1152 MET cc_start: 0.8696 (mmm) cc_final: 0.8163 (mmm) REVERT: B 1169 MET cc_start: 0.8966 (mtm) cc_final: 0.8646 (mpp) REVERT: C 37 MET cc_start: 0.9063 (mtm) cc_final: 0.8764 (mtm) REVERT: C 220 ASP cc_start: 0.8703 (t0) cc_final: 0.8386 (t0) REVERT: D 23 ASN cc_start: 0.7431 (t0) cc_final: 0.7125 (t0) REVERT: D 56 ARG cc_start: 0.7978 (ttp80) cc_final: 0.7414 (ttp80) REVERT: D 65 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8417 (mm-30) REVERT: D 68 ARG cc_start: 0.8501 (mtt180) cc_final: 0.8011 (tpm170) REVERT: D 142 LYS cc_start: 0.8783 (tttt) cc_final: 0.8159 (ptmt) REVERT: D 156 ASP cc_start: 0.8197 (p0) cc_final: 0.7779 (p0) REVERT: E 114 ASN cc_start: 0.7998 (t0) cc_final: 0.7535 (t0) REVERT: E 182 ASP cc_start: 0.9051 (t0) cc_final: 0.8810 (t0) REVERT: F 81 THR cc_start: 0.9563 (m) cc_final: 0.8725 (p) REVERT: F 116 ASP cc_start: 0.9029 (t0) cc_final: 0.8674 (t70) REVERT: F 129 LYS cc_start: 0.9254 (mmtm) cc_final: 0.8845 (mmmm) REVERT: F 144 GLU cc_start: 0.8426 (mt-10) cc_final: 0.7968 (mt-10) REVERT: G 106 MET cc_start: 0.8444 (mtm) cc_final: 0.8070 (mtt) REVERT: G 111 THR cc_start: 0.8499 (p) cc_final: 0.8251 (t) REVERT: H 11 GLN cc_start: 0.8821 (tt0) cc_final: 0.8590 (tp-100) REVERT: H 37 LYS cc_start: 0.8359 (mptt) cc_final: 0.8151 (mmtm) REVERT: H 123 MET cc_start: 0.8595 (tmm) cc_final: 0.7904 (tmm) REVERT: I 4 PHE cc_start: 0.7768 (m-80) cc_final: 0.7274 (m-80) REVERT: I 12 ASN cc_start: 0.7899 (m-40) cc_final: 0.7697 (m-40) REVERT: I 36 GLU cc_start: 0.9221 (pt0) cc_final: 0.8795 (pt0) REVERT: I 44 TYR cc_start: 0.8968 (t80) cc_final: 0.8464 (t80) REVERT: I 62 ILE cc_start: 0.8865 (tt) cc_final: 0.8580 (tt) REVERT: I 68 LEU cc_start: 0.9215 (mt) cc_final: 0.8945 (mt) REVERT: I 87 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7694 (mt0) REVERT: J 27 GLU cc_start: 0.8586 (mt-10) cc_final: 0.7973 (mp0) REVERT: J 29 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8281 (tm-30) REVERT: J 32 GLU cc_start: 0.9152 (mp0) cc_final: 0.8704 (mp0) REVERT: J 49 MET cc_start: 0.9561 (tpp) cc_final: 0.8877 (mmm) REVERT: K 5 ASP cc_start: 0.8879 (t0) cc_final: 0.8494 (t0) REVERT: K 64 GLU cc_start: 0.8519 (mm-30) cc_final: 0.6976 (mm-30) REVERT: K 72 LYS cc_start: 0.9557 (mttt) cc_final: 0.9094 (mttp) REVERT: K 85 ASP cc_start: 0.9276 (m-30) cc_final: 0.9048 (m-30) REVERT: L 33 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7368 (mt-10) REVERT: L 47 ARG cc_start: 0.7860 (ttp-110) cc_final: 0.6870 (ttt90) outliers start: 76 outliers final: 42 residues processed: 471 average time/residue: 0.1949 time to fit residues: 149.8529 Evaluate side-chains 438 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 393 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 932 GLU Chi-restraints excluded: chain A residue 992 ASP Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1079 MET Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1199 ARG Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 837 ASP Chi-restraints excluded: chain B residue 1100 ASP Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain L residue 64 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 0 optimal weight: 10.0000 chunk 345 optimal weight: 2.9990 chunk 138 optimal weight: 7.9990 chunk 183 optimal weight: 0.3980 chunk 169 optimal weight: 10.0000 chunk 216 optimal weight: 0.8980 chunk 286 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 251 optimal weight: 0.6980 chunk 308 optimal weight: 0.0060 chunk 352 optimal weight: 3.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 975 HIS A1106 ASN ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 GLN ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 GLN C 188 HIS D 179 GLN H 11 GLN ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.080832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.058118 restraints weight = 94752.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.060017 restraints weight = 47340.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.061276 restraints weight = 29947.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.062085 restraints weight = 22173.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.062538 restraints weight = 18347.222| |-----------------------------------------------------------------------------| r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33905 Z= 0.128 Angle : 0.599 12.267 46198 Z= 0.311 Chirality : 0.044 0.247 5190 Planarity : 0.004 0.048 5630 Dihedral : 16.795 157.798 5346 Min Nonbonded Distance : 1.527 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.53 % Favored : 96.37 % Rotamer: Outliers : 1.34 % Allowed : 13.10 % Favored : 85.56 % 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: 0.35 (0.14), residues: 3854 helix: 1.35 (0.15), residues: 1343 sheet: -0.04 (0.21), residues: 596 loop : -0.42 (0.15), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 677 TYR 0.023 0.001 TYR G 44 PHE 0.021 0.002 PHE A 219 TRP 0.010 0.001 TRP C 192 HIS 0.010 0.001 HIS I 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (33873) covalent geometry : angle 0.58930 / 0.31 (46153) hydrogen bonds : bond 0.03830 / 2.60 ( 1420) hydrogen bonds : angle 4.88383 / 3.52 ( 3868) metal coordination : bond 0.00582 / 0.36 ( 32) metal coordination : angle 3.43515 / 2.36 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 462 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 LEU cc_start: 0.9547 (mt) cc_final: 0.9326 (mt) REVERT: A 455 MET cc_start: 0.8514 (ttp) cc_final: 0.8223 (ttm) REVERT: A 486 GLU cc_start: 0.8169 (tt0) cc_final: 0.7852 (tt0) REVERT: A 504 LEU cc_start: 0.9523 (OUTLIER) cc_final: 0.9304 (mp) REVERT: A 746 MET cc_start: 0.9169 (mtm) cc_final: 0.8948 (mtt) REVERT: A 873 MET cc_start: 0.9219 (mmp) cc_final: 0.8697 (mmm) REVERT: A 884 ASP cc_start: 0.7884 (t0) cc_final: 0.7499 (t0) REVERT: A 1050 GLU cc_start: 0.8860 (tt0) cc_final: 0.8625 (tt0) REVERT: A 1062 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7538 (mt-10) REVERT: A 1110 ASN cc_start: 0.8773 (m-40) cc_final: 0.8213 (p0) REVERT: A 1192 LEU cc_start: 0.8529 (tp) cc_final: 0.8306 (tp) REVERT: A 1196 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8192 (mm-30) REVERT: A 1269 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8237 (mp0) REVERT: B 101 MET cc_start: 0.9029 (mtt) cc_final: 0.8756 (mtp) REVERT: B 216 GLU cc_start: 0.8321 (tt0) cc_final: 0.8088 (tt0) REVERT: B 388 CYS cc_start: 0.9232 (t) cc_final: 0.8798 (t) REVERT: B 563 MET cc_start: 0.8447 (ttp) cc_final: 0.7952 (ptm) REVERT: B 615 MET cc_start: 0.7859 (mtm) cc_final: 0.7523 (mtp) REVERT: B 769 TYR cc_start: 0.9004 (m-10) cc_final: 0.8703 (m-80) REVERT: B 796 LEU cc_start: 0.9351 (mt) cc_final: 0.9086 (mt) REVERT: