Starting phenix.real_space_refine on Sun Aug 9 10:27:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sbu_54739/08_2026/9sbu_54739.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sbu_54739/08_2026/9sbu_54739.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sbu_54739/08_2026/9sbu_54739.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sbu_54739/08_2026/9sbu_54739.map" model { file = "/net/cci-nas-00/data/ceres_data/9sbu_54739/08_2026/9sbu_54739.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sbu_54739/08_2026/9sbu_54739.cif" } resolution = 3.83 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= 0.022 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33083 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 10942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1390, 10942 Classifications: {'peptide': 1390} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1327} Chain breaks: 7 Chain: "B" Number of atoms: 9155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1150, 9155 Classifications: {'peptide': 1150} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 1100} Chain breaks: 6 Chain: "C" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2095 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain: "D" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1327 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 164} Chain breaks: 2 Chain: "E" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1744 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1340 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1077 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Chain: "I" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 909 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 904 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "N" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 905 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "R" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 197 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna3p': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 886 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 35 Unusual residues: {' MG': 2, ' ZN': 2, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 457 SG CYS A 67 106.762 71.071 94.966 1.00217.52 S ATOM 479 SG CYS A 70 106.255 67.658 93.288 1.00224.85 S ATOM 532 SG CYS A 77 103.533 70.312 93.102 1.00214.43 S ATOM 762 SG CYS A 107 81.170 76.707 135.365 1.00253.89 S ATOM 786 SG CYS A 110 82.757 73.434 136.063 1.00246.55 S ATOM 1091 SG CYS A 148 79.467 74.386 137.869 1.00268.63 S ATOM 1105 SG CYS A 167 82.767 76.210 138.678 1.00257.56 S ATOM 19603 SG CYS B1163 98.545 58.627 104.877 1.00222.81 S ATOM 19621 SG CYS B1166 96.965 61.912 105.399 1.00224.25 S ATOM 19746 SG CYS B1182 100.763 61.624 104.794 1.00229.84 S ATOM 19765 SG CYS B1185 98.997 60.587 108.149 1.00232.00 S ATOM 20753 SG CYS C 86 93.309 75.804 26.125 1.00277.48 S ATOM 20770 SG CYS C 88 96.372 77.805 26.140 1.00278.52 S ATOM 20803 SG CYS C 92 94.304 79.442 24.597 1.00250.18 S ATOM 20826 SG CYS C 95 92.676 79.364 27.643 1.00261.41 S ATOM 28411 SG CYS I 7 38.759 127.038 127.512 1.00418.34 S ATOM 28436 SG CYS I 10 42.519 126.587 127.438 1.00410.33 S ATOM 28602 SG CYS I 29 40.473 123.982 129.223 1.00421.18 S ATOM 28626 SG CYS I 32 40.744 127.419 130.724 1.00424.58 S ATOM 28953 SG CYS I 75 17.007 118.467 88.398 1.00482.20 S ATOM 28975 SG CYS I 78 16.529 121.886 87.045 1.00479.26 S ATOM 29191 SG CYS I 103 20.058 120.477 87.325 1.00469.93 S ATOM 29211 SG CYS I 106 18.224 121.530 90.454 1.00471.95 S ATOM 29313 SG CYS J 7 64.054 91.804 37.989 1.00183.43 S ATOM 29336 SG CYS J 10 63.890 89.573 34.963 1.00193.99 S ATOM 29616 SG CYS J 45 60.709 90.348 36.736 1.00183.67 S ATOM 29622 SG CYS J 46 62.542 92.780 34.443 1.00191.90 S ATOM 30745 SG CYS L 31 97.333 115.157 54.409 1.00330.62 S ATOM 30765 SG CYS L 34 98.368 116.647 51.088 1.00322.80 S ATOM 30869 SG CYS L 48 101.020 115.641 53.661 1.00332.52 S ATOM 30892 SG CYS L 51 98.842 118.610 54.382 1.00333.29 S Time building chain proxies: 6.82, per 1000 atoms: 0.21 Number of scatterers: 33083 At special positions: 0 Unit cell: (152.329, 156.681, 184.971, 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: 2.46 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1804 " pdb="ZN ZN A1804 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 67 " pdb=" ZN A1805 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 148 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " 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 I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb=" ZN J 101 " 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 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " Number of angles added : 45 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 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: 144 helices and 46 sheets defined 39.2% alpha, 19.2% beta 40 base pairs and 77 stacking pairs defined. Time for finding SS restraints: 4.28 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 203 through 213 removed outlier: 3.673A pdb=" N HIS A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 222 Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 260 through 283 removed outlier: 3.617A 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: 3.708A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 524 through 536 removed outlier: 3.784A pdb=" N LEU A 528 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 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: 4.015A 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 removed outlier: 3.535A pdb=" N ILE A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 797 Processing helix chain 'A' and resid 809 through 829 removed outlier: 3.759A pdb=" N GLU A 822 " --> pdb=" O MET A 818 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 845 removed outlier: 3.711A 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: 3.547A pdb=" N LEU A 920 " --> pdb=" O GLY A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 959 through 972 removed outlier: 3.521A pdb=" N ILE A 963 " --> pdb=" O ASN A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 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: 3.793A 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: 4.509A pdb=" N VAL A1098 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Proline residue: A1099 - end of helix Processing helix chain 'A' and resid 1130 through 1139 Processing helix chain 'A' and resid 1142 through 1145 Processing helix chain 'A' and resid 1166 through 1173 Processing helix chain 'A' and resid 1198 through 1205 Processing helix chain 'A' and resid 1208 through 1221 Processing helix chain 'A' and resid 1257 through 1271 removed outlier: 3.611A pdb=" N ILE A1271 " --> pdb=" O MET A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1317 removed outlier: 3.713A pdb=" N MET A1317 " --> pdb=" O LEU A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1340 removed outlier: 3.507A pdb=" N ILE A1335 " --> pdb=" O SER A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1357 Processing helix chain 'A' and resid 1364 through 1376 removed outlier: 3.997A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1401 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1431 Processing helix chain 'A' and resid 1447 through 1452 Processing helix chain 'B' and resid 29 through 37 removed outlier: 4.021A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 66 removed outlier: 3.541A pdb=" N LEU B 48 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASP B 66 " --> pdb=" O ILE B 62 " (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 289 Processing helix chain 'B' and resid 293 through 303 removed outlier: 3.587A pdb=" N ILE B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLU B 299 " --> pdb=" O GLY B 295 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR B 303 " --> pdb=" O GLU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 322 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 370 through 390 removed outlier: 3.560A pdb=" N LYS B 374 " --> pdb=" O PHE B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 438 removed outlier: 3.533A pdb=" N LEU B 412 " --> pdb=" O LEU B 408 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU B 438 " --> pdb=" O ARG B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.534A pdb=" N THR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.654A pdb=" N ARG B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 565 through 569 Processing helix chain 'B' and resid 592 through 607 Processing helix chain 'B' and resid 654 through 667 removed outlier: 3.528A 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: 3.799A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 removed outlier: 3.561A 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: 3.628A pdb=" N ASN B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 775 removed outlier: 3.784A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 788 Processing helix chain 'B' and resid 809 through 813 Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 995 through 999 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.224A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.790A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1061 removed outlier: 3.716A 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 1175 through 1178 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 69 removed outlier: 3.558A pdb=" N LEU C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 206 through 210 Processing helix chain 'C' and resid 239 through 266 Processing helix chain 'D' and resid 51 through 73 Processing helix chain 'D' and resid 118 through 134 removed outlier: 3.501A pdb=" N GLN D 132 " --> pdb=" O VAL D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 151 Processing helix chain 'D' and resid 156 through 171 removed outlier: 3.775A pdb=" N THR