Starting phenix.real_space_refine on Sun Aug 9 09:46:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sbr_54736/08_2026/9sbr_54736.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sbr_54736/08_2026/9sbr_54736.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9sbr_54736/08_2026/9sbr_54736.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sbr_54736/08_2026/9sbr_54736.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9sbr_54736/08_2026/9sbr_54736.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sbr_54736/08_2026/9sbr_54736.map" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 96 5.49 5 Mg 2 5.21 5 S 182 5.16 5 C 20464 2.51 5 N 5738 2.21 5 O 6424 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: 32914 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 10853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1378, 10853 Classifications: {'peptide': 1378} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1315} Chain breaks: 9 Chain: "B" Number of atoms: 9155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1150, 9155 Classifications: {'peptide': 1150} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 1100} Chain breaks: 6 Chain: "C" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2095 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain: "D" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1327 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 164} Chain breaks: 2 Chain: "E" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1744 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1340 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1077 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Chain: "I" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 909 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 904 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "N" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 825 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain breaks: 1 Chain: "R" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 197 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna3p': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 886 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 2, ' ZN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 457 SG CYS A 67 106.839 70.607 95.198 1.00234.76 S ATOM 479 SG CYS A 70 106.484 67.348 93.210 1.00242.87 S ATOM 532 SG CYS A 77 103.751 69.880 93.165 1.00216.96 S ATOM 762 SG CYS A 107 81.477 76.484 135.414 1.00268.15 S ATOM 786 SG CYS A 110 82.788 73.060 135.993 1.00255.48 S ATOM 1091 SG CYS A 148 79.470 74.064 137.560 1.00290.45 S ATOM 1105 SG CYS A 167 82.662 75.724 138.849 1.00276.60 S ATOM 19514 SG CYS B1163 98.613 58.162 104.958 1.00240.56 S ATOM 19532 SG CYS B1166 97.289 61.696 105.048 1.00229.48 S ATOM 19657 SG CYS B1182 101.016 60.943 104.501 1.00245.70 S ATOM 19676 SG CYS B1185 99.412 60.526 107.937 1.00235.21 S ATOM 20664 SG CYS C 86 93.229 75.961 26.704 1.00284.98 S ATOM 20681 SG CYS C 88 95.694 78.158 28.221 1.00305.80 S ATOM 20714 SG CYS C 92 94.479 79.216 24.921 1.00261.59 S ATOM 20737 SG CYS C 95 92.065 79.433 27.878 1.00276.97 S ATOM 28322 SG CYS I 7 37.723 127.742 126.612 1.00434.31 S ATOM 28347 SG CYS I 10 41.431 126.977 126.316 1.00421.81 S ATOM 28513 SG CYS I 29 39.271 124.632 128.323 1.00443.53 S ATOM 28537 SG CYS I 32 39.884 127.979 129.733 1.00440.37 S ATOM 28864 SG CYS I 75 16.474 119.791 87.458 1.00510.18 S ATOM 28886 SG CYS I 78 16.362 123.486 86.399 1.00506.55 S ATOM 29102 SG CYS I 103 19.603 121.505 86.206 1.00483.25 S ATOM 29122 SG CYS I 106 18.168 122.482 89.560 1.00492.61 S ATOM 29224 SG CYS J 7 64.022 91.749 38.110 1.00188.88 S ATOM 29247 SG CYS J 10 64.070 89.727 34.921 1.00195.87 S ATOM 29527 SG CYS J 45 60.794 90.559 36.489 1.00189.37 S ATOM 29533 SG CYS J 46 62.831 93.166 34.628 1.00215.91 S ATOM 30656 SG CYS L 31 96.825 115.245 54.715 1.00362.78 S ATOM 30676 SG CYS L 34 98.013 116.723 51.500 1.00361.26 S ATOM 30780 SG CYS L 48 100.547 115.745 54.280 1.00366.50 S ATOM 30803 SG CYS L 51 98.317 118.752 54.736 1.00372.40 S Time building chain proxies: 6.83, per 1000 atoms: 0.21 Number of scatterers: 32914 At special positions: 0 Unit cell: (152.329, 156.681, 183.883, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 182 16.00 P 96 15.00 Mg 2 11.99 O 6424 8.00 N 5738 7.00 C 20464 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: 3.16 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 67 " pdb=" ZN A1804 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 167 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " 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 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " 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 78 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " Number of angles added : 45 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7318 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 47 sheets defined 39.3% alpha, 19.6% beta 43 base pairs and 76 stacking pairs defined. Time for finding SS restraints: 4.16 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 95 through 105 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 203 through 213 removed outlier: 3.730A pdb=" N HIS A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 222 removed outlier: 3.509A pdb=" N PHE A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 234 Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 260 through 283 removed outlier: 3.508A 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: 3.671A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 506 through 510 Processing helix chain 'A' and resid 524 through 536 removed outlier: 3.701A pdb=" N LEU A 528 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.651A pdb=" N VAL A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 582 removed outlier: 3.836A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 661 Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 672 through 699 removed outlier: 3.538A pdb=" N ALA A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 737 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 removed outlier: 3.525A pdb=" N ILE A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 845 removed outlier: 3.550A pdb=" N GLU A 822 " --> pdb=" O MET A 818 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR A 831 " --> pdb=" O THR A 827 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU A 833 " --> pdb=" O VAL A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 874 through 876 No H-bonds generated for 'chain 'A' and resid 874 through 876' Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 909 through 913 Processing helix chain 'A' and resid 915 through 920 Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 959 through 972 Processing helix chain 'A' and resid 982 through 995 removed outlier: 3.520A pdb=" N GLN A 994 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU A 995 " --> pdb=" O LYS A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1015 Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1038 through 1056 Processing helix chain 'A' and resid 1063 through 1079 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1096 through 1107 Processing helix chain 'A' and resid 1130 through 1139 Processing helix chain 'A' and resid 1142 through 1145 Processing helix chain 'A' and resid 1166 through 1174 removed outlier: 3.977A pdb=" N PHE A1174 " --> pdb=" O ILE A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1205 Processing helix chain 'A' and resid 1208 through 1221 Processing helix chain 'A' and resid 1257 through 1271 Processing helix chain 'A' and resid 1312 through 1317 removed outlier: 3.636A pdb=" N MET A1317 " --> pdb=" O LEU A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1340 Processing helix chain 'A' and resid 1340 through 1357 Processing helix chain 'A' and resid 1364 through 1376 removed outlier: 4.018A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1401 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1431 removed outlier: 3.568A pdb=" N ASN A1427 " --> pdb=" O GLY A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1439 Processing helix chain 'A' and resid 1447 through 1452 Processing helix chain 'B' and resid 29 through 37 removed outlier: 4.236A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 66 removed outlier: 3.644A pdb=" N LEU B 48 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASP B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 293 through 303 removed outlier: 3.533A pdb=" N ILE B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) removed outlier: 3.811A 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 Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 438 Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.799A pdb=" N THR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 473 removed outlier: 4.477A pdb=" N MET B 473 " --> pdb=" O LYS B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.585A pdb=" N ARG B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 565 through 569 Processing helix chain 'B' and resid 592 through 607 Processing helix chain 'B' and resid 654 through 667 Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.714A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 Processing helix chain 'B' and resid 744 through 749 Processing helix chain 'B' and resid 750 through 755 removed outlier: 4.122A pdb=" N ILE B 755 " --> pdb=" O VAL B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 762 removed outlier: 3.587A pdb=" N ASN B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 775 removed outlier: 3.617A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 788 Processing helix chain 'B' and resid 806 through 813 removed outlier: 3.685A pdb=" N GLU B 810 " --> pdb=" O ARG B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 849 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.455A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.843A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1061 removed outlier: 3.745A pdb=" N GLU B1061 " --> pdb=" O LYS B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1153 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 69 removed outlier: 3.533A 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 30 through 34 removed outlier: 3.674A pdb=" N GLN D 34 " --> pdb=" O GLN D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 73 Processing helix chain 'D' and resid 118 through 132 Processing helix chain 'D' and resid 138 through 151 Processing helix chain 'D' and resid 156 through 171 removed outlier: 3.702A pdb=" N VAL D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 removed outlier: 3.876A pdb=" N GLY D 181 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 196 through 199 Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'E' and resid 4 through 27 Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.531A pdb=" N VAL