Starting phenix.real_space_refine on Sun Aug 9 10:05:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sbt_54738/08_2026/9sbt_54738.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sbt_54738/08_2026/9sbt_54738.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9sbt_54738/08_2026/9sbt_54738.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sbt_54738/08_2026/9sbt_54738.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9sbt_54738/08_2026/9sbt_54738.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sbt_54738/08_2026/9sbt_54738.map" } resolution = 3.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 96 5.49 5 Mg 2 5.21 5 S 182 5.16 5 C 20512 2.51 5 N 5750 2.21 5 O 6437 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: 32987 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 10926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1387, 10926 Classifications: {'peptide': 1387} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1324} Chain breaks: 9 Chain: "B" Number of atoms: 9155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1150, 9155 Classifications: {'peptide': 1150} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 1100} Chain breaks: 6 Chain: "C" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2095 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain: "D" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1327 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 164} Chain breaks: 2 Chain: "E" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1744 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1340 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1077 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Chain: "I" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 909 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 904 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "N" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 825 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain breaks: 1 Chain: "R" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 197 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna3p': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 886 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 35 Unusual residues: {' MG': 2, ' ZN': 2, 'ATP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 457 SG CYS A 67 106.863 71.022 94.998 1.00222.53 S ATOM 479 SG CYS A 70 106.489 67.665 93.159 1.00235.26 S ATOM 532 SG CYS A 77 103.581 70.104 93.237 1.00218.90 S ATOM 762 SG CYS A 107 81.183 76.579 135.401 1.00264.78 S ATOM 786 SG CYS A 110 83.057 73.423 136.286 1.00257.66 S ATOM 1091 SG CYS A 148 79.668 74.112 137.873 1.00289.58 S ATOM 1105 SG CYS A 167 82.701 76.297 138.789 1.00268.93 S ATOM 19587 SG CYS B1163 98.568 58.618 105.004 1.00220.00 S ATOM 19605 SG CYS B1166 97.150 61.969 105.529 1.00227.01 S ATOM 19730 SG CYS B1182 100.910 61.510 104.779 1.00236.48 S ATOM 19749 SG CYS B1185 99.466 60.584 108.212 1.00238.66 S ATOM 20737 SG CYS C 86 93.417 75.633 26.592 1.00270.69 S ATOM 20754 SG CYS C 88 95.184 78.087 28.774 1.00291.63 S ATOM 20787 SG CYS C 92 94.663 78.981 25.168 1.00251.30 S ATOM 20810 SG CYS C 95 91.747 78.948 27.689 1.00245.31 S ATOM 28395 SG CYS I 7 39.182 127.240 127.025 1.00417.47 S ATOM 28420 SG CYS I 10 42.913 126.621 126.782 1.00405.14 S ATOM 28586 SG CYS I 29 40.724 123.978 128.435 1.00418.05 S ATOM 28610 SG CYS I 32 41.462 127.187 130.174 1.00420.56 S ATOM 28937 SG CYS I 75 16.876 119.544 87.729 1.00502.96 S ATOM 28959 SG CYS I 78 16.642 123.149 86.895 1.00506.00 S ATOM 29175 SG CYS I 103 20.050 121.419 86.635 1.00489.85 S ATOM 29195 SG CYS I 106 18.516 122.009 90.066 1.00501.72 S ATOM 29297 SG CYS J 7 64.119 91.621 37.958 1.00177.68 S ATOM 29320 SG CYS J 10 63.937 89.482 34.844 1.00195.07 S ATOM 29600 SG CYS J 45 60.745 90.279 36.606 1.00186.98 S ATOM 29606 SG CYS J 46 62.674 92.729 34.420 1.00199.56 S ATOM 30729 SG CYS L 31 97.185 115.088 54.003 1.00339.83 S ATOM 30749 SG CYS L 34 98.511 117.066 51.080 1.00344.80 S ATOM 30853 SG CYS L 48 100.856 115.704 53.749 1.00347.84 S ATOM 30876 SG CYS L 51 98.561 118.634 54.583 1.00352.91 S Time building chain proxies: 6.19, per 1000 atoms: 0.19 Number of scatterers: 32987 At special positions: 0 Unit cell: (153.417, 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 6437 8.00 N 5750 7.00 C 20512 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1804 " pdb="ZN ZN A1804 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 67 " pdb=" ZN A1805 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 148 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " Number of angles added : 45 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7336 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 48 sheets defined 39.6% alpha, 19.5% beta 41 base pairs and 77 stacking pairs defined. Time for finding SS restraints: 3.50 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 203 through 212 Processing helix chain 'A' and resid 215 through 221 Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.578A pdb=" N ILE A 235 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 260 through 283 removed outlier: 3.516A pdb=" N PHE A 264 " --> pdb=" O ASP A 260 " (cutoff:3.500A) removed outlier: 3.726A 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: 3.857A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 507 through 511 Processing helix chain 'A' and resid 525 through 536 removed outlier: 4.051A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.582A pdb=" N VAL A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 579 Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 659 removed outlier: 3.518A pdb=" N HIS A 659 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 672 through 699 removed outlier: 3.599A pdb=" N ALA A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 699 " --> pdb=" O LYS A 695 " (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: 3.574A pdb=" N ILE A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 798 Processing helix chain 'A' and resid 809 through 829 removed outlier: 3.891A pdb=" N GLY A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 824 " --> pdb=" O GLY A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 846 removed outlier: 4.188A pdb=" N GLU A 833 " --> pdb=" O VAL A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 874 through 876 No H-bonds generated for 'chain 'A' and resid 874 through 876' Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 909 through 913 Processing helix chain 'A' and resid 915 through 920 removed outlier: 3.581A pdb=" N LEU A 920 " --> pdb=" O GLY A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 959 through 972 Processing helix chain 'A' and resid 982 through 995 removed outlier: 3.596A 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 1083 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1084 through 1086 No H-bonds generated for 'chain 'A' and resid 1084 through 1086' Processing helix chain 'A' and resid 1092 through 1107 removed outlier: 4.547A pdb=" N VAL A1098 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Proline residue: A1099 - end of helix Processing helix chain 'A' and resid 1130 through 1139 Processing helix chain 'A' and resid 1142 through 1145 Processing helix chain 'A' and resid 1166 through 1174 removed outlier: 4.102A 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 1220 removed outlier: 3.615A pdb=" N VAL A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE A1220 " --> pdb=" O ILE A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1270 Processing helix chain 'A' and resid 1312 through 1317 removed outlier: 3.570A 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: 4.023A 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: 3.601A 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 removed outlier: 3.640A pdb=" N VAL A1451 " --> pdb=" O GLU A1447 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A1452 " --> pdb=" O GLU A1448 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1447 through 1452' Processing helix chain 'B' and resid 29 through 37 removed outlier: 3.897A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 66 removed outlier: 3.626A pdb=" N LEU B 48 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 4.537A 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 120 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 293 through 303 removed outlier: 3.611A pdb=" N ILE B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU B 299 " --> pdb=" O GLY B 295 " (cutoff:3.500A) removed outlier: 4.065A 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 removed outlier: 3.515A pdb=" N GLU B 438 " --> pdb=" O ARG B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.797A pdb=" N THR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 473 removed outlier: 4.614A pdb=" N MET B 473 " --> pdb=" O LYS B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.667A pdb=" N ARG B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 592 through 607 Processing helix chain 'B' and resid 654 through 667 Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.872A 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 752 through 756 Processing helix chain 'B' and resid 758 through 762 removed outlier: 3.627A pdb=" N ASN B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 775 removed outlier: 3.672A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 788 removed outlier: 3.571A pdb=" N TYR B 785 " --> pdb=" O LEU B 782 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ASN B 786 " --> pdb=" O THR B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.269A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.764A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 