D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY D 171 " --> pdb=" O LEU D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 196 through 199 Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'E' and resid 4 through 27 removed outlier: 3.559A pdb=" N GLY E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 44 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 91 through 103 removed outlier: 3.927A pdb=" N THR E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 124 removed outlier: 3.778A pdb=" N MET E 121 " --> pdb=" O THR E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 141 Processing helix chain 'E' and resid 143 through 147 removed outlier: 3.687A pdb=" N HIS E 146 " --> pdb=" O ASN E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.568A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'H' and resid 129 through 133 Processing helix chain 'I' and resid 59 through 65 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 40 Processing helix chain 'J' and resid 43 through 53 removed outlier: 3.774A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N HIS J 53 " --> pdb=" O MET J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 removed outlier: 3.508A pdb=" N PHE J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 42 through 53 removed outlier: 3.537A pdb=" N GLU K 49 " --> pdb=" O LEU K 45 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP K 53 " --> pdb=" O GLU K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 83 Processing sheet with id=AA3, first strand: chain 'A' and resid 173 through 177 Processing sheet with id=AA4, first strand: chain 'A' and resid 250 through 252 Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 344 removed outlier: 3.697A pdb=" N LYS A 343 " --> pdb=" O PHE B1130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.614A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N HIS A 490 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET A 456 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE A 468 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL A 352 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N LEU A 470 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N SER A 354 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 375 through 379 removed outlier: 4.106A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 512 through 513 Processing sheet with id=AA9, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AB1, first strand: chain 'A' and resid 588 through 590 removed outlier: 7.103A 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: 6.608A 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: 4.198A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU A1192 " --> pdb=" O ILE A1152 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ILE A1152 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ARG A1194 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N SER A1150 " --> pdb=" O ARG A1194 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLU A1196 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR I 44 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 49 through 50 removed outlier: 3.944A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N VAL A1443 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 49 through 50 removed outlier: 3.944A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 71 through 73 removed outlier: 5.383A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLY B 127 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N SER B 125 " --> pdb=" O PRO B 100 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA B 153 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU B 138 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 5.488A 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: 5.383A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLY B 127 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N SER B 125 " --> pdb=" O PRO B 100 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.737A 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: 6.233A 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: 4.248A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (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 585 through 590 removed outlier: 5.247A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 640 through 641 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 796 removed outlier: 3.593A pdb=" N ILE B 795 " --> pdb=" O LEU B 854 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN B 951 " --> pdb=" O ARG B 967 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.593A pdb=" N ILE B 795 " --> pdb=" O LEU B 854 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN B 951 " --> pdb=" O ARG B 967 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU L 27 " --> pdb=" O LEU L 40 " (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: 7.069A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE B1012 " --> pdb=" O ALA B 826 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR B1092 " --> pdb=" O GLN B 821 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 873 through 874 Processing sheet with id=AD5, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.688A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD7, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD8, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.770A pdb=" N ASP C 19 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN C 231 " --> pdb=" O GLU C 177 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.535A pdb=" N GLU C 152 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N THR C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LYS C 154 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N VAL C 51 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR C 156 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL C 49 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL C 158 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA C 45 " --> pdb=" O LYS C 160 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 111 through 114 Processing sheet with id=AE2, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AE3, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.284A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.902A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 169 through 170 removed outlier: 5.033A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N LYS G 107 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N GLY G 161 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N PHE G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR G 90 " --> pdb=" O GLN G 102 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 130 through 131 removed outlier: 3.835A pdb=" N TYR G 130 " --> pdb=" O ILE G 137 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE G 137 " --> pdb=" O TYR G 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'H' and resid 4 through 16 removed outlier: 5.519A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY H 99 " --> pdb=" O ALA H 140 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 15 through 18 Processing sheet with id=AE9, first strand: chain 'I' and resid 83 through 86 Processing sheet with id=AF1, first strand: chain 'K' and resid 19 through 24 removed outlier: 4.718A pdb=" N ALA K 30 " --> pdb=" O ASP K 24 " (cutoff:3.500A) 1352 hydrogen bonds defined for protein. 3687 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 105 hydrogen bonds 210 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 77 stacking parallelities Total time for adding SS restraints: 10.48 Time building geometry restraints manager: 3.24 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: 5428 1.31 - 1.44: 8965 1.44 - 1.57: 18991 1.57 - 1.69: 196 1.69 - 1.82: 292 Bond restraints: 33872 Sorted by residual: bond pdb=" C4 ATP A1801 " pdb=" N9 ATP A1801 " ideal model delta sigma weight residual 1.374 1.181 0.193 1.00e-02 1.00e+04 3.71e+02 bond pdb=" C8 ATP A1801 " pdb=" N9 ATP A1801 " ideal model delta sigma weight residual 1.370 1.213 0.157 1.20e-02 6.94e+03 1.71e+02 bond pdb=" C6 ATP A1801 " pdb=" N6 ATP A1801 " ideal model delta sigma weight residual 1.337 1.448 -0.111 1.10e-02 8.26e+03 1.02e+02 bond pdb=" C5 ATP A1801 " pdb=" C6 ATP A1801 " ideal model delta sigma weight residual 1.409 1.334 0.075 1.00e-02 1.00e+04 5.61e+01 bond pdb=" C5 ATP A1801 " pdb=" N7 ATP A1801 " ideal model delta sigma weight residual 1.387 1.455 -0.068 1.00e-02 1.00e+04 4.65e+01 ... (remaining 33867 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.08: 46015 4.08 - 8.16: 130 8.16 - 12.24: 3 12.24 - 16.32: 1 16.32 - 20.40: 1 Bond angle restraints: 46150 Sorted by residual: angle pdb=" PB ATP A1801 " pdb=" O3B ATP A1801 " pdb=" PG ATP A1801 " ideal model delta sigma weight residual 139.87 119.47 20.40 1.00e+00 1.00e+00 4.16e+02 angle pdb=" C4 ATP A1801 " pdb=" N9 ATP A1801 " pdb=" C8 ATP A1801 " ideal model delta sigma weight residual 105.72 119.76 -14.04 1.00e+00 1.00e+00 1.97e+02 angle pdb=" PA ATP A1801 " pdb=" O3A ATP A1801 " pdb=" PB ATP A1801 " ideal model delta sigma weight residual 136.83 125.82 11.01 1.00e+00 1.00e+00 1.21e+02 angle pdb=" N1 ATP A1801 " pdb=" C2 ATP A1801 " pdb=" N3 ATP A1801 " ideal model delta sigma weight residual 128.69 120.28 8.41 1.00e+00 1.00e+00 7.07e+01 angle pdb=" N HIS A 706 " pdb=" CA HIS A 706 " pdb=" C HIS A 706 " ideal model delta sigma weight residual 111.33 104.32 7.01 1.21e+00 6.83e-01 3.36e+01 ... (remaining 46145 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.24: 19575 28.24 - 56.49: 726 56.49 - 84.73: 160 84.73 - 112.97: 3 112.97 - 141.21: 2 Dihedral angle restraints: 20466 sinusoidal: 9132 harmonic: 11334 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 180.00 153.67 26.33 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA VAL E 88 " pdb=" C VAL E 88 " pdb=" N GLY E 89 " pdb=" CA GLY E 89 " ideal model delta harmonic sigma weight residual 