Starting phenix.real_space_refine on Tue Sep 15 22:37:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6j4x_0672/09_2026/6j4x_0672.cif Found real_map, /net/cci-nas-00/data/ceres_data/6j4x_0672/09_2026/6j4x_0672.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6j4x_0672/09_2026/6j4x_0672.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6j4x_0672/09_2026/6j4x_0672.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6j4x_0672/09_2026/6j4x_0672.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6j4x_0672/09_2026/6j4x_0672.map" model { file = "/net/cci-nas-00/data/ceres_data/6j4x_0672/09_2026/6j4x_0672.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6j4x_0672/09_2026/6j4x_0672.cif" } resolution = 4.3 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= 0.003 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 10 6.06 5 P 264 5.49 5 Mg 1 5.21 5 S 214 5.16 5 C 28267 2.51 5 N 8207 2.21 5 O 9222 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.17s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 46185 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 11116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1411, 11116 Classifications: {'peptide': 1411} Link IDs: {'PCIS': 3, 'PTRANS': 65, 'TRANS': 1342} Chain breaks: 5 Chain: "B" Number of atoms: 9228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1157, 9228 Classifications: {'peptide': 1157} Link IDs: {'PTRANS': 52, 'TRANS': 1104} Chain breaks: 5 Chain: "C" Number of atoms: 2098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2098 Classifications: {'peptide': 263} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 249} Chain: "D" Number of atoms: 1314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1314 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 4, 'TRANS': 163} Chain breaks: 2 Chain: "E" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1740 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 202} Chain: "F" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 677 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "G" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1324 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 160} Chain: "H" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1052 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain breaks: 1 Chain: "I" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 917 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "J" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 545 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "K" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 932 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} 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: {'PTRANS': 1, 'TRANS': 43} Chain: "P" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 341 Classifications: {'RNAv2': 16} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 7, 'rna3p_pyr': 7} Link IDs: {'rna2p': 2, 'rna3p': 13} Chain: "T" Number of atoms: 2589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 2589 Classifications: {'DNA': 127} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 126} Chain: "N" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 2509 Classifications: {'DNA': 122} Link IDs: {'rna3p': 121} Chain breaks: 1 Chain: "M" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 505 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "V" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 792 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "W" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2226 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 12, 'TRANS': 262} Chain breaks: 4 Chain: "a" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 797 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "b" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "c" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 796 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "d" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "e" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 796 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "f" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "g" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "h" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "V" 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 527 SG CYS A 67 73.577 60.508 140.102 1.00103.22 S ATOM 549 SG CYS A 70 77.057 59.634 141.022 1.00 94.73 S ATOM 594 SG CYS A 77 75.918 63.210 141.554 1.00 74.48 S ATOM 829 SG CYS A 107 77.945 82.686 97.238 1.00142.68 S ATOM 851 SG CYS A 110 79.324 79.340 96.554 1.00152.38 S ATOM 1222 SG CYS A 168 76.038 82.685 94.220 1.00155.44 S ATOM 19876 SG CYS B1163 87.319 60.338 127.387 1.00 76.06 S ATOM 19894 SG CYS B1166 85.470 63.703 126.260 1.00 77.90 S ATOM 20017 SG CYS B1182 83.516 60.195 127.381 1.00108.37 S ATOM 20040 SG CYS B1185 85.716 60.449 124.035 1.00109.59 S ATOM 20985 SG CYS C 85 86.079 75.547 206.827 1.00126.06 S ATOM 21033 SG CYS C 91 81.822 76.415 208.572 1.00108.11 S ATOM 21056 SG CYS C 94 83.315 78.818 205.080 1.00108.09 S ATOM 29164 SG CYS I 78 81.707 166.207 144.902 1.00173.59 S ATOM 29380 SG CYS I 103 81.954 162.577 144.361 1.00166.64 S ATOM 28780 SG CYS I 29 63.593 145.512 104.205 1.00154.71 S ATOM 28805 SG CYS I 32 60.601 147.800 102.574 1.00153.57 S ATOM 29521 SG CYS J 7 87.611 109.099 194.123 1.00 34.60 S ATOM 29544 SG CYS J 10 90.084 108.526 196.764 1.00 33.65 S ATOM 29820 SG CYS J 44 91.024 111.401 194.839 1.00 40.97 S ATOM 29826 SG CYS J 45 88.234 111.352 197.765 1.00 40.49 S ATOM 30988 SG CYS L 33 46.718 94.023 183.252 1.00114.61 S ATOM 31003 SG CYS L 36 44.691 94.373 186.460 1.00124.33 S ATOM 31113 SG CYS L 50 44.100 91.607 183.424 1.00122.63 S ATOM 31137 SG CYS L 53 43.611 95.602 182.322 1.00130.70 S ATOM 36833 SG CYS M 25 52.353 106.665 98.282 1.00198.31 S ATOM 36858 SG CYS M 28 52.687 103.230 97.876 1.00168.76 S ATOM 37016 SG CYS M 49 55.560 104.895 96.820 1.00180.55 S ATOM 37040 SG CYS M 52 52.600 105.042 94.545 1.00191.36 S ATOM 37277 SG CYS V 12 20.540 81.220 119.214 1.00 34.75 S ATOM 37299 SG CYS V 15 21.596 84.072 116.893 1.00 22.76 S ATOM 37401 SG CYS V 29 18.834 84.760 118.886 1.00 18.00 S ATOM 37422 SG CYS V 32 18.415 82.163 116.029 1.00 25.35 S Time building chain proxies: 8.54, per 1000 atoms: 0.18 Number of scatterers: 46185 At special positions: 0 Unit cell: (174.33, 177.31, 232.44, 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 10 29.99 S 214 16.00 P 264 15.00 Mg 1 11.99 O 9222 8.00 N 8207 7.00 C 28267 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.83 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 67 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 168 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 91 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 85 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 78 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 32 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 50 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 53 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 33 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 52 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 25 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 49 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 28 " pdb=" ZN V 300 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 12 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 15 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 29 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 32 " Number of angles added : 33 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9586 Finding SS restraints... Secondary structure from input PDB file: 201 helices and 60 sheets defined 43.1% alpha, 17.3% beta 108 base pairs and 205 stacking pairs defined. Time for finding SS restraints: 6.11 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 95 through 106 removed outlier: 3.652A pdb=" N GLU A 104 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS A 105 " --> pdb=" O LYS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 4.041A pdb=" N ARG A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 204 through 214 removed outlier: 3.559A pdb=" N VAL A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS A 214 " --> pdb=" O ASN A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 223 Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 261 through 279 removed outlier: 3.508A pdb=" N GLN A 278 " --> pdb=" O ASN A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 306 removed outlier: 3.622A pdb=" N MET A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 331 removed outlier: 3.585A pdb=" N LEU A 330 " --> pdb=" O ILE A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 