E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 47 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 91 through 104 removed outlier: 3.567A pdb=" N THR E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS E 103 " --> pdb=" O HIS E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 124 Processing helix chain 'E' and resid 138 through 141 Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.581A pdb=" N GLU G 32 " --> pdb=" O THR G 28 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) 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 'I' and resid 59 through 65 removed outlier: 4.017A pdb=" N GLY I 63 " --> pdb=" O GLN I 60 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP I 65 " --> pdb=" O ILE I 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 40 removed outlier: 3.561A pdb=" N GLY J 40 " --> pdb=" O LEU J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 53 removed outlier: 3.992A pdb=" N HIS J 53 " --> pdb=" O MET J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 removed outlier: 3.547A pdb=" N PHE J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU J 61 " --> pdb=" O ILE J 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 56 through 61' Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 53 removed outlier: 4.018A pdb=" N ASN K 44 " --> pdb=" O HIS K 40 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (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 90 removed outlier: 9.973A pdb=" N LEU A 86 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 11.194A pdb=" N LYS A 88 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N CYS A 238 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 173 through 177 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 345 removed outlier: 3.616A 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: 3.581A pdb=" N SER A 348 " --> pdb=" O ARG B1106 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS A 490 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET A 456 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL A 364 " --> pdb=" O LYS A 461 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE A 463 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL A 366 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N PHE A 468 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL A 352 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N LEU A 470 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N SER A 354 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.666A pdb=" N ARG A 434 " --> pdb=" O TYR A 376 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.828A 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: 7.011A 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: 6.614A 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 removed outlier: 3.552A pdb=" N LEU A1116 " --> pdb=" O THR A1308 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.237A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU A1192 " --> pdb=" O ILE A1152 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE A1152 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ARG A1194 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N SER A1150 " --> pdb=" O ARG A1194 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLU A1196 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR I 44 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 5 through 6 removed outlier: 5.182A pdb=" N VAL A1443 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 48 through 50 removed outlier: 4.663A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 69 through 73 removed outlier: 5.195A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N VAL B 132 " --> pdb=" O SER B 156 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N SER B 156 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LYS B 134 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N GLU B 154 " --> pdb=" O LYS B 134 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N THR B 136 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE B 152 " --> pdb=" O THR B 136 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 69 through 73 removed outlier: 5.195A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AC3, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC4, first strand: chain 'B' and resid 404 through 407 removed outlier: 6.060A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 224 through 227 removed outlier: 4.169A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC7, first strand: chain 'B' and resid 650 through 651 removed outlier: 3.561A pdb=" N GLU B 650 " --> pdb=" O GLU B 641 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS B 741 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 585 through 590 removed outlier: 5.283A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ARG B 579 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ILE B 626 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N PHE B 581 " --> pdb=" O ILE B 626 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU B 623 " --> pdb=" O ASP B 618 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 792 through 793 removed outlier: 3.728A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 7.652A 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 793 removed outlier: 3.728A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD3, first strand: chain 'B' and resid 821 through 825 removed outlier: 7.122A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 873 through 874 removed outlier: 3.577A pdb=" N THR B 873 " --> pdb=" O THR B 915 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 910 through 912 Processing sheet with id=AD6, first strand: chain 'B' and resid 1069 through 1070 Processing sheet with id=AD7, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD8, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD9, first strand: chain 'C' and resid 7 through 13 removed outlier: 5.552A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.798A pdb=" N GLU C 152 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N THR C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LYS C 154 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N VAL C 51 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N THR C 156 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL C 49 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL C 158 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA C 45 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 111 through 114 removed outlier: 6.533A pdb=" N THR C 111 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LYS C 146 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL C 113 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AE4, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.488A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.825A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 169 through 170 removed outlier: 3.713A pdb=" N LYS G 146 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE G 160 " --> pdb=" O GLU G 148 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N CYS G 150 " --> pdb=" O HIS G 158 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N HIS G 158 " --> pdb=" O CYS G 150 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS G 107 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA G 159 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE G 99 " --> pdb=" O VAL G 110 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR G 90 " --> pdb=" O GLN G 102 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.542A pdb=" N SER G 129 " --> pdb=" O ASN G 122 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 4 through 16 removed outlier: 5.527A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU H 14 " --> pdb=" O GLU H 27 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 15 through 19 removed outlier: 3.573A pdb=" N ARG I 24 " --> pdb=" O ASP I 19 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE I 27 " --> pdb=" O GLU I 36 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU I 36 " --> pdb=" O PHE I 27 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 70 through 71 removed outlier: 3.552A pdb=" N SER I 71 " --> pdb=" O ASN I 83 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 19 through 23 1351 hydrogen bonds defined for protein. 3702 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 112 hydrogen bonds 224 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 76 stacking parallelities Total time for adding SS restraints: 10.21 Time building geometry restraints manager: 4.24 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: 5408 1.31 - 1.44: 8886 1.44 - 1.56: 18915 1.56 - 1.69: 187 1.69 - 1.81: 292 Bond restraints: 33688 Sorted by residual: bond pdb=" C4 ATP T 101 " pdb=" N9 ATP T 101 " ideal model delta sigma weight residual 1.374 1.184 0.190 1.00e-02 1.00e+04 3.62e+02 bond pdb=" C8 ATP T 101 " pdb=" N9 ATP T 101 " ideal model delta sigma weight residual 1.370 1.212 0.158 1.20e-02 6.94e+03 1.73e+02 bond pdb=" C6 ATP T 101 " pdb=" N6 ATP T 101 " ideal model delta sigma weight residual 1.337 1.451 -0.114 1.10e-02 8.26e+03 1.08e+02 bond pdb=" C5 ATP T 101 " pdb=" N7 ATP T 101 " ideal model delta sigma weight residual 1.387 1.457 -0.070 1.00e-02 1.00e+04 4.95e+01 bond pdb=" C5 ATP T 101 " pdb=" C6 ATP T 101 " ideal model delta sigma weight residual 1.409 1.339 0.070 1.00e-02 1.00e+04 4.89e+01 ... (remaining 33683 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.17: 45608 3.17 - 6.33: 221 6.33 - 9.50: 43 9.50 - 12.66: 2 12.66 - 15.83: 3 Bond angle restraints: 45877 Sorted by residual: angle pdb=" PB ATP T 101 " pdb=" O3B ATP T 101 " pdb=" PG ATP T 101 " ideal model delta sigma weight residual 139.87 124.04 15.83 1.00e+00 1.00e+00 2.51e+02 angle pdb=" C4 ATP T 101 " pdb=" N9 ATP T 101 " pdb=" C8 ATP T 101 " ideal model delta sigma weight residual 105.72 119.73 -14.01 1.00e+00 1.00e+00 1.96e+02 angle pdb=" PA ATP T 101 " pdb=" O3A ATP T 101 " pdb=" PB ATP T 101 " ideal model delta sigma weight residual 136.83 123.84 12.99 1.00e+00 1.00e+00 1.69e+02 angle pdb=" N1 ATP T 101 " pdb=" C2 ATP T 101 " pdb=" N3 ATP T 101 " ideal model delta sigma weight residual 128.69 120.25 8.44 1.00e+00 1.00e+00 7.13e+01 angle pdb=" O4' DT N 50 " pdb=" C4' DT N 50 " pdb=" C3' DT N 50 " ideal model delta sigma weight residual 106.00 102.27 3.73 6.00e-01 2.78e+00 3.86e+01 ... (remaining 45872 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.65: 19599 29.65 - 59.29: 706 59.29 - 88.94: 57 88.94 - 118.58: 4 118.58 - 148.23: 3 Dihedral angle restraints: 20369 sinusoidal: 9071 harmonic: 11298 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 180.00 152.96 27.04 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA HIS A1173 " pdb=" C HIS A1173 " pdb=" N PHE A1174 " pdb=" CA PHE A1174 " ideal model delta harmonic sigma weight residual 180.00 160.52 19.48 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA ILE C 38 " pdb=" C