180.00 159.62 20.38 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" C4' DT T 50 " pdb=" C3' DT T 50 " pdb=" O3' DT T 50 " pdb=" P DG T 51 " ideal model delta sinusoidal sigma weight residual 220.00 78.79 141.21 1 3.50e+01 8.16e-04 1.39e+01 ... (remaining 20463 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 3804 0.043 - 0.086: 995 0.086 - 0.129: 371 0.129 - 0.172: 17 0.172 - 0.215: 3 Chirality restraints: 5190 Sorted by residual: chirality pdb=" C2' ATP A1801 " pdb=" C1' ATP A1801 " pdb=" C3' ATP A1801 " pdb=" O2' ATP A1801 " both_signs ideal model delta sigma weight residual False -2.68 -2.47 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CB VAL A 474 " pdb=" CA VAL A 474 " pdb=" CG1 VAL A 474 " pdb=" CG2 VAL A 474 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" C3' DT N 43 " pdb=" C4' DT N 43 " pdb=" O3' DT N 43 " pdb=" C2' DT N 43 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.61e-01 ... (remaining 5187 not shown) Planarity restraints: 5629 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 635 " 0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO B 636 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 636 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 636 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 500 " 0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO B 501 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 501 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 501 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A1434 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.50e+00 pdb=" N PRO A1435 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A1435 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A1435 " 0.026 5.00e-02 4.00e+02 ... (remaining 5626 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 168 2.43 - 3.04: 21654 3.04 - 3.66: 50510 3.66 - 4.28: 75270 4.28 - 4.90: 123782 Nonbonded interactions: 271384 Sorted by model distance: nonbonded pdb=" O2A ATP A1801 " pdb="MG MG A1802 " model vdw 1.807 2.170 nonbonded pdb=" O2G ATP A1801 " pdb="MG MG A1802 " model vdw 1.899 2.170 nonbonded pdb=" O2B ATP A1801 " pdb="MG MG A1802 " model vdw 1.907 2.170 nonbonded pdb=" OD1 ASP A 485 " pdb="MG MG A1803 " model vdw 2.054 2.170 nonbonded pdb=" OD2 ASP A 481 " pdb="MG MG A1802 " model vdw 2.119 2.170 ... (remaining 271379 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: 3.210 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: 0.050 Extract box with map and model: 0.490 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 40.270 Find NCS groups from input model: 0.180 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.193 33904 Z= 0.345 Angle : 0.678 26.850 46195 Z= 0.429 Chirality : 0.043 0.215 5190 Planarity : 0.004 0.052 5629 Dihedral : 14.587 141.215 13126 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.88 % Favored : 94.96 % Rotamer: Outliers : 0.20 % Allowed : 0.09 % Favored : 99.71 % 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: 0.54 (0.14), residues: 3852 helix: 1.71 (0.15), residues: 1313 sheet: -0.23 (0.22), residues: 607 loop : -0.34 (0.15), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1222 TYR 0.030 0.001 TYR B 797 PHE 0.018 0.001 PHE A 219 TRP 0.018 0.001 TRP B 561 HIS 0.012 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.35 (33872) covalent geometry : angle 0.64279 / 0.43 (46150) hydrogen bonds : bond 0.19200 / 12.98 ( 1423) hydrogen bonds : angle 6.88986 / 4.96 ( 3897) metal coordination : bond 0.00991 / 0.65 ( 32) metal coordination : angle 6.89090 / 3.81 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 563 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8286 (mtt) cc_final: 0.8047 (mmm) REVERT: A 88 LYS cc_start: 0.9040 (mttt) cc_final: 0.8718 (mtpp) REVERT: A 124 GLN cc_start: 0.9330 (mt0) cc_final: 0.8973 (mp10) REVERT: A 205 GLU cc_start: 0.9276 (tt0) cc_final: 0.8972 (tm-30) REVERT: A 320 ARG cc_start: 0.8879 (mtm110) cc_final: 0.8667 (ttp-110) REVERT: A 453 MET cc_start: 0.9117 (mpp) cc_final: 0.8633 (mmm) REVERT: A 539 THR cc_start: 0.9068 (m) cc_final: 0.8787 (p) REVERT: A 748 MET cc_start: 0.9137 (mtm) cc_final: 0.8903 (mtm) REVERT: A 838 GLN cc_start: 0.9272 (tp40) cc_final: 0.8478 (tm-30) REVERT: A 873 MET cc_start: 0.9407 (mmp) cc_final: 0.8488 (mmp) REVERT: A 903 ASN cc_start: 0.8789 (m110) cc_final: 0.8586 (m110) REVERT: A 919 ILE cc_start: 0.9078 (mm) cc_final: 0.8833 (mm) REVERT: A 1063 MET cc_start: 0.9449 (mmm) cc_final: 0.8935 (mmt) REVERT: A 1071 SER cc_start: 0.9092 (m) cc_final: 0.8873 (p) REVERT: A 1259 MET cc_start: 0.6983 (mmp) cc_final: 0.6650 (tmm) REVERT: A 1285 MET cc_start: 0.8911 (mmt) cc_final: 0.8566 (mtp) REVERT: A 1315 GLU cc_start: 0.9325 (tt0) cc_final: 0.8807 (tm-30) REVERT: A 1336 MET cc_start: 0.9187 (ttt) cc_final: 0.8760 (tpt) REVERT: A 1444 MET cc_start: 0.8908 (mmm) cc_final: 0.8567 (mmm) REVERT: A 1454 MET cc_start: 0.8622 (mtp) cc_final: 0.8410 (mtp) REVERT: B 164 LYS cc_start: 0.8844 (mttt) cc_final: 0.8593 (mppt) REVERT: B 239 GLU cc_start: 0.8574 (pt0) cc_final: 0.8341 (tm-30) REVERT: B 310 MET cc_start: 0.9124 (mtp) cc_final: 0.8717 (mmm) REVERT: B 514 LEU cc_start: 0.9728 (tp) cc_final: 0.9076 (tt) REVERT: B 552 MET cc_start: 0.9271 (mmm) cc_final: 0.8963 (tpp) REVERT: B 563 MET cc_start: 0.9283 (ttp) cc_final: 0.9058 (tmm) REVERT: B 615 MET cc_start: 0.8949 (mtm) cc_final: 0.8654 (mtm) REVERT: B 629 ASP cc_start: 0.8637 (t0) cc_final: 0.8364 (p0) REVERT: B 747 MET cc_start: 0.9305 (mmm) cc_final: 0.9073 (mmm) REVERT: B 778 MET cc_start: 0.9370 (ttm) cc_final: 0.9084 (ttm) REVERT: B 809 MET cc_start: 0.8962 (mtt) cc_final: 0.8641 (mtp) REVERT: B 875 GLU cc_start: 0.8807 (pt0) cc_final: 0.8414 (pm20) REVERT: B 877 PRO cc_start: 0.7799 (Cg_exo) cc_final: 0.7379 (Cg_endo) REVERT: B 895 ASP cc_start: 0.9020 (m-30) cc_final: 0.8766 (t0) REVERT: B 999 MET cc_start: 0.9550 (mmt) cc_final: 0.9273 (mmm) REVERT: B 1111 MET cc_start: 0.8061 (mmm) cc_final: 0.7477 (mmt) REVERT: B 1120 GLU cc_start: 0.8868 (tt0) cc_final: 0.8348 (tt0) REVERT: B 1152 MET cc_start: 0.8461 (mmm) cc_final: 0.8236 (mmm) REVERT: C 15 LYS cc_start: 0.9348 (ptpt) cc_final: 0.8716 (tptp) REVERT: C 50 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8156 (mm-30) REVERT: C 57 VAL cc_start: 0.9470 (m) cc_final: 0.9080 (p) REVERT: C 190 ASP cc_start: 0.8897 (t0) cc_final: 0.8657 (t0) REVERT: D 9 GLN cc_start: 0.1992 (mt0) cc_final: 0.1277 (mt0) REVERT: D 38 ILE cc_start: 0.7528 (mt) cc_final: 0.7268 (mt) REVERT: D 41 GLN cc_start: 0.8918 (mp10) cc_final: 0.8701 (mp10) REVERT: D 65 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7932 (tt0) REVERT: D 67 ARG cc_start: 0.7825 (ttm170) cc_final: 0.7561 (tpm170) REVERT: D 140 ASP cc_start: 0.7309 (m-30) cc_final: 0.6552 (m-30) REVERT: D 210 ILE cc_start: 0.9316 (mt) cc_final: 0.9073 (tp) REVERT: E 32 GLN cc_start: 0.9197 (tt0) cc_final: 0.8819 (tp-100) REVERT: E 57 MET cc_start: 0.9186 (mtm) cc_final: 0.8753 (ptp) REVERT: E 58 MET cc_start: 0.9296 (mtp) cc_final: 0.8891 (mtp) REVERT: E 74 ASP cc_start: 0.9568 (m-30) cc_final: 0.9278 (p0) REVERT: E 121 MET cc_start: 0.9318 (mtm) cc_final: 0.9058 (mpp) REVERT: E 214 CYS cc_start: 0.9476 (t) cc_final: 0.9162 (t) REVERT: E 215 MET cc_start: 0.8317 (ptt) cc_final: 0.7578 (ppp) REVERT: F 89 GLU cc_start: 0.9336 (mt-10) cc_final: 0.9100 (mt-10) REVERT: F 111 LEU cc_start: 0.9263 (mt) cc_final: 0.8970 (mm) REVERT: F 112 GLU cc_start: 0.9142 (mp0) cc_final: 0.8737 (mp0) REVERT: F 116 ASP cc_start: 0.8726 (t0) cc_final: 0.8170 (t0) REVERT: F 119 ARG cc_start: 0.9438 (tpp80) cc_final: 0.9129 (tpp80) REVERT: F 123 LYS cc_start: 0.9209 (tttm) cc_final: 0.8867 (tttp) REVERT: F 128 LYS cc_start: 0.9358 (mmtp) cc_final: 0.8969 (mmmm) REVERT: F 129 LYS cc_start: 0.8802 (mmtm) cc_final: 0.8559 (mmmm) REVERT: F 149 GLU cc_start: 0.9183 (tt0) cc_final: 0.8450 (tm-30) REVERT: F 150 GLU cc_start: 0.8854 (pt0) cc_final: 0.8598 (pt0) REVERT: G 3 PHE cc_start: 0.8558 (m-80) cc_final: 0.8239 (m-80) REVERT: G 22 MET cc_start: 0.8669 (ttp) cc_final: 0.8332 (ttm) REVERT: G 28 THR cc_start: 0.8862 (m) cc_final: 0.8438 (p) REVERT: G 35 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7107 (mt-10) REVERT: G 73 LYS cc_start: 0.8466 (mmtp) cc_final: 0.8256 (mtpt) REVERT: G 82 PHE cc_start: 0.5840 (m-80) cc_final: 0.5538 (m-80) REVERT: G 121 PHE cc_start: 0.1529 (t80) cc_final: 0.1034 (t80) REVERT: H 14 GLU cc_start: 0.9127 (tt0) cc_final: 0.8926 (mm-30) REVERT: H 24 CYS cc_start: 0.9022 (m) cc_final: 0.8749 (m) REVERT: H 27 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8743 (mp0) REVERT: H 32 THR cc_start: 0.9369 (m) cc_final: 0.9006 (p) REVERT: H 35 GLN cc_start: 0.8409 (mt0) cc_final: 0.7716 (pm20) REVERT: H 77 ARG cc_start: 0.8131 (ptt90) cc_final: 0.7917 (ptm160) REVERT: I 15 TYR cc_start: 0.4230 (m-80) cc_final: 0.3962 (m-80) REVERT: J 58 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8818 (tm-30) REVERT: K 11 LEU cc_start: 0.8691 (mt) cc_final: 0.8365 (mt) REVERT: K 20 LYS cc_start: 0.9096 (tttp) cc_final: 0.8605 (tttm) REVERT: K 22 ASP cc_start: 0.8486 (m-30) cc_final: 0.8148 (m-30) REVERT: K 49 GLU cc_start: 0.9170 (mm-30) cc_final: 0.8706 (tp30) REVERT: K 54 ARG cc_start: 0.9455 (mtm180) cc_final: 0.9179 (mmm-85) REVERT: L 60 ARG cc_start: 0.8045 (ttm-80) cc_final: 0.7679 (ttm-80) outliers start: 7 outliers final: 0 residues processed: 569 average time/residue: 0.2160 time to fit residues: 195.0173 Evaluate side-chains 351 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 1.281 ------------------------------------------------------------------------------- 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: 50.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.0770 chunk 132 optimal weight: 0.3980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 7.9990 overall best weight: 2.