341 Processing helix chain 'A' and resid 369 through 375 Processing helix chain 'A' and resid 385 through 396 removed outlier: 3.608A pdb=" N GLU A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 425 Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 475 through 480 removed outlier: 3.718A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 506 removed outlier: 3.501A pdb=" N ALA A 500 " --> pdb=" O GLU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 511 Processing helix chain 'A' and resid 525 through 536 removed outlier: 3.519A pdb=" N LYS A 534 " --> pdb=" O CYS A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 553 removed outlier: 3.947A pdb=" N ASN A 549 " --> pdb=" O GLU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 583 removed outlier: 3.958A pdb=" N ALA A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 639 through 662 removed outlier: 3.754A pdb=" N PHE A 647 " --> pdb=" O CYS A 643 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 671 Processing helix chain 'A' and resid 673 through 700 removed outlier: 3.583A pdb=" N LYS A 678 " --> pdb=" O ALA A 674 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 738 removed outlier: 3.683A pdb=" N LEU A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 751 Processing helix chain 'A' and resid 755 through 764 removed outlier: 3.589A pdb=" N ILE A 759 " --> pdb=" O SER A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 798 Processing helix chain 'A' and resid 810 through 847 removed outlier: 4.736A pdb=" N ALA A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU A 834 " --> pdb=" O VAL A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 875 through 877 No H-bonds generated for 'chain 'A' and resid 875 through 877' Processing helix chain 'A' and resid 890 through 899 Processing helix chain 'A' and resid 904 through 908 Processing helix chain 'A' and resid 910 through 914 removed outlier: 3.626A pdb=" N VAL A 913 " --> pdb=" O LYS A 910 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A 914 " --> pdb=" O PRO A 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 910 through 914' Processing helix chain 'A' and resid 923 through 947 removed outlier: 3.991A pdb=" N GLU A 929 " --> pdb=" O GLU A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 973 Processing helix chain 'A' and resid 984 through 996 Processing helix chain 'A' and resid 1006 through 1017 removed outlier: 3.632A pdb=" N THR A1017 " --> pdb=" O GLN A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1028 Processing helix chain 'A' and resid 1029 through 1035 Processing helix chain 'A' and resid 1040 through 1058 removed outlier: 3.601A pdb=" N GLN A1056 " --> pdb=" O GLU A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1079 Proline residue: A1077 - end of helix Processing helix chain 'A' and resid 1098 through 1108 removed outlier: 3.594A pdb=" N ARG A1102 " --> pdb=" O LEU A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1128 Processing helix chain 'A' and resid 1129 through 1141 Processing helix chain 'A' and resid 1145 through 1148 No H-bonds generated for 'chain 'A' and resid 1145 through 1148' Processing helix chain 'A' and resid 1168 through 1177 removed outlier: 3.546A pdb=" N ALA A1174 " --> pdb=" O ASP A1170 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER A1177 " --> pdb=" O GLU A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1207 Processing helix chain 'A' and resid 1210 through 1223 removed outlier: 3.726A pdb=" N VAL A1221 " --> pdb=" O LYS A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1272 removed outlier: 3.897A pdb=" N LYS A1264 " --> pdb=" O ASP A1260 " (cutoff:3.500A) Processing helix chain 'A' and resid 1315 through 1321 removed outlier: 3.630A pdb=" N ALA A1321 " --> pdb=" O ALA A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1334 through 1343 removed outlier: 3.565A pdb=" N SER A1340 " --> pdb=" O VAL A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1362 removed outlier: 3.582A pdb=" N SER A1349 " --> pdb=" O GLU A1345 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ASP A1362 " --> pdb=" O VAL A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1380 removed outlier: 4.107A pdb=" N MET A1371 " --> pdb=" O ASN A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1393 Processing helix chain 'A' and resid 1398 through 1404 Processing helix chain 'A' and resid 1407 through 1418 Processing helix chain 'A' and resid 1426 through 1433 removed outlier: 3.665A pdb=" N ASN A1430 " --> pdb=" O GLY A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1439 through 1442 Processing helix chain 'A' and resid 1449 through 1454 removed outlier: 3.699A pdb=" N THR A1454 " --> pdb=" O GLU A1450 " (cutoff:3.500A) Processing helix chain 'A' and resid 1455 through 1456 No H-bonds generated for 'chain 'A' and resid 1455 through 1456' Processing helix chain 'A' and resid 1457 through 1461 removed outlier: 3.591A pdb=" N TYR A1460 " --> pdb=" O PRO A1457 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 29 Processing helix chain 'B' and resid 31 through 44 removed outlier: 3.715A pdb=" N SER B 37 " --> pdb=" O GLN B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 51 Processing helix chain 'B' and resid 100 through 107 Processing helix chain 'B' and resid 176 through 183 removed outlier: 3.602A pdb=" N LEU B 180 " --> pdb=" O ASP B 176 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS B 182 " --> pdb=" O VAL B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 280 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 299 through 312 Proline residue: B 308 - end of helix Processing helix chain 'B' and resid 318 through 328 Processing helix chain 'B' and resid 337 through 351 removed outlier: 3.643A pdb=" N ILE B 342 " --> pdb=" O ARG B 338 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N GLN B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP B 347 " --> pdb=" O GLN B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 383 removed outlier: 4.262A pdb=" N LYS B 367 " --> pdb=" O PHE B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 395 No H-bonds generated for 'chain 'B' and resid 393 through 395' Processing helix chain 'B' and resid 401 through 429 removed outlier: 3.906A pdb=" N ARG B 427 " --> pdb=" O ARG B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 457 Processing helix chain 'B' and resid 461 through 465 Processing helix chain 'B' and resid 480 through 489 removed outlier: 3.563A pdb=" N ARG B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 512 Processing helix chain 'B' and resid 544 through 554 Processing helix chain 'B' and resid 558 through 562 removed outlier: 3.690A pdb=" N TYR B 562 " --> pdb=" O LEU B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 600 removed outlier: 3.851A pdb=" N LEU B 589 " --> pdb=" O ASP B 585 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER B 591 " --> pdb=" O SER B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 658 Processing helix chain 'B' and resid 677 through 683 removed outlier: 3.637A pdb=" N LEU B 681 " --> pdb=" O GLY B 677 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 682 " --> pdb=" O TRP B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 696 removed outlier: 3.699A pdb=" N GLU B 696 " --> pdb=" O GLY B 692 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 692 through 696' Processing helix chain 'B' and resid 703 through 708 removed outlier: 3.577A pdb=" N GLN B 708 " --> pdb=" O GLU B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 Processing helix chain 'B' and resid 752 through 756 Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'B' and resid 763 through 774 removed outlier: 3.907A pdb=" N ASN B 767 " --> pdb=" O GLN B 763 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR B 768 " --> pdb=" O SER B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 777 No H-bonds generated for 'chain 'B' and resid 775 through 777' Processing helix chain 'B' and resid 806 through 811 Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 995 through 999 Processing helix chain 'B' and resid 1013 through 1017 Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.917A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1061 removed outlier: 3.507A pdb=" N LEU B1058 " --> pdb=" O ALA B1054 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1121 through 1125 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1151 Processing helix chain 'B' and resid 1198 through 1210 Processing helix chain 'C' and resid 25 through 39 Processing helix chain 'C' and resid 58 through 68 removed outlier: 3.742A pdb=" N LEU C 68 " --> pdb=" O HIS C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 79 Processing helix chain 'C' and resid 81 through 