B 864 LYS cc_start: 0.9056 (mtmt) cc_final: 0.8387 (pptt) REVERT: B 906 SER cc_start: 0.8375 (p) cc_final: 0.8092 (t) REVERT: B 1072 MET cc_start: 0.8860 (mtp) cc_final: 0.8491 (mtp) REVERT: B 1151 LEU cc_start: 0.9543 (OUTLIER) cc_final: 0.9290 (mp) REVERT: B 1152 MET cc_start: 0.8786 (mmm) cc_final: 0.8374 (mmm) REVERT: B 1206 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8328 (mt-10) REVERT: C 37 MET cc_start: 0.8997 (mtm) cc_final: 0.8625 (mtm) REVERT: C 60 ASP cc_start: 0.8509 (m-30) cc_final: 0.8205 (t0) REVERT: C 220 ASP cc_start: 0.8620 (t0) cc_final: 0.8258 (t0) REVERT: D 23 ASN cc_start: 0.7588 (t0) cc_final: 0.7378 (t0) REVERT: D 56 ARG cc_start: 0.7902 (ttp80) cc_final: 0.7562 (ttp80) REVERT: D 65 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8432 (mp0) REVERT: D 68 ARG cc_start: 0.8455 (mtt180) cc_final: 0.8006 (tpm170) REVERT: D 142 LYS cc_start: 0.8674 (tttt) cc_final: 0.8104 (ptmt) REVERT: D 145 MET cc_start: 0.9180 (OUTLIER) cc_final: 0.8966 (mmm) REVERT: D 153 ARG cc_start: 0.7603 (ttp-170) cc_final: 0.7076 (ttt-90) REVERT: D 156 ASP cc_start: 0.8157 (p0) cc_final: 0.7698 (p0) REVERT: E 22 MET cc_start: 0.9653 (ttp) cc_final: 0.9206 (tmm) REVERT: E 182 ASP cc_start: 0.9014 (t0) cc_final: 0.8768 (t0) REVERT: E 208 TYR cc_start: 0.9208 (t80) cc_final: 0.8972 (t80) REVERT: F 81 THR cc_start: 0.9574 (m) cc_final: 0.8872 (p) REVERT: F 85 MET cc_start: 0.8881 (tmm) cc_final: 0.8635 (tmm) REVERT: F 116 ASP cc_start: 0.8980 (t0) cc_final: 0.8639 (t70) REVERT: F 129 LYS cc_start: 0.9144 (mmtm) cc_final: 0.8600 (mmmm) REVERT: F 144 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8109 (mt-10) REVERT: G 1 MET cc_start: 0.7270 (tmm) cc_final: 0.6764 (tmm) REVERT: G 50 ASP cc_start: 0.8271 (t0) cc_final: 0.7988 (t0) REVERT: G 106 MET cc_start: 0.8398 (mtm) cc_final: 0.8072 (mtt) REVERT: G 111 THR cc_start: 0.8491 (p) cc_final: 0.8227 (t) REVERT: G 115 MET cc_start: 0.7220 (mtp) cc_final: 0.6558 (ptp) REVERT: H 37 LYS cc_start: 0.8435 (mptt) cc_final: 0.8140 (mmtt) REVERT: H 130 ARG cc_start: 0.9021 (mtp-110) cc_final: 0.8629 (mmm160) REVERT: I 4 PHE cc_start: 0.7737 (m-80) cc_final: 0.7301 (m-80) REVERT: I 12 ASN cc_start: 0.7991 (m-40) cc_final: 0.7737 (t0) REVERT: I 27 PHE cc_start: 0.8106 (m-80) cc_final: 0.7761 (m-80) REVERT: I 36 GLU cc_start: 0.9056 (pt0) cc_final: 0.8744 (pt0) REVERT: I 44 TYR cc_start: 0.8816 (t80) cc_final: 0.8442 (t80) REVERT: I 62 ILE cc_start: 0.8779 (tt) cc_final: 0.8486 (tt) REVERT: I 68 LEU cc_start: 0.9241 (mt) cc_final: 0.8917 (mt) REVERT: J 27 GLU cc_start: 0.8498 (mt-10) cc_final: 0.7996 (mt-10) REVERT: J 29 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8196 (tm-30) REVERT: J 32 GLU cc_start: 0.9230 (mp0) cc_final: 0.8795 (mm-30) REVERT: K 85 ASP cc_start: 0.9203 (m-30) cc_final: 0.8996 (m-30) REVERT: L 33 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7625 (mt-10) REVERT: L 47 ARG cc_start: 0.7779 (ttp-110) cc_final: 0.6745 (ttt90) outliers start: 46 outliers final: 26 residues processed: 490 average time/residue: 0.1847 time to fit residues: 150.2101 Evaluate side-chains 442 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 412 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1079 MET Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 1151 LEU Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 93 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 46 optimal weight: 6.9990 chunk 140 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 182 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 138 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 862 GLN B 951 GLN ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN I 87 GLN ** I 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 23 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.079084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.056575 restraints weight = 96395.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.058389 restraints weight = 49387.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.059593 restraints weight = 31719.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.060383 restraints weight = 23731.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.060870 restraints weight = 19688.062| |-----------------------------------------------------------------------------| r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 33905 Z= 0.244 Angle : 0.640 11.576 46198 Z= 0.327 Chirality : 0.045 0.260 5190 Planarity : 0.004 0.049 5630 Dihedral : 16.779 158.099 5346 Min Nonbonded Distance : 1.220 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.49 % Favored : 95.41 % Rotamer: Outliers : 2.01 % Allowed : 13.95 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.14), residues: 3854 helix: 1.34 (0.15), residues: 1335 sheet: -0.18 (0.21), residues: 607 loop : -0.48 (0.15), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 56 TYR 0.033 0.002 TYR H 95 PHE 0.029 0.002 PHE D 175 TRP 0.009 0.001 TRP B 31 HIS 0.008 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.24 (33873) covalent geometry : angle 0.62954 / 0.33 (46153) hydrogen bonds : bond 0.03856 / 2.60 ( 1420) hydrogen bonds : angle 4.91668 / 3.55 ( 3868) metal coordination : bond 0.01010 / 0.64 ( 32) metal coordination : angle 3.69133 / 2.68 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 417 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.9448 (mmm) cc_final: 0.9159 (mtp) REVERT: A 415 LEU cc_start: 0.9544 (mt) cc_final: 0.9271 (mt) REVERT: A 455 MET cc_start: 0.8552 (ttp) cc_final: 0.8306 (ttm) REVERT: A 486 GLU cc_start: 0.8213 (tt0) cc_final: 0.7982 (tt0) REVERT: A 504 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9285 (mp) REVERT: A 873 MET cc_start: 0.9253 (mmp) cc_final: 0.8801 (mmm) REVERT: A 884 ASP cc_start: 0.7941 (t0) cc_final: 0.7524 (t0) REVERT: A 1050 GLU cc_start: 0.8884 (tt0) cc_final: 0.8671 (tt0) REVERT: A 1070 GLN cc_start: 0.9355 (mt0) cc_final: 0.9151 (mt0) REVERT: A 1110 ASN cc_start: 0.8845 (m-40) cc_final: 0.8229 (p0) REVERT: A 1196 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8225 (mm-30) REVERT: A 1267 MET cc_start: 0.7949 (mtm) cc_final: 0.7721 (mtm) REVERT: A 1269 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8247 (mp0) REVERT: B 101 MET cc_start: 0.9065 (mtt) cc_final: 0.8787 (mtp) REVERT: B 216 GLU cc_start: 0.8329 (tt0) cc_final: 0.8112 (tt0) REVERT: B 388 CYS cc_start: 0.9270 (t) cc_final: 0.8860 (t) REVERT: B 563 MET cc_start: 0.8510 (ttp) cc_final: 0.8078 (ptm) REVERT: B 860 MET cc_start: 0.8790 (ttp) cc_final: 0.8089 (tmm) REVERT: B 864 LYS cc_start: 0.8902 (mtmt) cc_final: 0.8362 (pttp) REVERT: B 906 SER cc_start: 0.8413 (p) cc_final: 0.8113 (t) REVERT: B 1072 MET