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 339 ASN A 358 ASN ** A 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 698 GLN ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 ASN B 761 HIS B 986 GLN C 203 GLN D 37 GLN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 HIS K 104 ASN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.087016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.058709 restraints weight = 95409.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.060603 restraints weight = 48649.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.061827 restraints weight = 32202.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.062587 restraints weight = 25076.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 66)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.063032 restraints weight = 21651.060| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 33904 Z= 0.186 Angle : 0.676 31.992 46195 Z= 0.340 Chirality : 0.046 0.341 5190 Planarity : 0.005 0.079 5629 Dihedral : 16.876 141.253 5345 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.39 % Favored : 95.53 % Rotamer: Outliers : 0.90 % Allowed : 6.35 % Favored : 92.75 % 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: 0.49 (0.14), residues: 3852 helix: 1.59 (0.14), residues: 1331 sheet: -0.19 (0.22), residues: 601 loop : -0.35 (0.15), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 730 TYR 0.020 0.001 TYR H 95 PHE 0.028 0.001 PHE A1084 TRP 0.013 0.001 TRP A1044 HIS 0.010 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.19 (33872) covalent geometry : angle 0.63307 / 0.34 (46150) hydrogen bonds : bond 0.04879 / 3.29 ( 1423) hydrogen bonds : angle 5.28822 / 3.81 ( 3897) metal coordination : bond 0.00872 / 0.59 ( 32) metal coordination : angle 7.63592 / 4.34 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 379 time to evaluate : 1.168 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 88 LYS cc_start: 0.9396 (mttt) cc_final: 0.9182 (mtpp) REVERT: A 122 MET cc_start: 0.9337 (tpp) cc_final: 0.9120 (tpp) REVERT: A 453 MET cc_start: 0.8700 (mpp) cc_final: 0.8349 (mmm) REVERT: A 838 GLN cc_start: 0.9240 (tp40) cc_final: 0.8392 (tm-30) REVERT: A 849 MET cc_start: 0.8691 (ttp) cc_final: 0.8490 (ttm) REVERT: A 873 MET cc_start: 0.9479 (mmp) cc_final: 0.8570 (mmp) REVERT: A 919 ILE cc_start: 0.9438 (mm) cc_final: 0.9188 (mm) REVERT: A 1062 GLU cc_start: 0.8659 (tp30) cc_final: 0.8078 (tp30) REVERT: A 1071 SER cc_start: 0.9483 (m) cc_final: 0.9157 (p) REVERT: A 1259 MET cc_start: 0.7264 (mmp) cc_final: 0.6947 (tmm) REVERT: A 1284 MET cc_start: 0.8258 (mtm) cc_final: 0.7963 (mtt) REVERT: B 173 MET cc_start: 0.9301 (ttm) cc_final: 0.8824 (ttp) REVERT: B 313 MET cc_start: 0.9198 (mmm) cc_final: 0.8823 (mmm) REVERT: B 526 GLU cc_start: 0.8212 (tt0) cc_final: 0.7930 (tt0) REVERT: B 563 MET cc_start: 0.8942 (ttp) cc_final: 0.8508 (tmm) REVERT: B 615 MET cc_start: 0.8384 (mtm) cc_final: 0.8057 (mtm) REVERT: B 875 GLU cc_start: 0.8961 (pt0) cc_final: 0.8552 (pm20) REVERT: C 15 LYS cc_start: 0.8830 (ptpt) cc_final: 0.8587 (tptp) REVERT: C 57 VAL cc_start: 0.9338 (m) cc_final: 0.9073 (p) REVERT: D 34 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8237 (mt0) REVERT: D 65 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8313 (tt0) REVERT: D 139 LYS cc_start: 0.7620 (mmtt) cc_final: 0.7384 (mmtt) REVERT: D 175 PHE cc_start: 0.7754 (t80) cc_final: 0.7550 (t80) REVERT: E 58 MET cc_start: 0.8875 (mtp) cc_final: 0.8580 (mtp) REVERT: F 116 ASP cc_start: 0.8811 (t0) cc_final: 0.8354 (t0) REVERT: F 150 GLU cc_start: 0.8747 (pt0) cc_final: 0.8536 (pt0) REVERT: G 3 PHE cc_start: 0.8927 (m-80) cc_final: 0.8492 (m-80) REVERT: G 32 GLU cc_start: 0.9081 (mm-30) cc_final: 0.8641 (tm-30) REVERT: H 32 THR cc_start: 0.9461 (m) cc_final: 0.9239 (p) REVERT: I 91 ARG cc_start: 0.8430 (mmm-85) cc_final: 0.8116 (mtp85) REVERT: K 20 LYS cc_start: 0.8936 (tttp) cc_final: 0.8625 (tttm) REVERT: K 22 ASP cc_start: 0.8415 (m-30) cc_final: 0.7818 (m-30) REVERT: L 29 TYR cc_start: 0.8260 (m-80) cc_final: 0.7936 (m-80) outliers start: 31 outliers final: 21 residues processed: 397 average time/residue: 0.2060 time to fit residues: 132.7273 Evaluate side-chains 344 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 322 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 1102 LYS Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 887 HIS Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain D residue 34 GLN Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 104 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 242 optimal weight: 8.9990 chunk 191 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 373 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 333 optimal weight: 6.9990 chunk 304 optimal weight: 9.9990 chunk 239 optimal weight: 5.9990 chunk 7 optimal weight: 0.0970 chunk 249 optimal weight: 4.9990 chunk 222 optimal weight: 10.0000 overall best weight: 3.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN ** A 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 GLN ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 763 GLN C 188 HIS C 203 GLN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 HIS G 97 HIS K 104 ASN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.085872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.057638 restraints weight = 95914.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.059472 restraints weight = 49485.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.060656 restraints weight = 33010.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.061396 restraints weight = 25777.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.061831 restraints weight = 22288.084| |-----------------------------------------------------------------------------| r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 33904 Z= 0.243 Angle : 0.677 31.696 46195 Z= 0.338 Chirality : 0.046 0.348 5190 Planarity : 0.004 0.061 5629 Dihedral : 16.829 141.076 5345 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.80 % Favored : 95.12 % Rotamer: Outliers : 1.34 % Allowed : 9.73 % Favored : 88.93 % 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: 0.31 (0.14), residues: 3852 helix: 1.42 (0.14), residues: 1349 sheet: -0.21 (0.22), residues: 605 loop : -0.48 (0.15), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 617 TYR 0.020 0.001 TYR G 51 PHE 0.023 0.002 PHE G 121 TRP 0.011 0.001 TRP A1044 HIS 0.008 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.24 (33872) covalent geometry : angle 0.63644 / 0.34 (46150) hydrogen bonds : bond 0.04332 / 2.92 ( 1423) hydrogen bonds : angle 5.02214 / 3.61 ( 3897) metal coordination : bond 0.01059 / 0.70 ( 32) metal coordination : angle 7.38245 / 4.11 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 332 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.9434 (mttt) cc_final: 0.9179 (mtpp) REVERT: A 122 MET cc_start: 0.9368 (tpp) cc_final: 0.9146 (tpp) REVERT: A 453 MET cc_start: 0.8720 (mpp) cc_final: 0.8390 (mmm) REVERT: A 455 MET cc_start: 0.8089 (ttm) cc_final: 0.7886 (ttm) REVERT: A 838 GLN cc_start: 0.9221 (tp40) cc_final: 0.8343 (tm-30) REVERT: A 873 MET cc_start: 0.9514 (mmp) cc_final: 0.9025 (mmp) REVERT: A 912 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8851 (pp) REVERT: A 919 ILE cc_start: 0.9461 (mm) cc_final: 0.9202 (mm) REVERT: A 1062 GLU cc_start: 0.8654 (tp30) cc_final: 0.8025 (tp30) REVERT: A 1071 SER cc_start: 0.9532 (m) cc_final: 0.9242 (p) REVERT: A 1259 MET cc_start: 0.7191 (mmp) cc_final: 0.6912 (tmm) REVERT: A 1284 MET cc_start: 0.8408 (mtm) cc_final: 0.8172 (mtp) REVERT: B 173 MET cc_start: 0.9281 (ttm) cc_final: 0.8802 (ttp) REVERT: B 310 MET cc_start: 0.9156 (mmm) cc_final: 0.8956 (mmm) REVERT: B 526 GLU cc_start: 0.8227 (tt0) cc_final: 0.7945 (tt0) REVERT: B 615 MET cc_start: 0.8414 (mtm) cc_final: 0.8094 (mtm) REVERT: B 809 MET cc_start: 0.8799 (mtp) cc_final: 0.8595 (mtp) REVERT: B 875 GLU cc_start: 0.8984 (pt0) cc_final: 0.8538 (pm20) REVERT: B 1152 MET cc_start: 0.8720 (mmm) cc_final: 0.8295 (mmm) REVERT: C 15 LYS cc_start: 0.8846 (ptpt) cc_final: 0.8603 (tptp) REVERT: C 57 VAL cc_start: 0.9356 (m) cc_final: 0.9079 (p) REVERT: D 34 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8111 (mt0) REVERT: D 65 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8321 (tt0) REVERT: D 175 PHE cc_start: 0.7725 (t80) cc_final: 0.7511 (t80) REVERT: E 32 GLN cc_start: 0.8483 (tp-100) cc_final: 0.8200 (tp-100) REVERT: E 58 MET cc_start: 0.8888 (mtp) cc_final: 0.8569 (mtp) REVERT: E 121 MET cc_start: 0.8964 (mpp) cc_final: 0.8481 (mpp) REVERT: F 110 ASP cc_start: 0.7493 (t0) cc_final: 0.6443 (t0) REVERT: F 111 LEU cc_start: 0.9478 (mm) cc_final: 0.9273 (mp) REVERT: F 112 GLU cc_start: 0.8571 (mp0) cc_final: 0.8110 (mp0) REVERT: F 116 ASP cc_start: 0.8812 (t0) cc_final: 0.8397 (t0) REVERT: G 3 PHE cc_start: 0.8981 (m-80) cc_final: 0.8405 (m-80) REVERT: G 32 GLU cc_start: 0.9145 (mm-30) cc_final: 0.8686 (tm-30) REVERT: H 32 THR cc_start: 0.9478 (m) cc_final: 0.9236 (p) REVERT: I 17 ARG cc_start: 0.6785 (tpm170) cc_final: 0.6134 (tpt170) REVERT: I 97 MET cc_start: 0.7999 (tpp) cc_final: 0.7773 (tpt) REVERT: K 20 LYS cc_start: 0.8935 (tttp) cc_final: 0.8640 (tttm) REVERT: K 22 ASP cc_start: 0.8455 (m-30) cc_final: 0.7731 (m-30) outliers start: 46 outliers final: 28 residues processed: 356 average time/residue: 0.2077 time to fit residues: 121.6555 Evaluate side-chains 339 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 309 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 1102 LYS Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 887 HIS Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain D residue 34 GLN Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 104 ASN 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: 4.9990 chunk 138 optimal weight: 2.9990 chunk 183 optimal weight: 7.9990 chunk 169 optimal weight: 6.9990 chunk 216 optimal weight: 5.9990 chunk 286 optimal weight: 7.9990 chunk 108 optimal weight: 9.9990 chunk 251 optimal weight: 1.9990 chunk 308 optimal weight: 8.9990 chunk 352 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 700 ASN ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 HIS ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** 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 = 0.3449 r_free = 0.3449 target = 0.085291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.056944 restraints weight = 95755.