removed outlier: 3.700A pdb=" N GLU B1061 " --> pdb=" O LYS B1057 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N HIS B1062 " --> pdb=" O LEU B1058 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1153 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 40 removed outlier: 3.539A pdb=" N ALA C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 removed outlier: 3.519A 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 removed outlier: 3.903A pdb=" N GLU C 210 " --> pdb=" O CYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 266 removed outlier: 3.657A pdb=" N ASP C 266 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 34 removed outlier: 3.650A 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 removed outlier: 3.533A pdb=" N VAL D 128 " --> pdb=" O GLU D 124 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU D 129 " --> pdb=" O SER D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 151 Processing helix chain 'D' and resid 156 through 169 removed outlier: 3.659A pdb=" N VAL D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 removed outlier: 3.596A pdb=" N GLY D 181 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 196 through 199 removed outlier: 3.515A pdb=" N ASN D 199 " --> pdb=" O PRO D 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 196 through 199' Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'E' and resid 4 through 27 removed outlier: 3.597A pdb=" N GLY E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 47 Processing helix chain 'E' and resid 54 through 59 removed outlier: 3.940A pdb=" N SER E 59 " --> pdb=" O LYS E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 92 through 104 removed outlier: 3.668A pdb=" N LYS E 103 " --> pdb=" O HIS E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 124 removed outlier: 3.599A pdb=" N MET E 121 " --> pdb=" O THR E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 141 Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.565A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 128 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.530A pdb=" N GLU G 32 " --> pdb=" O THR G 28 " (cutoff:3.500A) removed outlier: 3.612A 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 45 through 47 No H-bonds generated for 'chain 'H' and resid 45 through 47' Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'H' and resid 129 through 133 Processing helix chain 'I' and resid 59 through 65 removed outlier: 4.044A pdb=" N GLY I 63 " --> pdb=" O GLN I 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 40 removed outlier: 3.578A pdb=" N GLY J 40 " --> pdb=" O LEU J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.736A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 removed outlier: 3.544A pdb=" N LEU J 61 " --> pdb=" O ILE J 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 53 removed outlier: 3.653A pdb=" N ASN K 44 " --> pdb=" O HIS K 40 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP K 53 " --> pdb=" O GLU K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 90 removed outlier: 7.097A pdb=" N THR A 237 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 177 Processing sheet with id=AA4, first strand: chain 'A' and resid 250 through 252 removed outlier: 3.664A pdb=" N PHE A 252 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 345 removed outlier: 3.671A pdb=" N LYS A 343 " --> pdb=" O PHE B1130 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU B1128 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.750A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N HIS A 490 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET A 456 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N PHE A 468 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL A 352 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N LEU A 470 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 6.214A 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: 3.504A pdb=" N ARG A 434 " --> pdb=" O TYR A 376 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LYS A 431 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL A 405 " --> pdb=" O LYS A 431 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLU A 433 " --> pdb=" O LYS A 403 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AA9, first strand: chain 'A' and resid 588 through 590 removed outlier: 7.128A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 766 through 767 removed outlier: 3.564A pdb=" N GLY A 766 " --> pdb=" O VAL A 800 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 849 through 850 removed outlier: 6.653A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 878 through 882 Processing sheet with id=AB4, first strand: chain 'A' and resid 1282 through 1292 Processing sheet with id=AB5, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.011A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL A1242 " --> pdb=" O TRP A1191 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N TRP A1191 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU A1192 " --> pdb=" O ILE A1152 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE A1152 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ARG A1194 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER A1150 " --> pdb=" O ARG A1194 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLU A1196 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TYR I 44 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 48 through 50 removed outlier: 4.492A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY G 59 " --> pdb=" O ILE A1445 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N VAL A1443 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 48 through 50 removed outlier: 4.492A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 69 through 73 removed outlier: 5.864A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL B 132 " --> pdb=" O SER B 156 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N SER B 156 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LYS B 134 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLU B 154 " --> pdb=" O LYS B 134 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N THR B 136 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE B 152 " --> pdb=" O THR B 136 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 69 through 73 removed outlier: 5.864A pdb=" N ARG B 86 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ALA B 139 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AC2, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC3, first strand: chain 'B' and resid 404 through 407 removed outlier: 6.051A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 224 through 227 removed outlier: 3.898A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC6, first strand: chain 'B' and resid 585 through 590 removed outlier: 5.234A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 640 through 641 removed outlier: 3.504A pdb=" N GLU B 641 " --> pdb=" O GLU B 650 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU B 650 " --> pdb=" O GLU B 641 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 703 through 704 Processing sheet with id=AC9, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.575A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.575A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU L 27 " --> pdb=" O LEU L 40 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD3, first strand: chain 'B' and resid 821 through 825 removed outlier: 6.996A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.620A 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 Processing sheet with id=AD5, first strand: chain 'B' and resid 910 through 912 Processing sheet with id=AD6, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD7, first strand: chain 'B' and resid 1069 through 1070 Processing sheet with id=AD8, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD9, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AE1, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.196A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN C 231 " --> pdb=" O GLU C 177 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.706A pdb=" N GLU C 152 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N THR C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LYS C 154 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N VAL C 51 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR C 156 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL C 49 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL C 158 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 111 through 114 removed outlier: 3.645A pdb=" N CYS C 145 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AE5, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.278A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.889A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE E 199 " --> pdb=" O LYS E 152 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 169 through 170 removed outlier: 6.108A pdb=" N ILE G 160 " --> pdb=" O GLU G 148 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N CYS G 150 " --> pdb=" O HIS G 158 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N HIS G 158 " --> pdb=" O CYS G 150 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LYS G 107 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA G 159 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE G 99 " --> pdb=" O VAL G 110 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR G 90 " --> pdb=" O GLN G 102 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 120 through 122 Processing sheet with id=AE9, first strand: chain 'H' and resid 4 through 16 removed outlier: 5.547A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY H 127 " --> pdb=" O ILE H 112 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 15 through 19 removed outlier: 3.596A pdb=" N PHE I 27 " --> pdb=" O GLU I 36 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU I 36 " --> pdb=" O PHE I 27 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 70 through 71 removed outlier: 3.656A pdb=" N SER I 71 " --> pdb=" O ASN I 83 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 19 through 23 1337 hydrogen bonds defined for protein. 