cc_start: 0.8943 (mtp) cc_final: 0.8575 (mtp) REVERT: B 1152 MET cc_start: 0.8801 (mmm) cc_final: 0.8388 (mmm) REVERT: B 1206 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8400 (mt-10) REVERT: C 37 MET cc_start: 0.9048 (mtm) cc_final: 0.8658 (mtm) REVERT: C 60 ASP cc_start: 0.8558 (OUTLIER) cc_final: 0.8066 (t0) REVERT: C 220 ASP cc_start: 0.8698 (t0) cc_final: 0.8343 (t0) REVERT: D 23 ASN cc_start: 0.7416 (t0) cc_final: 0.7203 (t0) REVERT: D 56 ARG cc_start: 0.7753 (ttp80) cc_final: 0.7533 (ttp80) REVERT: D 65 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8502 (mp0) REVERT: D 68 ARG cc_start: 0.8503 (mtt180) cc_final: 0.8056 (tpm170) REVERT: D 131 GLU cc_start: 0.8511 (mm-30) cc_final: 0.7882 (pt0) REVERT: D 142 LYS cc_start: 0.8751 (tttt) cc_final: 0.8189 (ptmt) REVERT: D 145 MET cc_start: 0.9212 (OUTLIER) cc_final: 0.9000 (mmm) REVERT: D 156 ASP cc_start: 0.8143 (p0) cc_final: 0.7651 (p0) REVERT: E 22 MET cc_start: 0.9664 (ttp) cc_final: 0.9144 (tmm) REVERT: E 114 ASN cc_start: 0.7739 (t0) cc_final: 0.7294 (t0) REVERT: E 182 ASP cc_start: 0.9051 (t0) cc_final: 0.8846 (t0) REVERT: F 81 THR cc_start: 0.9589 (m) cc_final: 0.9094 (p) REVERT: F 116 ASP cc_start: 0.9023 (t0) cc_final: 0.8656 (t70) REVERT: F 129 LYS cc_start: 0.9151 (mmtm) cc_final: 0.8682 (mmmm) REVERT: F 144 GLU cc_start: 0.8509 (mt-10) cc_final: 0.7881 (mt-10) REVERT: G 1 MET cc_start: 0.7328 (tmm) cc_final: 0.6856 (tmm) REVERT: G 106 MET cc_start: 0.8437 (mtm) cc_final: 0.8136 (mtt) REVERT: G 111 THR cc_start: 0.8489 (p) cc_final: 0.8246 (t) REVERT: H 37 LYS cc_start: 0.8491 (mptt) cc_final: 0.8072 (mmtt) REVERT: H 41 ASP cc_start: 0.8810 (m-30) cc_final: 0.8269 (m-30) REVERT: H 123 MET cc_start: 0.8545 (tmm) cc_final: 0.7947 (tmm) REVERT: H 130 ARG cc_start: 0.9040 (mtp-110) cc_final: 0.8655 (mmm160) REVERT: I 4 PHE cc_start: 0.7798 (m-80) cc_final: 0.7327 (m-80) REVERT: I 12 ASN cc_start: 0.7897 (m-40) cc_final: 0.7647 (t0) REVERT: I 27 PHE cc_start: 0.8060 (m-80) cc_final: 0.7761 (m-80) REVERT: I 36 GLU cc_start: 0.9115 (pt0) cc_final: 0.8750 (pt0) REVERT: I 44 TYR cc_start: 0.8853 (t80) cc_final: 0.8467 (t80) REVERT: I 62 ILE cc_start: 0.8823 (tt) cc_final: 0.8556 (tt) REVERT: I 68 LEU cc_start: 0.9233 (mt) cc_final: 0.8954 (mt) REVERT: J 27 GLU cc_start: 0.8474 (mt-10) cc_final: 0.7915 (mt-10) REVERT: J 29 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8206 (tm-30) REVERT: J 49 MET cc_start: 0.9505 (tpp) cc_final: 0.8989 (mmm) REVERT: K 5 ASP cc_start: 0.8925 (t0) cc_final: 0.8533 (t0) REVERT: K 64 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8200 (mm-30) REVERT: K 72 LYS cc_start: 0.9538 (mttt) cc_final: 0.9291 (mtmm) REVERT: K 85 ASP cc_start: 0.9233 (m-30) cc_final: 0.9024 (m-30) REVERT: L 47 ARG cc_start: 0.7742 (ttp-110) cc_final: 0.6738 (ttt90) REVERT: L 53 HIS cc_start: 0.7281 (t-170) cc_final: 0.6902 (t-170) outliers start: 69 outliers final: 44 residues processed: 458 average time/residue: 0.1779 time to fit residues: 135.2211 Evaluate side-chains 447 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 400 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 408 ASP Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1079 MET Chi-restraints excluded: chain A residue 1206 ASP Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 837 ASP Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 1071 VAL Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 64 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 317 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 159 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 143 optimal weight: 0.8980 chunk 114 optimal weight: 20.0000 chunk 150 optimal weight: 6.9990 chunk 144 optimal weight: 0.0870 chunk 31 optimal weight: 3.9990 chunk 293 optimal weight: 20.0000 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 HIS ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 862 GLN B 951 GLN ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN ** I 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.080800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.058130 restraints weight = 94927.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.059994 restraints weight = 48288.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.061241 restraints weight = 30866.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.062054 restraints weight = 22963.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.062554 restraints weight = 18976.173| |-----------------------------------------------------------------------------| r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33905 Z= 0.125 Angle : 0.579 12.453 46198 Z= 0.299 Chirality : 0.044 0.240 5190 Planarity : 0.004 0.050 5630 Dihedral : 16.690 155.633 5346 Min Nonbonded Distance : 1.024 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.76 % Favored : 96.13 % Rotamer: Outliers : 1.66 % Allowed : 15.08 % Favored : 83.26 % 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: 3854 helix: 1.44 (0.15), residues: 1345 sheet: -0.12 (0.21), residues: 606 loop : -0.43 (0.15), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 153 TYR 0.029 0.001 TYR H 95 PHE 0.031 0.001 PHE D 175 TRP 0.009 0.001 TRP C 192 HIS 0.010 0.001 HIS A 706 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (33873) covalent geometry : angle 0.57068 / 0.30 (46153) hydrogen bonds : bond 0.03496 / 2.37 ( 1420) hydrogen bonds : angle 4.69616 / 3.38 ( 3868) metal coordination : bond 0.00542 / 0.33 ( 32) metal coordination : angle 3.19563 / 2.22 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 441 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.9456 (mmm) cc_final: 0.9154 (mtp) REVERT: A 415 LEU cc_start: 0.9522 (mt) cc_final: 0.9307 (mt) REVERT: A 455 MET cc_start: 0.8504 (ttp) cc_final: 0.8235 (ttm) REVERT: A 504 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9278 (mp) REVERT: A 542 GLU cc_start: 0.7685 (mp0) cc_final: 0.7443 (mp0) REVERT: A 873 MET cc_start: 0.9154 (mmp) cc_final: 0.8894 (mmp) REVERT: A 1050 GLU cc_start: 0.8864 (tt0) cc_final: 0.8645 (tt0) REVERT: A 1110 ASN cc_start: 0.8798 (m-40) cc_final: 0.8309 (p0) REVERT: A 1192 LEU cc_start: 0.8416 (tp) cc_final: 0.8119 (tp) REVERT: A 1196 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8230 (mm-30) REVERT: A 1269 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8243 (mp0) REVERT: B 101 MET cc_start: 0.9037 (mtt) cc_final: 0.8752 (mtp) REVERT: B 216 GLU cc_start: 0.8310 (tt0) cc_final: 0.8055 (tt0) REVERT: B 388 CYS cc_start: 0.9215 (t) cc_final: 0.8770 (t) REVERT: B 418 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8988 (ttmt) REVERT: B 444 MET cc_start: 0.7617 (mmp) cc_final: 0.7263 (mmp) REVERT: B 769 TYR