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.058756 restraints weight = 50037.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.059926 restraints weight = 33624.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.060620 restraints weight = 26402.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.061079 restraints weight = 22963.638| |-----------------------------------------------------------------------------| r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 33904 Z= 0.257 Angle : 0.665 30.954 46195 Z= 0.332 Chirality : 0.045 0.321 5190 Planarity : 0.004 0.056 5629 Dihedral : 16.870 141.044 5345 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.70 % Favored : 95.22 % Rotamer: Outliers : 1.72 % Allowed : 11.09 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.14), residues: 3852 helix: 1.46 (0.14), residues: 1337 sheet: -0.39 (0.21), residues: 617 loop : -0.51 (0.15), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 617 TYR 0.014 0.001 TYR H 95 PHE 0.024 0.002 PHE A 219 TRP 0.011 0.001 TRP B 561 HIS 0.008 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.26 (33872) covalent geometry : angle 0.62529 / 0.33 (46150) hydrogen bonds : bond 0.04026 / 2.71 ( 1423) hydrogen bonds : angle 4.90184 / 3.52 ( 3897) metal coordination : bond 0.01093 / 0.72 ( 32) metal coordination : angle 7.24460 / 4.04 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 323 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8167 (mmt) cc_final: 0.7862 (mmt) REVERT: A 88 LYS cc_start: 0.9441 (mttt) cc_final: 0.9170 (mtpp) REVERT: A 122 MET cc_start: 0.9365 (tpp) cc_final: 0.8974 (tpp) REVERT: A 453 MET cc_start: 0.8762 (mpp) cc_final: 0.8397 (mmm) REVERT: A 470 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9021 (pp) REVERT: A 838 GLN cc_start: 0.9210 (tp40) cc_final: 0.8333 (tm-30) REVERT: A 873 MET cc_start: 0.9502 (mmp) cc_final: 0.9039 (mmp) REVERT: A 912 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8870 (pp) REVERT: A 919 ILE cc_start: 0.9450 (mm) cc_final: 0.9177 (mm) REVERT: A 1062 GLU cc_start: 0.8643 (tp30) cc_final: 0.8026 (tp30) REVERT: A 1071 SER cc_start: 0.9528 (m) cc_final: 0.9223 (p) REVERT: A 1259 MET cc_start: 0.7077 (mmp) cc_final: 0.6846 (tmm) REVERT: B 173 MET cc_start: 0.9241 (ttm) cc_final: 0.8775 (ttp) REVERT: B 310 MET cc_start: 0.9102 (mmm) cc_final: 0.8473 (mmt) REVERT: B 526 GLU cc_start: 0.8237 (tt0) cc_final: 0.7958 (tt0) REVERT: B 615 MET cc_start: 0.8422 (mtm) cc_final: 0.8095 (mtm) REVERT: B 809 MET cc_start: 0.8867 (mtp) cc_final: 0.8288 (mtp) REVERT: B 875 GLU cc_start: 0.9017 (pt0) cc_final: 0.8568 (pm20) REVERT: C 15 LYS cc_start: 0.8870 (ptpt) cc_final: 0.8641 (tptp) REVERT: C 57 VAL cc_start: 0.9382 (m) cc_final: 0.9097 (p) REVERT: D 34 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8205 (mt0) REVERT: D 65 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8261 (tt0) REVERT: E 32 GLN cc_start: 0.8542 (tp-100) cc_final: 0.8184 (tp-100) REVERT: E 58 MET cc_start: 0.8855 (mtp) cc_final: 0.8557 (mtp) REVERT: E 121 MET cc_start: 0.9057 (mpp) cc_final: 0.8635 (mpp) REVERT: F 110 ASP cc_start: 0.7771 (t0) cc_final: 0.6791 (t0) REVERT: F 111 LEU cc_start: 0.9505 (mm) cc_final: 0.9243 (mp) REVERT: F 112 GLU cc_start: 0.8693 (mp0) cc_final: 0.8140 (mp0) REVERT: F 116 ASP cc_start: 0.8821 (t0) cc_final: 0.8417 (t0) REVERT: G 3 PHE cc_start: 0.8933 (m-80) cc_final: 0.8306 (m-80) REVERT: G 32 GLU cc_start: 0.9206 (mm-30) cc_final: 0.8707 (tm-30) REVERT: H 32 THR cc_start: 0.9494 (m) cc_final: 0.9250 (p) REVERT: I 17 ARG cc_start: 0.6775 (tpm170) cc_final: 0.6157 (tpt170) REVERT: J 49 MET cc_start: 0.9192 (mmm) cc_final: 0.8973 (mmm) outliers start: 59 outliers final: 40 residues processed: 358 average time/residue: 0.2066 time to fit residues: 122.0229 Evaluate side-chains 348 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 305 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 1102 LYS Chi-restraints excluded: chain A residue 1207 LEU Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1355 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain B residue 887 HIS Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain D residue 34 GLN Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 137 GLN Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 104 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 46 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 111 optimal weight: 20.0000 chunk 182 optimal weight: 0.0870 chunk 71 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 548 ASN B 46 GLN ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN G 24 GLN ** G 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 104 ASN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.087288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.059065 restraints weight = 94112.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.060955 restraints weight = 47971.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.062174 restraints weight = 31766.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.062939 restraints weight = 24690.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.063400 restraints weight = 21290.709| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33904 Z= 0.116 Angle : 0.587 28.804 46195 Z= 0.295 Chirality : 0.043 0.333 5190 Planarity : 0.004 0.052 5629 Dihedral : 16.790 139.858 5345 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.69 % Favored : 96.24 % Rotamer: Outliers : 1.49 % Allowed : 11.91 % 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: 0.47 (0.14), residues: 3852 helix: 1.62 (0.15), residues: 1343 sheet: -0.31 (0.21), residues: 612 loop : -0.37 (0.15), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 192 TYR 0.026 0.001 TYR A1153 PHE 0.023 0.001 PHE A 219 TRP 0.012 0.001 TRP A1044 HIS 0.006 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (33872) covalent geometry : angle 0.55214 / 0.29 (46150) hydrogen bonds : bond 0.03529 / 2.38 ( 1423) hydrogen bonds : angle 4.62592 / 3.33 ( 3897) metal coordination : bond 0.00569 / 0.40 ( 32) metal coordination : angle 6.36186 / 3.49 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 342 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8190 (mmt) cc_final: 0.7928 (mmt) REVERT: A 88 LYS cc_start: 0.9430 (mttt) cc_final: 0.9157 (mtpp) REVERT: A 122 MET cc_start: 0.9335 (tpp) cc_final: 0.8967 (tpp) REVERT: A 445 ASN cc_start: 0.8803 (t0) cc_final: 0.8379 (t0) REVERT: A 453 MET cc_start: 0.8700 (mpp) cc_final: 0.8337 (mmm) REVERT: A 470 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8944 (pp) REVERT: A 708 MET cc_start: 0.7333 (mpp) cc_final: 0.6956 (tpt) REVERT: A 838 GLN cc_start: 0.9160 (tp40) cc_final: 0.8364 (tm-30) REVERT: A 873 MET cc_start: 0.9482 (mmp) cc_final: 0.8582 (mmp) REVERT: A 912 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8838 (pp) REVERT: A 919 ILE cc_start: 0.9400 (mm) cc_final: 0.9115 (mm) REVERT: A 1062 GLU cc_start: 0.8607 (tp30) cc_final: 0.7929 (tp30) REVERT: A 1070 GLN cc_start: 0.9242 (mt0) cc_final: 0.8984 (mt0) REVERT: A 1071 SER cc_start: 0.9476 (m) cc_final: 0.9152 (p) REVERT: A 1259 MET cc_start: 0.7058 (mmp) cc_final: 0.6846 (tmm) REVERT: A 1284 MET cc_start: 0.8359 (mtm) cc_final: 0.8086 (mtt) REVERT: B 310 MET cc_start: 0.9111 (mmm) cc_final: 0.8488 (mmt) REVERT: B 313 MET cc_start: 0.9271 (mmm) cc_final: 0.8921 (mmm) REVERT: B 507 LYS cc_start: 0.8077 (pttm) cc_final: 0.7595 (pttt) REVERT: B 526 GLU cc_start: 0.8066 (tt0) cc_final: 0.7721 (tt0) REVERT: B 552 MET cc_start: 0.8332 (mmm) cc_final: 0.7899 (tmm) REVERT: B 563 MET cc_start: 0.8759 (tmm) cc_final: 0.8357 (tmm) REVERT: B 615 MET cc_start: 0.8366 (mtm) cc_final: 0.8052 (mtm) REVERT: B 809 MET cc_start: 0.8866 (mtp) cc_final: 0.8355 (mtp) REVERT: B 875 GLU cc_start: 0.8983 (pt0) cc_final: 0.8539 (pm20) REVERT: B 1152 MET cc_start: 0.8693 (mmm) cc_final: 0.8112 (mmm) REVERT: C 57 VAL cc_start: 0.9303 (m) cc_final: 0.9014 (p) REVERT: D 34 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8133 (mt0) REVERT: D 65 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8263 (tt0) REVERT: E 32 GLN cc_start: 0.8567 (tp-100) cc_final: 0.8166 (tp-100) REVERT: E 58 MET cc_start: 0.8823 (mtp) cc_final: 0.8505 (mtp) REVERT: E 121 MET cc_start: 0.9158 (mpp) cc_final: 0.8667 (mpp) REVERT: F 111 LEU cc_start: 0.9499 (mm) cc_final: 0.9248 (mp) REVERT: F 112 GLU cc_start: 0.8696 (mp0) cc_final: 0.8475 (mp0) REVERT: F 116 ASP cc_start: 0.8780 (t0) cc_final: 0.8360 (t0) REVERT: F 128 LYS cc_start: 0.9639 (mmtp) cc_final: 0.9399 (mmtm) REVERT: G 1 MET cc_start: 0.7523 (tpt) cc_final: 0.7125 (tpt) REVERT: G 3 PHE cc_start: 0.9019 (m-80) cc_final: 0.8592 (m-80) REVERT: G 32 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8760 (tm-30) REVERT: G 33 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8072 (mm-30) REVERT: G 60 ARG cc_start: 0.8526 (ttp80) cc_final: 0.8298 (ttp80) REVERT: H 32 THR cc_start: 0.9477 (m) cc_final: 0.9226 (p) REVERT: H 136 LYS cc_start: 0.9257 (mmmm) cc_final: 0.8922 (mmtp) REVERT: I 1 MET cc_start: 0.6403 (tpp) cc_final: 0.5347 (tpp) REVERT: I 17 ARG cc_start: 0.7036 (tpm170) cc_final: 0.6508 (tpt170) REVERT: J 3 VAL cc_start: 0.9645 (OUTLIER) cc_final: 0.9416 (m) REVERT: J 49 MET cc_start: 0.9092 (mmm) cc_final: 0.8747 (mpp) outliers start: 51 outliers final: 27 residues processed: 375 average time/residue: 0.2097 time to fit residues: 129.7194 Evaluate side-chains 344 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 313 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 887 HIS Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain D residue 34 GLN Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 137 GLN Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 104 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 317 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 159 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 chunk 143 optimal weight: 9.9990 chunk 114 optimal weight: 8.9990 chunk 150 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 293 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 HIS ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 GLN ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN G 24 GLN G 97 HIS ** G 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 104 ASN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.083541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.055463 restraints weight = 96695.