3663 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 107 hydrogen bonds 214 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 77 stacking parallelities Total time for adding SS restraints: 10.01 Time building geometry restraints manager: 3.57 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: 5414 1.31 - 1.44: 8914 1.44 - 1.56: 18957 1.56 - 1.69: 187 1.69 - 1.81: 292 Bond restraints: 33764 Sorted by residual: bond pdb=" C4 ATP A1801 " pdb=" N9 ATP A1801 " ideal model delta sigma weight residual 1.374 1.183 0.191 1.00e-02 1.00e+04 3.63e+02 bond pdb=" C8 ATP A1801 " pdb=" N9 ATP A1801 " ideal model delta sigma weight residual 1.370 1.213 0.157 1.20e-02 6.94e+03 1.71e+02 bond pdb=" C6 ATP A1801 " pdb=" N6 ATP A1801 " ideal model delta sigma weight residual 1.337 1.448 -0.111 1.10e-02 8.26e+03 1.02e+02 bond pdb=" C5 ATP A1801 " pdb=" C6 ATP A1801 " ideal model delta sigma weight residual 1.409 1.335 0.074 1.00e-02 1.00e+04 5.48e+01 bond pdb=" C5 ATP A1801 " pdb=" N7 ATP A1801 " ideal model delta sigma weight residual 1.387 1.455 -0.068 1.00e-02 1.00e+04 4.60e+01 ... (remaining 33759 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.80: 45837 3.80 - 7.61: 140 7.61 - 11.41: 1 11.41 - 15.21: 2 15.21 - 19.01: 1 Bond angle restraints: 45981 Sorted by residual: angle pdb=" PB ATP A1801 " pdb=" O3B ATP A1801 " pdb=" PG ATP A1801 " ideal model delta sigma weight residual 139.87 120.86 19.01 1.00e+00 1.00e+00 3.62e+02 angle pdb=" PA ATP A1801 " pdb=" O3A ATP A1801 " pdb=" PB ATP A1801 " ideal model delta sigma weight residual 136.83 122.20 14.63 1.00e+00 1.00e+00 2.14e+02 angle pdb=" C4 ATP A1801 " pdb=" N9 ATP A1801 " pdb=" C8 ATP A1801 " ideal model delta sigma weight residual 105.72 119.67 -13.95 1.00e+00 1.00e+00 1.94e+02 angle pdb=" N1 ATP A1801 " pdb=" C2 ATP A1801 " pdb=" N3 ATP A1801 " ideal model delta sigma weight residual 128.69 120.08 8.61 1.00e+00 1.00e+00 7.42e+01 angle pdb=" O4' DT N 50 " pdb=" C4' DT N 50 " pdb=" C3' DT N 50 " ideal model delta sigma weight residual 106.00 102.29 3.71 6.00e-01 2.78e+00 3.83e+01 ... (remaining 45976 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.81: 19575 28.81 - 57.63: 720 57.63 - 86.44: 108 86.44 - 115.26: 3 115.26 - 144.07: 3 Dihedral angle restraints: 20409 sinusoidal: 9084 harmonic: 11325 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 180.00 152.64 27.36 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA GLU A 398 " pdb=" C GLU A 398 " pdb=" N HIS A 399 " pdb=" CA HIS A 399 " ideal model delta harmonic sigma weight residual 180.00 -155.85 -24.15 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA PHE A 22 " pdb=" C PHE A 22 " pdb=" N SER A 23 " pdb=" CA SER A 23 " ideal model delta harmonic sigma weight residual 180.00 159.87 20.13 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 20406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 3615 0.037 - 0.075: 1049 0.075 - 0.112: 430 0.112 - 0.150: 74 0.150 - 0.187: 3 Chirality restraints: 5171 Sorted by residual: chirality pdb=" C2' ATP A1801 " pdb=" C1' ATP A1801 " pdb=" C3' ATP A1801 " pdb=" O2' ATP A1801 " both_signs ideal model delta sigma weight residual False -2.68 -2.49 -0.19 2.00e-01 2.50e+01 8.75e-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 7.56e-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 6.51e-01 ... (remaining 5168 not shown) Planarity restraints: 5620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 710 " -0.009 2.00e-02 2.50e+03 1.73e-02 3.01e+00 pdb=" C LEU A 710 " 0.030 2.00e-02 2.50e+03 pdb=" O LEU A 710 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG A 711 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 797 " -0.014 2.00e-02 2.50e+03 1.23e-02 3.00e+00 pdb=" CG TYR B 797 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR B 797 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR B 797 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B 797 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 797 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 797 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 797 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 480 " 0.008 2.00e-02 2.50e+03 1.72e-02 2.97e+00 pdb=" C ALA A 480 " -0.030 2.00e-02 2.50e+03 pdb=" O ALA A 480 " 0.011 2.00e-02 2.50e+03 pdb=" N ASP A 481 " 0.010 2.00e-02 2.50e+03 ... (remaining 5617 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 43 2.30 - 2.95: 15243 2.95 - 3.60: 49365 3.60 - 4.25: 77458 4.25 - 4.90: 128277 Nonbonded interactions: 270386 Sorted by model distance: nonbonded pdb=" O2A ATP A1801 " pdb="MG MG A1803 " model vdw 1.647 2.170 nonbonded pdb=" OD2 ASP A 481 " pdb="MG MG A1802 " model vdw 1.671 2.170 nonbonded pdb=" O2B ATP A1801 " pdb="MG MG A1802 " model vdw 1.722 2.170 nonbonded pdb=" O2A ATP A1801 " pdb="MG MG A1802 " model vdw 1.744 2.170 nonbonded pdb="MG MG A1802 " pdb="MG MG A1803 " model vdw 1.864 1.300 ... (remaining 270381 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 37.410 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 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 0.191 33796 Z= 0.324 Angle : 0.635 19.015 46026 Z= 0.423 Chirality : 0.042 0.187 5171 Planarity : 0.003 0.043 5620 Dihedral : 14.531 144.071 13073 Min Nonbonded Distance : 1.647 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.14 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.14), residues: 3845 helix: 1.65 (0.15), residues: 1299 sheet: 0.10 (0.22), residues: 608 loop : -0.32 (0.15), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 337 TYR 0.031 0.001 TYR B 797 PHE 0.018 0.001 PHE B 37 TRP 0.011 0.001 TRP B 561 HIS 0.009 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.32 (33764) covalent geometry : angle 0.62847 / 0.42 (45981) hydrogen bonds : bond 0.18490 / 12.69 ( 1405) hydrogen bonds : angle 6.96056 / 4.91 ( 3877) metal coordination : bond 0.00659 / 0.46 ( 32) metal coordination : angle 2.96775 / 1.92 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 3433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 595 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8091 (mtt) cc_final: 0.7720 (mtp) REVERT: A 229 SER cc_start: 0.9314 (t) cc_final: 0.9030 (p) REVERT: A 250 ILE cc_start: 0.8670 (mm) cc_final: 0.8324 (tp) REVERT: A 323 LYS cc_start: 0.9317 (tttp) cc_final: 0.8958 (ttpt) REVERT: A 487 MET cc_start: 0.9228 (mtp) cc_final: 0.8861 (mtm) REVERT: A 496 GLU cc_start: 0.8702 (tt0) cc_final: 0.8453 (tm-30) REVERT: A 605 MET cc_start: 0.9309 (tpt) cc_final: 0.8655 (tpp) REVERT: A 748 MET cc_start: 0.8963 (mtm) cc_final: 0.8671 (mtp) REVERT: A 789 LYS cc_start: 0.9097 (mttt) cc_final: 0.8591 (mtpp) REVERT: A 846 GLU cc_start: 0.9109 (pt0) cc_final: 0.8766 (pt0) REVERT: A 849 MET cc_start: 0.8582 (ttp) cc_final: 0.8056 (ttm) REVERT: A 873 MET cc_start: 0.9446 (mmp) cc_final: 0.8658 (mmp) REVERT: A 878 ILE cc_start: 0.9145 (mt) cc_final: 0.8930 (mm) REVERT: A 966 ASN cc_start: 0.8864 (m-40) cc_final: 0.8565 (t0) REVERT: A 995 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8582 (tm-30) REVERT: A 1005 GLU cc_start: 0.9365 (mm-30) cc_final: 0.9052 (tp30) REVERT: A 1071 SER cc_start: 0.9310 (m) cc_final: 0.8918 (p) REVERT: A 1086 PHE cc_start: 0.8415 (m-80) cc_final: 0.8179 (t80) REVERT: A 1315 GLU cc_start: 0.9381 (tt0) cc_final: 0.8866 (tm-30) REVERT: A 1378 GLN cc_start: 0.9305 (mt0) cc_final: 0.9072 (mm110) REVERT: A 1424 VAL cc_start: 0.8828 (m) cc_final: 0.8555 (p) REVERT: A 1444 MET cc_start: 0.8725 (mmp) cc_final: 0.8248 (mmm) REVERT: A 1454 MET cc_start: 0.8698 (mtp) cc_final: 0.8230 (tmm) REVERT: B 470 LYS cc_start: 0.8632 (mppt) cc_final: 0.8414 (mmtt) REVERT: B 473 MET cc_start: 0.8994 (mmp) cc_final: 0.8185 (pmm) REVERT: B 498 THR cc_start: 0.9128 (m) cc_final: 0.8651 (p) REVERT: B 526 GLU cc_start: 0.9272 (tt0) cc_final: 0.8891 (tm-30) REVERT: B 615 MET cc_start: 0.8620 (mtm) cc_final: 0.8368 (mtm) REVERT: B 662 MET cc_start: 0.9360 (mtm) cc_final: 0.9103 (mmm) REVERT: B 747 MET cc_start: 0.9158 (mmm) cc_final: 0.8950 (mmp) REVERT: B 809 MET cc_start: 0.8920 (mtt) cc_final: 0.8454 (mtp) REVERT: B 1028 GLU cc_start: 0.9052 (tt0) cc_final: 0.8794 (tt0) REVERT: B 1032 SER cc_start: 0.9349 (m) cc_final: 0.8916 (t) REVERT: B 1072 MET cc_start: 0.8937 (mtp) cc_final: 0.8578 (mtp) REVERT: B 1082 MET cc_start: 0.8772 (tpp) cc_final: 0.8479 (tpp) REVERT: B 1111 MET cc_start: 0.8325 (mmm) cc_final: 0.7798 (mmt) REVERT: B 1120 GLU cc_start: 0.8586 (tt0) cc_final: 0.8347 (tt0) REVERT: B 1152 MET cc_start: 0.8146 (mmm) cc_final: 0.7748 (tpt) REVERT: C 40 GLU cc_start: 0.8803 (mt-10) cc_final: 0.7821 (tm-30) REVERT: C 75 MET cc_start: 0.8934 (mmm) cc_final: 0.8525 (tpt) REVERT: D 23 ASN cc_start: 0.8347 (t0) cc_final: 0.7967 (t0) REVERT: D 50 LEU cc_start: 0.8517 (mt) cc_final: 0.8317 (mp) REVERT: D 57 LEU cc_start: 0.9233 (mt) cc_final: 0.8954 (pp) REVERT: D 140 ASP cc_start: 0.8633 (m-30) cc_final: 0.8084 (t0) REVERT: D 142 LYS cc_start: 0.8523 (tttt) cc_final: 0.8075 (tmtt) REVERT: D 147 TYR cc_start: 0.7174 (t80) cc_final: 0.6953 (t80) REVERT: D 151 PHE cc_start: 0.4632 (m-80) cc_final: 0.4382 (m-10) REVERT: D 209 ARG