ILE C 38 " pdb=" N ALA C 39 " pdb=" CA ALA C 39 " ideal model delta harmonic sigma weight residual 180.00 -160.90 -19.10 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 20366 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3509 0.036 - 0.071: 1080 0.071 - 0.107: 444 0.107 - 0.142: 121 0.142 - 0.178: 5 Chirality restraints: 5159 Sorted by residual: chirality pdb=" C2' ATP T 101 " pdb=" C1' ATP T 101 " pdb=" C3' ATP T 101 " pdb=" O2' ATP T 101 " both_signs ideal model delta sigma weight residual False -2.68 -2.50 -0.18 2.00e-01 2.50e+01 7.92e-01 chirality pdb=" C2' G R 9 " pdb=" C3' G R 9 " pdb=" O2' G R 9 " pdb=" C1' G R 9 " both_signs ideal model delta sigma weight residual False -2.62 -2.79 0.17 2.00e-01 2.50e+01 7.12e-01 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 -2.47 -0.16 2.00e-01 2.50e+01 6.16e-01 ... (remaining 5156 not shown) Planarity restraints: 5607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 710 " -0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C LEU A 710 " 0.059 2.00e-02 2.50e+03 pdb=" O LEU A 710 " -0.022 2.00e-02 2.50e+03 pdb=" N ARG A 711 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A1098 " 0.029 5.00e-02 4.00e+02 4.37e-02 3.05e+00 pdb=" N PRO A1099 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A1099 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1099 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 244 " -0.028 5.00e-02 4.00e+02 4.12e-02 2.71e+00 pdb=" N PRO A 245 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 245 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 245 " -0.023 5.00e-02 4.00e+02 ... (remaining 5604 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 229 2.49 - 3.09: 24406 3.09 - 3.70: 51187 3.70 - 4.30: 73480 4.30 - 4.90: 120488 Nonbonded interactions: 269790 Sorted by model distance: nonbonded pdb="MG MG A1801 " pdb=" O2A ATP T 101 " model vdw 1.891 2.170 nonbonded pdb="MG MG A1801 " pdb=" O2G ATP T 101 " model vdw 1.896 2.170 nonbonded pdb="MG MG A1801 " pdb=" O2B ATP T 101 " model vdw 1.900 2.170 nonbonded pdb=" OD2 ASP A 481 " pdb="MG MG A1801 " model vdw 1.958 2.170 nonbonded pdb=" O LYS A1205 " pdb=" NH2 ARG A1274 " model vdw 2.178 3.120 ... (remaining 269785 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: 3.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 39.810 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 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 0.190 33720 Z= 0.345 Angle : 0.647 15.830 45922 Z= 0.425 Chirality : 0.042 0.178 5159 Planarity : 0.004 0.045 5607 Dihedral : 14.368 148.226 13051 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.48 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: 0.94 (0.14), residues: 3836 helix: 2.05 (0.15), residues: 1309 sheet: 0.30 (0.21), residues: 603 loop : -0.22 (0.15), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1366 TYR 0.025 0.001 TYR B 797 PHE 0.019 0.001 PHE A 815 TRP 0.018 0.001 TRP A 552 HIS 0.007 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.35 (33688) covalent geometry : angle 0.64079 / 0.43 (45877) hydrogen bonds : bond 0.19053 / 12.52 ( 1425) hydrogen bonds : angle 6.82425 / 4.85 ( 3926) metal coordination : bond 0.00738 / 0.49 ( 32) metal coordination : angle 2.85901 / 1.86 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 588 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ASP cc_start: 0.9292 (t0) cc_final: 0.8586 (p0) REVERT: A 277 GLU cc_start: 0.9685 (tt0) cc_final: 0.9469 (tm-30) REVERT: A 346 ASP cc_start: 0.9008 (m-30) cc_final: 0.8652 (m-30) REVERT: A 453 MET cc_start: 0.9334 (mpp) cc_final: 0.8707 (mpp) REVERT: A 456 MET cc_start: 0.9197 (mtm) cc_final: 0.8719 (mtt) REVERT: A 486 GLU cc_start: 0.9118 (tt0) cc_final: 0.8810 (tt0) REVERT: A 487 MET cc_start: 0.9435 (mtp) cc_final: 0.8840 (mtt) REVERT: A 496 GLU cc_start: 0.8915 (tt0) cc_final: 0.8458 (tm-30) REVERT: A 605 MET cc_start: 0.9309 (tpp) cc_final: 0.9017 (tpp) REVERT: A 748 MET cc_start: 0.9150 (mtm) cc_final: 0.8938 (mtp) REVERT: A 838 GLN cc_start: 0.9385 (tp40) cc_final: 0.8952 (tm-30) REVERT: A 842 VAL cc_start: 0.9474 (t) cc_final: 0.9240 (p) REVERT: A 849 MET cc_start: 0.8391 (ttp) cc_final: 0.7904 (ttm) REVERT: A 873 MET cc_start: 0.9384 (mmp) cc_final: 0.9063 (mmp) REVERT: A 919 ILE cc_start: 0.9449 (mm) cc_final: 0.9231 (mm) REVERT: A 1261 LYS cc_start: 0.8904 (mtpp) cc_final: 0.8632 (tptp) REVERT: A 1277 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8271 (tm-30) REVERT: A 1315 GLU cc_start: 0.9464 (tt0) cc_final: 0.8996 (tm-30) REVERT: A 1336 MET cc_start: 0.9453 (tmm) cc_final: 0.9245 (tmm) REVERT: A 1444 MET cc_start: 0.8941 (mmt) cc_final: 0.8553 (mmm) REVERT: B 101 MET cc_start: 0.9342 (mtt) cc_final: 0.9016 (mmm) REVERT: B 164 LYS cc_start: 0.9063 (mttt) cc_final: 0.8813 (mppt) REVERT: B 173 MET cc_start: 0.9247 (ttm) cc_final: 0.8929 (ttp) REVERT: B 239 GLU cc_start: 0.9094 (pt0) cc_final: 0.8555 (tm-30) REVERT: B 563 MET cc_start: 0.9237 (ttp) cc_final: 0.8968 (tmm) REVERT: B 615 MET cc_start: 0.8859 (mtm) cc_final: 0.8120 (ptt) REVERT: B 629 ASP cc_start: 0.9082 (t0) cc_final: 0.8879 (t0) REVERT: B 662 MET cc_start: 0.9560 (mtm) cc_final: 0.9307 (mtm) REVERT: B 703 ILE cc_start: 0.9412 (mt) cc_final: 0.8823 (tp) REVERT: B 782 LEU cc_start: 0.9032 (mt) cc_final: 0.8627 (mt) REVERT: B 836 GLU cc_start: 0.9383 (mm-30) cc_final: 0.9092 (mm-30) REVERT: B 842 ASN cc_start: 0.9189 (t0) cc_final: 0.8973 (t0) REVERT: B 875 GLU cc_start: 0.9199 (pt0) cc_final: 0.8923 (pp20) REVERT: B 999 MET cc_start: 0.9624 (mmt) cc_final: 0.9155 (mmm) REVERT: B 1021 MET cc_start: 0.9472 (mtm) cc_final: 0.9182 (mtp) REVERT: B 1072 MET cc_start: 0.8801 (mmm) cc_final: 0.8558 (mmm) REVERT: B 1111 MET cc_start: 0.8777 (mmm) cc_final: 0.8124 (mmm) REVERT: B 1128 LEU cc_start: 0.9058 (mt) cc_final: 0.8791 (mt) REVERT: B 1206 GLU cc_start: 0.9477 (mt-10) cc_final: 0.9254 (mt-10) REVERT: C 190 ASP cc_start: 0.9376 (t0) cc_final: 0.9052 (m-30) REVERT: C 211 ASP cc_start: 0.9579 (m-30) cc_final: 0.9359 (p0) REVERT: D 29 LEU cc_start: 0.7171 (mt) cc_final: 0.6656 (mm) REVERT: D 67 ARG cc_start: 0.8371 (ttm170) cc_final: 0.8130 (mmm160) REVERT: D 129 LEU cc_start: 0.7910 (tp) cc_final: 0.7441 (pp) REVERT: D 151 PHE cc_start: 0.4287 (m-80) cc_final: 0.3634 (m-10) REVERT: D 179 GLN cc_start: 0.7696 (mm110) cc_final: 0.7476 (tm-30) REVERT: E 33 GLU cc_start: 0.9551 (tt0) cc_final: 0.9286 (tm-30) REVERT: E 48 ASP cc_start: 0.9316 (t70) cc_final: 0.9114 (t70) REVERT: E 58 MET cc_start: 0.9345 (mtp) cc_final: 0.8965 (mtm) REVERT: E 112 TYR cc_start: 0.9147 (p90) cc_final: 0.8834 (p90) REVERT: E 214 CYS cc_start: 0.9300 (t) cc_final: 0.8914 (t) REVERT: F 89 GLU cc_start: 0.9350 (mt-10) cc_final: 0.9079 (mt-10) REVERT: F 100 GLN cc_start: 0.9192 (mt0) cc_final: 0.8934 (mt0) REVERT: F 114 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8571 (tm-30) REVERT: F 120 ILE cc_start: 0.9422 (mm) cc_final: 0.8892 (mm) REVERT: F 122 MET cc_start: 0.8974 (mtp) cc_final: 0.8745 (mtm) REVERT: F 130 ILE cc_start: 0.9595 (mt) cc_final: 0.9335 (mp) REVERT: F 144 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8234 (mt-10) REVERT: G 1 MET cc_start: 0.6289 (mmm) cc_final: 0.5446 (mmm) REVERT: G 41 LYS cc_start: 0.8988 (tppt) cc_final: 0.8762 (tppt) REVERT: G 53 ASN cc_start: 0.9041 (m-40) cc_final: 0.8806 (t0) REVERT: G 57 GLN cc_start: 0.7890 (mt0) cc_final: 0.7482 (mt0) REVERT: G 75 ARG cc_start: 0.8653 (ttm170) cc_final: 0.8007 (ttp-170) REVERT: G 82 PHE cc_start: 0.4440 (m-80) cc_final: 0.4050 (m-80) REVERT: G 115 MET cc_start: 0.6491 (mtp) cc_final: 0.5191 (ptp) REVERT: G 142 ARG cc_start: 0.6282 (mtp85) cc_final: 0.5858 (mmt90) REVERT: H 14 GLU cc_start: 0.9214 (tt0) cc_final: 0.8100 (tm-30) REVERT: H 27 GLU cc_start: 0.9384 (mt-10) cc_final: 0.8915 (mp0) REVERT: H 64 ASN cc_start: 0.9480 (m-40) cc_final: 0.8936 (t0) REVERT: H 103 LYS cc_start: 0.8535 (tptt) cc_final: 0.8331 (tppt) REVERT: H 105 GLU cc_start: 0.8687 (tt0) cc_final: 0.7806 (tm-30) REVERT: H 106 GLU cc_start: 0.8881 (tp30) cc_final: 0.8600 (tp30) REVERT: H 107 VAL cc_start: 0.8703 (t) cc_final: 0.7955 (t) REVERT: H 116 TYR cc_start: 0.9133 (m-80) cc_final: 0.8908 (m-80) REVERT: H 136 LYS cc_start: 0.8727 (mmtp) cc_final: 0.8428 (mptt) REVERT: H 137 GLN cc_start: 0.9191 (tt0) cc_final: 0.8492 (tm-30) REVERT: I 44 TYR cc_start: 0.6781 (t80) cc_final: 0.6012 (t80) REVERT: I 97 MET cc_start: 0.7685 (mtp) cc_final: 0.7048 (mmm) REVERT: J 1 MET cc_start: 0.8515 (mtm) cc_final: 0.8274 (mtm) REVERT: J 26 GLN cc_start: 0.9569 (tt0) cc_final: 0.9316 (pt0) REVERT: J 29 GLU cc_start: 0.9552 (mt-10) cc_final: 0.9305 (mp0) REVERT: J 49 MET cc_start: 0.9441 (tpp) cc_final: 0.8943 (tpp) REVERT: J 58 GLU cc_start: 0.9364 (mm-30) cc_final: 0.9046 (tm-30) REVERT: K 38 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8543 (mm-30) REVERT: K 39 ASP cc_start: 0.8991 (p0) cc_final: 0.8670 (p0) REVERT: K 49 GLU cc_start: 0.9446 (mm-30) cc_final: 0.9246 (tp30) REVERT: K 91 CYS cc_start: 0.9396 (m) cc_final: 0.9162 (t) REVERT: K 106 GLU cc_start: 0.9613 (mt-10) cc_final: 0.9275 (mt-10) REVERT: L 54 ARG cc_start: 0.7655 (mtt-85) cc_final: 0.7142 (mtt-85) REVERT: L 60 ARG cc_start: 0.8551 (ttm-80) cc_final: 0.8183 (ttm110) outliers start: 0 outliers final: 0 residues processed: 588 average time/residue: 0.2233 time to fit residues: 206.1612 Evaluate side-chains 363 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.3980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.0570 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 631 HIS ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1173 HIS A1218 GLN A1367 HIS B 46 GLN ** B 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 ASN B 733 HIS B 734 HIS B 984 HIS C 31 ASN C 203 GLN ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN G 122 ASN I 46 HIS ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.080743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.055920 restraints weight = 114865.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.057672 restraints weight = 59651.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.058815 restraints weight = 39341.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.059529 restraints weight = 30267.