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.057204 restraints weight = 51124.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.058334 restraints weight = 34456.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.059035 restraints weight = 27112.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.059458 restraints weight = 23551.314| |-----------------------------------------------------------------------------| r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.115 33904 Z= 0.420 Angle : 0.797 30.148 46195 Z= 0.397 Chirality : 0.048 0.252 5190 Planarity : 0.005 0.060 5629 Dihedral : 16.961 140.869 5345 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.43 % Favored : 94.50 % Rotamer: Outliers : 1.98 % Allowed : 12.78 % Favored : 85.24 % 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: 0.03 (0.14), residues: 3852 helix: 1.24 (0.14), residues: 1334 sheet: -0.54 (0.21), residues: 613 loop : -0.61 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 617 TYR 0.023 0.002 TYR G 51 PHE 0.024 0.002 PHE A 219 TRP 0.014 0.002 TRP B 561 HIS 0.009 0.002 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00931 / 0.42 (33872) covalent geometry : angle 0.76462 / 0.40 (46150) hydrogen bonds : bond 0.04359 / 2.93 ( 1423) hydrogen bonds : angle 5.00537 / 3.59 ( 3897) metal coordination : bond 0.01680 / 1.07 ( 32) metal coordination : angle 7.28842 / 4.11 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 299 time to evaluate : 1.289 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 88 LYS cc_start: 0.9439 (mttt) cc_final: 0.9101 (mtpp) REVERT: A 122 MET cc_start: 0.9397 (tpp) cc_final: 0.9028 (tpp) REVERT: A 453 MET cc_start: 0.8856 (mpp) cc_final: 0.8539 (mmm) REVERT: A 470 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9065 (pp) REVERT: A 708 MET cc_start: 0.7292 (mpp) cc_final: 0.6814 (tpt) REVERT: A 838 GLN cc_start: 0.9271 (tp40) cc_final: 0.8327 (tm-30) REVERT: A 873 MET cc_start: 0.9497 (mmp) cc_final: 0.9047 (mmp) REVERT: A 912 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8854 (pp) REVERT: A 919 ILE cc_start: 0.9450 (mm) cc_final: 0.9163 (mm) REVERT: A 1071 SER cc_start: 0.9558 (m) cc_final: 0.9248 (p) REVERT: A 1153 TYR cc_start: 0.7960 (m-10) cc_final: 0.7618 (m-10) REVERT: A 1259 MET cc_start: 0.7011 (mmp) cc_final: 0.6777 (tmm) REVERT: A 1284 MET cc_start: 0.8418 (mtm) cc_final: 0.8163 (mtp) REVERT: A 1444 MET cc_start: 0.8873 (mmm) cc_final: 0.8528 (mmt) REVERT: B 310 MET cc_start: 0.9025 (mmm) cc_final: 0.8474 (mmm) REVERT: B 507 LYS cc_start: 0.8244 (pttm) cc_final: 0.7745 (mtmt) REVERT: B 563 MET cc_start: 0.8691 (tmm) cc_final: 0.8374 (tmm) REVERT: B 615 MET cc_start: 0.8481 (mtm) cc_final: 0.8152 (mtm) REVERT: B 809 MET cc_start: 0.8955 (mtp) cc_final: 0.8356 (mtp) REVERT: B 875 GLU cc_start: 0.9037 (pt0) cc_final: 0.8524 (pm20) REVERT: D 34 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8199 (mt0) REVERT: E 32 GLN cc_start: 0.8619 (tp-100) cc_final: 0.8241 (tp-100) REVERT: E 58 MET cc_start: 0.8827 (mtp) cc_final: 0.8575 (mtp) REVERT: E 121 MET cc_start: 0.9187 (mpp) cc_final: 0.8703 (mpp) REVERT: F 110 ASP cc_start: 0.7770 (t0) cc_final: 0.6697 (t0) REVERT: F 112 GLU cc_start: 0.8669 (mp0) cc_final: 0.8004 (mp0) REVERT: F 116 ASP cc_start: 0.8864 (t0) cc_final: 0.8509 (t0) REVERT: G 1 MET cc_start: 0.7248 (tpt) cc_final: 0.6968 (tpt) REVERT: G 3 PHE cc_start: 0.8999 (m-80) cc_final: 0.8399 (m-80) REVERT: H 27 GLU cc_start: 0.7516 (mp0) cc_final: 0.7301 (mp0) REVERT: H 136 LYS cc_start: 0.9300 (mmmm) cc_final: 0.9067 (mmtp) REVERT: I 1 MET cc_start: 0.6650 (tpp) cc_final: 0.5421 (tpp) REVERT: J 3 VAL cc_start: 0.9676 (OUTLIER) cc_final: 0.9467 (m) REVERT: J 49 MET cc_start: 0.9199 (mmm) cc_final: 0.8941 (mmm) outliers start: 68 outliers final: 49 residues processed: 347 average time/residue: 0.2061 time to fit residues: 118.4166 Evaluate side-chains 346 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 293 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 1058 VAL Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain B residue 887 HIS Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1139 ILE Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain D residue 34 GLN Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 137 GLN Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 61 LEU Chi-restraints excluded: chain K residue 77 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 382 optimal weight: 2.9990 chunk 3 optimal weight: 0.3980 chunk 200 optimal weight: 0.9980 chunk 306 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 354 optimal weight: 0.9990 chunk 270 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 357 optimal weight: 1.9990 chunk 254 optimal weight: 4.9990 chunk 351 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 GLN B 513 GLN ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN G 97 HIS ** G 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 GLN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.086637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.058303 restraints weight = 94332.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.060174 restraints weight = 48417.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.061366 restraints weight = 32151.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.062121 restraints weight = 25180.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.062520 restraints weight = 21740.472| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33904 Z= 0.120 Angle : 0.603 28.172 46195 Z= 0.303 Chirality : 0.043 0.314 5190 Planarity : 0.004 0.050 5629 Dihedral : 16.872 140.110 5345 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.63 % Favored : 96.29 % Rotamer: Outliers : 1.40 % Allowed : 13.57 % Favored : 85.03 % 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: 0.39 (0.14), residues: 3852 helix: 1.59 (0.15), residues: 1338 sheet: -0.40 (0.21), residues: 608 loop : -0.43 (0.15), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 617 TYR 0.024 0.001 TYR G 51 PHE 0.022 0.001 PHE A 219 TRP 0.011 0.001 TRP A1044 HIS 0.007 0.001 HIS L 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (33872) covalent geometry : angle 0.57041 / 0.30 (46150) hydrogen bonds : bond 0.03511 / 2.35 ( 1423) hydrogen bonds : angle 4.58248 / 3.29 ( 3897) metal coordination : bond 0.00573 / 0.41 ( 32) metal coordination : angle 6.24894 / 3.45 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 339 time to evaluate : 1.320 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 88 LYS cc_start: 0.9430 (mttt) cc_final: 0.9130 (mtpp) REVERT: A 122 MET cc_start: 0.9336 (tpp) cc_final: 0.8961 (tpp) REVERT: A 445 ASN cc_start: 0.8937 (t0) cc_final: 0.8455 (t0) REVERT: A 453 MET cc_start: 0.8703 (mpp) cc_final: 0.8344 (mmm) REVERT: A 455 MET cc_start: 0.7968 (ttm) cc_final: 0.7673 (ttm) REVERT: A 470 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.9038 (pp) REVERT: A 708 MET cc_start: 0.7443 (mpp) cc_final: 0.6895 (tpt) REVERT: A 838 GLN cc_start: 0.9152 (tp40) cc_final: 0.8334 (tm-30) REVERT: A 873 MET cc_start: 0.9471 (mmp) cc_final: 0.8650 (mmp) REVERT: A 912 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8841 (pp) REVERT: A 919 ILE cc_start: 0.9371 (mm) cc_final: 0.9069 (mm) REVERT: A 1070 GLN cc_start: 0.9244 (mt0) cc_final: 0.9001 (mt0) REVERT: A 1071 SER cc_start: 0.9474 (m) cc_final: 0.9144 (p) REVERT: A 1153 TYR cc_start: 0.7741 (m-10) cc_final: 0.7407 (m-10) REVERT: A 1284 MET cc_start: 0.8278 (mtm) cc_final: 0.7992 (mtp) REVERT: A 1444 MET cc_start: 0.8814 (mmm) cc_final: 0.8583 (mmt) REVERT: B 310 MET cc_start: 0.9013 (mmm) cc_final: 0.8488 (mmm) REVERT: B 313 MET cc_start: 0.9292 (mmm) cc_final: 0.8859 (mmm) REVERT: B 507 LYS cc_start: 0.8270 (pttm) cc_final: 0.7855 (pttt) REVERT: B 526 GLU cc_start: 0.8102 (tt0) cc_final: 0.7787 (tt0) REVERT: B 552 MET cc_start: 0.8299 (mmm) cc_final: 0.7883 (tmm) REVERT: B 563 MET cc_start: 0.8754 (tmm) cc_final: 0.8431 (tmm) REVERT: B 615 MET cc_start: 0.8380 (mtm) cc_final: 0.8076 (mtm) REVERT: B 809 MET cc_start: 0.8909 (mtp) cc_final: 0.8411 (mtp) REVERT: B 875 GLU cc_start: 0.9019 (pt0) cc_final: 0.8514 (pm20) REVERT: B 999 MET cc_start: 0.8876 (mmm) cc_final: 0.8522 (mmm) REVERT: B 1152 MET cc_start: 0.8658 (mmm) cc_final: 0.8086 (mmm) REVERT: C 57 VAL cc_start: 0.9258 (m) cc_final: 0.8967 (p) REVERT: D 34 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8078 (mt0) REVERT: D 65 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8257 (tt0) REVERT: E 32 GLN cc_start: 0.8654 (tp-100) cc_final: 0.8215 (tp-100) REVERT: E 58 MET cc_start: 0.8804 (mtp) cc_final: 0.8579 (mtp) REVERT: E 121 MET cc_start: 0.9182 (mpp) cc_final: 0.8769 (mpp) REVERT: F 111 LEU cc_start: 0.9488 (mm) cc_final: 0.9245 (mp) REVERT: F 112 GLU cc_start: 0.8684 (mp0) cc_final: 0.8452 (mp0) REVERT: F 116 ASP cc_start: 0.8776 (t0) cc_final: 0.8444 (t0) REVERT: F 128 LYS cc_start: 0.9642 (mmtp) cc_final: 0.9336 (mmtm) REVERT: G 1 MET cc_start: 0.7290 (tpt) cc_final: 0.6895 (tpt) REVERT: G 3 PHE cc_start: 0.8969 (m-80) cc_final: 0.8563 (m-80) REVERT: G 32 