cc_start: 0.7783 (tmt170) cc_final: 0.7562 (tmt170) REVERT: E 32 GLN cc_start: 0.9473 (tt0) cc_final: 0.9219 (tp-100) REVERT: E 36 GLU cc_start: 0.9608 (mt-10) cc_final: 0.9249 (mm-30) REVERT: E 192 ARG cc_start: 0.9227 (ttt180) cc_final: 0.8726 (ttm-80) REVERT: E 201 LYS cc_start: 0.9278 (mtmt) cc_final: 0.9042 (mmmt) REVERT: F 109 VAL cc_start: 0.9167 (t) cc_final: 0.8802 (p) REVERT: F 116 ASP cc_start: 0.8564 (t0) cc_final: 0.8135 (t0) REVERT: F 119 ARG cc_start: 0.9331 (tpp80) cc_final: 0.8942 (tpp80) REVERT: F 130 ILE cc_start: 0.9366 (mt) cc_final: 0.9150 (mm) REVERT: F 151 LEU cc_start: 0.9330 (mt) cc_final: 0.9105 (mm) REVERT: G 44 TYR cc_start: 0.5672 (m-80) cc_final: 0.5113 (m-80) REVERT: G 46 LEU cc_start: 0.8956 (mt) cc_final: 0.8593 (mp) REVERT: G 69 GLU cc_start: 0.8742 (tt0) cc_final: 0.8372 (tm-30) REVERT: G 114 LEU cc_start: 0.7536 (mt) cc_final: 0.7316 (mt) REVERT: H 12 VAL cc_start: 0.9540 (t) cc_final: 0.9204 (m) REVERT: H 52 GLN cc_start: 0.9234 (mt0) cc_final: 0.9013 (mp10) REVERT: H 105 GLU cc_start: 0.8246 (tt0) cc_final: 0.7899 (tm-30) REVERT: H 107 VAL cc_start: 0.8985 (t) cc_final: 0.8620 (t) REVERT: H 110 ASP cc_start: 0.8790 (p0) cc_final: 0.8332 (t0) REVERT: H 123 MET cc_start: 0.9208 (ttt) cc_final: 0.8918 (ttp) REVERT: H 129 TYR cc_start: 0.8574 (p90) cc_final: 0.8190 (p90) REVERT: H 136 LYS cc_start: 0.9378 (mmtp) cc_final: 0.9130 (mptt) REVERT: I 8 ARG cc_start: 0.6400 (tmm160) cc_final: 0.6030 (mtm-85) REVERT: I 90 GLN cc_start: 0.8178 (tp-100) cc_final: 0.7285 (tm-30) REVERT: J 27 GLU cc_start: 0.9201 (tm-30) cc_final: 0.8836 (pt0) REVERT: K 26 LYS cc_start: 0.9220 (mmmt) cc_final: 0.8966 (mtmt) REVERT: K 108 GLU cc_start: 0.9404 (mm-30) cc_final: 0.9032 (tt0) REVERT: L 29 TYR cc_start: 0.6863 (m-80) cc_final: 0.6628 (m-80) REVERT: L 56 LEU cc_start: 0.8672 (mt) cc_final: 0.8407 (mm) REVERT: L 61 THR cc_start: 0.8235 (p) cc_final: 0.7984 (p) REVERT: L 63 ARG cc_start: 0.8134 (mtm-85) cc_final: 0.7096 (tpp-160) outliers start: 0 outliers final: 0 residues processed: 595 average time/residue: 0.2352 time to fit residues: 219.7789 Evaluate side-chains 359 residues out of total 3433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 HIS A 742 ASN A1085 HIS ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 HIS B 862 GLN B1025 HIS B1093 GLN B1117 GLN D 143 ASN E 54 GLN I 90 GLN ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.085717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.058225 restraints weight = 100179.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.060058 restraints weight = 51718.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.061246 restraints weight = 34319.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.061980 restraints weight = 26626.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.062418 restraints weight = 22899.605| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 33796 Z= 0.252 Angle : 0.687 18.366 46026 Z= 0.354 Chirality : 0.047 0.302 5171 Planarity : 0.005 0.061 5620 Dihedral : 16.430 143.975 5293 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.50 % Favored : 95.42 % Rotamer: Outliers : 1.19 % Allowed : 7.14 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.14), residues: 3845 helix: 1.44 (0.14), residues: 1325 sheet: 0.07 (0.22), residues: 576 loop : -0.46 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 337 TYR 0.021 0.002 TYR B 797 PHE 0.025 0.002 PHE D 33 TRP 0.016 0.001 TRP B 561 HIS 0.008 0.001 HIS D 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.25 (33764) covalent geometry : angle 0.67076 / 0.35 (45981) hydrogen bonds : bond 0.04889 / 3.32 ( 1405) hydrogen bonds : angle 5.42981 / 3.83 ( 3877) metal coordination : bond 0.00973 / 0.67 ( 32) metal coordination : angle 4.80094 / 2.84 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 393 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8382 (mtt) cc_final: 0.7907 (mtp) REVERT: A 304 MET cc_start: 0.9240 (mtt) cc_final: 0.8957 (mmt) REVERT: A 605 MET cc_start: 0.9268 (tpt) cc_final: 0.8946 (tpp) REVERT: A 873 MET cc_start: 0.9152 (mmp) cc_final: 0.8456 (mmp) REVERT: A 1071 SER cc_start: 0.9652 (m) cc_final: 0.9211 (p) REVERT: A 1111 MET cc_start: 0.8098 (ttm) cc_final: 0.7722 (ttm) REVERT: A 1444 MET cc_start: 0.8250 (mmp) cc_final: 0.7187 (mmm) REVERT: B 470 LYS cc_start: 0.8226 (mppt) cc_final: 0.7958 (mmtt) REVERT: B 1032 SER cc_start: 0.9392 (m) cc_final: 0.8949 (t) REVERT: B 1072 MET cc_start: 0.8077 (mtp) cc_final: 0.7614 (mtp) REVERT: B 1128 LEU cc_start: 0.9438 (mt) cc_final: 0.9218 (mp) REVERT: B 1152 MET cc_start: 0.8551 (mmm) cc_final: 0.8201 (tpt) REVERT: D 50 LEU cc_start: 0.8797 (mt) cc_final: 0.8244 (mt) REVERT: D 57 LEU cc_start: 0.9345 (mt) cc_final: 0.8911 (pp) REVERT: D 140 ASP cc_start: 0.8818 (m-30) cc_final: 0.8418 (t70) REVERT: D 147 TYR cc_start: 0.7516 (t80) cc_final: 0.7253 (t80) REVERT: E 25 ASP cc_start: 0.9211 (m-30) cc_final: 0.8936 (m-30) REVERT: F 89 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8391 (mt-10) REVERT: F 116 ASP cc_start: 0.9131 (t0) cc_final: 0.8890 (t0) REVERT: F 124 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8476 (mt-10) REVERT: G 1 MET cc_start: 0.6713 (mmm) cc_final: 0.6331 (mmm) REVERT: G 6 ASP cc_start: 0.7514 (m-30) cc_final: 0.7152 (m-30) REVERT: G 44 TYR cc_start: 0.5994 (m-80) cc_final: 0.5563 (m-80) REVERT: G 46 LEU cc_start: 0.9014 (mt) cc_final: 0.8763 (mp) REVERT: G 50 ASP cc_start: 0.8216 (t0) cc_final: 0.7767 (t0) REVERT: G 158 HIS cc_start: 0.8564 (OUTLIER) cc_final: 0.8317 (t-90) REVERT: H 106 GLU cc_start: 0.8844 (tp30) cc_final: 0.8593 (tp30) REVERT: H 107 VAL cc_start: 0.9156 (t) cc_final: 0.8681 (t) REVERT: H 110 ASP cc_start: 0.7755 (p0) cc_final: 0.7548 (t0) REVERT: I 1 MET cc_start: 0.6238 (tpp) cc_final: 0.5732 (tpp) REVERT: I 90 GLN cc_start: 0.8291 (tp40) cc_final: 0.7726 (tm-30) REVERT: L 29 TYR cc_start: 0.7733 (m-80) cc_final: 0.7528 (m-80) REVERT: L 63 ARG cc_start: 0.7991 (mtm-85) cc_final: 0.7327 (tpp-160) outliers start: 41 outliers final: 26 residues processed: 415 average time/residue: 0.2211 time to fit residues: 146.4743 Evaluate side-chains 354 residues out of total 3433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 327 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 158 HIS Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain L residue 30 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 206 optimal weight: 9.9990 chunk 192 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 302 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 211 optimal weight: 0.7980 chunk 295 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 294 optimal weight: 5.9990 chunk 359 optimal weight: 0.0970 chunk 49 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 HIS A 975 HIS ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1432 GLN B 46 GLN ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 HIS D 23 ASN D 143 ASN D 150 ASN K 2 ASN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.086964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.059235 restraints weight = 98975.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.061108 restraints weight = 51041.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.062317 restraints weight = 33858.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.063073 restraints weight = 26290.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.063518 restraints weight = 22597.290| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33796 Z= 0.146 Angle : 0.602 16.058 46026 Z= 0.313 Chirality : 0.044 0.223 5171 Planarity : 0.004 0.046 5620 Dihedral : 16.325 141.532 5293 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.46 % Favored : 96.46 % Rotamer: Outliers : 0.84 % Allowed : 9.76 % Favored : 89.40 % 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: 0.45 (0.14), residues: 3845 helix: 1.47 (0.14), residues: 1338 sheet: 0.06 (0.22), residues: 578 loop : -0.42 (0.14), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 87 TYR 0.020 0.001 TYR G 51 PHE 0.022 0.001 PHE A 219 TRP 0.010 0.001 TRP B 561 HIS 0.008 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (33764) covalent geometry : angle 0.58881 / 0.31 (45981) hydrogen bonds : bond 0.04041 / 2.73 ( 1405) hydrogen bonds : angle 4.97797 / 3.51 ( 3877) metal coordination : bond 0.00606 / 0.42 ( 32) metal coordination : angle 3.98691 / 2.37 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 385 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8379 (mtt) cc_final: 0.7948 (mtp) REVERT: A 546 VAL cc_start: 0.9552 (t) cc_final: 0.9339 (t) REVERT: A 605 MET cc_start: 0.9237 (tpt) cc_final: 0.8991 (tpp) REVERT: A 830 LYS cc_start: 0.8971 (mmmm) cc_final: 0.8678 (mmtm) REVERT: A 873 MET cc_start: 0.9174 (mmp) cc_final: 0.8519 (mmp) REVERT: A 1071 SER cc_start: 0.9644 (m) cc_final: 0.9222 (p) REVERT: A 1203 ASN cc_start: 0.8612 (m110) cc_final: 0.8046 (m110) REVERT: A 1284 MET cc_start: 0.7968 (mtp) cc_final: 0.7732 (mtt) REVERT: B 470 LYS cc_start: 0.8148 (mppt) cc_final: 0.7916 (mmtt) REVERT: B 1032 SER cc_start: 0.9351 (m) cc_final: 0.8933 (t) REVERT: B 1152 MET cc_start: 0.8568 (mmm) cc_final: 0.8215 (tpt) REVERT: D 50 LEU cc_start: 0.8829 (mt) cc_final: 0.8582 (mp) REVERT: D 57 LEU cc_start: 0.9339 (mt) cc_final: 0.8870 (pp) REVERT: D 67 ARG cc_start: 0.5839 (mmm-85) cc_final: 0.5068 (mmm-85) REVERT: D 140 ASP cc_start: 0.8728 (m-30) cc_final: 0.8330 (t70) REVERT: D 153 ARG cc_start: 0.7083 (ttt180) cc_final: 0.6765 (ttm170) REVERT: E 25 ASP cc_start: 0.9159 (m-30) cc_final: 0.8888 (m-30) REVERT: F 89 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8427 (mt-10) REVERT: G 1 MET cc_start: 0.6513 (mmm) cc_final: 0.6252 (mmm) REVERT: G 6 ASP cc_start: 0.7515 (m-30) cc_final: 0.7242 (m-30) REVERT: G 44 TYR cc_start: 0.5688 (m-80) cc_final: 0.5327 (m-80) REVERT: G 46 LEU cc_start: 0.8954 (mt) cc_final: 0.8626 (mp) REVERT: G 50 ASP cc_start: 0.8344 (t0) cc_final: 0.7803 (t0) REVERT: G 158 HIS cc_start: 0.8535 (OUTLIER) cc_final: 0.8239 (t-90) REVERT: H 139 ASN cc_start: 0.8856 (m-40) cc_final: 0.8608 (m-40) REVERT: I 1 MET cc_start: 0.5811 (tpp) cc_final: 0.5077 (tpp) REVERT: I 90 GLN cc_start: 0.8135 (tp40) cc_final: 0.7622 (tm-30) REVERT: L 29 TYR cc_start: 0.7857 (m-80) cc_final: 0.7494 (m-80) REVERT: L 63 ARG cc_start: 0.8038 (mtm-85) cc_final: 0.7385 (tpp-160) outliers start: 29 outliers final: 16 residues processed: 401 average time/residue: 0.1970 time to fit residues: 127.0045 Evaluate side-chains 350 residues out of total 3433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 333 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 158 HIS Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain L residue 30 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 39 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 324 optimal weight: 20.0000 chunk 72 optimal weight: 9.9990 chunk 376 optimal weight: 5.9990 chunk 356 optimal weight: 5.9990 chunk 301 optimal weight: 0.9990 chunk 167 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 ASN E 32 GLN ** G 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 GLN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.083980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.056929 restraints weight = 99559.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.058624 restraints weight = 52673.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.059730 restraints weight = 35427.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.060419 restraints weight = 27738.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.060839 restraints weight = 23946.979| |-----------------------------------------------------------------------------| r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 33796 Z= 0.225 Angle : 0.634 15.127 46026 Z= 0.326 Chirality : 0.044 0.274 5171 Planarity : 0.004 0.054 5620 Dihedral : 16.344 141.247 5293 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.93 % Favored : 95.99 % Rotamer: Outliers : 1.57 % Allowed : 10.75 % Favored : 87.68 % 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: 0.37 (0.14), residues: 3845 helix: 1.46 (0.14), residues: 1331 sheet: -0.10 (0.22), residues: 584 loop : -0.46 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 56 TYR 0.023 0.001 TYR B 830 PHE 0.021 0.001 PHE A 219 TRP 0.010 0.001 TRP A1044 HIS 0.007 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.23 (33764) covalent geometry : angle 0.62189 / 0.33 (45981) hydrogen bonds : bond 0.03867 / 2.62 ( 1405) hydrogen bonds : angle 4.88941 / 3.45 ( 3877) metal coordination : bond 0.00844 / 0.57 ( 32) metal coordination : angle 3.93424 / 2.31 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 345 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8384 (mtt) cc_final: 0.7912 (mtp) REVERT: A 133 LYS cc_start: 0.9527 (mmmt) cc_final: 0.9278 (mmmt) REVERT: A 304 MET cc_start: 0.9194 (mmt) cc_final: 0.8658 (mmt) REVERT: A 470 LEU cc_start: 0.9616 (OUTLIER) cc_final: 0.9358 (pp) REVERT: A 546 VAL cc_start: 0.9577 (t) cc_final: 0.9339 (t) REVERT: A 605 MET cc_start: 0.9323 (tpt) cc_final: 0.9016 (tpp) REVERT: A 708 MET cc_start: 0.3191 (ttm) cc_final: 0.2984 (ttm) REVERT: A 873 MET cc_start: 0.9176 (mmp) cc_final: 0.8275 (mmp) REVERT: A 1071 SER cc_start: 0.9642 (m) cc_final: 0.9222 (p) REVERT: B 224 GLN cc_start: 0.8230 (mt0) cc_final: 0.7939 (mt0) REVERT: B 470 LYS cc_start: 0.8196 (mppt) cc_final: 0.7926 (mmtt) REVERT: B 615 MET cc_start: 0.8369 (mpp) cc_final: 0.8047 (mpp) REVERT: B 1032 SER cc_start: 0.9411 (m) cc_final: 0.8940 (t) REVERT: B 1072 MET cc_start: 0.7958 (mtp) cc_final: 0.7558 (mtp) REVERT: B 1152 MET cc_start: 0.8571 (mmm) cc_final: 0.8189 (tpt) REVERT: C 29 MET cc_start: 0.9254 (tpp) cc_final: 0.9026 (tpp) REVERT: C 40 GLU cc_start: 0.7555 (tm-30) cc_final: 0.7183 (tm-30) REVERT: D 50 LEU cc_start: 0.8860 (mt) cc_final: 0.8343 (mt) REVERT: D 57 LEU cc_start: 0.9324 (mt) cc_final: 0.8842 (pp) REVERT: D 67 ARG cc_start: 0.6001 (mmm-85) cc_final: 0.5162 (mmm-85) REVERT: D 124 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7708 (tp30) REVERT: D 140 ASP cc_start: 0.8772 (m-30) cc_final: 0.8268 (t70) REVERT: D 147 TYR cc_start: 0.7025 (t80) cc_final: 0.6628 (t80) REVERT: D 153 ARG cc_start: 0.7123 (ttt180) cc_final: 0.6776 (ttm170) REVERT: E 25 ASP cc_start: 0.9192 (m-30) cc_final: 0.8884 (m-30) REVERT: E 32 GLN cc_start: 0.8922 (tp-100) cc_final: 0.8595 (tp-100) REVERT: E 84 ASP cc_start: 0.9213 (OUTLIER) cc_final: 0.8983 (m-30) REVERT: E 215 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.6282 (tpt) REVERT: G 1 MET cc_start: 0.6342 (mmm) cc_final: 0.6106 (mmm) REVERT: G 44 TYR cc_start: 0.5602 (m-80) cc_final: 0.5198 (m-80) REVERT: G 46 LEU cc_start: 0.9087 (mt) cc_final: 0.8807 (mp) REVERT: G 50 ASP cc_start: 0.8533 (t0) cc_final: 0.8079 (t0) REVERT: G 69 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7621 (tm-30) REVERT: G 158 HIS cc_start: 0.8530 (OUTLIER) cc_final: 0.8194 (t-90) REVERT: H 139 ASN cc_start: 0.8857 (m-40) cc_final: 0.8554 (m-40) REVERT: I 1 MET cc_start: 0.5877 (tpp) cc_final: 0.5221 (tpp) REVERT: I 90 GLN cc_start: 0.7975 (tp40) cc_final: 0.7299 (tm-30) REVERT: K 22 ASP cc_start: 0.8510 (t0) cc_final: 0.8277 (t0) REVERT: K 49 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8322 (tp30) REVERT: L 63 ARG cc_start: 0.8116 (mtm-85) cc_final: 0.7406 (tpp-160) outliers start: 54 outliers final: 29 residues processed: 381 average time/residue: 0.2163 time to fit residues: 133.7050 Evaluate side-chains 360 residues out of total 3433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 327 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain F residue 82 THR 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 74 TYR Chi-restraints excluded: chain G residue 158 HIS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 65 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 188 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 171 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 277 optimal weight: 2.9990 chunk 269 optimal weight: 7.9990 chunk 292 optimal weight: 10.0000 chunk 260 optimal weight: 5.9990 chunk 289 optimal weight: 9.9990 chunk 121 optimal weight: 9.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 ASN ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 GLN B 440 HIS ** B1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 ASN F 104 ASN ** G 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 104 ASN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.083146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.055943 restraints weight = 100584.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.057645 restraints weight = 52964.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.058756 restraints weight = 35583.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.059442 restraints weight = 27860.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.059864 restraints weight = 24034.297| |-----------------------------------------------------------------------------| r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 33796 Z= 0.277 Angle : 0.665 16.569 46026 Z= 0.340 Chirality : 0.045 0.239 5171 Planarity : 0.004 0.044 5620 Dihedral : 16.400 142.049 5293 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.47 % Favored : 95.45 % Rotamer: Outliers : 1.72 % Allowed : 12.00 % Favored : 86.28 % 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: 0.25 (0.14), residues: 3845 helix: 1.40 (0.14), residues: 1331 sheet: -0.17 (0.22), residues: 576 loop : -0.56 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 87 TYR 0.015 0.002 TYR J 44 PHE 0.023 0.002 PHE L 67 TRP 0.010 0.001 TRP B 308 HIS 0.008 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.28 (33764) covalent geometry : angle 0.65078 / 0.34 (45981) hydrogen bonds : bond 0.03950 / 2.66 ( 1405) hydrogen bonds : angle 4.86350 / 3.44 ( 3877) metal coordination : bond 0.01039 / 0.69 ( 32) metal coordination : angle 4.37989 / 2.58 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 330 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8381 (mtt) cc_final: 0.7922 (mtp) REVERT: A 122 MET cc_start: 0.9247 (tpp) cc_final: 0.8516 (tpp) REVERT: A 133 LYS cc_start: 0.9545 (mmmt) cc_final: 0.9338 (mmmt) REVERT: A 304 MET cc_start: 0.9363 (mmt) cc_final: 0.8682 (mmt) REVERT: A 470 LEU cc_start: 0.9624 (OUTLIER) cc_final: 0.9344 (pp) REVERT: A 546 VAL cc_start: 0.9560 (t) cc_final: 0.9356 (t) REVERT: A 605 MET cc_start: 0.9326 (tpt) cc_final: 0.9040 (tpp) REVERT: A 873 MET cc_start: 0.9154 (mmp) cc_final: 0.8414 (mmp) REVERT: A 1071 SER cc_start: 0.9657 (m) cc_final: 0.9245 (p) REVERT: B 224 GLN cc_start: 0.8278 (mt0) cc_final: 0.7961 (mt0) REVERT: B 310 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8699 (mtm) REVERT: B 470 LYS cc_start: 0.8212 (mppt) cc_final: 0.7955 (mmtt) REVERT: B 615 MET cc_start: 0.8394 (mpp) cc_final: 0.8002 (mpp) REVERT: B 1032 SER cc_start: 0.9419 (m) cc_final: 0.9011 (t) REVERT: B 1072 MET cc_start: 0.7998 (mtp) cc_final: 0.7638 (mtp) REVERT: C 29 MET cc_start: 0.9291 (tpp) cc_final: 0.9059 (tpp) REVERT: C 40 GLU cc_start: 0.7555 (tm-30) cc_final: 0.7159 (tm-30) REVERT: D 50 LEU cc_start: 0.8862 (mt) cc_final: 0.8315 (mt) REVERT: D 57 LEU cc_start: 0.9336 (mt) cc_final: 0.8862 (pp) REVERT: D 140 ASP cc_start: 0.8758 (m-30) cc_final: 0.8247 (t70) REVERT: D 147 TYR cc_start: 0.7164 (t80) cc_final: 