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.059896 restraints weight = 25850.988| |-----------------------------------------------------------------------------| r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 33720 Z= 0.137 Angle : 0.650 18.705 45922 Z= 0.336 Chirality : 0.046 0.258 5159 Planarity : 0.004 0.062 5607 Dihedral : 16.712 139.435 5284 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.44 % Favored : 96.45 % Rotamer: Outliers : 0.88 % Allowed : 6.31 % Favored : 92.82 % 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: 0.66 (0.14), residues: 3836 helix: 1.68 (0.14), residues: 1347 sheet: 0.08 (0.21), residues: 586 loop : -0.29 (0.15), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 47 TYR 0.018 0.001 TYR B 797 PHE 0.025 0.002 PHE A 444 TRP 0.012 0.001 TRP B 466 HIS 0.011 0.001 HIS C 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (33688) covalent geometry : angle 0.63084 / 0.33 (45877) hydrogen bonds : bond 0.04813 / 3.18 ( 1425) hydrogen bonds : angle 5.16683 / 3.69 ( 3926) metal coordination : bond 0.00593 / 0.40 ( 32) metal coordination : angle 4.99547 / 3.44 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 438 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.9463 (mmm) cc_final: 0.8810 (tpp) REVERT: A 146 MET cc_start: 0.8910 (mmm) cc_final: 0.8686 (mpp) REVERT: A 177 ASP cc_start: 0.8874 (t0) cc_final: 0.8626 (p0) REVERT: A 605 MET cc_start: 0.9305 (tpp) cc_final: 0.8869 (tpp) REVERT: A 748 MET cc_start: 0.8904 (mtm) cc_final: 0.8677 (mtm) REVERT: A 838 GLN cc_start: 0.9303 (tp40) cc_final: 0.8738 (tm-30) REVERT: A 842 VAL cc_start: 0.9691 (t) cc_final: 0.9465 (p) REVERT: A 849 MET cc_start: 0.8136 (ttp) cc_final: 0.7935 (ttm) REVERT: A 873 MET cc_start: 0.8836 (mmp) cc_final: 0.8610 (mmp) REVERT: A 1195 LEU cc_start: 0.9112 (mp) cc_final: 0.8682 (tt) REVERT: A 1261 LYS cc_start: 0.8810 (mtpp) cc_final: 0.8599 (tptp) REVERT: A 1276 VAL cc_start: 0.9320 (t) cc_final: 0.8675 (p) REVERT: A 1411 GLU cc_start: 0.8874 (tp30) cc_final: 0.8417 (tm-30) REVERT: A 1444 MET cc_start: 0.8848 (mmt) cc_final: 0.8454 (mmm) REVERT: B 224 GLN cc_start: 0.9182 (mt0) cc_final: 0.8929 (mp10) REVERT: B 239 GLU cc_start: 0.9093 (pt0) cc_final: 0.8829 (tm-30) REVERT: B 308 TRP cc_start: 0.8240 (p-90) cc_final: 0.7938 (p-90) REVERT: B 615 MET cc_start: 0.8277 (mtm) cc_final: 0.8020 (ptt) REVERT: B 703 ILE cc_start: 0.9542 (mt) cc_final: 0.9263 (tp) REVERT: B 782 LEU cc_start: 0.8871 (mt) cc_final: 0.8460 (mt) REVERT: B 789 MET cc_start: 0.9441 (mmm) cc_final: 0.9163 (mmm) REVERT: B 841 MET cc_start: 0.8707 (ttm) cc_final: 0.8485 (ttm) REVERT: B 1111 MET cc_start: 0.8770 (mmm) cc_final: 0.8357 (mmm) REVERT: B 1206 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8783 (mt-10) REVERT: C 190 ASP cc_start: 0.8786 (t0) cc_final: 0.8544 (m-30) REVERT: D 38 ILE cc_start: 0.8717 (mm) cc_final: 0.8493 (mm) REVERT: D 67 ARG cc_start: 0.8221 (ttm170) cc_final: 0.8020 (mmm160) REVERT: D 128 VAL cc_start: 0.8840 (t) cc_final: 0.8572 (p) REVERT: D 129 LEU cc_start: 0.8170 (tp) cc_final: 0.7663 (pp) REVERT: D 138 ASN cc_start: 0.8346 (p0) cc_final: 0.8042 (p0) REVERT: D 151 PHE cc_start: 0.4758 (m-80) cc_final: 0.4311 (m-10) REVERT: D 175 PHE cc_start: 0.6720 (t80) cc_final: 0.6337 (t80) REVERT: E 25 ASP cc_start: 0.9099 (m-30) cc_final: 0.8707 (m-30) REVERT: E 58 MET cc_start: 0.8887 (mtp) cc_final: 0.8633 (mtm) REVERT: E 121 MET cc_start: 0.9144 (mmm) cc_final: 0.8944 (mmm) REVERT: E 214 CYS cc_start: 0.8743 (t) cc_final: 0.8448 (t) REVERT: F 96 THR cc_start: 0.9648 (m) cc_final: 0.9411 (p) REVERT: F 103 MET cc_start: 0.8988 (mtt) cc_final: 0.8642 (mtp) REVERT: F 116 ASP cc_start: 0.9128 (t0) cc_final: 0.8358 (t0) REVERT: F 120 ILE cc_start: 0.9707 (mm) cc_final: 0.9123 (mm) REVERT: F 122 MET cc_start: 0.8971 (mtp) cc_final: 0.8721 (mtm) REVERT: F 124 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8250 (mm-30) REVERT: F 149 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8607 (tm-30) REVERT: G 24 GLN cc_start: 0.8877 (pm20) cc_final: 0.8524 (tp40) REVERT: G 44 TYR cc_start: 0.8040 (m-80) cc_final: 0.7468 (m-80) REVERT: G 57 GLN cc_start: 0.8587 (mt0) cc_final: 0.8067 (mt0) REVERT: G 75 ARG cc_start: 0.8834 (ttm170) cc_final: 0.8087 (ttp-170) REVERT: G 102 GLN cc_start: 0.6510 (tp40) cc_final: 0.6212 (tp40) REVERT: G 115 MET cc_start: 0.6120 (mtp) cc_final: 0.4435 (ptp) REVERT: G 142 ARG cc_start: 0.6708 (mtp85) cc_final: 0.5971 (mmt90) REVERT: H 14 GLU cc_start: 0.8745 (tt0) cc_final: 0.8369 (tm-30) REVERT: H 64 ASN cc_start: 0.8948 (m-40) cc_final: 0.8731 (t0) REVERT: H 100 THR cc_start: 0.9423 (m) cc_final: 0.9185 (p) REVERT: H 105 GLU cc_start: 0.8747 (tt0) cc_final: 0.8130 (tm-30) REVERT: I 44 TYR cc_start: 0.7689 (t80) cc_final: 0.6836 (t80) REVERT: I 45 ARG cc_start: 0.7789 (ttt-90) cc_final: 0.7436 (ttt180) REVERT: I 97 MET cc_start: 0.8076 (mtp) cc_final: 0.7736 (mmm) REVERT: J 27 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8214 (mt-10) REVERT: J 49 MET cc_start: 0.9513 (tpp) cc_final: 0.9310 (tpp) REVERT: K 6 ARG cc_start: 0.9019 (mmm-85) cc_final: 0.8646 (mmm160) REVERT: K 54 ARG cc_start: 0.7574 (mmm160) cc_final: 0.6956 (tpt90) REVERT: L 29 TYR cc_start: 0.8655 (m-10) cc_final: 0.8003 (m-10) REVERT: L 33 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8160 (pt0) REVERT: L 38 LEU cc_start: 0.8779 (tt) cc_final: 0.8556 (tt) REVERT: L 54 ARG cc_start: 0.7920 (mtt-85) cc_final: 0.7446 (mtt-85) REVERT: L 56 LEU cc_start: 0.8712 (pp) cc_final: 0.8485 (mm) REVERT: L 60 ARG cc_start: 0.8908 (ttm-80) cc_final: 0.8327 (ttm110) outliers start: 30 outliers final: 20 residues processed: 454 average time/residue: 0.2128 time to fit residues: 156.6627 Evaluate side-chains 384 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 363 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 992 ASP Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 733 HIS Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 839 MET Chi-restraints excluded: chain B residue 1057 LYS Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain L residue 41 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 184 optimal weight: 8.9990 chunk 121 optimal weight: 2.9990 chunk 234 optimal weight: 0.0980 chunk 133 optimal weight: 6.9990 chunk 298 optimal weight: 10.0000 chunk 191 optimal weight: 8.9990 chunk 164 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 206 optimal weight: 10.0000 chunk 369 optimal weight: 3.9990 chunk 371 optimal weight: 9.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 733 HIS D 179 GLN E 143 ASN F 100 GLN G 10 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 = 0.3424 r_free = 0.3424 target = 0.079013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.054504 restraints weight = 116061.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.056147 restraints weight = 60651.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.057246 restraints weight = 40288.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.057941 restraints weight = 31099.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.058326 restraints weight = 26582.309| |-----------------------------------------------------------------------------| r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 33720 Z= 0.214 Angle : 0.649 19.110 45922 Z= 0.332 Chirality : 0.045 0.244 5159 Planarity : 0.004 0.053 5607 Dihedral : 16.654 139.910 5284 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.14 % Favored : 95.72 % Rotamer: Outliers : 1.69 % Allowed : 8.44 % Favored : 89.87 % 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: 0.56 (0.14), residues: 3836 helix: 1.69 (0.14), residues: 1348 sheet: -0.14 (0.21), residues: 605 loop : -0.37 (0.15), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 30 TYR 0.021 0.001 TYR G 44 PHE 0.016 0.001 PHE A 252 TRP 0.011 0.001 TRP B 561 HIS 0.019 0.001 HIS B 733 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.21 (33688) covalent geometry : angle 0.62949 / 0.33 (45877) hydrogen bonds : bond 0.04372 / 2.92 ( 1425) hydrogen bonds : angle 4.94837 / 3.53 ( 3926) metal coordination : bond 0.00763 / 0.51 ( 32) metal coordination : angle 5.10315 / 3.51 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 363 time to evaluate : 1.210 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 108 MET cc_start: 0.7635 (ppp) cc_final: 0.7322 (ppp) REVERT: A 146 MET cc_start: 0.8908 (mmm) cc_final: 0.8660 (mpp) REVERT: A 177 ASP cc_start: 0.8903 (t0) cc_final: 0.8676 (p0) REVERT: A 605 MET cc_start: 0.9295 (tpp) cc_final: 0.8836 (tpp) REVERT: A 748 MET cc_start: 0.8976 (mtm) cc_final: 0.8673 (mtm) REVERT: A 838 GLN cc_start: 0.9344 (tp40) cc_final: 0.8709 (tm-30) REVERT: A 842 VAL cc_start: 0.9705 (t) cc_final: 0.9399 (p) REVERT: A 849 MET cc_start: 0.8313 (ttp) cc_final: 0.8068 (ttm) REVERT: A 1261 LYS cc_start: 0.8805 (mtpp) cc_final: 0.8592 (tptt) REVERT: A 1411 GLU cc_start: 0.8914 (tp30) cc_final: 0.8201 (tm-30) REVERT: A 1444 MET cc_start: 0.8874 (mmt) cc_final: 0.8425 (mmm) REVERT: B 239 GLU cc_start: 0.9159 (pt0) cc_final: 0.8844 (tm-30) REVERT: B 615 MET cc_start: 0.8369 (mtm) cc_final: 0.8039 (ptt) REVERT: B 703 ILE cc_start: 0.9552 (mt) cc_final: 0.9283 (tp) REVERT: B 782 LEU cc_start: 0.8997 (mt) cc_final: 0.8551 (mt) REVERT: B 1057 LYS cc_start: 0.9491 (OUTLIER) cc_final: 0.9286 (ttpp) REVERT: B 1111 MET cc_start: 0.8835 (mmm) cc_final: 0.8295 (mmm) REVERT: B 1152 MET cc_start: 0.8799 (mmm) cc_final: 0.8441 (mmm) REVERT: B 1206 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8787 (mt-10) REVERT: C 190 ASP cc_start: 0.8870 (t0) cc_final: 0.8591 (m-30) REVERT: D 67 ARG cc_start: 0.8195 (ttm170) cc_final: 0.7973 (mmm160) REVERT: D 129 LEU cc_start: 0.8096 (tp) cc_final: 0.7787 (mt) REVERT: D 151 PHE cc_start: 0.4837 (m-80) cc_final: 0.4396 (m-10) REVERT: D 155 ARG cc_start: 0.6053 (tpt90) cc_final: 0.5841 (tpt90) REVERT: D 157 GLN cc_start: 0.8217 (pp30) cc_final: 0.7169 (mp10) REVERT: E 25 ASP cc_start: 0.9142 (m-30) cc_final: 0.8733 (m-30) REVERT: E 58 MET cc_start: 0.8912 (mtp) cc_final: 0.8574 (mtm) REVERT: E 121 MET cc_start: 0.9246 (mmm) cc_final: 0.8963 (mmm) REVERT: E 214 CYS cc_start: 0.8694 (t) cc_final: 0.8413 (t) REVERT: F 87 LYS cc_start: 0.9359 (ptpt) cc_final: 0.9086 (ptpp) REVERT: F 100 GLN cc_start: 0.9118 (mt0) cc_final: 0.8839 (mt0) REVERT: F 103 MET cc_start: 0.8962 (mtt) cc_final: 0.8726 (mtp) REVERT: F 116 ASP cc_start: 0.8895 (t0) cc_final: 0.8495 (t0) REVERT: F 122 MET cc_start: 0.8968 (mtp) cc_final: 0.8719 (mtm) REVERT: G 57 GLN cc_start: 0.8641 (mt0) cc_final: 0.8416 (mt0) REVERT: G 75 ARG cc_start: 0.8817 (ttm170) cc_final: 0.8078 (ttp-170) REVERT: G 115 MET cc_start: 0.6141 (mtp) cc_final: 0.4720 (ptt) REVERT: G 121 PHE cc_start: 0.4455 (t80) cc_final: 0.4250 (t80) REVERT: G 142 ARG cc_start: 0.6581 (mtp85) cc_final: 0.5956 (mmt90) REVERT: H 105 GLU cc_start: 0.8844 (tt0) cc_final: 0.8201 (tm-30) REVERT: H 109 LYS cc_start: 0.8384 (tptm) cc_final: 0.8161 (tptp) REVERT: I 44 TYR cc_start: 0.7704 (t80) cc_final: 0.6840 (t80) REVERT: I 97 MET cc_start: 0.8074 (mtp) cc_final: 0.7649 (mmm) REVERT: J 49 MET cc_start: 0.9538 (tpp) cc_final: 0.9140 (tpp) REVERT: K 54 ARG cc_start: 0.7656 (mmm160) cc_final: 0.7062 (tpt90) REVERT: L 29 TYR cc_start: 0.8688 (m-10) cc_final: 0.7844 (m-10) REVERT: L 38 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8283 (tt) REVERT: L 54 ARG cc_start: 0.7833 (mtt-85) cc_final: 0.7296 (mtt-85) REVERT: L 56 LEU cc_start: 0.8428 (pp) cc_final: 0.8192 (mm) REVERT: L 60 ARG cc_start: 0.8920 (ttm-80) cc_final: 0.8321 (ttm110) outliers start: 58 outliers final: 31 residues processed: 395 average time/residue: 0.2150 time to fit residues: 138.0952 Evaluate side-chains 356 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 323 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1274 ARG Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 839 MET Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1057 LYS Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 46 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 292 optimal weight: 20.0000 chunk 352 optimal weight: 0.0470 chunk 175 optimal weight: 8.9990 chunk 312 optimal weight: 5.9990 chunk 164 optimal weight: 6.9990 chunk 375 optimal weight: 0.3980 chunk 255 optimal weight: 6.9990 chunk 158 optimal weight: 20.0000 chunk 47 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 chunk 191 optimal weight: 10.0000 overall best weight: 3.4884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1140 HIS ** B 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN J 26 GLN L 53 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.077854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.052806 restraints weight = 115227.