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8709 (tm-30) REVERT: H 32 THR cc_start: 0.9475 (m) cc_final: 0.9236 (p) REVERT: I 1 MET cc_start: 0.6623 (tpp) cc_final: 0.5482 (tpp) REVERT: I 17 ARG cc_start: 0.7235 (tpm170) cc_final: 0.6435 (tpt170) REVERT: J 3 VAL cc_start: 0.9642 (OUTLIER) cc_final: 0.9409 (m) REVERT: J 49 MET cc_start: 0.9131 (mmm) cc_final: 0.8778 (mpp) outliers start: 48 outliers final: 31 residues processed: 368 average time/residue: 0.2032 time to fit residues: 124.3946 Evaluate side-chains 357 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 322 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain B residue 887 HIS Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 8 PHE Chi-restraints excluded: chain D residue 34 GLN 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 35 GLN Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 137 GLN Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 25 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 20 optimal weight: 0.0370 chunk 80 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 363 optimal weight: 7.9990 chunk 243 optimal weight: 9.9990 chunk 331 optimal weight: 0.9980 chunk 139 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 126 optimal weight: 2.9990 chunk 275 optimal weight: 0.7980 overall best weight: 1.5662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN G 97 HIS ** G 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 GLN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.086408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.058200 restraints weight = 94431.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.060070 restraints weight = 48465.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.061266 restraints weight = 32105.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.062009 restraints weight = 25021.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.062462 restraints weight = 21629.397| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 33904 Z= 0.141 Angle : 0.595 27.426 46195 Z= 0.298 Chirality : 0.043 0.258 5190 Planarity : 0.004 0.050 5629 Dihedral : 16.808 139.260 5345 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.08 % Favored : 95.85 % Rotamer: Outliers : 1.25 % Allowed : 14.30 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.14), residues: 3852 helix: 1.63 (0.15), residues: 1333 sheet: -0.40 (0.21), residues: 620 loop : -0.40 (0.15), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1241 TYR 0.024 0.001 TYR G 51 PHE 0.027 0.001 PHE G 82 TRP 0.010 0.001 TRP A1044 HIS 0.006 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (33872) covalent geometry : angle 0.56450 / 0.30 (46150) hydrogen bonds : bond 0.03390 / 2.28 ( 1423) hydrogen bonds : angle 4.52707 / 3.25 ( 3897) metal coordination : bond 0.00609 / 0.42 ( 32) metal coordination : angle 6.09177 / 3.34 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 328 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.9438 (mttt) cc_final: 0.9116 (mtpp) REVERT: A 122 MET cc_start: 0.9329 (tpp) cc_final: 0.8992 (tpp) REVERT: A 453 MET cc_start: 0.8724 (mpp) cc_final: 0.8343 (mmm) REVERT: A 455 MET cc_start: 0.8095 (ttm) cc_final: 0.7875 (ttm) REVERT: A 470 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.9038 (pp) REVERT: A 708 MET cc_start: 0.7444 (mpp) cc_final: 0.6957 (tpt) REVERT: A 838 GLN cc_start: 0.9181 (tp40) cc_final: 0.8348 (tm-30) REVERT: A 873 MET cc_start: 0.9460 (mmp) cc_final: 0.8657 (mmp) REVERT: A 912 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8848 (pp) REVERT: A 919 ILE cc_start: 0.9371 (mm) cc_final: 0.9073 (mm) REVERT: A 1070 GLN cc_start: 0.9264 (mt0) cc_final: 0.8998 (mt0) REVERT: A 1071 SER cc_start: 0.9480 (m) cc_final: 0.9149 (p) REVERT: A 1079 MET cc_start: 0.8460 (ttp) cc_final: 0.8246 (tmm) REVERT: A 1111 MET cc_start: 0.8683 (ptp) cc_final: 0.8439 (ptm) REVERT: A 1153 TYR cc_start: 0.7655 (m-10) cc_final: 0.7398 (m-10) REVERT: A 1284 MET cc_start: 0.8183 (mtm) cc_final: 0.7950 (mtp) REVERT: A 1444 MET cc_start: 0.8855 (mmm) cc_final: 0.8627 (mmt) REVERT: B 173 MET cc_start: 0.9312 (ttm) cc_final: 0.8886 (ttp) REVERT: B 310 MET cc_start: 0.9040 (mmm) cc_final: 0.8437 (mmm) REVERT: B 313 MET cc_start: 0.9288 (mmm) cc_final: 0.8887 (mmm) REVERT: B 507 LYS cc_start: 0.8304 (pttm) cc_final: 0.7880 (pttt) REVERT: B 526 GLU cc_start: 0.8127 (tt0) cc_final: 0.7774 (tt0) REVERT: B 552 MET cc_start: 0.8333 (mmm) cc_final: 0.7900 (tmm) REVERT: B 563 MET cc_start: 0.8726 (tmm) cc_final: 0.8397 (tmm) REVERT: B 615 MET cc_start: 0.8419 (mtm) cc_final: 0.8131 (mtm) REVERT: B 809 MET cc_start: 0.8936 (mtp) cc_final: 0.8422 (mtp) REVERT: B 875 GLU cc_start: 0.9014 (pt0) cc_final: 0.8551 (pm20) REVERT: B 1152 MET cc_start: 0.8705 (mmm) cc_final: 0.8501 (mmm) REVERT: C 57 VAL cc_start: 0.9267 (m) cc_final: 0.8985 (p) REVERT: D 34 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8048 (mt0) REVERT: D 65 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8246 (tt0) REVERT: E 32 GLN cc_start: 0.8660 (tp-100) cc_final: 0.8203 (tp-100) REVERT: E 58 MET cc_start: 0.8817 (mtp) cc_final: 0.8585 (mtp) REVERT: E 121 MET cc_start: 0.9185 (mpp) cc_final: 0.8854 (mpp) REVERT: F 88 TYR cc_start: 0.8827 (m-80) cc_final: 0.8608 (m-10) REVERT: F 111 LEU cc_start: 0.9504 (mm) cc_final: 0.9258 (mp) REVERT: F 116 ASP cc_start: 0.8751 (t0) cc_final: 0.8354 (t0) REVERT: F 128 LYS cc_start: 0.9642 (mmtp) cc_final: 0.9339 (mmtm) REVERT: G 1 MET cc_start: 0.7188 (tpt) cc_final: 0.6971 (tpt) REVERT: G 3 PHE cc_start: 0.8984 (m-80) cc_final: 0.8507 (m-80) REVERT: G 32 GLU cc_start: 0.9145 (mm-30) cc_final: 0.8683 (tm-30) REVERT: G 69 GLU cc_start: 0.8336 (tt0) cc_final: 0.7871 (tt0) REVERT: H 32 THR cc_start: 0.9468 (m) cc_final: 0.9229 (p) REVERT: H 136 LYS cc_start: 0.9236 (mmmm) cc_final: 0.8940 (mmtp) REVERT: I 17 ARG cc_start: 0.7254 (tpm170) cc_final: 0.6456 (tpt170) REVERT: I 91 ARG cc_start: 0.8573 (mmm-85) cc_final: 0.8097 (mtp85) REVERT: J 3 VAL cc_start: 0.9644 (OUTLIER) cc_final: 0.9409 (m) REVERT: J 49 MET cc_start: 0.9164 (mmm) cc_final: 0.8874 (mmm) outliers start: 43 outliers final: 35 residues processed: 355 average time/residue: 0.2189 time to fit residues: 128.4231 Evaluate side-chains 358 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 319 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain B residue 887 HIS Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 908 GLU Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 34 GLN 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 35 GLN Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 137 GLN Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 61 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 58 optimal weight: 0.2980 chunk 377 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 196 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 331 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 247 optimal weight: 0.9980 chunk 163 optimal weight: 9.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN G 53 ASN G 97 HIS ** G 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 GLN ** L 53 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 = 0.3489 r_free = 0.3489 target = 0.087066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.058788 restraints weight = 94051.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.060680 restraints weight = 48282.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.061888 restraints weight = 32035.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.062642 restraints weight = 24980.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.063072 restraints weight = 21566.619| |-----------------------------------------------------------------------------| r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33904 Z= 0.119 Angle : 0.597 26.559 46195 Z= 0.298 Chirality : 0.043 0.273 5190 Planarity : 0.004 0.050 5629 Dihedral : 16.770 138.873 5345 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.87 % Favored : 96.05 % Rotamer: Outliers : 1.43 % Allowed : 14.09 % Favored : 84.48 % 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: 0.46 (0.14), residues: 3852 helix: 1.65 (0.15), residues: 1334 sheet: -0.34 (0.21), residues: 623 loop : -0.39 (0.15), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 60 TYR 0.026 0.001 TYR H 129 PHE 0.022 0.001 PHE A 219 TRP 0.011 0.001 TRP A1044 HIS 0.006 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (33872) covalent geometry : angle 0.56871 / 0.30 (46150) hydrogen bonds : bond 0.03256 / 2.19 ( 1423) hydrogen bonds : angle 4.44570 / 3.19 ( 3897) metal coordination : bond 0.00530 / 0.37 ( 32) metal coordination : angle 5.79652 / 3.17 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 337 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.9438 (mttt) cc_final: 0.9119 (mtpp) REVERT: A 122 MET cc_start: 0.9317 (tpp) cc_final: 0.8980 (tpp) REVERT: A 351 THR cc_start: 0.9162 (OUTLIER) cc_final: 0.8804 (p) REVERT: A 453 MET cc_start: 0.8671 (mpp) cc_final: 0.8267 (mmm) REVERT: A 454 SER cc_start: 0.9356 (m) cc_final: 0.9110 (p) REVERT: A 455 MET cc_start: 0.8218 (ttm) cc_final: 0.7665 (ttm) REVERT: A 470 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9039 (pp) REVERT: A 708 MET cc_start: 0.7452 (mpp) cc_final: 0.6968 (tpt) REVERT: A 838 GLN cc_start: 0.9139 (tp40) cc_final: 0.8347 (tm-30) REVERT: A 873 MET cc_start: 0.9455 (mmp) cc_final: 0.8657 (mmp) REVERT: A 912 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8858 (pp) REVERT: A 919 ILE cc_start: 0.9369 (mm) cc_final: 0.9070 (mm) REVERT: A 1070 GLN cc_start: 0.9257 (mt0) cc_final: 0.8977 (mt0) REVERT: A 1071 SER cc_start: 0.9472 (m) cc_final: 0.9121 (p) REVERT: A 1153 TYR cc_start: 0.7529 (m-10) cc_final: 0.7215 (m-10) REVERT: A 1444 MET cc_start: 0.8807 (mmm) cc_final: 0.8530 (mmt) REVERT: B 173 MET cc_start: 0.9290 (ttm) cc_final: 0.8885 (ttp) REVERT: B 310 MET cc_start: 0.9049 (mmm) cc_final: 0.8528 (mmm) REVERT: B 507 LYS cc_start: 0.8299 (pttm) cc_final: 0.7884 (pttt) REVERT: B 526 GLU cc_start: 0.8054 (tt0) cc_final: 0.7674 (tt0) REVERT: B 563 MET cc_start: 0.8719 (tmm) cc_final: 0.8386 (tmm) REVERT: B 615 MET cc_start: 0.8382 (mtm) cc_final: 0.8098 (mtm) REVERT: B 809 MET cc_start: 0.8939 (mtp) cc_final: 0.8446 (mtp) REVERT: B 875 GLU cc_start: 0.8946 (pt0) cc_final: 0.8542 (pm20) REVERT: B 1152 MET cc_start: 0.8711 (mmm) cc_final: 0.8496 (mmm) REVERT: C 57 VAL cc_start: 0.9205 (m) cc_final: 0.8932 (p) REVERT: D 34 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8031 (mt0) REVERT: E 32 GLN cc_start: 0.8664 (tp-100) cc_final: 0.8199 (tp-100) REVERT: E 58 MET cc_start: 0.8795 (mtp) cc_final: 0.8572 (mtp) REVERT: E 121 MET cc_start: 0.9169 (mpp) cc_final: 0.8864 (mpp) REVERT: F 116 ASP cc_start: 0.8700 (t0) cc_final: 0.8295 (t0) REVERT: F 128 LYS cc_start: 0.9644 (mmtp) cc_final: 0.9355 (mmtm) REVERT: G 3 PHE cc_start: 0.8957 (m-80) cc_final: 0.8372 (m-80) REVERT: G 32 GLU cc_start: 0.9159 (mm-30) cc_final: 0.8777 (tm-30) REVERT: G 57 GLN cc_start: 0.8329 (mt0) cc_final: 0.7827 (mp10) REVERT: H 32 THR cc_start: 0.9449 (m) cc_final: 0.9220 (p) REVERT: H 35 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8218 (mt0) REVERT: H 136 LYS cc_start: 0.9235 (mmmm) cc_final: 0.8935 (mmtp) REVERT: I 17 ARG cc_start: 0.7218 (tpm170) cc_final: 0.6509 (tpt170) REVERT: I 91 ARG cc_start: 0.8563 (mmm-85) cc_final: 0.7934 (mtp180) REVERT: J 3 VAL cc_start: 0.9637 (OUTLIER) cc_final: 0.9396 (m) REVERT: J 49 MET cc_start: 0.9140 (mmm) cc_final: 0.8770 (mpp) outliers start: 49 outliers final: 36 residues processed: 368 average time/residue: 0.1975 time to fit residues: 120.0657 Evaluate side-chains 365 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 323 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 887 HIS Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 908 GLU Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 8 PHE Chi-restraints excluded: chain D residue 34 GLN Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 53 ASN Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 137 GLN Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 25 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 308 optimal weight: 0.7980 chunk 268 optimal weight: 6.9990 chunk 200 optimal weight: 4.9990 chunk 176 optimal weight: 7.9990 chunk 232 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 314 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 164 optimal weight: 4.9990 chunk 321 optimal weight: 0.7980 chunk 241 optimal weight: 7.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN G 53 ASN G 97 HIS ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.086938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.058712 restraints weight = 94866.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.060586 restraints weight = 48566.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.061790 restraints weight = 32220.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.062552 restraints weight = 25131.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.063003 restraints weight = 21703.888| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.190 33904 Z= 0.161 Angle : 0.705 59.185 46195 Z= 0.377 Chirality : 0.043 0.267 5190 Planarity : 0.004 0.097 5629 Dihedral : 16.768 138.858 5345 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.84 % Favored : 96.08 % Rotamer: Outliers : 1.31 % Allowed : 14.12 % Favored : 84.57 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.14), residues: 3852 helix: 1.63 (0.15), residues: 1334 sheet: -0.34 (0.21), residues: 623 loop : -0.38 (0.15), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 335 TYR 0.025 0.001 TYR H 129 PHE 0.022 0.001 PHE A 219 TRP 0.024 0.001 TRP A1228 HIS 0.006 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (33872) covalent geometry : angle 0.68125 / 0.38 (46150) hydrogen bonds : bond 0.03263 / 2.19 ( 1423) hydrogen bonds : angle 4.44306 / 3.19 ( 3897) metal coordination : bond 0.00558 / 0.39 ( 32) metal coordination : angle 5.79471 / 3.17 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7704 Ramachandran restraints generated. 3852 Oldfield, 0 Emsley, 3852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 323 time to evaluate : 1.276 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 88 LYS cc_start: 0.9441 (mttt) cc_final: 0.9123 (mtpp) REVERT: A 122 MET cc_start: 0.9314 (tpp) cc_final: 0.8979 (tpp) REVERT: A 351 THR cc_start: 0.9171 (OUTLIER) cc_final: 0.8806 (p) REVERT: A 453 MET cc_start: 0.8687 (mpp) cc_final: 0.8282 (mmm) REVERT: A 454 SER cc_start: 0.9351 (m) cc_final: 0.9112 (p) REVERT: A 455 MET cc_start: 0.8145 (ttm) cc_final: 0.7793 (ttm) REVERT: A 470 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.9042 (pp) REVERT: A 708 MET cc_start: 0.7341 (mpp) cc_final: 0.6873 (tpt) REVERT: A 838 GLN cc_start: 0.9143 (tp40) cc_final: 0.8353 (tm-30) REVERT: A 873 MET cc_start: 0.9458 (mmp) cc_final: 0.8658 (mmp) REVERT: A 912 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8861 (pp) REVERT: A 919 ILE cc_start: 0.9370 (mm) cc_final: 0.9072 (mm) REVERT: A 1070 GLN cc_start: 0.9250 (mt0) cc_final: 0.8973 (mt0) REVERT: A 1071 SER cc_start: 0.9475 (m) cc_final: 0.9123 (p) REVERT: A 1153 TYR cc_start: 0.7543 (m-10) cc_final: 0.7218 (m-10) REVERT: A 1444 MET cc_start: 0.8793 (mmm) cc_final: 0.8538 (mmt) REVERT: B 173 MET cc_start: 0.9291 (ttm) cc_final: 0.8890 (ttp) REVERT: B 310 MET cc_start: 0.9038 (mmm) cc_final: 0.8515 (mmm) REVERT: B 507 LYS cc_start: 0.8303 (pttm) cc_final: 0.7891 (pttt) REVERT: B 526 GLU cc_start: 0.8056 (tt0) cc_final: 0.7677 (tt0) REVERT: B 563 MET cc_start: 0.8721 (tmm) cc_final: 0.8387 (tmm) REVERT: B 615 MET cc_start: 0.8381 (mtm) cc_final: 0.8099 (mtm) REVERT: B 809 MET cc_start: 0.8937 (mtp) cc_final: 0.8450 (mtp) REVERT: B 875 GLU cc_start: 0.8940 (pt0) cc_final: 0.8541 (pm20) REVERT: B 1152 MET cc_start: 0.8705 (mmm) cc_final: 0.8499 (mmm) REVERT: C 57 VAL cc_start: 0.9205 (m) cc_final: 0.8933 (p) REVERT: D 34 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.8036 (mt0) REVERT: E 32 GLN cc_start: 0.8665 (tp-100) cc_final: 0.8202 (tp-100) REVERT: E 58 MET cc_start: 0.8801 (mtp) cc_final: 0.8575 (mtp) REVERT: E 121 MET cc_start: 0.9170 (mpp) cc_final: 0.8873 (mpp) REVERT: F 116 ASP cc_start: 0.8704 (t0) cc_final: 0.8295 (t0) REVERT: F 128 LYS cc_start: 0.9646 (mmtp) cc_final: 0.9356 (mmtm) REVERT: G 1 MET cc_start: 0.6747 (tpt) cc_final: 0.6503 (tpt) REVERT: G 3 PHE cc_start: 0.8823 (m-80) cc_final: 0.8541 (m-10) REVERT: G 32 GLU cc_start: 0.9116 (mm-30) cc_final: 0.8772 (tm-30) REVERT: G 57 GLN cc_start: 0.8333 (mt0) cc_final: 0.7832 (mp10) REVERT: H 32 THR cc_start: 0.9453 (m) cc_final: 0.9222 (p) REVERT: H 136 LYS cc_start: 0.9237 (mmmm) cc_final: 0.8933 (mmtp) REVERT: I 17 ARG cc_start: 0.7197 (tpm170) cc_final: 0.6467 (tpt170) REVERT: I 91 ARG cc_start: 0.8569 (mmm-85) cc_final: 0.7941 (mtp180) REVERT: J 3 VAL cc_start: 0.9629 (OUTLIER) cc_final: 0.9389 (m) REVERT: J 49 MET cc_start: 0.9140 (mmm) cc_final: 0.8773 (mpp) outliers start: 45 outliers final: 40 residues processed: 354 average time/residue: 0.2068 time to fit residues: 120.4318 Evaluate side-chains 367 residues out of total 3434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 322 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 432 MET Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain B residue 887 HIS Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 908 GLU Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 1072 MET Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 34 GLN Chi-restraints excluded: chain E residue 156 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 23 VAL Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 137 GLN Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 61 LEU Chi-restraints excluded: chain K residue 104 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 352 optimal weight: 0.8980 chunk 284 optimal weight: 5.9990 chunk 354 optimal weight: 5.9990 chunk 214 optimal weight: 0.7980 chunk 374 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 343 optimal weight: 1.9990 chunk 296 optimal weight: 8.9990 chunk 250 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 HIS ** I 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** 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 = 0.3486 r_free = 0.3486 target = 0.086962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.058764 restraints weight = 94225.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.060640 restraints weight = 48436.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.061847 restraints weight = 32175.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.062598 restraints weight = 25114.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.063046 restraints weight = 21699.899| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.190 33904 Z= 0.161 Angle : 0.705 59.185 46195 Z= 0.377 Chirality : 0.043 0.267 5190 Planarity : 0.004 0.097 5629 Dihedral : 16.768 138.858 5345 Min Nonbonded Distance : 1.535 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.84 % Favored : 96.08 % Rotamer: Outliers : 1.31 % Allowed : 14.18 % Favored : 84.51 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.14), residues: 3852 helix: 1.63 (0.15), residues: 1334 sheet: -0.34 (0.21), residues: 623 loop : -0.38 (0.15), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 335 TYR 0.025 0.001 TYR H 129 PHE 0.022 0.001 PHE A 219 TRP 0.024 0.001 TRP A1228 HIS 0.006 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (33872) covalent geometry : angle 0.68125 / 0.38 (46150) hydrogen bonds : bond 0.03263 / 2.19 ( 1423) hydrogen bonds : angle 4.44306 / 3.19 ( 3897) metal coordination : bond 0.00558 / 0.39 ( 32) metal coordination : angle 5.79471 / 3.17 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5953.65 seconds wall clock time: 103 minutes 48.75 seconds (6228.75 seconds total)