cc_start: 0.9018 (m-10) cc_final: 0.8698 (m-80) REVERT: B 860 MET cc_start: 0.8774 (ttp) cc_final: 0.8109 (tmm) REVERT: B 864 LYS cc_start: 0.8853 (mtmt) cc_final: 0.8266 (pttp) REVERT: B 906 SER cc_start: 0.8353 (p) cc_final: 0.8097 (t) REVERT: B 1072 MET cc_start: 0.8875 (mtp) cc_final: 0.8673 (mtp) REVERT: B 1152 MET cc_start: 0.8828 (mmm) cc_final: 0.8422 (mmm) REVERT: B 1206 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8398 (mt-10) REVERT: C 33 LEU cc_start: 0.9419 (tp) cc_final: 0.8635 (tp) REVERT: C 37 MET cc_start: 0.9022 (mtm) cc_final: 0.8504 (mtm) REVERT: C 60 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.8136 (t0) REVERT: C 220 ASP cc_start: 0.8606 (t0) cc_final: 0.8226 (t0) REVERT: D 56 ARG cc_start: 0.7755 (ttp80) cc_final: 0.7236 (mtp85) REVERT: D 65 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8466 (mp0) REVERT: D 68 ARG cc_start: 0.8520 (mtt180) cc_final: 0.8056 (tpm170) REVERT: D 131 GLU cc_start: 0.8475 (mm-30) cc_final: 0.7799 (pt0) REVERT: D 142 LYS cc_start: 0.8781 (tttt) cc_final: 0.8268 (ptpt) REVERT: D 153 ARG cc_start: 0.7681 (ttt-90) cc_final: 0.7423 (tmt170) REVERT: D 156 ASP cc_start: 0.8028 (p0) cc_final: 0.7510 (p0) REVERT: D 176 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8690 (mp0) REVERT: E 22 MET cc_start: 0.9657 (ttp) cc_final: 0.9167 (tmm) REVERT: E 182 ASP cc_start: 0.9028 (t0) cc_final: 0.8818 (t0) REVERT: E 208 TYR cc_start: 0.9206 (t80) cc_final: 0.8952 (t80) REVERT: F 81 THR cc_start: 0.9588 (m) cc_final: 0.8941 (p) REVERT: F 89 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8421 (mt-10) REVERT: F 116 ASP cc_start: 0.9022 (t0) cc_final: 0.8655 (t70) REVERT: F 129 LYS cc_start: 0.9096 (mmtm) cc_final: 0.8613 (mmmm) REVERT: F 144 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8179 (mt-10) REVERT: G 1 MET cc_start: 0.7322 (tmm) cc_final: 0.6824 (tmm) REVERT: G 13 LEU cc_start: 0.9108 (tt) cc_final: 0.8855 (tt) REVERT: G 50 ASP cc_start: 0.8221 (t0) cc_final: 0.7987 (t0) REVERT: G 106 MET cc_start: 0.8446 (mtm) cc_final: 0.8008 (mtt) REVERT: G 111 THR cc_start: 0.8441 (p) cc_final: 0.8166 (t) REVERT: G 115 MET cc_start: 0.7215 (mtp) cc_final: 0.6568 (ptp) REVERT: H 41 ASP cc_start: 0.8809 (m-30) cc_final: 0.8271 (m-30) REVERT: H 130 ARG cc_start: 0.9025 (mtp-110) cc_final: 0.8620 (mmm160) REVERT: H 138 GLU cc_start: 0.8414 (pm20) cc_final: 0.7760 (pm20) REVERT: I 4 PHE cc_start: 0.7726 (m-80) cc_final: 0.7258 (m-80) REVERT: I 12 ASN cc_start: 0.7945 (m-40) cc_final: 0.6739 (m110) REVERT: I 36 GLU cc_start: 0.9101 (pt0) cc_final: 0.8776 (pt0) REVERT: I 44 TYR cc_start: 0.8891 (t80) cc_final: 0.8525 (t80) REVERT: I 62 ILE cc_start: 0.8841 (tt) cc_final: 0.8571 (tt) REVERT: I 65 ASP cc_start: 0.8789 (t70) cc_final: 0.8414 (t0) REVERT: I 68 LEU cc_start: 0.9234 (mt) cc_final: 0.8986 (mt) REVERT: J 27 GLU cc_start: 0.8462 (mt-10) cc_final: 0.7832 (mt-10) REVERT: J 29 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8147 (tm-30) REVERT: J 32 GLU cc_start: 0.9169 (mp0) cc_final: 0.8735 (mm-30) REVERT: K 5 ASP cc_start: 0.8984 (t0) cc_final: 0.8656 (t0) REVERT: K 64 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8127 (mm-30) REVERT: K 72 LYS cc_start: 0.9467 (mttt) cc_final: 0.9209 (mtmm) REVERT: K 85 ASP cc_start: 0.9216 (m-30) cc_final: 0.9013 (m-30) REVERT: L 33 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7339 (mt-10) REVERT: L 47 ARG cc_start: 0.7830 (ttp-110) cc_final: 0.6731 (ttt90) outliers start: 57 outliers final: 39 residues processed: 474 average time/residue: 0.1911 time to fit residues: 150.2735 Evaluate side-chains 449 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 406 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1079 MET Chi-restraints excluded: chain A residue 1206 ASP Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 1071 VAL Chi-restraints excluded: chain B residue 1100 ASP Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1183 LYS Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 382 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 200 optimal weight: 0.0020 chunk 306 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 354 optimal weight: 7.9990 chunk 270 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 357 optimal weight: 7.9990 chunk 254 optimal weight: 1.9990 chunk 351 optimal weight: 10.0000 overall best weight: 3.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1040 ASN ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN ** F 100 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 = 0.3239 r_free = 0.3239 target = 0.079045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.056514 restraints weight = 96817.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.058338 restraints weight = 49507.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.059537 restraints weight = 31766.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.060333 restraints weight = 23812.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.060831 restraints weight = 19732.729| |-----------------------------------------------------------------------------| r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 33905 Z= 0.236 Angle : 0.637 11.933 46198 Z= 0.326 Chirality : 0.044 0.255 5190 Planarity : 0.004 0.050 5630 Dihedral : 16.719 157.079 5346 Min Nonbonded Distance : 0.948 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.70 % Favored : 95.20 % Rotamer: Outliers : 2.01 % Allowed : 15.61 % Favored : 82.38 % 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: 0.29 (0.14), residues: 3854 helix: 1.38 (0.15), residues: 1344 sheet: -0.29 (0.21), residues: 621 loop : -0.45 (0.15), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 476 TYR 0.026 0.001 TYR H 95 PHE 0.033 0.002 PHE D 175 TRP 0.009 0.001 TRP B 31 HIS 0.009 0.001 HIS A 706 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.24 (33873) covalent geometry : angle 0.62873 / 0.33 (46153) hydrogen bonds : bond 0.03751 / 2.53 ( 1420) hydrogen bonds : angle 4.77974 / 3.44 ( 3868) metal coordination : bond 0.00984 / 0.61 ( 32) metal coordination : angle 3.37804 / 2.48 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 405 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.9314 (OUTLIER) cc_final: 0.9097 (tp30) REVERT: A 304 MET cc_start: 0.9473 (mmm) cc_final: 0.9030 (mtp) REVERT: A 455 MET cc_start: 0.8534 (ttp) cc_final: 0.8309 (ttm) REVERT: A 486 GLU cc_start: 0.8229 (tt0) cc_final: 0.7951 (tt0) REVERT: A 504 LEU cc_start: 0.9544 (OUTLIER) cc_final: 0.9313 (mp) REVERT: A 1062 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7630 (mt-10) REVERT: A 1110 ASN cc_start: 0.8847 (m-40) cc_final: 0.8318 (p0) REVERT: A 1192 LEU cc_start: 0.8347 (tp) cc_final: 0.8094 (tp) REVERT: A 1259 MET cc_start: 0.8678 (mmm) cc_final: 0.8423 (mmm) REVERT: A 1269 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8233 (mp0) REVERT: B 101 MET cc_start: 0.9059 (mtt) cc_final: 0.8779 (mtp) REVERT: B 216 GLU cc_start: 0.8332 (tt0) cc_final: 0.8112 (tt0) REVERT: B 388 CYS cc_start: 0.9243 (t) cc_final: 0.8833 (t) REVERT: B 860 MET cc_start: 0.8757 (ttp) cc_final: 0.8110 (tmm) REVERT: B 864 LYS cc_start: 0.8844 (mtmt) cc_final: 0.8273 (pttp) REVERT: B 906 SER cc_start: 0.8372 (p) cc_final: 0.8066 (t) REVERT: B 1072 MET cc_start: 0.8965 (mtp) cc_final: 0.8561 (mtp) REVERT: B 1152 MET cc_start: 0.8808 (mmm) cc_final: 0.8482 (mmm) REVERT: B 1206 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8450 (mt-10) REVERT: C 37 MET cc_start: 0.9057 (mtm) cc_final: 0.8720 (mtm) REVERT: C 60 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.8192 (t0) REVERT: C 220 ASP cc_start: 0.8687 (t0) cc_final: 0.8322 (t0) REVERT: D 56 ARG cc_start: 0.7956 (ttp80) cc_final: 0.7730 (ttp80) REVERT: D 65 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8523 (mp0) REVERT: D 68 ARG cc_start: 0.8535 (mtt180) cc_final: 0.8084 (tpm170) REVERT: D 131 GLU cc_start: 0.8497 (mm-30) cc_final: 0.7811 (pt0) REVERT: D 142 LYS cc_start: 0.8802 (tttt) cc_final: 0.8344 (ptpt) REVERT: D 153 ARG cc_start: 0.7796 (ttt-90) cc_final: 0.7472 (tmt170) REVERT: D 156 ASP cc_start: 0.8062 (p0) cc_final: 0.7514 (p0) REVERT: D 176 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8585 (mt-10) REVERT: E 182 ASP cc_start: 0.9042 (t0) cc_final: 0.8825 (t0) REVERT: F 81 THR cc_start: 0.9586 (m) cc_final: 0.8953 (p) REVERT: F 116 ASP cc_start: 0.9052 (t0) cc_final: 0.8676 (t70) REVERT: F 129 LYS cc_start: 0.9143 (mmtm) cc_final: 0.8652 (mmmm) REVERT: F 144 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8271 (mt-10) REVERT: G 1 MET cc_start: 0.7408 (tmm) cc_final: 0.6902 (tmm) REVERT: G 13 LEU cc_start: 0.9104 (tt) cc_final: 0.8846 (tt) REVERT: G 106 MET cc_start: 0.8387 (mtm) cc_final: 0.8160 (mtt) REVERT: G 111 THR cc_start: 0.8451 (p) cc_final: 0.8213 (t) REVERT: H 37 LYS cc_start: 0.8446 (mptt) cc_final: 0.8048 (mmtm) REVERT: H 130 ARG cc_start: 0.9065 (mtp-110) cc_final: 0.8646 (mmm160) REVERT: H 138 GLU cc_start: 0.8460 (pm20) cc_final: 0.7755 (pm20) REVERT: I 4 PHE cc_start: 0.7842 (m-80) cc_final: 0.7337 (m-80) REVERT: I 9 ASP cc_start: 0.7765 (m-30) cc_final: 0.7559 (m-30) REVERT: I 12 ASN cc_start: 0.8012 (m-40) cc_final: 0.6849 (m110) REVERT: I 36 GLU cc_start: 0.9171 (pt0) cc_final: 0.8814 (pt0) REVERT: I 44 TYR cc_start: 0.8856 (t80) cc_final: 0.8477 (t80) REVERT: I 62 ILE cc_start: 0.8873 (tt) cc_final: 0.8629 (tt) REVERT: I 65 ASP cc_start: 0.8806 (t70) cc_final: 0.8448 (t0) REVERT: I 68 LEU cc_start: 0.9235 (mt) cc_final: 0.8966 (mt) REVERT: I 87 GLN cc_start: 0.7441 (mt0) cc_final: 0.7196 (mt0) REVERT: J 27 GLU cc_start: 0.8535 (mt-10) cc_final: 0.7825 (mt-10) REVERT: J 28 ASP cc_start: 0.8529 (p0) cc_final: 0.8296 (p0) REVERT: J 29 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8150 (tm-30) REVERT: J 32 GLU cc_start: 0.9228 (mp0) cc_final: 0.8758 (mm-30) REVERT: J 58 GLU cc_start: 0.8317 (tm-30) cc_final: 0.8111 (tm-30) REVERT: K 5 ASP cc_start: 0.9062 (t0) cc_final: 0.8841 (t0) REVERT: K 64 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8147 (mm-30) REVERT: K 72 LYS cc_start: 0.9537 (mttt) cc_final: 0.9288 (mtmm) REVERT: K 85 ASP cc_start: 0.9234 (m-30) cc_final: 0.9028 (m-30) REVERT: L 33 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7653 (mt-10) REVERT: L 47 ARG cc_start: 0.7832 (ttp-110) cc_final: 0.6732 (ttt90) outliers start: 69 outliers final: 46 residues processed: 452 average time/residue: 0.1783 time to fit residues: 133.5538 Evaluate side-chains 440 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 389 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 932 GLU Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 1071 VAL Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1183 LYS Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 86 PHE Chi-restraints excluded: chain I residue 111 THR 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 93 SER Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 64 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 20 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 363 optimal weight: 10.0000 chunk 243 optimal weight: 9.9990 chunk 331 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 275 optimal weight: 0.0060 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN I 108 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.080657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.057869 restraints weight = 95315.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.059753 restraints weight = 47899.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.061029 restraints weight = 30485.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.061845 restraints weight = 22592.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.062374 restraints weight = 18666.226| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33905 Z= 0.124 Angle : 0.585 11.734 46198 Z= 0.301 Chirality : 0.043 0.237 5190 Planarity : 0.004 0.050 5630 Dihedral : 16.646 155.036 5346 Min Nonbonded Distance : 1.001 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.66 % Favored : 96.24 % Rotamer: Outliers : 1.66 % Allowed : 16.39 % Favored : 81.95 % 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: 3854 helix: 1.45 (0.15), residues: 1344 sheet: -0.18 (0.21), residues: 626 loop : -0.39 (0.15), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 192 TYR 0.022 0.001 TYR H 95 PHE 0.032 0.001 PHE D 175 TRP 0.009 0.001 TRP C 192 HIS 0.008 0.001 HIS A 706 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (33873) covalent geometry : angle 0.57832 / 0.30 (46153) hydrogen bonds : bond 0.03395 / 2.29 ( 1420) hydrogen bonds : angle 4.60921 / 3.31 ( 3868) metal coordination : bond 0.00549 / 0.34 ( 32) metal coordination : angle 2.89907 / 2.02 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 418 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 ASP cc_start: 0.8845 (m-30) cc_final: 0.8637 (p0) REVERT: A 304 MET cc_start: 0.9475 (mmm) cc_final: 0.9067 (mtp) REVERT: A 1110 ASN cc_start: 0.8771 (m-40) cc_final: 0.8307 (p0) REVERT: A 1192 LEU cc_start: 0.8360 (tp) cc_final: 0.8109 (tp) REVERT: A 1259 MET cc_start: 0.8639 (mmm) cc_final: 0.8373 (mmm) REVERT: A 1269 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8186 (mp0) REVERT: A 1444 MET cc_start: 0.8526 (mmt) cc_final: 0.8283 (mmt) REVERT: B 101 MET cc_start: 0.9014 (mtt) cc_final: 0.8736 (mtp) REVERT: B 216 GLU cc_start: 0.8287 (tt0) cc_final: 0.8062 (tt0) REVERT: B 388 CYS