85 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: 3.696A pdb=" N GLU C 210 " --> pdb=" O ALA C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 266 removed outlier: 3.504A pdb=" N GLU C 263 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG C 266 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 72 removed outlier: 3.577A pdb=" N LEU D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 90 Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 95 through 111 removed outlier: 3.522A pdb=" N VAL D 101 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 129 Processing helix chain 'D' and resid 138 through 148 removed outlier: 3.508A pdb=" N ILE D 142 " --> pdb=" O HIS D 138 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER D 146 " --> pdb=" O ILE D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 160 removed outlier: 3.772A pdb=" N THR D 158 " --> pdb=" O ASP D 154 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 167 removed outlier: 3.913A pdb=" N ALA D 164 " --> pdb=" O PRO D 161 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ALA D 165 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS D 166 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS D 167 " --> pdb=" O ALA D 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 161 through 167' Processing helix chain 'D' and resid 170 through 182 Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 37 through 46 Processing helix chain 'E' and resid 53 through 57 Processing helix chain 'E' and resid 64 through 71 Processing helix chain 'E' and resid 88 through 102 removed outlier: 3.507A pdb=" N ARG E 93 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASN E 94 " --> pdb=" O LYS E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 127 removed outlier: 3.723A pdb=" N ILE E 123 " --> pdb=" O ASN E 120 " (cutoff:3.500A) Proline residue: E 124 - end of helix removed outlier: 4.167A pdb=" N SER E 127 " --> pdb=" O PRO E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 140 Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 156 through 168 Processing helix chain 'E' and resid 170 through 174 removed outlier: 3.507A pdb=" N LEU E 174 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 188 Processing helix chain 'F' and resid 75 through 79 removed outlier: 3.597A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'G' and resid 50 through 54 removed outlier: 3.511A pdb=" N ILE G 54 " --> pdb=" O GLY G 51 " (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 87 through 92 removed outlier: 3.622A pdb=" N ASP H 91 " --> pdb=" O LEU H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 132 Processing helix chain 'H' and resid 133 through 135 No H-bonds generated for 'chain 'H' and resid 133 through 135' Processing helix chain 'I' and resid 61 through 65 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.933A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 61 removed outlier: 3.938A pdb=" N ARG J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 52 removed outlier: 3.954A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU K 49 " --> pdb=" O LEU K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 removed outlier: 3.615A pdb=" N ILE K 111 " --> pdb=" O GLU K 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 78 removed outlier: 3.656A pdb=" N ILE M 69 " --> pdb=" O GLN M 65 " (cutoff:3.500A) Processing helix chain 'V' and resid 20 through 27 removed outlier: 3.724A pdb=" N PHE V 24 " --> pdb=" O PRO V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 32 through 37 Processing helix chain 'V' and resid 42 through 49 Processing helix chain 'V' and resid 66 through 72 Processing helix chain 'V' and resid 91 through 101 Processing helix chain 'W' and resid 213 through 218 removed outlier: 3.884A pdb=" N ILE W 218 " --> pdb=" O ARG W 215 " (cutoff:3.500A) Processing helix chain 'W' and resid 235 through 251 Processing helix chain 'W' and resid 278 through 287 removed outlier: 3.804A pdb=" N ILE W 282 " --> pdb=" O LYS W 278 " (cutoff:3.500A) Processing helix chain 'W' and resid 302 through 304 No H-bonds generated for 'chain 'W' and resid 302 through 304' Processing helix chain 'W' and resid 305 through 310 removed outlier: 3.619A pdb=" N LEU W 309 " --> pdb=" O GLU W 305 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU W 310 " --> pdb=" O TYR W 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 305 through 310' Processing helix chain 'W' and resid 395 through 403 Processing helix chain 'W' and resid 443 through 450 Processing helix chain 'a' and resid 44 through 57 removed outlier: 3.817A pdb=" N LEU a 48 " --> pdb=" O GLY a 44 " (cutoff:3.500A) Processing helix chain 'a' and resid 63 through 76 removed outlier: 3.977A pdb=" N PHE a 67 " --> pdb=" O ARG a 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 114 removed outlier: 3.736A pdb=" N ILE a 89 " --> pdb=" O GLN a 85 " (cutoff:3.500A) Processing helix chain 'a' and resid 120 through 131 removed outlier: 3.854A pdb=" N ILE a 124 " --> pdb=" O MET a 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 24 through 29 Processing helix chain 'b' and resid 30 through 41 Processing helix chain 'b' and resid 50 through 77 Processing helix chain 'b' and resid 82 through 94 Processing helix chain 'c' and resid 17 through 21 Processing helix chain 'c' and resid 26 through 36 removed outlier: 3.608A pdb=" N VAL c 30 " --> pdb=" O PRO c 26 " (cutoff:3.500A) Processing helix chain 'c' and resid 46 through 74 Processing helix chain 'c' and resid 79 through 90 removed outlier: 3.725A pdb=" N LEU c 83 " --> pdb=" O ILE c 79 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP c 90 " --> pdb=" O ALA c 86 " (cutoff:3.500A) Processing helix chain 'c' and resid 90 through 97 Processing helix chain 'c' and resid 112 through 116 Processing helix chain 'd' and resid 34 through 46 Processing helix chain 'd' and resid 52 through 80 Processing helix chain 'd' and resid 87 through 99 removed outlier: 3.665A pdb=" N ILE d 91 " --> pdb=" O THR d 87 " (cutoff:3.500A) Processing helix chain 'd' and resid 100 through 121 removed outlier: 3.901A pdb=" N ALA d 121 " --> pdb=" O LYS d 117 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 55 Processing helix chain 'e' and resid 63 through 76 removed outlier: 3.826A pdb=" N PHE e 67 " --> pdb=" O ARG e 63 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 114 Processing helix chain 'e' and resid 120 through 132 removed outlier: 3.651A pdb=" N ILE e 124 " --> pdb=" O MET e 120 " (cutoff:3.500A) Processing helix chain 'f' and resid 25 through 29 Processing helix chain 'f' and resid 30 through 42 Processing helix chain 'f' and resid 49 through 77 Processing helix chain 'f' and resid 82 through 93 Processing helix chain 'g' and resid 16 through 22 Processing helix chain 'g' and resid 26 through 36 removed outlier: 3.567A pdb=" N VAL g 30 " --> pdb=" O PRO g 26 " (cutoff:3.500A) Processing helix chain 'g' and resid 45 through 72 removed outlier: 4.467A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU g 65 " --> pdb=" O GLU g 61 " (cutoff:3.500A) Processing helix chain 'g' and resid 79 through 90 Processing helix chain 'g' and resid 91 through 97 Processing helix chain 'h' and resid 34 through 46 Processing helix chain 'h' and resid 52 through 82 Processing helix chain 'h' and resid 87 through 99 removed outlier: 3.711A pdb=" N ILE h 91 " --> pdb=" O THR h 87 " (cutoff:3.500A) Processing helix chain 'h' and resid 100 through 121 Processing sheet with id=AA1, first strand: chain 'A' and resid 1421 through 1422 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 91 removed outlier: 6.892A pdb=" N THR A 238 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 10.888A pdb=" N LYS A 88 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 10.402A pdb=" N ILE A 236 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 178 removed outlier: 3.763A pdb=" N GLY A 184 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS A 201 " --> pdb=" O GLY A 184 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N TRP A 186 " --> pdb=" O GLU A 199 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU A 199 " --> pdb=" O TRP A 186 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 251 through 252 removed outlier: 3.589A pdb=" N ILE A 251 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 344 through 346 removed outlier: 3.761A pdb=" N LEU B1128 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.561A pdb=" N SER A 349 " --> pdb=" O ARG B1106 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR A 352 " --> pdb=" O MET A 488 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL A 365 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N MET A 464 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL A 367 " --> pdb=" O MET A 464 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 376 through 380 removed outlier: 3.834A pdb=" N TYR A 405 " --> pdb=" O GLU A 434 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N HIS A 436 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ALA A 403 " --> pdb=" O HIS A 436 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 406 " --> pdb=" O ILE A 414 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 513 through 514 removed outlier: 3.755A pdb=" N LYS A 519 " --> pdb=" O SER A 514 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 541 through 543 Processing sheet with id=AB1, first strand: chain 'A' and resid 566 through 568 removed outlier: 6.466A pdb=" N VAL H 95 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE H 29 " --> pdb=" O THR H 11 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE H 27 " --> pdb=" O GLN H 13 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N LEU H 121 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N LYS H 112 " --> pdb=" O PHE H 103 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N PHE H 103 " --> pdb=" O LYS H 112 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TYR H 114 " --> pdb=" O TYR H 101 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 589 through 591 removed outlier: 7.035A pdb=" N LEU A 607 " --> pdb=" O MET A 614 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 767 through 768 Processing sheet with id=AB4, first strand: chain 'A' and resid 850 through 851 removed outlier: 6.837A pdb=" N THR A 857 " --> pdb=" O ILE A 865 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 879 through 883 Processing sheet with id=AB6, first strand: chain 'A' and resid 1284 through 1295 removed outlier: 4.196A pdb=" N LYS A1284 " --> pdb=" O ASP A1312 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A1118 " --> pdb=" O THR A1311 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1143 through 1144 removed outlier: 7.228A pdb=" N THR A1143 " --> pdb=" O LEU A1276 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1226 through 1230 removed outlier: 3.581A pdb=" N ARG A1243 " --> pdb=" O PHE A1227 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU A1238 " --> pdb=" O LEU A1199 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL A1244 " --> pdb=" O TRP A1193 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N TRP A1193 " --> pdb=" O VAL A1244 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N SER A1150 " --> pdb=" O GLU I 47 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLU I 47 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR A1152 " --> pdb=" O ARG I 45 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ARG I 45 " --> pdb=" O THR A1152 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE A1154 " --> pdb=" O VAL I 43 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1444 through 1448 Processing sheet with id=AC1, first strand: chain 'B' and resid 55 through 57 removed outlier: 5.189A pdb=" N ASP B 118 " --> pdb=" O GLY B 80 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ILE B 82 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N TYR B 116 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N LEU B 84 " --> pdb=" O PRO B 114 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY B 159 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU B 117 " --> pdb=" O HIS B 157 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N HIS B 157 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 88 through 90 Processing sheet with id=AC3, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC4, first strand: chain 'B' and resid 397 through 400 removed outlier: 3.514A pdb=" N ALA B 205 " --> pdb=" O ARG B 490 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 215 through 218 removed outlier: 4.037A pdb=" N HIS B 227 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER B 243 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN B 246 " --> pdb=" O THR B 264 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 537 through 538 Processing sheet with id=AC7, first strand: chain 'B' and resid 537 through 538 Processing sheet with id=AC8, first strand: chain 'B' and resid 578 through 583 removed outlier: 5.767A pdb=" N TRP B 579 " --> pdb=" O VAL B 575 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B 575 " --> pdb=" O TRP B 579 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY B 581 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 792 through 796 removed outlier: 6.881A pdb=" N PHE B 963 " --> pdb=" O LEU B 954 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.801A 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: 6.881A pdb=" N PHE B 963 " --> pdb=" O LEU B 954 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N VAL B 952 " --> pdb=" O LYS L 60 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE L 40 " --> pdb=" O TYR L 31 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD3, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 7.047A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 873 through 874 removed outlier: 3.555A pdb=" N ASP B 936 " --> pdb=" O LEU B 883 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.824A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) 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 1157 through 1163 Processing sheet with id=AD8, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD9, first strand: chain 'C' and resid 6 through 12 removed outlier: 6.870A pdb=" N GLU C 18 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ALA C 12 " --> pdb=" O GLU C 16 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLU C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU C 233 " --> pdb=" O ALA C 175 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.927A pdb=" N GLU C 152 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASN C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASN C 154 " --> pdb=" O LYS C 51 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LYS C 160 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ILE C 45 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLY C 162 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU C 43 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE L 67 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 71 through 73 removed outlier: 4.779A pdb=" N GLU C 131 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 111 through 114 removed outlier: 3.553A pdb=" N CYS C 145 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 4 through 6 removed outlier: 4.643A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TRP G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ILE G 45 " --> pdb=" O TRP G 79 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 50 through 51 removed outlier: 4.521A pdb=" N PHE G 2 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 37 through 39 Processing sheet with id=AE7, first strand: chain 'E' and resid 27 through 28 removed outlier: 4.229A pdb=" N ASN E 62 " --> pdb=" O PHE E 28 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 86 through 87 removed outlier: 3.638A pdb=" N VAL E 87 " --> pdb=" O ASN E 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'E' and resid 152 through 154 Processing sheet with id=AF1, first strand: chain 'G' and resid 169 through 170 removed outlier: 5.866A pdb=" N VAL G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N SER G 162 " --> pdb=" O VAL G 147 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASN G 107 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N GLY G 161 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU G 106 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLY G 98 " --> pdb=" O VAL G 94 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N VAL G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE G 100 " --> pdb=" O SER G 92 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE G 90 " --> pdb=" O ASP G 102 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL G 143 " --> pdb=" O ALA G 89 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 120 through 122 removed outlier: 4.483A pdb=" N VAL G 120 " --> pdb=" O MET G 131 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET G 131 " --> pdb=" O VAL G 120 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA G 129 " --> pdb=" O ASN G 122 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 15 through 19 Processing sheet with id=AF4, first strand: chain 'I' and resid 70 through 71 removed outlier: 3.524A pdb=" N SER I 71 " --> pdb=" O CYS I 83 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N CYS I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF6, first strand: chain 'M' and resid 17 through 20 Processing sheet with