0.6854 (t80) REVERT: E 25 ASP cc_start: 0.9248 (m-30) cc_final: 0.8891 (m-30) REVERT: E 32 GLN cc_start: 0.8916 (tp-100) cc_final: 0.8608 (tp-100) REVERT: E 106 GLN cc_start: 0.8725 (mm-40) cc_final: 0.8325 (tp-100) REVERT: E 215 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.6458 (tpt) REVERT: F 124 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8593 (tt0) REVERT: G 1 MET cc_start: 0.6422 (mmm) cc_final: 0.6140 (mmm) REVERT: G 44 TYR cc_start: 0.5659 (m-80) cc_final: 0.5214 (m-80) REVERT: G 46 LEU cc_start: 0.9113 (mt) cc_final: 0.8806 (mp) REVERT: G 50 ASP cc_start: 0.8522 (t0) cc_final: 0.8057 (t0) REVERT: G 69 GLU cc_start: 0.8352 (tm-30) cc_final: 0.7686 (tm-30) REVERT: G 158 HIS cc_start: 0.8508 (OUTLIER) cc_final: 0.8167 (t-90) REVERT: H 139 ASN cc_start: 0.8998 (m-40) cc_final: 0.8748 (m-40) REVERT: I 1 MET cc_start: 0.6104 (tpp) cc_final: 0.5147 (tpt) REVERT: K 22 ASP cc_start: 0.8529 (t0) cc_final: 0.8254 (t0) REVERT: K 49 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8288 (tp30) REVERT: L 63 ARG cc_start: 0.8111 (mtm-85) cc_final: 0.7471 (tpp-160) outliers start: 59 outliers final: 38 residues processed: 368 average time/residue: 0.2043 time to fit residues: 123.1343 Evaluate side-chains 352 residues out of total 3433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 310 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1202 LEU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain F residue 82 THR 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 74 TYR Chi-restraints excluded: chain G residue 158 HIS Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 65 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 279 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 379 optimal weight: 2.9990 chunk 325 optimal weight: 5.9990 chunk 283 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 249 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 chunk 47 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 316 GLN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 ASN ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1432 GLN B 494 HIS ** B1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 ASN ** G 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3527 r_free = 0.3527 target = 0.086640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.059616 restraints weight = 100406.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.061418 restraints weight = 53390.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.062590 restraints weight = 35946.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.063314 restraints weight = 28227.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 65)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.063740 restraints weight = 24454.199| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 33796 Z= 0.174 Angle : 0.605 15.071 46026 Z= 0.310 Chirality : 0.044 0.380 5171 Planarity : 0.004 0.054 5620 Dihedral : 16.366 140.932 5293 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.85 % Favored : 96.10 % Rotamer: Outliers : 1.51 % Allowed : 12.93 % Favored : 85.55 % 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: 0.33 (0.14), residues: 3845 helix: 1.48 (0.14), residues: 1331 sheet: -0.20 (0.21), residues: 575 loop : -0.49 (0.14), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 87 TYR 0.016 0.001 TYR B 769 PHE 0.020 0.001 PHE A 219 TRP 0.015 0.001 TRP B 308 HIS 0.007 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (33764) covalent geometry : angle 0.59386 / 0.31 (45981) hydrogen bonds : bond 0.03621 / 2.45 ( 1405) hydrogen bonds : angle 4.67817 / 3.30 ( 3877) metal coordination : bond 0.00683 / 0.46 ( 32) metal coordination : angle 3.80471 / 2.27 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 332 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8348 (mtt) cc_final: 0.7906 (mtp) REVERT: A 122 MET cc_start: 0.9243 (tpp) cc_final: 0.8454 (tpp) REVERT: A 304 MET cc_start: 0.9406 (mmt) cc_final: 0.8746 (mmt) REVERT: A 470 LEU cc_start: 0.9620 (OUTLIER) cc_final: 0.9373 (pp) REVERT: A 605 MET cc_start: 0.9299 (tpt) cc_final: 0.9014 (tpp) REVERT: A 849 MET cc_start: 0.8603 (tpp) cc_final: 0.8380 (tpt) REVERT: A 873 MET cc_start: 0.9123 (mmp) cc_final: 0.8348 (mmp) REVERT: A 1071 SER cc_start: 0.9646 (m) cc_final: 0.9215 (p) REVERT: A 1260 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7310 (mt) REVERT: A 1284 MET cc_start: 0.8059 (mtt) cc_final: 0.7848 (mtt) REVERT: A 1444 MET cc_start: 0.8863 (mmm) cc_final: 0.8514 (mmm) REVERT: B 224 GLN cc_start: 0.8323 (mt0) cc_final: 0.8039 (mt0) REVERT: B 310 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8689 (mtm) REVERT: B 470 LYS cc_start: 0.8187 (mppt) cc_final: 0.7945 (mmtt) REVERT: B 615 MET cc_start: 0.8386 (mpp) cc_final: 0.7879 (mpp) REVERT: B 1032 SER cc_start: 0.9388 (m) cc_final: 0.8904 (t) REVERT: B 1072 MET cc_start: 0.7865 (mtp) cc_final: 0.7474 (mtp) REVERT: C 29 MET cc_start: 0.9255 (tpp) cc_final: 0.9004 (tpp) REVERT: C 40 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7137 (tm-30) REVERT: C 75 MET cc_start: 0.8886 (mmm) cc_final: 0.8668 (tpp) REVERT: D 50 LEU cc_start: 0.8877 (mt) cc_final: 0.8357 (mt) REVERT: D 57 LEU cc_start: 0.9327 (mt) cc_final: 0.8862 (pp) REVERT: D 140 ASP cc_start: 0.8721 (m-30) cc_final: 0.8114 (t70) REVERT: D 147 TYR cc_start: 0.7083 (t80) cc_final: 0.6781 (t80) REVERT: E 25 ASP cc_start: 0.9195 (m-30) cc_final: 0.8854 (m-30) REVERT: E 32 GLN cc_start: 0.8920 (tp-100) cc_final: 0.8579 (tp-100) REVERT: E 58 MET cc_start: 0.8741 (mtm) cc_final: 0.8480 (mtp) REVERT: E 106 GLN cc_start: 0.8638 (mm-40) cc_final: 0.8280 (tp40) REVERT: E 215 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.6405 (tpt) REVERT: F 124 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8585 (tt0) REVERT: G 1 MET cc_start: 0.6677 (mmm) cc_final: 0.6279 (mmm) REVERT: G 44 TYR cc_start: 0.5562 (m-80) cc_final: 0.5089 (m-80) REVERT: G 46 LEU cc_start: 0.9123 (mt) cc_final: 0.8799 (mp) REVERT: G 50 ASP cc_start: 0.8509 (t0) cc_final: 0.8140 (t0) REVERT: G 69 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7695 (tm-30) REVERT: G 158 HIS cc_start: 0.8426 (OUTLIER) cc_final: 0.8099 (t-90) REVERT: H 139 ASN cc_start: 0.8967 (m-40) cc_final: 0.8686 (m-40) REVERT: I 1 MET cc_start: 0.6038 (tpp) cc_final: 0.5080 (tpt) REVERT: K 22 ASP cc_start: 0.8541 (t0) cc_final: 0.8133 (t0) REVERT: K 49 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8370 (tp30) REVERT: K 106 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8439 (mt-10) REVERT: L 63 ARG cc_start: 0.8053 (mtm-85) cc_final: 0.7447 (tpp-160) outliers start: 52 outliers final: 37 residues processed: 366 average time/residue: 0.1999 time to fit residues: 119.8171 Evaluate side-chains 359 residues out of total 3433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 316 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 124 GLU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 74 TYR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 158 HIS Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 168 optimal weight: 6.9990 chunk 298 optimal weight: 0.8980 chunk 171 optimal weight: 9.9990 chunk 233 optimal weight: 7.9990 chunk 324 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 34 optimal weight: 7.9990 chunk 255 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 260 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 overall best weight: 1.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 ASN ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 ASN ** G 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.087320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.060235 restraints weight = 100565.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.062092 restraints weight = 53272.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.063274 restraints weight = 35731.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.064015 restraints weight = 28003.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.064445 restraints weight = 24222.452| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33796 Z= 0.142 Angle : 0.585 12.040 46026 Z= 0.298 Chirality : 0.043 0.350 5171 Planarity : 0.004 0.048 5620 Dihedral : 16.306 139.757 5293 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.59 % Favored : 96.36 % Rotamer: Outliers : 1.66 % Allowed : 13.11 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.14), residues: 3845 helix: 1.55 (0.15), residues: 1334 sheet: -0.18 (0.21), residues: 578 loop : -0.45 (0.15), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 90 TYR 0.017 0.001 TYR B 769 PHE 0.026 0.001 PHE A1225 TRP 0.016 0.001 TRP B 308 HIS 0.007 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (33764) covalent geometry : angle 0.57652 / 0.30 (45981) hydrogen bonds : bond 0.03432 / 2.32 ( 1405) hydrogen bonds : angle 4.55302 / 3.21 ( 3877) metal coordination : bond 0.00528 / 0.36 ( 32) metal coordination : angle 3.27836 / 1.99 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 340 time to evaluate : 1.263 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 74 MET cc_start: 0.8359 (mtt) cc_final: 0.7927 (mtp) REVERT: A 133 LYS cc_start: 0.9321 (mmmt) cc_final: 0.9092 (ptpp) REVERT: A 146 MET cc_start: 0.8466 (mpp) cc_final: 0.8192 (mmt) REVERT: A 304 MET cc_start: 0.9405 (mmt) cc_final: 0.8696 (mmt) REVERT: A 470 LEU cc_start: 0.9626 (OUTLIER) cc_final: 0.9380 (pp) REVERT: A 605 MET cc_start: 0.9285 (tpt) cc_final: 0.9024 (tpp) REVERT: A 873 MET cc_start: 0.9116 (mmp) cc_final: 0.8356 (mmp) REVERT: A 1071 SER cc_start: 0.9635 (m) cc_final: 0.9211 (p) REVERT: A 1209 MET cc_start: 0.7572 (ttp) cc_final: 0.7319 (ttp) REVERT: A 1260 