cc_start: 0.9181 (t) cc_final: 0.8734 (t) REVERT: B 563 MET cc_start: 0.8742 (ttp) cc_final: 0.8289 (ptm) REVERT: B 769 TYR cc_start: 0.8995 (m-10) cc_final: 0.8766 (m-80) REVERT: B 860 MET cc_start: 0.8750 (ttp) cc_final: 0.8138 (tmm) REVERT: B 864 LYS cc_start: 0.8903 (mtmt) cc_final: 0.8265 (pttp) REVERT: B 906 SER cc_start: 0.8327 (p) cc_final: 0.8053 (t) REVERT: B 1072 MET cc_start: 0.8869 (mtp) cc_final: 0.8482 (mtp) REVERT: B 1152 MET cc_start: 0.8893 (mmm) cc_final: 0.8615 (mmm) REVERT: B 1206 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8408 (mt-10) REVERT: C 37 MET cc_start: 0.9031 (mtm) cc_final: 0.8714 (mtm) REVERT: C 60 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.8085 (t0) REVERT: C 62 PHE cc_start: 0.9102 (t80) cc_final: 0.8898 (t80) REVERT: C 220 ASP cc_start: 0.8584 (t0) cc_final: 0.8200 (t0) REVERT: D 56 ARG cc_start: 0.7938 (ttp80) cc_final: 0.7646 (ttp80) REVERT: D 65 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8478 (mp0) REVERT: D 68 ARG cc_start: 0.8552 (mtt180) cc_final: 0.8106 (tpm170) REVERT: D 131 GLU cc_start: 0.8476 (mm-30) cc_final: 0.7847 (pt0) REVERT: D 142 LYS cc_start: 0.8782 (tttt) cc_final: 0.8333 (ptpt) REVERT: D 153 ARG cc_start: 0.7685 (ttt-90) cc_final: 0.7409 (tmt170) REVERT: D 156 ASP cc_start: 0.7964 (p0) cc_final: 0.7512 (p0) REVERT: D 176 GLU cc_start: 0.9001 (OUTLIER) cc_final: 0.8569 (mt-10) REVERT: F 81 THR cc_start: 0.9590 (m) cc_final: 0.8902 (p) REVERT: F 116 ASP cc_start: 0.9033 (t0) cc_final: 0.8672 (t70) REVERT: F 129 LYS cc_start: 0.9083 (mmtm) cc_final: 0.8574 (mmmm) REVERT: F 144 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8243 (mt-10) REVERT: G 1 MET cc_start: 0.7402 (tmm) cc_final: 0.6898 (tmm) REVERT: G 13 LEU cc_start: 0.9099 (tt) cc_final: 0.8862 (tt) REVERT: G 111 THR cc_start: 0.8448 (p) cc_final: 0.8043 (t) REVERT: H 37 LYS cc_start: 0.8582 (mptt) cc_final: 0.8161 (mmtm) REVERT: H 41 ASP cc_start: 0.8824 (m-30) cc_final: 0.8457 (m-30) REVERT: H 130 ARG cc_start: 0.9005 (mtp-110) cc_final: 0.8590 (mmm160) REVERT: H 138 GLU cc_start: 0.8549 (pm20) cc_final: 0.7860 (pm20) REVERT: I 4 PHE cc_start: 0.7777 (m-80) cc_final: 0.7306 (m-80) REVERT: I 9 ASP cc_start: 0.7796 (m-30) cc_final: 0.7578 (m-30) REVERT: I 12 ASN cc_start: 0.7983 (m-40) cc_final: 0.6801 (m110) REVERT: I 36 GLU cc_start: 0.9154 (pt0) cc_final: 0.8801 (pt0) REVERT: I 44 TYR cc_start: 0.8871 (t80) cc_final: 0.8600 (t80) REVERT: I 62 ILE cc_start: 0.8874 (tt) cc_final: 0.8622 (tt) REVERT: I 65 ASP cc_start: 0.8815 (t70) cc_final: 0.8466 (t0) REVERT: I 68 LEU cc_start: 0.9233 (mt) cc_final: 0.8975 (mt) REVERT: I 87 GLN cc_start: 0.7499 (mt0) cc_final: 0.7169 (mt0) REVERT: I 101 PHE cc_start: 0.7614 (m-10) cc_final: 0.7299 (m-10) REVERT: J 27 GLU cc_start: 0.8511 (mt-10) cc_final: 0.7789 (mt-10) REVERT: J 29 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8123 (tm-30) REVERT: J 32 GLU cc_start: 0.9220 (mp0) cc_final: 0.8801 (mm-30) REVERT: J 58 GLU cc_start: 0.8328 (tm-30) cc_final: 0.8123 (tm-30) REVERT: K 5 ASP cc_start: 0.9101 (t0) cc_final: 0.8883 (t0) REVERT: K 64 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8118 (mm-30) REVERT: K 72 LYS cc_start: 0.9507 (mttt) cc_final: 0.9258 (mtmm) REVERT: L 33 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7721 (mt-10) REVERT: L 47 ARG cc_start: 0.7895 (ttp-110) cc_final: 0.6780 (ttt90) outliers start: 57 outliers final: 46 residues processed: 455 average time/residue: 0.2141 time to fit residues: 162.5995 Evaluate side-chains 447 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 399 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain A residue 1206 ASP Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 1071 VAL Chi-restraints excluded: chain B residue 1100 ASP Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1183 LYS Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 111 THR 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 93 SER Chi-restraints excluded: chain L residue 57 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 58 optimal weight: 10.0000 chunk 377 optimal weight: 0.0370 chunk 167 optimal weight: 9.9990 chunk 196 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 331 optimal weight: 0.0570 chunk 134 optimal weight: 6.9990 chunk 247 optimal weight: 10.0000 chunk 163 optimal weight: 9.9990 overall best weight: 1.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 458 HIS ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 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 = 0.3267 r_free = 0.3267 target = 0.080425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.057764 restraints weight = 95377.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.059618 restraints weight = 48617.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.060831 restraints weight = 31153.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.061630 restraints weight = 23304.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.062139 restraints weight = 19360.335| |-----------------------------------------------------------------------------| r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33905 Z= 0.146 Angle : 0.597 11.237 46198 Z= 0.306 Chirality : 0.043 0.241 5190 Planarity : 0.004 0.046 5630 Dihedral : 16.626 155.064 5346 Min Nonbonded Distance : 0.991 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.05 % Favored : 95.82 % Rotamer: Outliers : 1.40 % Allowed : 17.01 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.14), residues: 3854 helix: 1.43 (0.15), residues: 1348 sheet: -0.16 (0.21), residues: 620 loop : -0.41 (0.15), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 63 TYR 0.027 0.001 TYR G 44 PHE 0.033 0.001 PHE D 175 TRP 0.009 0.001 TRP C 192 HIS 0.008 0.001 HIS A 706 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (33873) covalent geometry : angle 0.59134 / 0.31 (46153) hydrogen bonds : bond 0.03382 / 2.29 ( 1420) hydrogen bonds : angle 4.57119 / 3.29 ( 3868) metal coordination : bond 0.00623 / 0.38 ( 32) metal coordination : angle 2.79799 / 1.97 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 402 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.8272 (mmp) cc_final: 0.8063 (mmp) REVERT: A 261 ASP cc_start: 0.8866 (m-30) cc_final: 0.8635 (p0) REVERT: A 293 GLU cc_start: 0.9278 (OUTLIER) cc_final: 0.9069 (tp30) REVERT: A 304 MET cc_start: 0.9479 (mmm) cc_final: 0.9109 (mtp) REVERT: A 486 GLU cc_start: 0.8203 (tt0) cc_final: 0.7760 (tt0) REVERT: A 504 LEU cc_start: 0.9559 (mm) cc_final: 0.9299 (mp) REVERT: A 1110 ASN cc_start: 0.8785 (m-40) cc_final: 0.8322 (p0) REVERT: A 1192 LEU cc_start: 0.8459 (tp) cc_final: 0.8215 (tp) REVERT: A 1259 MET cc_start: 0.8630 (mmm) cc_final: 0.8362 (mmm) REVERT: B 101 MET cc_start: 0.9049 (mtt) cc_final: 0.8759 (mtp) REVERT: B 216 GLU cc_start: 0.8319 (tt0) cc_final: 0.8071 (tt0) REVERT: B 388 CYS cc_start: 0.9197 (t) cc_final: 0.8752 (t) REVERT: B 563 MET cc_start: 0.8643 (ttp) cc_final: 0.8127 (ptm) REVERT: B 769 TYR cc_start: 0.9038 (m-10) cc_final: 0.8739 (m-80) REVERT: B 860 MET cc_start: 0.8760 (ttp) cc_final: 0.8155 (tmm) REVERT: B 864 LYS cc_start: 0.8899 (mtmt) cc_final: 0.8256 (pttp) REVERT: B 906 SER cc_start: 0.8322 (p) cc_final: 0.8060 (t) REVERT: B 1072 MET cc_start: 0.8914 (mtp) cc_final: 0.8523 (mtp) REVERT: B 1152 MET cc_start: 0.8910 (mmm) cc_final: 0.8576 (mmm) REVERT: B 1206 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8427 (mt-10) REVERT: C 37 MET cc_start: 0.9040 (mtm) cc_final: 0.8685 (mtm) REVERT: C 60 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.7854 (t0) REVERT: C 62 PHE cc_start: 0.9100 (t80) cc_final: 0.8878 (t80) REVERT: C 220 ASP cc_start: 0.8612 (t0) cc_final: 0.8223 (t0) REVERT: D 56 ARG cc_start: 0.8038 (ttp80) cc_final: 0.7329 (ttp80) REVERT: D 65 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8509 (mp0) REVERT: D 68 ARG cc_start: 0.8568 (mtt180) cc_final: 0.8105 (tpm170) REVERT: D 131 GLU cc_start: 0.8475 (mm-30) cc_final: 0.7849 (pt0) REVERT: D 142 LYS cc_start: 0.8764 (tttt) cc_final: 0.8350 (ptpt) REVERT: D 153 ARG cc_start: 0.7697 (ttt-90) cc_final: 0.7401 (tmt170) REVERT: D 156 ASP cc_start: 0.8013 (p0) cc_final: 0.7597 (p0) REVERT: D 176 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8589 (mt-10) REVERT: F 81 THR cc_start: 0.9597 (m) cc_final: 0.8940 (p) REVERT: F 116 ASP cc_start: 0.9039 (t0) cc_final: 0.8665 (t70) REVERT: F 129 LYS cc_start: 0.9074 (mmtm) cc_final: 0.8584 (mmmm) REVERT: F 144 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8265 (mt-10) REVERT: G 1 MET cc_start: 0.7465 (tmm) cc_final: 0.6931 (tmm) REVERT: G 13 LEU cc_start: 0.9103 (tt) cc_final: 0.8851 (tt) REVERT: G 111 THR cc_start: 0.8363 (p) cc_final: 0.8034 (t) REVERT: G 115 MET cc_start: 0.7286 (mtp) cc_final: 0.6551 (ptp) REVERT: G 122 ASN cc_start: 0.7343 (t0) cc_final: 0.6976 (p0) REVERT: H 37 LYS cc_start: 0.8566 (mptt) cc_final: 0.8118 (mmtm) REVERT: H 130 ARG cc_start: 0.9024 (mtp-110) cc_final: 0.8590 (mmm160) REVERT: H 138 GLU cc_start: 0.8543 (pm20) cc_final: 0.7823 (pm20) REVERT: I 4 PHE cc_start: 0.7797 (m-80) cc_final: 0.7327 (m-80) REVERT: I 12 ASN cc_start: 0.8077 (m-40) cc_final: 0.6916 (m110) REVERT: I 36 GLU cc_start: 0.9162 (pt0) cc_final: 0.8784 (pt0) REVERT: I 44 TYR cc_start: 0.8903 (t80) cc_final: 0.8643 (t80) REVERT: I 62 ILE cc_start: 0.8871 (tt) cc_final: 0.8627 (tt) REVERT: I 65 ASP cc_start: 0.8805 (t70) cc_final: 0.8452 (t0) REVERT: I 68 LEU cc_start: 0.9226 (mt) cc_final: 0.8960 (mt) REVERT: I 87 GLN cc_start: 0.7486 (mt0) cc_final: 0.7141 (mt0) REVERT: I 101 PHE cc_start: 0.7652 (m-10) cc_final: 0.7313 (m-10) REVERT: J 27 GLU cc_start: 0.8572 (mt-10) cc_final: 0.7865 (mt-10) REVERT: J 29 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8146 (tm-30) REVERT: J 32 GLU cc_start: 0.9258 (mp0) cc_final: 0.8840 (mm-30) REVERT: J 58 GLU cc_start: 0.8341 (tm-30) cc_final: 0.8115 (tm-30) REVERT: K 5 ASP cc_start: 0.9116 (t0) cc_final: 0.8874 (t0) REVERT: K 64 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8129 (mm-30) REVERT: K 72 LYS cc_start: 0.9512 (mttt) cc_final: 0.9251 (mtmm) REVERT: L 33 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7669 (mt-10) REVERT: L 47 ARG cc_start: 0.7888 (ttp-110) cc_final: 0.6760 (ttt90) outliers start: 48 outliers final: 43 residues processed: 432 average time/residue: 0.2199 time to fit residues: 157.8864 Evaluate side-chains 440 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 394 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 999 MET Chi-restraints excluded: chain B residue 1071 VAL Chi-restraints excluded: chain B residue 1100 ASP Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1183 LYS Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 111 THR 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 42 LEU Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain L residue 57 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 308 optimal weight: 0.0030 chunk 268 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 176 optimal weight: 7.9990 chunk 232 optimal weight: 0.5980 chunk 49 optimal weight: 5.9990 chunk 314 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 chunk 321 optimal weight: 0.9990 chunk 241 optimal weight: 9.9990 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1130 GLN ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN ** G 102 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 = 0.3283 r_free = 0.3283 target = 0.081177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.058448 restraints weight = 95030.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.060357 restraints weight = 47555.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.061630 restraints weight = 30098.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.062465 restraints weight = 22200.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.062999 restraints weight = 18260.441| |-----------------------------------------------------------------------------| r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33905 Z= 0.119 Angle : 0.590 11.301 46198 Z= 0.302 Chirality : 0.043 0.234 5190 Planarity : 0.004 0.047 5630 Dihedral : 16.577 153.855 5346 Min Nonbonded Distance : 1.020 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.58 % Favored : 96.29 % Rotamer: Outliers : 1.37 % Allowed : 17.12 % Favored : 81.51 % 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: 0.41 (0.14), residues: 3854 helix: 1.42 (0.15), residues: 1355 sheet: -0.16 (0.21), residues: 626 loop : -0.37 (0.15), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 63 TYR 0.023 0.001 TYR H 95 PHE 0.033 0.001 PHE D 175 TRP 0.010 0.001 TRP C 192 HIS 0.007 0.001 HIS I 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (33873) covalent geometry : angle 0.58480 / 0.30 (46153) hydrogen bonds : bond 0.03258 / 2.20 ( 1420) hydrogen bonds : angle 4.49146 / 3.23 ( 3868) metal coordination : bond 0.00500 / 0.31 ( 32) metal coordination : angle 2.60540 / 1.78 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7708 Ramachandran restraints generated. 