id=AF7, first strand: chain 'V' and resid 18 through 19 Processing sheet with id=AF8, first strand: chain 'V' and resid 80 through 86 removed outlier: 7.010A pdb=" N GLY V 56 " --> pdb=" O VAL V 84 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL V 86 " --> pdb=" O PHE V 54 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N PHE V 54 " --> pdb=" O VAL V 86 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU V 57 " --> pdb=" O GLN W 264 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER W 261 " --> pdb=" O GLU W 275 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'W' and resid 407 through 410 removed outlier: 6.541A pdb=" N PHE W 413 " --> pdb=" O ASP W 409 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU W 420 " --> pdb=" O TYR W 427 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LYS W 353 " --> pdb=" O VAL W 340 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N VAL W 340 " --> pdb=" O LYS W 353 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'W' and resid 788 through 792 removed outlier: 6.692A pdb=" N ARG W 779 " --> pdb=" O LYS W 771 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N THR W 755 " --> pdb=" O GLU W 799 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'a' and resid 83 through 84 removed outlier: 6.673A pdb=" N ARG a 83 " --> pdb=" O VAL b 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'c' and resid 77 through 78 Processing sheet with id=AG4, first strand: chain 'e' and resid 83 through 84 removed outlier: 7.328A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.670A pdb=" N ARG g 42 " --> pdb=" O ILE h 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'g' and resid 77 through 78 1857 hydrogen bonds defined for protein. 5145 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 275 hydrogen bonds 546 hydrogen bond angles 0 basepair planarities 108 basepair parallelities 205 stacking parallelities Total time for adding SS restraints: 17.77 Time building geometry restraints manager: 5.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10797 1.33 - 1.45: 10971 1.45 - 1.57: 24917 1.57 - 1.70: 527 1.70 - 1.82: 342 Bond restraints: 47554 Sorted by residual: bond pdb=" C CYS V 29 " pdb=" N PRO V 30 " ideal model delta sigma weight residual 1.335 1.432 -0.098 1.19e-02 7.06e+03 6.75e+01 bond pdb=" CA ILE W 440 " pdb=" C ILE W 440 " ideal model delta sigma weight residual 1.521 1.431 0.090 1.21e-02 6.83e+03 5.52e+01 bond pdb=" C1' DC N -54 " pdb=" N1 DC N -54 " ideal model delta sigma weight residual 1.468 1.570 -0.102 1.40e-02 5.10e+03 5.36e+01 bond pdb=" C1' DG N -37 " pdb=" N9 DG N -37 " ideal model delta sigma weight residual 1.468 1.371 0.097 1.40e-02 5.10e+03 4.81e+01 bond pdb=" C1' DG N -19 " pdb=" N9 DG N -19 " ideal model delta sigma weight residual 1.468 1.376 0.092 1.40e-02 5.10e+03 4.35e+01 ... (remaining 47549 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.98: 64417 3.98 - 7.96: 840 7.96 - 11.94: 69 11.94 - 15.92: 8 15.92 - 19.90: 2 Bond angle restraints: 65336 Sorted by residual: angle pdb=" N GLN B 63 " pdb=" CA GLN B 63 " pdb=" C GLN B 63 " ideal model delta sigma weight residual 108.26 92.33 15.93 1.66e+00 3.63e-01 9.21e+01 angle pdb=" CA PRO W 389 " pdb=" N PRO W 389 " pdb=" CD PRO W 389 " ideal model delta sigma weight residual 112.00 99.51 12.49 1.40e+00 5.10e-01 7.96e+01 angle pdb=" N GLN B 63 " pdb=" CA GLN B 63 " pdb=" CB GLN B 63 " ideal model delta sigma weight residual 110.77 96.80 13.97 1.63e+00 3.76e-01 7.35e+01 angle pdb=" O CYS V 29 " pdb=" C CYS V 29 " pdb=" N PRO V 30 " ideal model delta sigma weight residual 121.31 114.30 7.01 8.50e-01 1.38e+00 6.80e+01 angle pdb=" C ARG W 388 " pdb=" N PRO W 389 " pdb=" CA PRO W 389 " ideal model delta sigma weight residual 119.84 128.69 -8.85 1.25e+00 6.40e-01 5.02e+01 ... (remaining 65331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.97: 26766 34.97 - 69.94: 1477 69.94 - 104.92: 61 104.92 - 139.89: 4 139.89 - 174.86: 1 Dihedral angle restraints: 28309 sinusoidal: 13469 harmonic: 14840 Sorted by residual: dihedral pdb=" C4' U P 0 " pdb=" C3' U P 0 " pdb=" C2' U P 0 " pdb=" C1' U P 0 " ideal model delta sinusoidal sigma weight residual 36.34 -36.71 73.06 1 3.10e+00 1.04e-01 7.08e+02 dihedral pdb=" C4' C P -5 " pdb=" C3' C P -5 " pdb=" C2' C P -5 " pdb=" C1' C P -5 " ideal model delta sinusoidal sigma weight residual 36.35 -36.14 72.49 1 3.10e+00 1.04e-01 6.98e+02 dihedral pdb=" O4' C P -5 " pdb=" C4' C P -5 " pdb=" C3' C P -5 " pdb=" C2' C P -5 " ideal model delta sinusoidal sigma weight residual -35.15 27.75 -62.90 1 4.00e+00 6.25e-02 3.27e+02 ... (remaining 28306 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 6859 0.130 - 0.259: 451 0.259 - 0.389: 12 0.389 - 0.519: 2 0.519 - 0.648: 2 Chirality restraints: 7326 Sorted by residual: chirality pdb=" CA GLN B 63 " pdb=" N GLN B 63 " pdb=" C GLN B 63 " pdb=" CB GLN B 63 " both_signs ideal model delta sigma weight residual False 2.51 3.16 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" CB ILE B 336 " pdb=" CA ILE B 336 " pdb=" CG1 ILE B 336 " pdb=" CG2 ILE B 336 " both_signs ideal model delta sigma weight residual False 2.64 2.05 0.59 2.00e-01 2.50e+01 8.73e+00 chirality pdb=" CA TYR B 811 " pdb=" N TYR B 811 " pdb=" C TYR B 811 " pdb=" CB TYR B 811 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.58e+00 ... (remaining 7323 not shown) Planarity restraints: 7516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 336 " -0.030 2.00e-02 2.50e+03 6.06e-02 3.67e+01 pdb=" C ILE B 336 " 0.105 2.00e-02 2.50e+03 pdb=" O ILE B 336 " -0.039 2.00e-02 2.50e+03 pdb=" N ARG B 337 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 89 " -0.019 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C ASP C 89 " 0.064 2.00e-02 2.50e+03 pdb=" O ASP C 89 " -0.023 2.00e-02 2.50e+03 pdb=" N TYR C 90 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 88 " -0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C GLU C 88 " 0.063 2.00e-02 2.50e+03 pdb=" O GLU C 88 " -0.024 2.00e-02 2.50e+03 pdb=" N ASP C 89 " -0.022 2.00e-02 2.50e+03 ... (remaining 7513 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 113 2.42 - 3.04: 26535 3.04 - 3.66: 69184 3.66 - 4.28: 104166 4.28 - 4.90: 166465 Nonbonded interactions: 366463 Sorted by model distance: nonbonded pdb=" O2 DC T 18 " pdb=" N2 DG N -18 " model vdw 1.803 3.120 nonbonded pdb=" NH1 ARG V 85 " pdb=" OD1 ASP V 87 " model vdw 2.071 3.120 nonbonded pdb=" CD ARG B 337 " pdb=" OE1 GLU M 78 " model vdw 2.125 3.440 nonbonded pdb=" OD1 ASP A 484 " pdb="MG MG A1803 " model vdw 2.148 2.170 nonbonded pdb=" O3' G P 10 " pdb="MG MG A1803 " model vdw 2.158 2.170 ... (remaining 366458 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 Found NCS groups: ncs_group { reference = (chain 'a' and resid 39 through 134) selection = (chain 'e' and resid 39 through 134) } ncs_group { reference = (chain 'b' and resid 25 through 102) selection = chain 'f' } ncs_group { reference = chain 'c' selection = (chain 'g' and resid 16 through 118) } ncs_group { reference = (chain 'd' and resid 31 through 121) selection = chain 'h' } 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: 0.970 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: 0.040 Extract box with map and model: 0.710 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 57.890 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.200 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:1.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6004 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 : 0.012 0.661 47588 Z= 0.609 Angle : 1.273 27.612 65369 Z= 0.774 Chirality : 0.070 0.648 7326 Planarity : 0.007 0.064 7516 Dihedral : 17.805 174.862 18723 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.65 % Allowed : 4.26 % Favored : 95.08 % Rotamer: Outliers : 0.74 % Allowed : 3.13 % Favored : 96.13 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % Twisted Proline : 0.45 % Twisted General : 0.04 % 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: -1.67 (0.11), residues: 5042 helix: -1.28 (0.10), residues: 1854 sheet: -0.74 (0.18), residues: 715 loop : -0.95 (0.12), residues: 2473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 25 TYR 0.050 0.004 TYR d 80 PHE 0.052 0.004 PHE A1176 TRP 0.037 0.004 TRP G 79 HIS 0.014 0.003 HIS f 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00938 / 0.56 (47554) covalent geometry : angle 1.23509 / 0.77 (65336) hydrogen bonds : bond 0.23071 / 15.37 ( 2101) hydrogen bonds : angle 7.32563 / 5.13 ( 5691) metal coordination : bond 0.26232 / 17.16 ( 34) metal coordination : angle 13.81581 / 9.04 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 654 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 347 ASP cc_start: 0.6829 (m-30) cc_final: 0.6608 (m-30) REVERT: A 709 MET cc_start: 0.6841 (mtt) cc_final: 0.6553 (mpp) REVERT: A 844 LYS cc_start: 0.8334 (mmmt) cc_final: 0.7902 (mmmm) REVERT: A 1065 MET cc_start: 0.7846 (mmm) cc_final: 0.7571 (mmm) REVERT: A 1072 GLN cc_start: 0.8251 (mt0) cc_final: 0.7940 (mt0) REVERT: A 1447 MET cc_start: 0.7573 (mmp) cc_final: 0.6336 (mmm) REVERT: B 183 MET cc_start: 0.7202 (mmm) cc_final: 0.6770 (mmp) REVERT: B 302 MET cc_start: 0.8164 (ttm) cc_final: 0.7949 (ttp) REVERT: B 486 SER cc_start: 0.8753 (m) cc_final: 0.8531 (p) REVERT: B 1098 MET cc_start: 0.6819 (mtm) cc_final: 0.6473 (mtp) REVERT: B 1138 MET cc_start: 0.6970 (mmm) cc_final: 0.6735 (mmm) REVERT: C 36 MET cc_start: 0.7437 (mtm) cc_final: 0.7191 (mtm) REVERT: D 46 HIS cc_start: 0.6349 (t-170) cc_final: 0.6109 (t70) REVERT: H 120 LEU cc_start: 0.8231 (mp) cc_final: 0.7971 (tt) REVERT: I 33 ASP cc_start: 0.8228 (m-30) cc_final: 0.7859 (p0) REVERT: I 68 LEU cc_start: 0.8196 (mt) cc_final: 0.7869 (mt) REVERT: W 788 THR cc_start: 0.8426 (m) cc_final: 0.8027 (t) outliers start: 33 outliers final: 7 residues processed: 682 average time/residue: 0.3028 time to fit residues: 333.1553 Evaluate side-chains 330 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 323 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 394 optimal weight: 40.0000 chunk 430 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 265 optimal weight: 6.9990 chunk 523 optimal weight: 6.9990 chunk 497 optimal weight: 20.0000 chunk 414 optimal weight: 40.0000 chunk 310 optimal weight: 6.9990 chunk 488 optimal weight: 8.9990 chunk 366 optimal weight: 5.9990 chunk 223 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 737 ASN ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 GLN B 794 ASN B 887 HIS B 975 GLN B 996 HIS C 13 GLN E 135 GLN E 145 HIS E 178 GLN H 13 GLN J 52 HIS M 29 ASN W 330 ASN W 339 GLN W 434 ASN W 784 ASN ** b 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 73 ASN c 82 HIS c 84 GLN d 64 ASN e 68 GLN ** f 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 31 HIS ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.066524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.045577 restraints weight = 386238.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 74)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.046889 restraints weight = 211504.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.047725 restraints weight = 144517.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.048245 restraints weight = 114067.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.048481 restraints weight = 98702.223| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 47588 Z= 0.242 Angle : 0.813 23.817 65369 Z= 0.424 Chirality : 0.052 1.162 7326 Planarity : 0.005 0.071 7516 Dihedral : 21.815 173.049 8502 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.80 % Favored : 96.97 % Rotamer: Outliers : 0.07 % Allowed : 1.99 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % 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: -0.24 (0.11), residues: 5042 helix: 0.41 (0.11), residues: 1906 sheet: -0.29 (0.18), residues: 732 loop : -0.47 (0.13), residues: 2404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 904 TYR 0.022 0.002 TYR d 80 PHE 0.042 0.002 PHE A1169 TRP 0.019 0.002 TRP B 18 HIS 0.025 0.002 HIS A 787 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.24 (47554) covalent geometry : angle 0.79955 / 0.42 (65336) hydrogen bonds : bond 0.06750 / 4.39 ( 2101) hydrogen bonds : angle 5.30899 / 3.72 ( 5691) metal coordination : bond 0.01367 / 0.77 ( 34) metal coordination : angle 6.61675 / 3.83 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 383 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 22 LEU cc_start: 0.9289 (mt) cc_final: 0.9051 (mt) REVERT: A 324 LYS cc_start: 0.9299 (mppt) cc_final: 0.9055 (mmtm) REVERT: A 464 MET cc_start: 0.9184 (ptm) cc_final: 0.6313 (ptp) REVERT: A 501 GLU cc_start: 0.9053 (tt0) cc_final: 0.8845 (tm-30) REVERT: A 505 LEU cc_start: 0.9524 (mt) cc_final: 0.9214 (tt) REVERT: A 535 MET cc_start: 0.9469 (ttp) cc_final: 0.9176 (ttp) REVERT: A 651 GLN cc_start: 0.9452 (mm-40) cc_final: 0.8720 (mm110) REVERT: A 677 MET cc_start: 0.9052 (mmp) cc_final: 0.8621 (mmp) REVERT: A 844 LYS cc_start: 0.9638 (mmmt) cc_final: 0.9389 (mmmt) REVERT: A 847 GLU cc_start: 0.8791 (pm20) cc_final: 0.8553 (pm20) REVERT: A 1065 MET cc_start: 0.8935 (mmm) cc_final: 0.8516 (mmm) REVERT: A 1447 MET cc_start: 0.8680 (mmp) cc_final: 0.8343 (mmm) REVERT: B 119 MET cc_start: 0.8979 (mmp) cc_final: 0.8428 (mmm) REVERT: B 278 PHE cc_start: 0.9131 (m-80) cc_final: 0.8796 (m-80) REVERT: B 773 MET cc_start: 0.9250 (mtm) cc_final: 0.8534 (ptp) REVERT: B 809 MET cc_start: 0.8626 (mtm) cc_final: 0.8140 (mtt) REVERT: B 812 LEU cc_start: 0.9629 (mt) cc_final: 0.9343 (tt) REVERT: B 839 MET cc_start: 0.8507 (pmm) cc_final: 0.8251 (pmm) REVERT: B 1098 MET cc_start: 0.8471 (mtm) cc_final: 0.8157 (mtp) REVERT: B 1100 ASP cc_start: 0.9222 (p0) cc_final: 0.8797 (p0) REVERT: B 1101 ASP cc_start: 0.9440 (m-30) cc_final: 0.9217 (m-30) REVERT: B 1133 MET cc_start: 0.8831 (mmp) cc_final: 0.8552 (mmp) REVERT: B 1152 MET cc_start: 0.8925 (tpt) cc_final: 0.8570 (tpt) REVERT: B 1208 MET cc_start: 0.9090 (mmm) cc_final: 0.8687 (mmm) REVERT: C 32 LEU cc_start: 0.9257 (tp) cc_final: 0.8697 (tp) REVERT: C 36 MET cc_start: 0.9162 (mtm) cc_final: 0.8750 (mtm) REVERT: C 138 TYR cc_start: 0.8122 (p90) cc_final: 0.7765 (p90) REVERT: D 46 HIS cc_start: 0.7690 (t-170) cc_final: 0.7392 (t70) REVERT: E 57 MET cc_start: 0.8628 (tpt) cc_final: 0.8409 (tpp) REVERT: H 42 ILE cc_start: 0.9245 (pt) cc_final: 0.8905 (mp) REVERT: I 9 GLU cc_start: 0.9233 (tm-30) cc_final: 0.8980 (pt0) REVERT: I 33 ASP cc_start: 0.9318 (m-30) cc_final: 0.8543 (p0) REVERT: J 48 MET cc_start: 0.9345 (mmm) cc_final: 0.9040 (mmm) REVERT: K 35 PHE cc_start: 0.9090 (m-80) cc_final: 0.8813 (m-80) REVERT: M 56 PHE cc_start: 0.5671 (t80) cc_final: 0.5363 (t80) REVERT: W 782 LEU cc_start: 0.9080 (mp) cc_final: 0.8494 (mp) REVERT: h 59 MET cc_start: 0.8637 (mmp) cc_final: 0.8379 (mmm) REVERT: h 76 ARG cc_start: 0.8625 (mpp80) cc_final: 0.8307 (mtp-110) outliers start: 3 outliers final: 0 residues processed: 384 average time/residue: 0.2801 time to fit residues: 176.1981 Evaluate side-chains 271 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 43 optimal weight: 8.9990 chunk 456 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 61.7449 > 50:) chunk 428 optimal weight: 30.0000 chunk 123 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 471 optimal weight: 40.0000 chunk 375 optimal weight: 5.9990 chunk 415 optimal weight: 20.0000 chunk 313 optimal weight: 5.9990 chunk 306 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN A 882 GLN ** A 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 GLN B 359 GLN ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 996 HIS E 31 GLN ** b 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 79 HIS ** e 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 27 GLN ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.065336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.046094 restraints weight = 427901.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.047148 restraints weight = 245404.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.047404 restraints weight = 173512.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.048100 restraints weight = 131891.