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.054399 restraints weight = 61375.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.055469 restraints weight = 41214.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.056139 restraints weight = 32084.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.056476 restraints weight = 27567.319| |-----------------------------------------------------------------------------| r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 33720 Z= 0.228 Angle : 0.648 15.467 45922 Z= 0.332 Chirality : 0.045 0.334 5159 Planarity : 0.004 0.051 5607 Dihedral : 16.708 140.448 5284 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.12 % Favored : 95.75 % Rotamer: Outliers : 1.99 % Allowed : 9.66 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.14), residues: 3836 helix: 1.68 (0.15), residues: 1334 sheet: -0.31 (0.21), residues: 615 loop : -0.41 (0.15), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 119 TYR 0.014 0.001 TYR H 95 PHE 0.022 0.001 PHE D 8 TRP 0.013 0.001 TRP B 561 HIS 0.006 0.001 HIS D 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.23 (33688) covalent geometry : angle 0.62950 / 0.33 (45877) hydrogen bonds : bond 0.04060 / 2.70 ( 1425) hydrogen bonds : angle 4.84138 / 3.45 ( 3926) metal coordination : bond 0.00827 / 0.56 ( 32) metal coordination : angle 5.00561 / 3.45 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 340 time to evaluate : 1.208 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 108 MET cc_start: 0.7680 (ppp) cc_final: 0.7348 (ppp) REVERT: A 146 MET cc_start: 0.8856 (mmm) cc_final: 0.8625 (mpp) REVERT: A 304 MET cc_start: 0.9295 (OUTLIER) cc_final: 0.8908 (mmm) REVERT: A 838 GLN cc_start: 0.9322 (tp40) cc_final: 0.8734 (tm-30) REVERT: A 842 VAL cc_start: 0.9707 (t) cc_final: 0.9443 (p) REVERT: A 1261 LYS cc_start: 0.8812 (mtpp) cc_final: 0.8600 (tptt) REVERT: A 1398 MET cc_start: 0.8707 (ttp) cc_final: 0.8494 (ttp) REVERT: A 1408 ILE cc_start: 0.9813 (mm) cc_final: 0.9612 (mt) REVERT: A 1411 GLU cc_start: 0.8862 (tp30) cc_final: 0.8222 (tm-30) REVERT: A 1444 MET cc_start: 0.8841 (mmt) cc_final: 0.8357 (mmm) REVERT: B 199 MET cc_start: 0.7916 (mmp) cc_final: 0.7705 (mmp) REVERT: B 239 GLU cc_start: 0.9147 (pt0) cc_final: 0.8832 (tm-30) REVERT: B 703 ILE cc_start: 0.9531 (mt) cc_final: 0.9303 (tp) REVERT: B 782 LEU cc_start: 0.9046 (mt) cc_final: 0.8644 (mt) REVERT: B 1111 MET cc_start: 0.8795 (mmm) cc_final: 0.8304 (mmm) REVERT: B 1152 MET cc_start: 0.8760 (mmm) cc_final: 0.8389 (mmm) REVERT: C 18 VAL cc_start: 0.9246 (OUTLIER) cc_final: 0.8867 (p) REVERT: C 37 MET cc_start: 0.8710 (mtm) cc_final: 0.8029 (mtm) REVERT: C 190 ASP cc_start: 0.8812 (t0) cc_final: 0.8549 (m-30) REVERT: D 128 VAL cc_start: 0.8801 (t) cc_final: 0.8524 (p) REVERT: D 129 LEU cc_start: 0.8022 (tp) cc_final: 0.7747 (mt) REVERT: D 151 PHE cc_start: 0.4587 (m-80) cc_final: 0.4173 (m-10) REVERT: D 155 ARG cc_start: 0.6050 (tpt90) cc_final: 0.5841 (tpt90) REVERT: D 179 GLN cc_start: 0.8144 (mm110) cc_final: 0.7689 (mm110) REVERT: E 25 ASP cc_start: 0.9124 (m-30) cc_final: 0.8708 (m-30) REVERT: E 58 MET cc_start: 0.8863 (mtp) cc_final: 0.8523 (mtm) REVERT: E 121 MET cc_start: 0.9250 (mmm) cc_final: 0.8950 (mmm) REVERT: F 87 LYS cc_start: 0.9319 (ptpt) cc_final: 0.9055 (ptpp) REVERT: F 103 MET cc_start: 0.9024 (mtt) cc_final: 0.8784 (mtp) REVERT: F 116 ASP cc_start: 0.8915 (t0) cc_final: 0.8539 (t0) REVERT: F 122 MET cc_start: 0.8968 (mtp) cc_final: 0.8751 (mtm) REVERT: F 144 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8122 (tt0) REVERT: G 57 GLN cc_start: 0.8709 (mt0) cc_final: 0.8489 (mt0) REVERT: G 75 ARG cc_start: 0.8844 (ttm170) cc_final: 0.8055 (ttp-170) REVERT: G 115 MET cc_start: 0.6328 (mtp) cc_final: 0.4683 (ptt) REVERT: G 142 ARG cc_start: 0.6502 (mtp85) cc_final: 0.5887 (mmt90) REVERT: H 14 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7489 (tm-30) REVERT: H 27 GLU cc_start: 0.8297 (mp0) cc_final: 0.7685 (mp0) REVERT: H 109 LYS cc_start: 0.8349 (tptm) cc_final: 0.8130 (tptp) REVERT: I 70 ARG cc_start: 0.8301 (mtt90) cc_final: 0.7735 (mtm110) REVERT: I 97 MET cc_start: 0.8115 (mtp) cc_final: 0.7563 (mmm) REVERT: J 49 MET cc_start: 0.9498 (tpp) cc_final: 0.9128 (tpp) REVERT: K 54 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.7085 (tpt90) REVERT: L 29 TYR cc_start: 0.8759 (m-10) cc_final: 0.7936 (m-10) REVERT: L 60 ARG cc_start: 0.8940 (ttm-80) cc_final: 0.8336 (ttm110) outliers start: 68 outliers final: 47 residues processed: 380 average time/residue: 0.1965 time to fit residues: 121.5022 Evaluate side-chains 369 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 319 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1078 GLN Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1274 ARG Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 658 ILE Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 839 MET Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain K residue 54 ARG Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 41 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 144 optimal weight: 10.0000 chunk 176 optimal weight: 1.9990 chunk 238 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 261 optimal weight: 10.0000 chunk 342 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 chunk 372 optimal weight: 0.4980 chunk 244 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 381 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.077593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.052485 restraints weight = 114124.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.054095 restraints weight = 59971.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.055151 restraints weight = 40012.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.055805 restraints weight = 31076.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.056179 restraints weight = 26706.716| |-----------------------------------------------------------------------------| r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33720 Z= 0.160 Angle : 0.607 16.947 45922 Z= 0.309 Chirality : 0.043 0.250 5159 Planarity : 0.004 0.054 5607 Dihedral : 16.693 139.634 5284 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.96 % Favored : 95.91 % Rotamer: Outliers : 1.64 % Allowed : 11.12 % Favored : 87.24 % 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: 0.50 (0.14), residues: 3836 helix: 1.69 (0.15), residues: 1335 sheet: -0.30 (0.21), residues: 609 loop : -0.38 (0.15), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 19 TYR 0.016 0.001 TYR G 51 PHE 0.027 0.001 PHE D 175 TRP 0.012 0.001 TRP B 466 HIS 0.006 0.001 HIS A1258 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (33688) covalent geometry : angle 0.58501 / 0.31 (45877) hydrogen bonds : bond 0.03798 / 2.54 ( 1425) hydrogen bonds : angle 4.69204 / 3.35 ( 3926) metal coordination : bond 0.00643 / 0.44 ( 32) metal coordination : angle 5.21392 / 3.55 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 344 time to evaluate : 1.027 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 68 GLN cc_start: 0.9430 (OUTLIER) cc_final: 0.8363 (pm20) REVERT: A 146 MET cc_start: 0.8879 (mmm) cc_final: 0.8647 (mpp) REVERT: A 838 GLN cc_start: 0.9337 (tp40) cc_final: 0.8745 (tm-30) REVERT: A 842 VAL cc_start: 0.9692 (t) cc_final: 0.9404 (p) REVERT: A 849 MET cc_start: 0.7750 (ttm) cc_final: 0.7470 (ttt) REVERT: A 1070 GLN cc_start: 0.9207 (mt0) cc_final: 0.8846 (mt0) REVERT: A 1206 ASP cc_start: 0.8110 (t0) cc_final: 0.7866 (m-30) REVERT: A 1261 LYS cc_start: 0.8800 (mtpp) cc_final: 0.8548 (tptt) REVERT: A 1411 GLU cc_start: 0.8928 (tp30) cc_final: 0.8272 (tm-30) REVERT: A 1444 MET cc_start: 0.8827 (mmt) cc_final: 0.8337 (mmm) REVERT: B 224 GLN cc_start: 0.9205 (mt0) cc_final: 0.8910 (mp10) REVERT: B 239 GLU cc_start: 0.9189 (pt0) cc_final: 0.8771 (tm-30) REVERT: B 703 ILE cc_start: 0.9542 (mt) cc_final: 0.9295 (tp) REVERT: B 782 LEU cc_start: 0.8982 (mt) cc_final: 0.8553 (mt) REVERT: B 1111 MET cc_start: 0.8798 (mmm) cc_final: 0.8313 (mmm) REVERT: B 1152 MET cc_start: 0.8743 (mmm) cc_final: 0.8368 (mmm) REVERT: C 190 ASP cc_start: 0.8791 (t0) cc_final: 0.8512 (m-30) REVERT: D 151 PHE cc_start: 0.4661 (m-80) cc_final: 0.4251 (m-10) REVERT: D 157 GLN cc_start: 0.8328 (pp30) cc_final: 0.7141 (mp10) REVERT: E 25 ASP cc_start: 0.9159 (m-30) cc_final: 0.8720 (m-30) REVERT: E 58 MET cc_start: 0.8892 (mtp) cc_final: 0.8517 (mtm) REVERT: E 121 MET cc_start: 0.9248 (mmm) cc_final: 0.8902 (mmm) REVERT: F 85 MET cc_start: 0.9053 (tmm) cc_final: 0.8680 (tmm) REVERT: F 87 LYS cc_start: 0.9346 (ptpt) cc_final: 0.9007 (ptpp) REVERT: F 103 MET cc_start: 0.9018 (mtt) cc_final: 0.8718 (mtp) REVERT: F 116 ASP cc_start: 0.8926 (t0) cc_final: 0.8547 (t0) REVERT: F 122 MET cc_start: 0.8971 (mtp) cc_final: 0.8749 (mtm) REVERT: F 144 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8041 (tt0) REVERT: G 57 GLN cc_start: 0.8690 (mt0) cc_final: 0.8461 (mt0) REVERT: G 75 ARG cc_start: 0.8855 (ttm170) cc_final: 0.8056 (ttp-170) REVERT: G 115 MET cc_start: 0.6358 (mtp) cc_final: 0.4697 (ptt) REVERT: G 142 ARG cc_start: 0.6502 (mtp85) cc_final: 0.5770 (mmt90) REVERT: H 109 LYS cc_start: 0.8400 (tptm) cc_final: 0.8160 (tptp) REVERT: I 44 TYR cc_start: 0.7706 (t80) cc_final: 0.6850 (t80) REVERT: I 97 MET cc_start: 0.8073 (mtp) cc_final: 0.7464 (mmm) REVERT: J 49 MET cc_start: 0.9520 (tpp) cc_final: 0.9195 (tpp) REVERT: K 2 ASN cc_start: 0.8943 (m-40) cc_final: 0.8625 (m-40) REVERT: K 54 ARG cc_start: 0.7662 (mmm160) cc_final: 0.7091 (tpt90) REVERT: L 29 TYR cc_start: 0.8647 (m-10) cc_final: 0.8042 (m-10) REVERT: L 60 ARG cc_start: 0.8937 (ttm-80) cc_final: 0.8335 (ttm110) outliers start: 56 outliers final: 42 residues processed: 378 average time/residue: 0.2040 time to fit residues: 124.6236 Evaluate side-chains 360 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 317 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1078 GLN Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1274 ARG Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 839 MET Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1057 LYS Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 41 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 22 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 237 optimal weight: 8.9990 chunk 8 optimal weight: 0.9980 chunk 249 optimal weight: 0.7980 chunk 189 optimal weight: 6.9990 chunk 334 optimal weight: 0.9980 chunk 12 optimal weight: 9.9990 chunk 226 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 131 optimal weight: 10.