3854 Oldfield, 0 Emsley, 3854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 428 time to evaluate : 1.240 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 220 THR cc_start: 0.9401 (m) cc_final: 0.9175 (p) REVERT: A 261 ASP cc_start: 0.8829 (m-30) cc_final: 0.8608 (p0) REVERT: A 304 MET cc_start: 0.9464 (mmm) cc_final: 0.9111 (mtp) REVERT: A 487 MET cc_start: 0.8714 (mtm) cc_final: 0.8365 (mtm) REVERT: A 528 LEU cc_start: 0.9323 (mt) cc_final: 0.9039 (mt) REVERT: A 873 MET cc_start: 0.9101 (mmp) cc_final: 0.8729 (mmm) REVERT: A 880 LYS cc_start: 0.9480 (tttt) cc_final: 0.9164 (ttmm) REVERT: A 1110 ASN cc_start: 0.8747 (m-40) cc_final: 0.8329 (p0) REVERT: A 1192 LEU cc_start: 0.8455 (tp) cc_final: 0.8205 (tp) REVERT: B 101 MET cc_start: 0.9029 (mtt) cc_final: 0.8743 (mtp) REVERT: B 216 GLU cc_start: 0.8241 (tt0) cc_final: 0.7994 (tt0) REVERT: B 388 CYS cc_start: 0.9222 (t) cc_final: 0.8743 (t) REVERT: B 444 MET cc_start: 0.7563 (mmp) cc_final: 0.7276 (mmp) REVERT: B 563 MET cc_start: 0.8590 (ttp) cc_final: 0.8101 (ptm) REVERT: B 769 TYR cc_start: 0.8999 (m-10) cc_final: 0.8747 (m-80) REVERT: B 860 MET cc_start: 0.8737 (ttp) cc_final: 0.8144 (tmm) REVERT: B 864 LYS cc_start: 0.8883 (mtmt) cc_final: 0.8242 (pttp) REVERT: B 906 SER cc_start: 0.8302 (p) cc_final: 0.8060 (t) REVERT: B 1072 MET cc_start: 0.8871 (mtp) cc_final: 0.8481 (mtp) REVERT: B 1206 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8465 (mt-10) REVERT: B 1210 MET cc_start: 0.8920 (ttm) cc_final: 0.8606 (ttm) REVERT: C 37 MET cc_start: 0.9063 (mtm) cc_final: 0.8770 (mtm) REVERT: C 60 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.7870 (t0) REVERT: C 62 PHE cc_start: 0.9062 (t80) cc_final: 0.8836 (t80) REVERT: C 220 ASP cc_start: 0.8582 (t0) cc_final: 0.8201 (t0) REVERT: D 48 ILE cc_start: 0.8801 (mm) cc_final: 0.8589 (tt) REVERT: D 56 ARG cc_start: 0.8036 (ttp80) cc_final: 0.7315 (ttp80) REVERT: D 65 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8497 (mp0) REVERT: D 68 ARG cc_start: 0.8561 (mtt180) cc_final: 0.8079 (tpm170) REVERT: D 131 GLU cc_start: 0.8441 (mm-30) cc_final: 0.7796 (pt0) REVERT: D 142 LYS cc_start: 0.8773 (tttt) cc_final: 0.8381 (ptpt) REVERT: D 153 ARG cc_start: 0.7739 (ttt-90) cc_final: 0.7424 (tmt170) REVERT: D 156 ASP cc_start: 0.8003 (p0) cc_final: 0.7608 (p0) REVERT: E 57 MET cc_start: 0.8476 (mtp) cc_final: 0.8176 (mtm) REVERT: F 81 THR cc_start: 0.9597 (m) cc_final: 0.8971 (p) REVERT: F 116 ASP cc_start: 0.9023 (t0) cc_final: 0.8666 (t70) REVERT: F 129 LYS cc_start: 0.9110 (mmtm) cc_final: 0.8557 (mmmm) REVERT: F 144 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8259 (mt-10) REVERT: G 13 LEU cc_start: 0.9117 (tt) cc_final: 0.8884 (tt) REVERT: G 50 ASP cc_start: 0.8280 (t0) cc_final: 0.8057 (t0) REVERT: G 111 THR cc_start: 0.8426 (p) cc_final: 0.8179 (t) REVERT: G 122 ASN cc_start: 0.7341 (t0) cc_final: 0.6981 (p0) REVERT: H 37 LYS cc_start: 0.8510 (mptt) cc_final: 0.8191 (mmtm) REVERT: H 130 ARG cc_start: 0.8979 (mtp-110) cc_final: 0.8566 (mmm160) REVERT: H 138 GLU cc_start: 0.8524 (pm20) cc_final: 0.7911 (pm20) REVERT: I 4 PHE cc_start: 0.7717 (m-80) cc_final: 0.7272 (m-80) REVERT: I 12 ASN cc_start: 0.8038 (m-40) cc_final: 0.6877 (m110) REVERT: I 36 GLU cc_start: 0.9153 (pt0) cc_final: 0.8782 (pt0) REVERT: I 44 TYR cc_start: 0.8891 (t80) cc_final: 0.8663 (t80) REVERT: I 62 ILE cc_start: 0.8886 (tt) cc_final: 0.8669 (tt) REVERT: I 68 LEU cc_start: 0.9240 (mt) cc_final: 0.9000 (mt) REVERT: I 87 GLN cc_start: 0.7461 (mt0) cc_final: 0.7177 (mt0) REVERT: I 101 PHE cc_start: 0.7641 (m-10) cc_final: 0.7365 (m-10) REVERT: J 27 GLU cc_start: 0.8607 (mt-10) cc_final: 0.7828 (mt-10) REVERT: J 29 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8085 (tm-30) REVERT: J 32 GLU cc_start: 0.9253 (mp0) cc_final: 0.8824 (mm-30) REVERT: J 58 GLU cc_start: 0.8390 (tm-30) cc_final: 0.8172 (tm-30) REVERT: K 5 ASP cc_start: 0.9162 (t0) cc_final: 0.8948 (t0) REVERT: K 64 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8019 (mm-30) REVERT: K 72 LYS cc_start: 0.9517 (mttt) cc_final: 0.9256 (mtmm) REVERT: K 85 ASP cc_start: 0.9085 (m-30) cc_final: 0.8815 (p0) REVERT: L 33 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7649 (mt-10) REVERT: L 47 ARG cc_start: 0.7913 (ttp-110) cc_final: 0.6799 (ttt90) outliers start: 47 outliers final: 39 residues processed: 455 average time/residue: 0.2181 time to fit residues: 164.1019 Evaluate side-chains 451 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 411 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 999 MET Chi-restraints excluded: chain B residue 1100 ASP Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1183 LYS Chi-restraints excluded: chain B residue 1213 THR Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 111 THR 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 93 SER Chi-restraints excluded: chain L residue 57 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 352 optimal weight: 0.9990 chunk 284 optimal weight: 0.9990 chunk 354 optimal weight: 2.9990 chunk 214 optimal weight: 0.7980 chunk 374 optimal weight: 0.0770 chunk 155 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 343 optimal weight: 10.0000 chunk 296 optimal weight: 2.9990 chunk 250 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 838 GLN ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 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 = 0.3286 r_free = 0.3286 target = 0.081335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.058634 restraints weight = 94639.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.060511 restraints weight = 48235.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.061757 restraints weight = 30822.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.062572 restraints weight = 22921.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.063080 restraints weight = 18943.203| |-----------------------------------------------------------------------------| r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33905 Z= 0.122 Angle : 0.589 11.151 46198 Z= 0.301 Chirality : 0.043 0.234 5190 Planarity : 0.004 0.047 5630 Dihedral : 16.556 153.652 5346 Min Nonbonded Distance : 1.022 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.79 % Favored : 96.08 % Rotamer: Outliers : 1.28 % Allowed : 17.47 % Favored : 81.25 % 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: 0.44 (0.14), residues: 3854 helix: 1.45 (0.15), residues: 1355 sheet: -0.10 (0.21), residues: 620 loop : -0.36 (0.15), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 63 TYR 0.022 0.001 TYR H 95 PHE 0.031 0.001 PHE D 175 TRP 0.009 0.001 TRP C 192 HIS 0.007 0.001 HIS I 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (33873) covalent geometry : angle 0.58452 / 0.30 (46153) hydrogen bonds : bond 0.03234 / 2.18 ( 1420) hydrogen bonds : angle 4.46323 / 3.21 ( 3868) metal coordination : bond 0.00483 / 0.29 ( 32) metal coordination : angle 2.51097 / 1.75 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5580.74 seconds wall clock time: 97 minutes 29.52 seconds (5849.52 seconds total)