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.047894 restraints weight = 111982.361| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 47588 Z= 0.246 Angle : 0.755 24.234 65369 Z= 0.392 Chirality : 0.048 0.618 7326 Planarity : 0.005 0.097 7516 Dihedral : 21.737 173.282 8502 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.19 % Favored : 96.57 % Rotamer: Outliers : 0.07 % Allowed : 2.71 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % 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: 0.14 (0.12), residues: 5042 helix: 0.90 (0.12), residues: 1930 sheet: -0.21 (0.19), residues: 731 loop : -0.39 (0.13), residues: 2381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG B1220 TYR 0.030 0.002 TYR G 17 PHE 0.041 0.002 PHE A 445 TRP 0.016 0.002 TRP B 554 HIS 0.015 0.002 HIS G 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.25 (47554) covalent geometry : angle 0.74129 / 0.39 (65336) hydrogen bonds : bond 0.06136 / 3.99 ( 2101) hydrogen bonds : angle 4.96505 / 3.47 ( 5691) metal coordination : bond 0.01371 / 0.75 ( 34) metal coordination : angle 6.52091 / 3.57 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 333 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LEU cc_start: 0.9179 (mt) cc_final: 0.8886 (mp) REVERT: A 146 MET cc_start: 0.8166 (pmm) cc_final: 0.7963 (ppp) REVERT: A 305 MET cc_start: 0.9347 (mmm) cc_final: 0.9125 (mmm) REVERT: A 437 LEU cc_start: 0.9536 (mt) cc_final: 0.9161 (mp) REVERT: A 457 MET cc_start: 0.9195 (mmp) cc_final: 0.8302 (mmm) REVERT: A 464 MET cc_start: 0.9429 (ptm) cc_final: 0.8844 (ptp) REVERT: A 488 MET cc_start: 0.9139 (ttt) cc_final: 0.8784 (ttt) REVERT: A 501 GLU cc_start: 0.8807 (tt0) cc_final: 0.8580 (tm-30) REVERT: A 535 MET cc_start: 0.9445 (ttp) cc_final: 0.9183 (ttp) REVERT: A 651 GLN cc_start: 0.9403 (mm-40) cc_final: 0.8729 (mm110) REVERT: A 677 MET cc_start: 0.9141 (mmp) cc_final: 0.8871 (mmp) REVERT: A 709 MET cc_start: 0.6481 (mtp) cc_final: 0.6171 (ttm) REVERT: A 738 LEU cc_start: 0.9100 (mt) cc_final: 0.8898 (mt) REVERT: A 839 GLN cc_start: 0.9208 (OUTLIER) cc_final: 0.8937 (pm20) REVERT: A 1065 MET cc_start: 0.9109 (mmm) cc_final: 0.8705 (mmm) REVERT: A 1072 GLN cc_start: 0.9270 (mt0) cc_final: 0.8912 (mt0) REVERT: A 1112 ASN cc_start: 0.9443 (p0) cc_final: 0.9233 (p0) REVERT: A 1371 MET cc_start: 0.9108 (mpp) cc_final: 0.8273 (mtm) REVERT: B 89 MET cc_start: 0.9269 (tpt) cc_final: 0.8570 (tpp) REVERT: B 190 MET cc_start: 0.8536 (mmp) cc_final: 0.8129 (mtp) REVERT: B 278 PHE cc_start: 0.9252 (m-80) cc_final: 0.8864 (m-80) REVERT: B 305 MET cc_start: 0.9492 (tpp) cc_final: 0.9169 (tpp) REVERT: B 699 MET cc_start: 0.8545 (tpp) cc_final: 0.8329 (tpp) REVERT: B 773 MET cc_start: 0.9381 (mtm) cc_final: 0.8534 (ptp) REVERT: B 778 MET cc_start: 0.7724 (mtp) cc_final: 0.7469 (mtm) REVERT: B 812 LEU cc_start: 0.9698 (mt) cc_final: 0.9379 (tt) REVERT: B 839 MET cc_start: 0.8495 (pmm) cc_final: 0.8165 (pmm) REVERT: B 968 MET cc_start: 0.8237 (tmm) cc_final: 0.7717 (tmm) REVERT: B 999 MET cc_start: 0.8605 (ttm) cc_final: 0.7823 (ttm) REVERT: B 1021 MET cc_start: 0.9071 (mpp) cc_final: 0.8657 (mpp) REVERT: B 1028 GLU cc_start: 0.8724 (tt0) cc_final: 0.8403 (tm-30) REVERT: B 1082 MET cc_start: 0.8894 (tpt) cc_final: 0.8589 (tpp) REVERT: B 1100 ASP cc_start: 0.9139 (p0) cc_final: 0.8750 (p0) REVERT: B 1101 ASP cc_start: 0.9550 (m-30) cc_final: 0.9264 (m-30) REVERT: B 1133 MET cc_start: 0.9053 (mmp) cc_final: 0.8613 (mmp) REVERT: B 1208 MET cc_start: 0.9151 (mmm) cc_final: 0.8826 (mmm) REVERT: C 20 MET cc_start: 0.9276 (tmm) cc_final: 0.9022 (tmm) REVERT: C 32 LEU cc_start: 0.9220 (tp) cc_final: 0.8483 (tp) REVERT: C 36 MET cc_start: 0.9267 (mtm) cc_final: 0.8592 (mtm) REVERT: C 138 TYR cc_start: 0.8569 (p90) cc_final: 0.8233 (p90) REVERT: D 46 HIS cc_start: 0.7633 (t-170) cc_final: 0.7400 (t70) REVERT: D 120 THR cc_start: 0.8357 (m) cc_final: 0.8148 (p) REVERT: G 85 GLU cc_start: 0.7022 (mm-30) cc_final: 0.5979 (mt-10) REVERT: I 9 GLU cc_start: 0.9335 (tm-30) cc_final: 0.8914 (pt0) REVERT: I 33 ASP cc_start: 0.9340 (m-30) cc_final: 0.8595 (p0) REVERT: J 48 MET cc_start: 0.9433 (mmm) cc_final: 0.9081 (mmm) REVERT: K 35 PHE cc_start: 0.8941 (m-80) cc_final: 0.8626 (m-80) REVERT: M 56 PHE cc_start: 0.5680 (t80) cc_final: 0.5451 (t80) REVERT: a 120 MET cc_start: 0.5938 (mtm) cc_final: 0.5324 (mtt) REVERT: e 120 MET cc_start: 0.7987 (mmm) cc_final: 0.7616 (mmp) REVERT: f 82 THR cc_start: 0.8423 (p) cc_final: 0.8211 (t) REVERT: f 84 MET cc_start: 0.8763 (mmp) cc_final: 0.8531 (mmp) REVERT: h 59 MET cc_start: 0.8901 (mmp) cc_final: 0.8648 (mmm) REVERT: h 76 ARG cc_start: 0.8673 (mpp80) cc_final: 0.8301 (ttp-170) outliers start: 3 outliers final: 0 residues processed: 334 average time/residue: 0.2548 time to fit residues: 142.4100 Evaluate side-chains 246 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 245 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 492 optimal weight: 5.9990 chunk 331 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 248 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 222 optimal weight: 20.0000 chunk 364 optimal weight: 7.9990 chunk 191 optimal weight: 9.9990 chunk 210 optimal weight: 6.9990 chunk 408 optimal weight: 50.0000 chunk 6 optimal weight: 7.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN ** A 787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS D 172 GLN F 100 GLN ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 ASN J 52 HIS ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 65 GLN ** b 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 76 GLN ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.065724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.045678 restraints weight = 426261.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.046939 restraints weight = 227734.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.047720 restraints weight = 153736.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.048278 restraints weight = 120998.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.048567 restraints weight = 104970.222| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 47588 Z= 0.156 Angle : 0.642 22.267 65369 Z= 0.339 Chirality : 0.045 0.458 7326 Planarity : 0.004 0.105 7516 Dihedral : 21.654 172.626 8502 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.90 % Favored : 96.87 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.12), residues: 5042 helix: 1.24 (0.12), residues: 1927 sheet: -0.13 (0.19), residues: 751 loop : -0.24 (0.13), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG A 435 TYR 0.024 0.001 TYR A 37 PHE 0.020 0.001 PHE B 278 TRP 0.014 0.001 TRP C 201 HIS 0.007 0.001 HIS b 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.16 (47554) covalent geometry : angle 0.62926 / 0.34 (65336) hydrogen bonds : bond 0.04819 / 3.10 ( 2101) hydrogen bonds : angle 4.75713 / 3.33 ( 5691) metal coordination : bond 0.00824 / 0.47 ( 34) metal coordination : angle 5.79864 / 3.28 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LEU cc_start: 0.9239 (mt) cc_final: 0.8540 (mp) REVERT: A 146 MET cc_start: 0.8141 (pmm) cc_final: 0.7941 (ppp) REVERT: A 457 MET cc_start: 0.9067 (mmp) cc_final: 0.8121 (mmm) REVERT: A 464 MET cc_start: 0.9284 (ptm) cc_final: 0.9041 (ptm) REVERT: A 488 MET cc_start: 0.9026 (ttt) cc_final: 0.8306 (mtp) REVERT: A 501 GLU cc_start: 0.8959 (tt0) cc_final: 0.8575 (tm-30) REVERT: A 535 MET cc_start: 0.9341 (ttp) cc_final: 0.9052 (ttp) REVERT: A 635 MET cc_start: 0.9211 (tpp) cc_final: 0.8998 (tpp) REVERT: A 677 MET cc_start: 0.9198 (mmp) cc_final: 0.8830 (mmp) REVERT: A 709 MET cc_start: 0.6336 (mtp) cc_final: 0.6033 (ttm) REVERT: A 819 MET cc_start: 0.9393 (mmm) cc_final: 0.9045 (mmt) REVERT: A 850 MET cc_start: 0.8791 (tpt) cc_final: 0.8453 (tpt) REVERT: A 1065 MET cc_start: 0.8920 (mmm) cc_final: 0.8332 (mmm) REVERT: A 1103 LEU cc_start: 0.9666 (tt) cc_final: 0.9247 (pp) REVERT: A 1433 LEU cc_start: 0.9455 (pp) cc_final: 0.8802 (pp) REVERT: A 1435 GLN cc_start: 0.8108 (mt0) cc_final: 0.7753 (mt0) REVERT: B 89 MET cc_start: 0.9260 (tpt) cc_final: 0.8520 (tpp) REVERT: B 119 MET cc_start: 0.8867 (mmp) cc_final: 0.8233 (mmp) REVERT: B 245 MET cc_start: 0.9155 (tmm) cc_final: 0.8947 (tmm) REVERT: B 278 PHE cc_start: 0.9193 (m-80) cc_final: 0.8752 (m-80) REVERT: B 305 MET cc_start: 0.9485 (tpp) cc_final: 0.9201 (tpp) REVERT: B 699 MET cc_start: 0.8567 (tpp) cc_final: 0.7965 (tpp) REVERT: B 773 MET cc_start: 0.9266 (mtm) cc_final: 0.8418 (ptp) REVERT: B 839 MET cc_start: 0.8557 (pmm) cc_final: 0.8251 (pmm) REVERT: B 968 MET cc_start: 0.8268 (tmm) cc_final: 0.7763 (tmm) REVERT: B 999 MET cc_start: 0.8536 (ttm) cc_final: 0.7904 (ttm) REVERT: B 1028 GLU cc_start: 0.8744 (tt0) cc_final: 0.8357 (tm-30) REVERT: B 1098 MET cc_start: 0.8368 (mtm) cc_final: 0.7344 (mpp) REVERT: B 1100 ASP cc_start: 0.9063 (p0) cc_final: 0.8668 (p0) REVERT: B 1101 ASP cc_start: 0.9485 (m-30) cc_final: 0.8697 (m-30) REVERT: B 1133 MET cc_start: 0.9069 (mmp) cc_final: 0.8737 (mmp) REVERT: B 1152 MET cc_start: 0.8889 (tpt) cc_final: 0.8586 (tpt) REVERT: C 32 LEU cc_start: 0.9156 (tp) cc_final: 0.8119 (tp) REVERT: C 36 MET cc_start: 0.9154 (mtm) cc_final: 0.8380 (mtm) REVERT: C 138 TYR cc_start: 0.8395 (p90) cc_final: 0.8041 (p90) REVERT: E 57 MET cc_start: 0.8351 (mmm) cc_final: 0.7948 (tpp) REVERT: F 103 MET cc_start: 0.9526 (tpp) cc_final: 0.9126 (tpp) REVERT: G 52 MET cc_start: 0.9047 (mmp) cc_final: 0.8786 (mmp) REVERT: G 85 GLU cc_start: 0.6850 (mm-30) cc_final: 0.5896 (mt-10) REVERT: I 9 GLU cc_start: 0.9216 (tm-30) cc_final: 0.8813 (pt0) REVERT: I 33 ASP cc_start: 0.8902 (m-30) cc_final: 0.8236 (p0) REVERT: J 48 MET cc_start: 0.9491 (mmm) cc_final: 0.8990 (mmm) REVERT: K 35 PHE cc_start: 0.8974 (m-80) cc_final: 0.8727 (m-80) REVERT: a 120 MET cc_start: 0.5943 (mtm) cc_final: 0.5326 (mtt) REVERT: e 120 MET cc_start: 0.8160 (mmm) cc_final: 0.7730 (mmp) REVERT: h 59 MET cc_start: 0.8775 (mmp) cc_final: 0.8467 (mmm) outliers start: 0 outliers final: 0 residues processed: 320 average time/residue: 0.2405 time to fit residues: 130.4298 Evaluate side-chains 244 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 306 optimal weight: 0.7980 chunk 409 optimal weight: 50.0000 chunk 119 optimal weight: 0.8980 chunk 248 optimal weight: 9.9990 chunk 512 optimal weight: 50.0000 chunk 438 optimal weight: 40.0000 chunk 267 optimal weight: 10.0000 chunk 275 optimal weight: 0.2980 chunk 101 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 274 optimal weight: 8.9990 overall best weight: 4.