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1203 ASN A1218 GLN B 433 GLN ** B1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN L 53 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.078273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.053127 restraints weight = 112623.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.054773 restraints weight = 58775.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.055838 restraints weight = 39056.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.056516 restraints weight = 30317.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.056853 restraints weight = 25977.887| |-----------------------------------------------------------------------------| r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33720 Z= 0.123 Angle : 0.590 14.960 45922 Z= 0.301 Chirality : 0.043 0.254 5159 Planarity : 0.004 0.056 5607 Dihedral : 16.651 138.667 5284 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.81 % Favored : 96.06 % Rotamer: Outliers : 1.52 % Allowed : 11.71 % Favored : 86.77 % 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: 0.52 (0.14), residues: 3836 helix: 1.69 (0.15), residues: 1335 sheet: -0.29 (0.21), residues: 602 loop : -0.36 (0.14), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 67 TYR 0.027 0.001 TYR B 830 PHE 0.023 0.001 PHE D 175 TRP 0.015 0.001 TRP A1228 HIS 0.005 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (33688) covalent geometry : angle 0.57231 / 0.30 (45877) hydrogen bonds : bond 0.03611 / 2.41 ( 1425) hydrogen bonds : angle 4.56365 / 3.26 ( 3926) metal coordination : bond 0.00492 / 0.34 ( 32) metal coordination : angle 4.63900 / 3.19 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 343 time to evaluate : 1.287 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 68 GLN cc_start: 0.9473 (OUTLIER) cc_final: 0.8525 (pm20) REVERT: A 146 MET cc_start: 0.8896 (mmm) cc_final: 0.8655 (mpp) REVERT: A 177 ASP cc_start: 0.9013 (t0) cc_final: 0.8718 (p0) REVERT: A 455 MET cc_start: 0.8421 (tpp) cc_final: 0.8041 (ttm) REVERT: A 487 MET cc_start: 0.8656 (mtp) cc_final: 0.8384 (ttt) REVERT: A 838 GLN cc_start: 0.9341 (tp40) cc_final: 0.8737 (tm-30) REVERT: A 842 VAL cc_start: 0.9675 (t) cc_final: 0.9384 (p) REVERT: A 956 LEU cc_start: 0.9545 (mt) cc_final: 0.9305 (mp) REVERT: A 1062 GLU cc_start: 0.8337 (tp30) cc_final: 0.8055 (tp30) REVERT: A 1070 GLN cc_start: 0.9184 (mt0) cc_final: 0.8840 (mt0) REVERT: A 1206 ASP cc_start: 0.8062 (t0) cc_final: 0.7827 (m-30) REVERT: A 1261 LYS cc_start: 0.8795 (mtpp) cc_final: 0.8554 (tptt) REVERT: A 1411 GLU cc_start: 0.8918 (tp30) cc_final: 0.8216 (tm-30) REVERT: A 1444 MET cc_start: 0.8796 (mmt) cc_final: 0.8302 (mmm) REVERT: B 224 GLN cc_start: 0.9188 (mt0) cc_final: 0.8921 (mp10) REVERT: B 239 GLU cc_start: 0.9173 (pt0) cc_final: 0.8777 (tm-30) REVERT: B 699 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8449 (tp30) REVERT: B 703 ILE cc_start: 0.9536 (mt) cc_final: 0.9300 (tp) REVERT: B 782 LEU cc_start: 0.8974 (mt) cc_final: 0.8572 (mt) REVERT: B 1111 MET cc_start: 0.8785 (mmm) cc_final: 0.8287 (mmm) REVERT: B 1152 MET cc_start: 0.8728 (mmm) cc_final: 0.8347 (mmm) REVERT: C 37 MET cc_start: 0.8736 (mtm) cc_final: 0.8061 (mtm) REVERT: C 190 ASP cc_start: 0.8852 (t0) cc_final: 0.8502 (m-30) REVERT: D 64 VAL cc_start: 0.9136 (t) cc_final: 0.8851 (t) REVERT: D 151 PHE cc_start: 0.4648 (m-80) cc_final: 0.4239 (m-10) REVERT: E 25 ASP cc_start: 0.9155 (m-30) cc_final: 0.8718 (m-30) REVERT: E 58 MET cc_start: 0.8860 (mtp) cc_final: 0.8492 (mtm) REVERT: E 121 MET cc_start: 0.9255 (mmm) cc_final: 0.8955 (mmm) REVERT: F 77 ASP cc_start: 0.8321 (p0) cc_final: 0.7378 (p0) REVERT: F 85 MET cc_start: 0.9060 (tmm) cc_final: 0.8819 (tmm) REVERT: F 87 LYS cc_start: 0.9275 (ptpt) cc_final: 0.8981 (ptpp) REVERT: F 88 TYR cc_start: 0.9035 (m-80) cc_final: 0.8325 (m-80) REVERT: F 116 ASP cc_start: 0.8942 (t0) cc_final: 0.8546 (t0) REVERT: F 122 MET cc_start: 0.8954 (mtp) cc_final: 0.8745 (mtm) REVERT: F 144 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8024 (tt0) REVERT: G 44 TYR cc_start: 0.8070 (m-80) cc_final: 0.7849 (m-80) REVERT: G 57 GLN cc_start: 0.8688 (mt0) cc_final: 0.8467 (mt0) REVERT: G 75 ARG cc_start: 0.8880 (ttm170) cc_final: 0.8092 (ttp-170) REVERT: G 115 MET cc_start: 0.6283 (mtp) cc_final: 0.4577 (ptt) REVERT: G 142 ARG cc_start: 0.6465 (mtp85) cc_final: 0.5673 (mmt90) REVERT: H 14 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7535 (tm-30) REVERT: H 27 GLU cc_start: 0.8499 (mp0) cc_final: 0.7845 (mp0) REVERT: H 109 LYS cc_start: 0.8387 (tptm) cc_final: 0.8140 (tptp) REVERT: I 44 TYR cc_start: 0.7691 (t80) cc_final: 0.6897 (t80) REVERT: I 97 MET cc_start: 0.8067 (mtp) cc_final: 0.7435 (mmm) REVERT: J 49 MET cc_start: 0.9487 (tpp) cc_final: 0.9241 (tpp) REVERT: K 2 ASN cc_start: 0.8940 (m-40) cc_final: 0.8608 (m-40) REVERT: K 54 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7117 (tpt90) REVERT: L 29 TYR cc_start: 0.8721 (m-10) cc_final: 0.8140 (m-10) REVERT: L 60 ARG cc_start: 0.8905 (ttm-80) cc_final: 0.8315 (ttm110) REVERT: L 63 ARG cc_start: 0.8470 (ptp-110) cc_final: 0.7914 (ptp-170) outliers start: 52 outliers final: 38 residues processed: 378 average time/residue: 0.2060 time to fit residues: 127.2756 Evaluate side-chains 362 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 322 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1078 GLN Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1274 ARG Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 839 MET Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain K residue 54 ARG Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 41 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 53 optimal weight: 0.7980 chunk 368 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 313 optimal weight: 4.9990 chunk 382 optimal weight: 0.3980 chunk 85 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 333 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN B1093 GLN ** B1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.078713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.053449 restraints weight = 111932.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.055116 restraints weight = 58184.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.056209 restraints weight = 38598.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.056887 restraints weight = 29853.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.057271 restraints weight = 25551.353| |-----------------------------------------------------------------------------| r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 33720 Z= 0.113 Angle : 0.590 13.601 45922 Z= 0.301 Chirality : 0.042 0.256 5159 Planarity : 0.004 0.052 5607 Dihedral : 16.610 138.087 5284 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.73 % Favored : 96.14 % Rotamer: Outliers : 1.43 % Allowed : 12.35 % Favored : 86.22 % 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: 3836 helix: 1.66 (0.15), residues: 1334 sheet: -0.24 (0.21), residues: 598 loop : -0.32 (0.15), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 19 TYR 0.018 0.001 TYR G 51 PHE 0.024 0.001 PHE D 70 TRP 0.013 0.001 TRP A1228 HIS 0.005 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (33688) covalent geometry : angle 0.57447 / 0.30 (45877) hydrogen bonds : bond 0.03510 / 2.35 ( 1425) hydrogen bonds : angle 4.44969 / 3.19 ( 3926) metal coordination : bond 0.00418 / 0.29 ( 32) metal coordination : angle 4.29675 / 2.99 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 353 time to evaluate : 1.162 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 68 GLN cc_start: 0.9487 (OUTLIER) cc_final: 0.8553 (pm20) REVERT: A 146 MET cc_start: 0.8815 (mmm) cc_final: 0.8596 (mpp) REVERT: A 177 ASP cc_start: 0.9027 (t0) cc_final: 0.8716 (p0) REVERT: A 654 ASN cc_start: 0.9123 (m-40) cc_final: 0.8916 (m110) REVERT: A 838 GLN cc_start: 0.9311 (tp40) cc_final: 0.8755 (tm-30) REVERT: A 842 VAL cc_start: 0.9669 (t) cc_final: 0.9373 (p) REVERT: A 956 LEU cc_start: 0.9533 (mt) cc_final: 0.9322 (mp) REVERT: A 1063 MET cc_start: 0.8929 (mmm) cc_final: 0.8673 (mmp) REVERT: A 1070 GLN cc_start: 0.9224 (mt0) cc_final: 0.8878 (mt0) REVERT: A 1206 ASP cc_start: 0.8195 (t0) cc_final: 0.7858 (m-30) REVERT: A 1261 LYS cc_start: 0.8800 (mtpp) cc_final: 0.8549 (tptt) REVERT: A 1411 GLU cc_start: 0.8935 (tp30) cc_final: 0.8300 (tm-30) REVERT: A 1444 MET cc_start: 0.8781 (mmt) cc_final: 0.8299 (mmm) REVERT: B 224 GLN cc_start: 0.9151 (mt0) cc_final: 0.8893 (mp10) REVERT: B 239 GLU cc_start: 0.9174 (pt0) cc_final: 0.8780 (tm-30) REVERT: B 699 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8437 (tp30) REVERT: B 703 ILE cc_start: 0.9535 (mt) cc_final: 0.9293 (tp) REVERT: B 775 LYS cc_start: 0.9470 (mtmt) cc_final: 0.9204 (mtmm) REVERT: B 782 LEU cc_start: 0.8988 (mt) cc_final: 0.8567 (mt) REVERT: B 1111 MET cc_start: 0.8783 (mmm) cc_final: 0.8280 (mmm) REVERT: B 1152 MET cc_start: 0.8739 (mmm) cc_final: 0.8350 (mmm) REVERT: C 190 ASP cc_start: 0.8871 (t0) cc_final: 0.8543 (m-30) REVERT: D 151 PHE cc_start: 0.4504 (m-80) cc_final: 0.4082 (m-10) REVERT: E 25 ASP cc_start: 0.9159 (m-30) cc_final: 0.8709 (m-30) REVERT: E 58 MET cc_start: 0.8769 (mtp) cc_final: 0.8538 (mtm) REVERT: E 121 MET cc_start: 0.9266 (mmm) cc_final: 0.8935 (mmm) REVERT: F 77 ASP cc_start: 0.8563 (p0) cc_final: 0.7962 (p0) REVERT: F 78 GLN cc_start: 0.9094 (OUTLIER) cc_final: 0.8788 (mp10) REVERT: F 85 MET cc_start: 0.9121 (tmm) cc_final: 0.8848 (tmm) REVERT: F 87 LYS cc_start: 0.9255 (ptpt) cc_final: 0.8941 (ptpp) REVERT: F 88 TYR cc_start: 0.9073 (m-80) cc_final: 0.8625 (m-80) REVERT: F 116 ASP cc_start: 0.8914 (t0) cc_final: 0.8500 (t0) REVERT: F 144 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8025 (tt0) REVERT: G 44 TYR cc_start: 0.8230 (m-80) cc_final: 0.7794 (m-80) REVERT: G 57 GLN cc_start: 0.8721 (mt0) cc_final: 0.8504 (mt0) REVERT: G 75 ARG cc_start: 0.8873 (ttm170) cc_final: 0.8091 (ttp-170) REVERT: G 115 MET cc_start: 0.6214 (mtp) cc_final: 0.4514 (ptt) REVERT: G 121 PHE cc_start: 0.4421 (t80) cc_final: 0.4201 (t80) REVERT: G 142 ARG cc_start: 0.6486 (mtp85) cc_final: 0.5683 (mmt90) REVERT: H 14 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7484 (tm-30) REVERT: H 27 GLU cc_start: 0.8575 (mp0) cc_final: 0.7818 (mp0) REVERT: H 109 LYS cc_start: 0.8397 (tptm) cc_final: 0.8139 (tptp) REVERT: I 44 TYR cc_start: 0.7683 (t80) cc_final: 0.6868 (t80) REVERT: I 97 MET cc_start: 0.8065 (mtp) cc_final: 0.7319 (mmm) REVERT: J 1 MET cc_start: 0.9526 (mpp) cc_final: 0.8538 (mpp) REVERT: J 49 MET cc_start: 0.9484 (tpp) cc_final: 0.9272 (tpp) REVERT: K 2 ASN cc_start: 0.8929 (m-40) cc_final: 0.8202 (m-40) REVERT: K 54 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7178 (tpt90) REVERT: L 29 TYR cc_start: 0.8749 (m-10) cc_final: 0.8216 (m-10) REVERT: L 33 GLU cc_start: 0.9229 (mm-30) cc_final: 0.8780 (mp0) REVERT: L 60 ARG cc_start: 0.8870 (ttm-80) cc_final: 0.8306 (ttm110) outliers start: 49 outliers final: 37 residues processed: 385 average time/residue: 0.2132 time to fit residues: 134.4915 Evaluate side-chains 372 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 332 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1078 GLN Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1274 ARG Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 839 MET Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain K residue 54 ARG Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 41 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 356 optimal weight: 0.9990 chunk 121 optimal weight: 0.5980 chunk 205 optimal weight: 10.0000 chunk 221 optimal weight: 0.0010 chunk 225 optimal weight: 0.4980 chunk 2 optimal weight: 0.8980 chunk 159 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 222 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN ** B1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.079129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.053926 restraints weight = 112148.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.055597 restraints weight = 58235.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.056700 restraints weight = 38594.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.057390 restraints weight = 29771.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.057821 restraints weight = 25432.835| |-----------------------------------------------------------------------------| r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 33720 Z= 0.108 Angle : 0.594 13.721 45922 Z= 0.302 Chirality : 0.043 0.258 5159 Planarity : 0.004 0.048 5607 Dihedral : 16.565 137.644 5284 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.70 % Favored : 96.17 % Rotamer: Outliers : 1.40 % Allowed : 12.70 % Favored : 85.90 % 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: 0.60 (0.14), residues: 3836 helix: 1.70 (0.15), residues: 1324 sheet: -0.17 (0.21), residues: 608 loop : -0.29 (0.15), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 19 TYR 0.019 0.001 TYR G 51 PHE 0.029 0.001 PHE D 154 TRP 0.013 0.001 TRP B 466 HIS 0.018 0.001 HIS L 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (33688) covalent geometry : angle 0.57919 / 0.30 (45877) hydrogen bonds : bond 0.03405 / 2.29 ( 1425) hydrogen bonds : angle 4.38819 / 3.15 ( 3926) metal coordination : bond 0.00456 / 0.29 ( 32) metal coordination : angle 4.19260 / 2.82 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 352 time to evaluate : 1.178 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 68 GLN cc_start: 0.9489 (OUTLIER) cc_final: 0.8650 (pm20) REVERT: A 146 MET cc_start: 0.8838 (mmm) cc_final: 0.8606 (mpp) REVERT: A 177 ASP cc_start: 0.9001 (t0) cc_final: 0.8710 (p0) REVERT: A 444 PHE cc_start: 0.8911 (t80) cc_final: 0.8642 (t80) REVERT: A 838 GLN cc_start: 0.9304 (tp40) cc_final: 0.8763 (tm-30) REVERT: A 842 VAL cc_start: 0.9672 (t) cc_final: 0.9388 (p) REVERT: A 845 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8645 (mm) REVERT: A 956 LEU cc_start: 0.9512 (mt) cc_final: 0.9295 (mp) REVERT: A 1062 GLU cc_start: 0.8305 (tp30) cc_final: 0.7271 (tp30) REVERT: A 1063 MET cc_start: 0.8993 (mmm) cc_final: 0.8734 (mmt) REVERT: A 1070 GLN cc_start: 0.9248 (mt0) cc_final: 0.8920 (mt0) REVERT: A 1206 ASP cc_start: 0.8216 (t0) cc_final: 0.7928 (m-30) REVERT: A 1261 LYS cc_start: 0.8833 (mtpp) cc_final: 0.8569 (tptt) REVERT: A 1411 GLU cc_start: 0.8926 (tp30) cc_final: 0.8300 (tm-30) REVERT: A 1444 MET cc_start: 0.8760 (mmt) cc_final: 0.8256 (mmm) REVERT: B 199 MET cc_start: 0.8034 (mmp) cc_final: 0.7788 (mmp) REVERT: B 224 GLN cc_start: 0.9130 (mt0) cc_final: 0.8891 (mp10) REVERT: B 239 GLU cc_start: 0.9155 (pt0) cc_final: 0.8782 (tm-30) REVERT: B 699 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8388 (tp30) REVERT: B 703 ILE cc_start: 0.9527 (mt) cc_final: 0.9311 (tp) REVERT: B 775 LYS cc_start: 0.9437 (mtmt) cc_final: 0.9179 (mtmm) REVERT: B 782 LEU cc_start: 0.8975 (mt) cc_final: 0.8576 (mt) REVERT: B 1111 MET cc_start: 0.8782 (mmm) cc_final: 0.8276 (mmm) REVERT: B 1152 MET cc_start: 0.8762 (mmm) cc_final: 0.8337 (mmm) REVERT: C 37 MET cc_start: 0.8728 (mtm) cc_final: 0.8241 (mtm) REVERT: C 190 ASP cc_start: 0.8863 (t0) cc_final: 0.8509 (m-30) REVERT: D 67 ARG cc_start: 0.7187 (ptp-110) cc_final: 0.6884 (ptp90) REVERT: D 151 PHE cc_start: 0.4334 (m-80) cc_final: 0.3897 (m-10) REVERT: E 25 ASP cc_start: 0.9150 (m-30) cc_final: 0.8685 (m-30) REVERT: E 58 MET cc_start: 0.8736 (mtp) cc_final: 0.8409 (mtm) REVERT: E 121 MET cc_start: 0.9268 (mmm) cc_final: 0.8925 (mmm) REVERT: E 192 ARG cc_start: 0.7730 (ttp80) cc_final: 0.7486 (tpt90) REVERT: F 77 ASP cc_start: 0.8502 (p0) cc_final: 0.7841 (p0) REVERT: F 78 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.8708 (mp10) REVERT: F 85 MET cc_start: 0.9132 (tmm) cc_final: 0.8876 (tmm) REVERT: F 87 LYS cc_start: 0.9197 (ptpt) cc_final: 0.8992 (pttp) REVERT: F 88 TYR cc_start: 0.8716 (m-80) cc_final: 0.8007 (m-80) REVERT: F 116 ASP cc_start: 0.8938 (t0) cc_final: 0.8512 (t0) REVERT: F 122 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.8639 (mtm) REVERT: F 144 GLU cc_start: 0.8424 (mt-10) cc_final: 0.7980 (tt0) REVERT: G 44 TYR cc_start: 0.8351 (m-80) cc_final: 0.8042 (m-80) REVERT: G 57 GLN cc_start: 0.8732 (mt0) cc_final: 0.8518 (mt0) REVERT: G 75 ARG cc_start: 0.8867 (ttm170) cc_final: 0.8090 (ttp-170) REVERT: G 115 MET cc_start: 0.6085 (mtp) cc_final: 0.4438 (ptt) REVERT: G 121 PHE cc_start: 0.4444 (t80) cc_final: 0.4222 (t80) REVERT: G 142 ARG cc_start: 0.6492 (mtp85) cc_final: 0.5732 (mmt90) REVERT: H 14 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7502 (tm-30) REVERT: H 27 GLU cc_start: 0.8650 (mp0) cc_final: 0.7867 (mp0) REVERT: H 109 LYS cc_start: 0.8404 (tptm) cc_final: 0.8157 (tptp) REVERT: H 123 MET cc_start: 0.9093 (tmm) cc_final: 0.8379 (tmm) REVERT: I 44 TYR cc_start: 0.7750 (t80) cc_final: 0.6954 (t80) REVERT: I 97 MET cc_start: 0.8085 (mtp) cc_final: 0.7326 (mmm) REVERT: J 1 MET cc_start: 0.9494 (mpp) cc_final: 0.8469 (mpp) REVERT: K 2 ASN cc_start: 0.8948 (m-40) cc_final: 0.8296 (m-40) REVERT: K 54 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.7146 (tpt90) REVERT: L 29 TYR cc_start: 0.8820 (m-10) cc_final: 0.8257 (m-10) REVERT: L 33 GLU cc_start: 0.9214 (mm-30) cc_final: 0.8716 (mp0) REVERT: L 60 ARG cc_start: 0.8887 (ttm-80) cc_final: 0.8328 (ttm110) REVERT: L 63 ARG cc_start: 0.8446 (ptp-110) cc_final: 0.7895 (ptp-170) outliers start: 48 outliers final: 35 residues processed: 382 average time/residue: 0.2204 time to fit residues: 136.4384 Evaluate side-chains 373 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 333 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1078 GLN Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1274 ARG Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 839 MET Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain K residue 54 ARG Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 175 optimal weight: 9.9990 chunk 188 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 323 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 69 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 266 optimal weight: 3.9990 chunk 319 optimal weight: 0.0470 chunk 387 optimal weight: 30.0000 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1427 ASN ** B 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN E 63 ASN F 100 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.077304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.052269 restraints weight = 114516.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.053873 restraints weight = 60606.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.054940 restraints weight = 40516.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.055604 restraints weight = 31452.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.056004 restraints weight = 26977.580| |-----------------------------------------------------------------------------| r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 33720 Z= 0.211 Angle : 0.642 17.531 45922 Z= 0.325 Chirality : 0.043 0.255 5159 Planarity : 0.004 0.045 5607 Dihedral : 16.588 139.056 5284 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.25 % Favored : 95.62 % Rotamer: Outliers : 1.37 % Allowed : 13.34 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.14), residues: 3836 helix: 1.72 (0.15), residues: 1319 sheet: -0.30 (0.21), residues: 615 loop : -0.29 (0.15), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 48 TYR 0.020 0.001 TYR B 830 PHE 0.024 0.001 PHE D 175 TRP 0.013 0.001 TRP B 561 HIS 0.006 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.21 (33688) covalent geometry : angle 0.62694 / 0.32 (45877) hydrogen bonds : bond 0.03621 / 2.41 ( 1425) hydrogen bonds : angle 4.50850 / 3.22 ( 3926) metal coordination : bond 0.00746 / 0.50 ( 32) metal coordination : angle 4.48468 / 3.05 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 328 time to evaluate : 1.167 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 68 GLN cc_start: 0.9540 (OUTLIER) cc_final: 0.8650 (pm20) REVERT: A 146 MET cc_start: 0.8844 (mmm) cc_final: 0.8584 (mpp) REVERT: A 177 ASP cc_start: 0.9032 (t0) cc_final: 0.8745 (p0) REVERT: A 838 GLN cc_start: 0.9335 (tp40) cc_final: 0.8746 (tm-30) REVERT: A 842 VAL cc_start: 0.9682 (t) cc_final: 0.9375 (p) REVERT: A 956 LEU cc_start: 0.9560 (mt) cc_final: 0.9326 (mp) REVERT: A 1062 GLU cc_start: 0.8323 (tp30) cc_final: 0.7874 (tp30) REVERT: A 1070 GLN cc_start: 0.9232 (mt0) cc_final: 0.8915 (mt0) REVERT: A 1206 ASP cc_start: 0.8279 (t0) cc_final: 0.7974 (m-30) REVERT: A 1261 LYS cc_start: 0.8759 (mtpp) cc_final: 0.8507 (tptt) REVERT: A 1411 GLU cc_start: 0.8924 (tp30) cc_final: 0.8331 (tm-30) REVERT: A 1444 MET cc_start: 0.8827 (mmt) cc_final: 0.8305 (mmm) REVERT: A 1454 MET cc_start: 0.8444 (tmm) cc_final: 0.8102 (tmm) REVERT: B 199 MET cc_start: 0.8097 (mmp) cc_final: 0.7815 (mmp) REVERT: B 224 GLN cc_start: 0.9158 (mt0) cc_final: 0.8916 (mp10) REVERT: B 239 GLU cc_start: 0.9179 (pt0) cc_final: 0.8677 (tm-30) REVERT: B 699 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8446 (tp30) REVERT: B 703 ILE cc_start: 0.9536 (mt) cc_final: 0.9320 (tp) REVERT: B 775 LYS cc_start: 0.9469 (mtmt) cc_final: 0.9214 (mtmm) REVERT: B 782 LEU