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7314 (mt) REVERT: A 1444 MET cc_start: 0.8822 (mmm) cc_final: 0.8554 (mmm) REVERT: B 224 GLN cc_start: 0.8254 (mt0) cc_final: 0.7943 (mt0) REVERT: B 310 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8656 (mtm) REVERT: B 470 LYS cc_start: 0.8214 (mppt) cc_final: 0.7951 (mmtt) REVERT: B 526 GLU cc_start: 0.8456 (tt0) cc_final: 0.8129 (tt0) REVERT: B 615 MET cc_start: 0.8397 (mpp) cc_final: 0.7944 (mpp) REVERT: B 1032 SER cc_start: 0.9364 (m) cc_final: 0.8886 (t) REVERT: B 1072 MET cc_start: 0.7955 (mtp) cc_final: 0.7606 (mtp) REVERT: B 1152 MET cc_start: 0.8527 (tpt) cc_final: 0.8054 (tpt) REVERT: C 29 MET cc_start: 0.9253 (tpp) cc_final: 0.9016 (tpp) REVERT: C 75 MET cc_start: 0.8914 (mmm) cc_final: 0.8467 (tpp) REVERT: D 50 LEU cc_start: 0.8847 (mt) cc_final: 0.8323 (mt) REVERT: D 57 LEU cc_start: 0.9314 (mt) cc_final: 0.8846 (pp) REVERT: D 139 LYS cc_start: 0.7654 (mmmt) cc_final: 0.7387 (mmmt) REVERT: D 140 ASP cc_start: 0.8716 (m-30) cc_final: 0.8170 (t70) REVERT: D 147 TYR cc_start: 0.7121 (t80) cc_final: 0.6865 (t80) REVERT: E 25 ASP cc_start: 0.9176 (m-30) cc_final: 0.8834 (m-30) REVERT: E 32 GLN cc_start: 0.8908 (tp-100) cc_final: 0.8559 (tp-100) REVERT: E 58 MET cc_start: 0.8795 (mtm) cc_final: 0.8529 (mtp) REVERT: E 215 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.6408 (tpt) REVERT: F 89 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8496 (mt-10) REVERT: F 124 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8587 (tt0) REVERT: G 1 MET cc_start: 0.6920 (mmm) cc_final: 0.6396 (mmm) REVERT: G 44 TYR cc_start: 0.5550 (m-80) cc_final: 0.5067 (m-80) REVERT: G 46 LEU cc_start: 0.9163 (mt) cc_final: 0.8894 (mp) REVERT: G 50 ASP cc_start: 0.8562 (t0) cc_final: 0.8192 (t0) REVERT: G 69 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7669 (tm-30) REVERT: G 153 GLN cc_start: 0.7822 (mp10) cc_final: 0.7172 (mp10) REVERT: G 158 HIS cc_start: 0.8397 (OUTLIER) cc_final: 0.8082 (t-90) REVERT: H 139 ASN cc_start: 0.8996 (m-40) cc_final: 0.8691 (m-40) REVERT: I 1 MET cc_start: 0.6104 (tpp) cc_final: 0.5091 (tpt) REVERT: K 22 ASP cc_start: 0.8509 (t0) cc_final: 0.8127 (t0) REVERT: K 49 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8343 (tp30) REVERT: K 106 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8396 (mt-10) REVERT: L 63 ARG cc_start: 0.8050 (mtm-85) cc_final: 0.7442 (tpp-160) outliers start: 57 outliers final: 37 residues processed: 379 average time/residue: 0.2117 time to fit residues: 131.7186 Evaluate side-chains 362 residues out of total 3433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 320 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 158 HIS Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 356 optimal weight: 0.0470 chunk 139 optimal weight: 6.9990 chunk 280 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 303 optimal weight: 0.7980 chunk 343 optimal weight: 5.9990 chunk 309 optimal weight: 5.9990 chunk 196 optimal weight: 3.9990 chunk 194 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 overall best weight: 3.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 ASN ** B1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 ASN ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.086057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.059158 restraints weight = 101455.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.060911 restraints weight = 53808.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.062064 restraints weight = 36307.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.062785 restraints weight = 28547.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.063204 restraints weight = 24739.211| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 33796 Z= 0.232 Angle : 0.648 12.811 46026 Z= 0.326 Chirality : 0.044 0.320 5171 Planarity : 0.004 0.055 5620 Dihedral : 16.331 140.507 5293 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.47 % Favored : 95.45 % Rotamer: Outliers : 1.51 % Allowed : 13.81 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.14), residues: 3845 helix: 1.47 (0.14), residues: 1340 sheet: -0.30 (0.21), residues: 581 loop : -0.53 (0.15), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 48 TYR 0.036 0.001 TYR B 830 PHE 0.024 0.001 PHE A1225 TRP 0.017 0.001 TRP B 308 HIS 0.007 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.23 (33764) covalent geometry : angle 0.63949 / 0.33 (45981) hydrogen bonds : bond 0.03599 / 2.43 ( 1405) hydrogen bonds : angle 4.64091 / 3.27 ( 3877) metal coordination : bond 0.00804 / 0.54 ( 32) metal coordination : angle 3.46990 / 2.07 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 323 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8346 (mtt) cc_final: 0.7952 (mtp) REVERT: A 304 MET cc_start: 0.9421 (mmt) cc_final: 0.8664 (mmt) REVERT: A 470 LEU cc_start: 0.9600 (OUTLIER) cc_final: 0.9360 (pp) REVERT: A 708 MET cc_start: 0.2894 (ttp) cc_final: 0.2316 (ptm) REVERT: A 873 MET cc_start: 0.9047 (mmp) cc_final: 0.8322 (mmp) REVERT: A 1071 SER cc_start: 0.9661 (m) cc_final: 0.9249 (p) REVERT: A 1209 MET cc_start: 0.7557 (ttp) cc_final: 0.7320 (ttp) REVERT: A 1260 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7334 (mt) REVERT: B 310 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8679 (mtm) REVERT: B 470 LYS cc_start: 0.8126 (mppt) cc_final: 0.7901 (mmtt) REVERT: B 615 MET cc_start: 0.8450 (mpp) cc_final: 0.8019 (mpp) REVERT: B 1032 SER cc_start: 0.9367 (m) cc_final: 0.8930 (t) REVERT: B 1072 MET cc_start: 0.7906 (mtp) cc_final: 0.7559 (mtp) REVERT: B 1152 MET cc_start: 0.8586 (tpt) cc_final: 0.8100 (tpt) REVERT: C 29 MET cc_start: 0.9212 (tpp) cc_final: 0.8964 (tpp) REVERT: C 75 MET cc_start: 0.8754 (mmm) cc_final: 0.8543 (tpp) REVERT: D 50 LEU cc_start: 0.8875 (mt) cc_final: 0.8316 (mt) REVERT: D 57 LEU cc_start: 0.9328 (mt) cc_final: 0.8858 (pp) REVERT: D 140 ASP cc_start: 0.8859 (m-30) cc_final: 0.8369 (t0) REVERT: D 142 LYS cc_start: 0.8240 (ptpp) cc_final: 0.8038 (pttm) REVERT: E 25 ASP cc_start: 0.9173 (m-30) cc_final: 0.8849 (m-30) REVERT: E 32 GLN cc_start: 0.8867 (tp-100) cc_final: 0.8574 (tp-100) REVERT: E 215 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.6532 (tpt) REVERT: G 1 MET cc_start: 0.6644 (mmm) cc_final: 0.6366 (mmm) REVERT: G 44 TYR cc_start: 0.5615 (m-80) cc_final: 0.4987 (m-80) REVERT: G 50 ASP cc_start: 0.8534 (t0) cc_final: 0.8156 (t0) REVERT: G 69 GLU cc_start: 0.8372 (tm-30) cc_final: 0.7755 (tm-30) REVERT: G 158 HIS cc_start: 0.8424 (OUTLIER) cc_final: 0.8087 (t-90) REVERT: H 139 ASN cc_start: 0.8938 (m-40) cc_final: 0.8675 (m-40) REVERT: I 1 MET cc_start: 0.6131 (tpp) cc_final: 0.5221 (tpt) REVERT: K 22 ASP cc_start: 0.8495 (t0) cc_final: 0.8099 (t0) REVERT: K 49 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8347 (tp30) REVERT: L 56 LEU cc_start: 0.9021 (mm) cc_final: 0.8804 (mm) REVERT: L 63 ARG cc_start: 0.8024 (mtm-85) cc_final: 0.7512 (tpp-160) outliers start: 52 outliers final: 41 residues processed: 355 average time/residue: 0.2183 time to fit residues: 126.6140 Evaluate side-chains 357 residues out of total 3433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 311 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 158 HIS Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 61 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 135 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 164 optimal weight: 0.0060 chunk 155 optimal weight: 3.9990 chunk 386 optimal weight: 50.0000 chunk 90 optimal weight: 0.8980 chunk 8 optimal weight: 0.0000 chunk 334 optimal weight: 0.8980 chunk 199 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 152 optimal weight: 2.9990 overall best weight: 0.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.088063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.061083 restraints weight = 99085.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.063044 restraints weight = 49459.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.064320 restraints weight = 32128.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.065101 restraints weight = 24608.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.065563 restraints weight = 21007.991| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 33796 Z= 0.111 Angle : 0.597 13.453 46026 Z= 0.301 Chirality : 0.043 0.324 5171 Planarity : 0.004 0.047 5620 Dihedral : 16.272 138.992 5293 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.17 % Favored : 96.80 % Rotamer: Outliers : 1.19 % Allowed : 14.33 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.14), residues: 3845 helix: 1.54 (0.14), residues: 1343 sheet: -0.24 (0.21), residues: 600 loop : -0.47 (0.15), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 87 TYR 0.038 0.001 TYR D 147 PHE 0.031 0.001 PHE J 8 TRP 0.021 0.001 TRP B 308 HIS 0.007 0.001 HIS A1173 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (33764) covalent geometry : angle 0.59134 / 0.30 (45981) hydrogen bonds : bond 0.03343 / 2.26 ( 1405) hydrogen bonds : angle 4.44527 / 3.13 ( 3877) metal coordination : bond 0.00463 / 0.32 ( 32) metal coordination : angle 2.77931 / 1.71 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 340 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8251 (mtt) cc_final: 0.7787 (mtp) REVERT: A 122 MET cc_start: 0.9181 (tpp) cc_final: 0.8439 (tpp) REVERT: A 146 MET cc_start: 0.8510 (mpp) cc_final: 0.8222 (mmt) REVERT: A 304 MET cc_start: 0.9408 (mmt) cc_final: 0.8706 (mmt) REVERT: A 470 LEU cc_start: 0.9627 (OUTLIER) cc_final: 0.9387 (pp) REVERT: A 479 ASN cc_start: 0.9089 (t0) cc_final: 0.8832 (t0) REVERT: A 708 MET cc_start: 0.2404 (ttp) cc_final: 0.1823 (ptm) REVERT: A 873 MET cc_start: 0.9090 (mmp) cc_final: 0.8272 (mmp) REVERT: A 1071 SER cc_start: 0.9631 (m) cc_final: 0.9197 (p) REVERT: A 1260 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7230 (mt) REVERT: B 310 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8205 (mtm) REVERT: B 470 LYS cc_start: 0.8195 (mppt) cc_final: 0.7883 (mmtt) REVERT: B 615 MET cc_start: 0.8358 (mpp) cc_final: 0.7844 (mpp) REVERT: B 809 MET cc_start: 0.8963 (mtp) cc_final: 0.8728 (ptp) REVERT: B 1032 SER cc_start: 0.9363 (m) cc_final: 0.8867 (t) REVERT: B 1072 MET cc_start: 0.8001 (mtp) cc_final: 0.7660 (mtp) REVERT: B 1152 MET cc_start: 0.8562 (tpt) cc_final: 0.8127 (tpt) REVERT: C 29 MET cc_start: 0.9302 (tpp) cc_final: 0.9070 (tpp) REVERT: C 75 MET cc_start: 0.8866 (mmm) cc_final: 0.8638 (tpt) REVERT: D 50 LEU cc_start: 0.8843 (mt) cc_final: 0.8314 (mt) REVERT: D 57 LEU cc_start: 0.9296 (mt) cc_final: 0.8766 (pp) REVERT: D 140 ASP cc_start: 0.8794 (m-30) cc_final: 0.8143 (t70) REVERT: D 147 TYR cc_start: 0.6898 (t80) cc_final: 0.6668 (t80) REVERT: E 25 ASP cc_start: 0.9211 (m-30) cc_final: 0.8892 (m-30) REVERT: E 32 GLN cc_start: 0.8926 (tp-100) cc_final: 0.8522 (tp-100) REVERT: E 58 MET cc_start: 0.8850 (mtm) cc_final: 0.8570 (mtp) REVERT: E 215 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.6358 (tpt) REVERT: F 114 GLU cc_start: 0.8518 (tp30) cc_final: 0.8309 (tp30) REVERT: G 1 MET cc_start: 0.6515 (mmm) cc_final: 0.6259 (mmm) REVERT: G 44 TYR cc_start: 0.5522 (m-80) cc_final: 0.5005 (m-80) REVERT: G 50 ASP cc_start: 0.8544 (t0) cc_final: 0.8155 (t0) REVERT: G 69 GLU cc_start: 0.8419 (tm-30) cc_final: 0.7712 (tm-30) REVERT: G 153 GLN cc_start: 0.8097 (mp10) cc_final: 0.7444 (mp10) REVERT: G 158 HIS cc_start: 0.8328 (OUTLIER) cc_final: 0.8002 (t-90) REVERT: H 139 ASN cc_start: 0.8950 (m-40) cc_final: 0.8673 (m-40) REVERT: I 1 MET cc_start: 0.6118 (tpp) cc_final: 0.5158 (tpt) REVERT: J 26 GLN cc_start: 0.8583 (tm-30) cc_final: 0.8368 (tm-30) REVERT: J 49 MET cc_start: 0.8906 (mtp) cc_final: 0.8576 (mtm) REVERT: K 22 ASP cc_start: 0.8486 (t0) cc_final: 0.8129 (t0) REVERT: K 49 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8328 (tp30) REVERT: L 56 LEU cc_start: 0.9077 (mm) cc_final: 0.8833 (mm) REVERT: L 63 ARG cc_start: 0.8082 (mtm-85) cc_final: 0.7426 (tpp-160) outliers start: 41 outliers final: 31 residues processed: 370 average time/residue: 0.2145 time to fit residues: 130.4969 Evaluate side-chains 358 residues out of total 3433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 322 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 322 PHE Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain B residue 1120 GLU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 158 HIS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain L residue 30 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 49 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 193 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 170 optimal weight: 9.9990 chunk 284 optimal weight: 9.9990 chunk 329 optimal weight: 4.9990 chunk 371 optimal weight: 9.9990 chunk 144 optimal weight: 20.0000 chunk 288 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 HIS ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 ASN ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.084132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.057708 restraints weight = 102714.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.059393 restraints weight = 54669.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.060502 restraints weight = 36866.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.061192 restraints weight = 28972.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.061597 restraints weight = 25069.244| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.088 33796 Z= 0.410 Angle : 0.807 16.320 46026 Z= 0.403 Chirality : 0.048 0.283 5171 Planarity : 0.005 0.052 5620 Dihedral : 16.385 141.912 5293 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.59 % Favored : 94.33 % Rotamer: Outliers : 1.34 % Allowed : 14.71 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.14), residues: 3845 helix: 1.22 (0.14), residues: 1335 sheet: -0.47 (0.21), residues: 580 loop : -0.69 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 209 TYR 0.033 0.002 TYR B 830 PHE 0.023 0.002 PHE A 655 TRP 0.020 0.002 TRP B 308 HIS 0.013 0.002 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00907 / 0.41 (33764) covalent geometry : angle 0.79634 / 0.40 (45981) hydrogen bonds : bond 0.04126 / 2.75 ( 1405) hydrogen bonds : angle 4.94195 / 3.49 ( 3877) metal coordination : bond 0.01527 / 1.02 ( 32) metal coordination : angle 4.25649 / 2.49 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 305 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8374 (mtt) cc_final: 0.7976 (mtp) REVERT: A 122 MET cc_start: 0.9290 (tpp) cc_final: 0.8544 (tpp) REVERT: A 304 MET cc_start: 0.9463 (mmt) cc_final: 0.8747 (mmt) REVERT: A 470 LEU cc_start: 0.9616 (OUTLIER) cc_final: 0.9186 (pp) REVERT: A 708 MET cc_start: 0.2907 (ttp) cc_final: 0.2471 (tpp) REVERT: A 873 MET cc_start: 0.9019 (mmp) cc_final: 0.8262 (mmp) REVERT: A 1071 SER cc_start: 0.9695 (m) cc_final: 0.9281 (p) REVERT: A 1260 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7329 (mt) REVERT: B 310 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8714 (mtm) REVERT: B 470 LYS cc_start: 0.8136 (mppt) cc_final: 0.7918 (mmtt) REVERT: B 542 MET cc_start: 0.8345 (mtp) cc_final: 0.7817 (mmm) REVERT: B 561 TRP cc_start: 0.8688 (OUTLIER) cc_final: 0.8242 (m-90) REVERT: B 615 MET cc_start: 0.8544 (mpp) cc_final: 0.8143 (mpp) REVERT: B 1072 MET cc_start: 0.8026 (mtp) cc_final: 0.7704 (mtp) REVERT: C 29 MET cc_start: 0.9306 (tpp) cc_final: 0.9051 (tpp) REVERT: C 75 MET cc_start: 0.8812 (mmm) cc_final: 0.8543 (tpp) REVERT: D 50 LEU cc_start: 0.8879 (mt) cc_final: 0.8298 (mt) REVERT: D 57 LEU cc_start: 0.9300 (mt) cc_final: 0.8752 (pp) REVERT: D 140 ASP cc_start: 0.8803 (m-30) cc_final: 0.8103 (t0) REVERT: E 25 ASP cc_start: 0.9244 (m-30) cc_final: 0.8864 (m-30) REVERT: E 32 GLN cc_start: 0.8934 (tp-100) cc_final: 0.8618 (tp-100) REVERT: E 215 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.6608 (tpt) REVERT: F 85 MET cc_start: 0.9165 (tmm) cc_final: 0.8958 (ttt) REVERT: G 44 TYR cc_start: 0.5592 (m-80) cc_final: 0.4872 (m-80) REVERT: G 50 ASP cc_start: 0.8464 (t0) cc_final: 0.8078 (t0) REVERT: G 69 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8020 (tm-30) REVERT: G 158 HIS cc_start: 0.8406 (OUTLIER) cc_final: 0.8036 (t-90) REVERT: H 139 ASN cc_start: 0.8998 (m-40) cc_final: 0.8740 (m-40) REVERT: I 1 MET cc_start: 0.6029 (tpp) cc_final: 0.4923 (tpt) REVERT: J 49 MET cc_start: 0.8966 (mtp) cc_final: 0.8560 (mtm) REVERT: K 22 ASP cc_start: 0.8571 (t0) cc_final: 0.8195 (t0) REVERT: K 49 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8509 (tp30) REVERT: L 56 LEU cc_start: 0.9081 (mm) cc_final: 0.8836 (mm) REVERT: L 63 ARG cc_start: 0.8125 (mtm-85) cc_final: 0.7505 (tpp-160) outliers start: 46 outliers final: 35 residues processed: 339 average time/residue: 0.2123 time to fit residues: 118.1001 Evaluate side-chains 341 residues out of total 3433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 300 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 CYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 790 ASP Chi-restraints excluded: chain A residue 1228 TRP Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 322 PHE Chi-restraints excluded: chain B residue 561 TRP Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 215 MET Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 158 HIS Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain L residue 30 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 380 optimal weight: 3.9990 chunk 150 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 chunk 236 optimal weight: 1.9990 chunk 334 optimal weight: 8.9990 chunk 2 optimal weight: 0.1980 chunk 245 optimal weight: 0.9990 chunk 315 optimal weight: 0.8980 chunk 212 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1062 HIS ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 ASN E 143 ASN ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.087266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.060454 restraints weight = 100737.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.062227 restraints weight = 52536.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.063410 restraints weight = 35282.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.064132 restraints weight = 27652.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.064560 restraints weight = 23933.927| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33796 Z= 0.128 Angle : 0.636 15.132 46026 Z= 0.316 Chirality : 0.044 0.312 5171 Planarity : 0.004 0.052 5620 Dihedral : 16.319 140.136 5293 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.49 % Favored : 96.46 % Rotamer: Outliers : 1.02 % Allowed : 14.94 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.14), residues: 3845 helix: 1.42 (0.14), residues: 1344 sheet: -0.35 (0.21), residues: 584 loop : -0.52 (0.15), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 209 TYR 0.035 0.001 TYR B 830 PHE 0.031 0.001 PHE A1225 TRP 0.022 0.001 TRP B 308 HIS 0.007 0.001 HIS B 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (33764) covalent geometry : angle 0.62783 / 0.32 (45981) hydrogen bonds : bond 0.03517 / 2.36 ( 1405) hydrogen bonds : angle 4.54393 / 3.20 ( 3877) metal coordination : bond 0.00524 / 0.36 ( 32) metal coordination : angle 3.34451 / 2.04 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6010.27 seconds wall clock time: 104 minutes 44.01 seconds (6284.01 seconds total)