cc_start: 0.9056 (mt) cc_final: 0.8652 (mt) REVERT: B 1111 MET cc_start: 0.8799 (mmm) cc_final: 0.8300 (mmm) REVERT: B 1152 MET cc_start: 0.8790 (mmm) cc_final: 0.8364 (mmm) REVERT: C 37 MET cc_start: 0.8778 (mtm) cc_final: 0.8034 (mtm) REVERT: C 75 MET cc_start: 0.8853 (tpp) cc_final: 0.8581 (tpt) REVERT: C 190 ASP cc_start: 0.8876 (t0) cc_final: 0.8571 (m-30) REVERT: D 151 PHE cc_start: 0.4300 (m-80) cc_final: 0.3665 (m-10) REVERT: E 25 ASP cc_start: 0.9179 (m-30) cc_final: 0.8720 (m-30) REVERT: E 58 MET cc_start: 0.8767 (mtp) cc_final: 0.8481 (mtm) REVERT: E 121 MET cc_start: 0.9269 (mmm) cc_final: 0.8940 (mmm) REVERT: E 137 GLU cc_start: 0.8838 (pm20) cc_final: 0.8379 (pm20) REVERT: F 77 ASP cc_start: 0.8501 (p0) cc_final: 0.7824 (p0) REVERT: F 78 GLN cc_start: 0.9147 (OUTLIER) cc_final: 0.8797 (mp10) REVERT: F 85 MET cc_start: 0.9196 (tmm) cc_final: 0.8914 (tmm) REVERT: F 88 TYR cc_start: 0.8983 (m-80) cc_final: 0.8619 (m-80) REVERT: F 116 ASP cc_start: 0.8985 (t0) cc_final: 0.8558 (t0) REVERT: F 122 MET cc_start: 0.8960 (mtm) cc_final: 0.8617 (mtm) REVERT: F 144 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8014 (tt0) REVERT: G 44 TYR cc_start: 0.8319 (m-80) cc_final: 0.8021 (m-80) REVERT: G 57 GLN cc_start: 0.8733 (mt0) cc_final: 0.8522 (mt0) REVERT: G 75 ARG cc_start: 0.8863 (ttm170) cc_final: 0.8109 (ttp-170) REVERT: G 115 MET cc_start: 0.6095 (mtp) cc_final: 0.4481 (ptt) REVERT: G 142 ARG cc_start: 0.6480 (mtp85) cc_final: 0.5747 (mmt90) REVERT: H 109 LYS cc_start: 0.8432 (tptm) cc_final: 0.8184 (tptp) REVERT: H 123 MET cc_start: 0.9116 (tmm) cc_final: 0.8407 (tmm) REVERT: I 44 TYR cc_start: 0.7710 (t80) cc_final: 0.6920 (t80) REVERT: I 97 MET cc_start: 0.8155 (mtp) cc_final: 0.7468 (mmm) REVERT: J 49 MET cc_start: 0.9451 (tpp) cc_final: 0.9212 (mmm) REVERT: K 2 ASN cc_start: 0.8975 (m-40) cc_final: 0.8374 (m-40) REVERT: K 54 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7201 (tpt90) REVERT: L 29 TYR cc_start: 0.8856 (m-10) cc_final: 0.8298 (m-10) REVERT: L 60 ARG cc_start: 0.8878 (ttm-80) cc_final: 0.8321 (ttm110) outliers start: 47 outliers final: 40 residues processed: 363 average time/residue: 0.2171 time to fit residues: 127.6492 Evaluate side-chains 367 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 324 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1078 GLN Chi-restraints excluded: chain A residue 1138 ILE Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1274 ARG Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 839 MET Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain K residue 54 ARG Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 41 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 71 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 116 optimal weight: 20.0000 chunk 9 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 chunk 108 optimal weight: 6.9990 chunk 254 optimal weight: 0.7980 chunk 345 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 206 optimal weight: 4.9990 chunk 287 optimal weight: 6.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.078230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.053089 restraints weight = 114270.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.054737 restraints weight = 59825.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.055822 restraints weight = 39852.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.056493 restraints weight = 30874.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.056910 restraints weight = 26481.836| |-----------------------------------------------------------------------------| r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33720 Z= 0.133 Angle : 0.626 17.968 45922 Z= 0.317 Chirality : 0.043 0.259 5159 Planarity : 0.004 0.045 5607 Dihedral : 16.592 138.836 5284 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.99 % Favored : 95.88 % Rotamer: Outliers : 1.28 % Allowed : 13.66 % Favored : 85.05 % 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: 0.57 (0.14), residues: 3836 helix: 1.69 (0.15), residues: 1318 sheet: -0.27 (0.21), residues: 610 loop : -0.27 (0.15), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 97 TYR 0.028 0.001 TYR I 15 PHE 0.040 0.001 PHE D 70 TRP 0.011 0.001 TRP B 466 HIS 0.006 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (33688) covalent geometry : angle 0.61140 / 0.32 (45877) hydrogen bonds : bond 0.03503 / 2.34 ( 1425) hydrogen bonds : angle 4.44483 / 3.19 ( 3926) metal coordination : bond 0.00476 / 0.34 ( 32) metal coordination : angle 4.29974 / 2.94 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 344 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9524 (OUTLIER) cc_final: 0.8638 (pm20) REVERT: A 122 MET cc_start: 0.9300 (mtp) cc_final: 0.9054 (mtm) REVERT: A 146 MET cc_start: 0.8874 (mmm) cc_final: 0.8602 (mpp) REVERT: A 177 ASP cc_start: 0.9030 (t0) cc_final: 0.8752 (p0) REVERT: A 444 PHE cc_start: 0.8887 (t80) cc_final: 0.8645 (t80) REVERT: A 838 GLN cc_start: 0.9333 (tp40) cc_final: 0.8743 (tm-30) REVERT: A 842 VAL cc_start: 0.9666 (t) cc_final: 0.9380 (p) REVERT: A 956 LEU cc_start: 0.9561 (mt) cc_final: 0.9334 (mp) REVERT: A 1062 GLU cc_start: 0.8314 (tp30) cc_final: 0.7708 (mm-30) REVERT: A 1063 MET cc_start: 0.9088 (mmt) cc_final: 0.8172 (mmm) REVERT: A 1070 GLN cc_start: 0.9179 (mt0) cc_final: 0.8889 (mt0) REVERT: A 1206 ASP cc_start: 0.8284 (t0) cc_final: 0.7936 (m-30) REVERT: A 1261 LYS cc_start: 0.8757 (mtpp) cc_final: 0.8504 (tptt) REVERT: A 1334 ASP cc_start: 0.9297 (m-30) cc_final: 0.9070 (m-30) REVERT: A 1411 GLU cc_start: 0.8887 (tp30) cc_final: 0.8285 (tm-30) REVERT: A 1444 MET cc_start: 0.8789 (mmt) cc_final: 0.8303 (mmm) REVERT: B 199 MET cc_start: 0.8123 (mmp) cc_final: 0.7853 (mmp) REVERT: B 224 GLN cc_start: 0.9142 (mt0) cc_final: 0.8896 (mp10) REVERT: B 239 GLU cc_start: 0.9162 (pt0) cc_final: 0.8769 (tm-30) REVERT: B 699 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8428 (tp30) REVERT: B 703 ILE cc_start: 0.9525 (mt) cc_final: 0.9316 (tp) REVERT: B 775 LYS cc_start: 0.9447 (mtmt) cc_final: 0.9195 (mtmm) REVERT: B 782 LEU cc_start: 0.8997 (mt) cc_final: 0.8599 (mt) REVERT: B 1111 MET cc_start: 0.8769 (mmm) cc_final: 0.8276 (mmm) REVERT: B 1152 MET cc_start: 0.8765 (mmm) cc_final: 0.8353 (mmm) REVERT: C 37 MET cc_start: 0.8763 (mtm) cc_final: 0.7978 (mtm) REVERT: C 75 MET cc_start: 0.8829 (tpp) cc_final: 0.8557 (tpt) REVERT: C 190 ASP cc_start: 0.8822 (t0) cc_final: 0.8505 (m-30) REVERT: D 67 ARG cc_start: 0.7458 (ptp-110) cc_final: 0.7087 (ptp90) REVERT: D 151 PHE cc_start: 0.4216 (m-80) cc_final: 0.3583 (m-10) REVERT: E 25 ASP cc_start: 0.9162 (m-30) cc_final: 0.8712 (m-30) REVERT: E 58 MET cc_start: 0.8717 (mtp) cc_final: 0.8396 (mtm) REVERT: E 121 MET cc_start: 0.9265 (mmm) cc_final: 0.8971 (mmm) REVERT: E 137 GLU cc_start: 0.8844 (pm20) cc_final: 0.8320 (pm20) REVERT: F 77 ASP cc_start: 0.8551 (p0) cc_final: 0.7869 (p0) REVERT: F 78 GLN cc_start: 0.9134 (OUTLIER) cc_final: 0.8767 (mp10) REVERT: F 85 MET cc_start: 0.9186 (tmm) cc_final: 0.8901 (tmm) REVERT: F 87 LYS cc_start: 0.9280 (ptpt) cc_final: 0.8959 (ptpp) REVERT: F 88 TYR cc_start: 0.8910 (m-80) cc_final: 0.8499 (m-80) REVERT: F 114 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7209 (tm-30) REVERT: F 116 ASP cc_start: 0.8984 (t0) cc_final: 0.8341 (t0) REVERT: F 122 MET cc_start: 0.8978 (mtm) cc_final: 0.8610 (mtm) REVERT: F 144 GLU cc_start: 0.8402 (mt-10) cc_final: 0.7943 (tt0) REVERT: G 44 TYR cc_start: 0.8384 (m-80) cc_final: 0.8058 (m-80) REVERT: G 57 GLN cc_start: 0.8709 (mt0) cc_final: 0.8492 (mt0) REVERT: G 75 ARG cc_start: 0.8861 (ttm170) cc_final: 0.8090 (ttp-170) REVERT: G 115 MET cc_start: 0.6081 (mtp) cc_final: 0.4465 (ptt) REVERT: G 142 ARG cc_start: 0.6427 (mtp85) cc_final: 0.5682 (mmt90) REVERT: H 109 LYS cc_start: 0.8407 (tptm) cc_final: 0.8153 (tptp) REVERT: H 123 MET cc_start: 0.9107 (tmm) cc_final: 0.8364 (tmm) REVERT: I 44 TYR cc_start: 0.7735 (t80) cc_final: 0.6933 (t80) REVERT: I 97 MET cc_start: 0.8143 (mtp) cc_final: 0.7466 (mmm) REVERT: J 49 MET cc_start: 0.9440 (tpp) cc_final: 0.9207 (mmm) REVERT: K 2 ASN cc_start: 0.8964 (m-40) cc_final: 0.8392 (m-40) REVERT: K 54 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7292 (tpt90) REVERT: L 29 TYR cc_start: 0.8876 (m-10) cc_final: 0.8307 (m-10) REVERT: L 60 ARG cc_start: 0.8886 (ttm-80) cc_final: 0.8314 (ttm110) REVERT: L 63 ARG cc_start: 0.8473 (ptp-110) cc_final: 0.7907 (ptp-170) outliers start: 44 outliers final: 34 residues processed: 375 average time/residue: 0.2218 time to fit residues: 135.4667 Evaluate side-chains 376 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 339 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1078 GLN Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1274 ARG Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 839 MET Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain K residue 54 ARG Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 41 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 100 optimal weight: 4.9990 chunk 188 optimal weight: 3.9990 chunk 222 optimal weight: 20.0000 chunk 123 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 283 optimal weight: 5.9990 chunk 198 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 157 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS F 100 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.077288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.052242 restraints weight = 114429.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.053846 restraints weight = 60501.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.054901 restraints weight = 40532.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.055545 restraints weight = 31503.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.055987 restraints weight = 27087.082| |-----------------------------------------------------------------------------| r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 33720 Z= 0.198 Angle : 0.647 17.597 45922 Z= 0.327 Chirality : 0.043 0.257 5159 Planarity : 0.004 0.045 5607 Dihedral : 16.601 139.361 5284 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.38 % Favored : 95.49 % Rotamer: Outliers : 1.34 % Allowed : 13.93 % Favored : 84.73 % 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: 3836 helix: 1.68 (0.15), residues: 1318 sheet: -0.31 (0.21), residues: 616 loop : -0.29 (0.15), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 67 TYR 0.031 0.001 TYR B1092 PHE 0.028 0.001 PHE D 70 TRP 0.014 0.001 TRP B 561 HIS 0.006 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.20 (33688) covalent geometry : angle 0.63370 / 0.33 (45877) hydrogen bonds : bond 0.03601 / 2.40 ( 1425) hydrogen bonds : angle 4.51159 / 3.23 ( 3926) metal coordination : bond 0.00696 / 0.48 ( 32) metal coordination : angle 4.29408 / 2.94 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5735.04 seconds wall clock time: 100 minutes 7.42 seconds (6007.42 seconds total)