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 GLN A 511 GLN ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN A 961 ASN ** A 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1112 ASN A1190 GLN ** A1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 GLN F 100 GLN ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.064178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.043399 restraints weight = 398886.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.044644 restraints weight = 218575.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.045457 restraints weight = 149926.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.045964 restraints weight = 118561.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.046077 restraints weight = 102928.836| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 47588 Z= 0.173 Angle : 0.644 21.005 65369 Z= 0.337 Chirality : 0.044 0.356 7326 Planarity : 0.004 0.061 7516 Dihedral : 21.573 172.771 8502 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.09 % Favored : 96.71 % Rotamer: Outliers : 0.04 % Allowed : 1.59 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % 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: 0.61 (0.12), residues: 5042 helix: 1.39 (0.12), residues: 1924 sheet: -0.11 (0.19), residues: 741 loop : -0.15 (0.13), residues: 2377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG A 200 TYR 0.043 0.002 TYR C 81 PHE 0.024 0.002 PHE B 169 TRP 0.013 0.001 TRP A 139 HIS 0.007 0.001 HIS A 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 (47554) covalent geometry : angle 0.63283 / 0.34 (65336) hydrogen bonds : bond 0.04767 / 3.08 ( 2101) hydrogen bonds : angle 4.60704 / 3.21 ( 5691) metal coordination : bond 0.00883 / 0.49 ( 34) metal coordination : angle 5.46707 / 3.01 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 298 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LEU cc_start: 0.9075 (mt) cc_final: 0.8616 (mp) REVERT: A 84 MET cc_start: 0.8648 (tpp) cc_final: 0.8227 (tpp) REVERT: A 139 TRP cc_start: 0.8946 (t60) cc_final: 0.8711 (t-100) REVERT: A 305 MET cc_start: 0.9444 (mmm) cc_final: 0.9238 (mmm) REVERT: A 456 MET cc_start: 0.8870 (ttp) cc_final: 0.8473 (ttp) REVERT: A 457 MET cc_start: 0.8911 (mmp) cc_final: 0.8009 (mmm) REVERT: A 464 MET cc_start: 0.9315 (ptm) cc_final: 0.9031 (ptm) REVERT: A 501 GLU cc_start: 0.9048 (tt0) cc_final: 0.8769 (mt-10) REVERT: A 505 LEU cc_start: 0.9531 (mp) cc_final: 0.9046 (tt) REVERT: A 535 MET cc_start: 0.9263 (ttp) cc_final: 0.8938 (ttp) REVERT: A 651 GLN cc_start: 0.9301 (mm-40) cc_final: 0.8602 (mm110) REVERT: A 677 MET cc_start: 0.9175 (mmp) cc_final: 0.8882 (mmp) REVERT: A 819 MET cc_start: 0.9333 (mmm) cc_final: 0.8821 (mmt) REVERT: A 827 ASP cc_start: 0.9207 (m-30) cc_final: 0.8864 (m-30) REVERT: A 839 GLN cc_start: 0.9192 (pm20) cc_final: 0.8841 (pm20) REVERT: A 850 MET cc_start: 0.8799 (tpt) cc_final: 0.8492 (tpt) REVERT: A 1065 MET cc_start: 0.8971 (mmm) cc_final: 0.8475 (mmm) REVERT: A 1074 ILE cc_start: 0.9384 (mm) cc_final: 0.9112 (tp) REVERT: B 89 MET cc_start: 0.9193 (tpt) cc_final: 0.8422 (tpp) REVERT: B 119 MET cc_start: 0.8863 (mmp) cc_final: 0.8193 (mmp) REVERT: B 190 MET cc_start: 0.8497 (mmp) cc_final: 0.8084 (mtp) REVERT: B 278 PHE cc_start: 0.9198 (m-80) cc_final: 0.8899 (m-80) REVERT: B 305 MET cc_start: 0.9331 (tpp) cc_final: 0.9042 (mmm) REVERT: B 699 MET cc_start: 0.8531 (tpp) cc_final: 0.7906 (tpp) REVERT: B 773 MET cc_start: 0.9188 (mtm) cc_final: 0.8379 (ptp) REVERT: B 968 MET cc_start: 0.8134 (tmm) cc_final: 0.7622 (tmm) REVERT: B 999 MET cc_start: 0.8649 (ttm) cc_final: 0.8331 (ttm) REVERT: B 1028 GLU cc_start: 0.8724 (tt0) cc_final: 0.8341 (tm-30) REVERT: B 1098 MET cc_start: 0.8347 (mtm) cc_final: 0.7873 (mpp) REVERT: B 1100 ASP cc_start: 0.9011 (p0) cc_final: 0.8632 (p0) REVERT: B 1101 ASP cc_start: 0.9453 (m-30) cc_final: 0.9155 (m-30) REVERT: B 1124 ARG cc_start: 0.8645 (mtt180) cc_final: 0.8366 (mmm-85) REVERT: B 1133 MET cc_start: 0.9109 (mmp) cc_final: 0.8682 (mmp) REVERT: C 32 LEU cc_start: 0.9083 (tp) cc_final: 0.7991 (tp) REVERT: C 36 MET cc_start: 0.9126 (mtm) cc_final: 0.8358 (mtm) REVERT: C 59 ASP cc_start: 0.8849 (p0) cc_final: 0.8585 (p0) REVERT: C 138 TYR cc_start: 0.8480 (p90) cc_final: 0.8211 (p90) REVERT: F 103 MET cc_start: 0.9494 (tpp) cc_final: 0.9232 (tpp) REVERT: G 85 GLU cc_start: 0.6914 (mm-30) cc_final: 0.5972 (mt-10) REVERT: H 96 MET cc_start: 0.8453 (mtm) cc_final: 0.8144 (mmp) REVERT: I 9 GLU cc_start: 0.9251 (tm-30) cc_final: 0.8755 (pt0) REVERT: I 33 ASP cc_start: 0.8822 (m-30) cc_final: 0.8084 (p0) REVERT: J 48 MET cc_start: 0.9557 (mmm) cc_final: 0.9123 (mmm) REVERT: K 35 PHE cc_start: 0.8999 (m-80) cc_final: 0.8751 (m-80) REVERT: a 120 MET cc_start: 0.5989 (mtm) cc_final: 0.5370 (mtt) REVERT: e 120 MET cc_start: 0.8340 (mmm) cc_final: 0.7932 (mmt) REVERT: h 59 MET cc_start: 0.8807 (mmp) cc_final: 0.8478 (mmm) REVERT: h 76 ARG cc_start: 0.8390 (mpp-170) cc_final: 0.7630 (ttp-170) outliers start: 2 outliers final: 0 residues processed: 299 average time/residue: 0.2345 time to fit residues: 119.3153 Evaluate side-chains 241 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 451 optimal weight: 50.0000 chunk 397 optimal weight: 50.0000 chunk 412 optimal weight: 50.0000 chunk 486 optimal weight: 7.9990 chunk 263 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 353 optimal weight: 0.9990 chunk 379 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 212 optimal weight: 2.9990 chunk 464 optimal weight: 50.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 GLN A 291 ASN A 300 HIS ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN A 961 ASN ** A 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1208 GLN ** A1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 ASN ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 GLN I 12 ASN I 89 GLN ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 774 ASN h 46 HIS ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.063231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.042475 restraints weight = 395505.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.043721 restraints weight = 220059.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.044498 restraints weight = 151391.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.044987 restraints weight = 120069.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.045208 restraints weight = 104791.683| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 47588 Z= 0.195 Angle : 0.651 20.671 65369 Z= 0.340 Chirality : 0.044 0.301 7326 Planarity : 0.004 0.091 7516 Dihedral : 21.568 173.336 8502 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.33 % Favored : 96.51 % Rotamer: Outliers : 0.04 % Allowed : 1.28 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % 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: 0.64 (0.12), residues: 5042 helix: 1.44 (0.12), residues: 1925 sheet: -0.13 (0.18), residues: 746 loop : -0.14 (0.13), residues: 2371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG W 779 TYR 0.032 0.001 TYR B1092 PHE 0.022 0.002 PHE B 100 TRP 0.013 0.001 TRP B 554 HIS 0.007 0.001 HIS A 660 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.20 (47554) covalent geometry : angle 0.63806 / 0.34 (65336) hydrogen bonds : bond 0.04825 / 3.12 ( 2101) hydrogen bonds : angle 4.62310 / 3.23 ( 5691) metal coordination : bond 0.01328 / 0.82 ( 34) metal coordination : angle 5.85443 / 3.24 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 293 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LEU cc_start: 0.9093 (mt) cc_final: 0.8251 (mp) REVERT: A 84 MET cc_start: 0.8666 (tpp) cc_final: 0.8189 (tpp) REVERT: A 457 MET cc_start: 0.8954 (mmp) cc_final: 0.8023 (mmm) REVERT: A 464 MET cc_start: 0.9230 (ptm) cc_final: 0.8934 (ptm) REVERT: A 501 GLU cc_start: 0.9144 (tt0) cc_final: 0.8578 (tm-30) REVERT: A 535 MET cc_start: 0.9272 (ttp) cc_final: 0.8985 (ttp) REVERT: A 677 MET cc_start: 0.9189 (mmp) cc_final: 0.8938 (mmp) REVERT: A 709 MET cc_start: 0.7084 (mmm) cc_final: 0.6531 (ttm) REVERT: A 819 MET cc_start: 0.9274 (mmm) cc_final: 0.8783 (mmt) REVERT: A 827 ASP cc_start: 0.9223 (m-30) cc_final: 0.8865 (m-30) REVERT: A 839 GLN cc_start: 0.9411 (pm20) cc_final: 0.9143 (pm20) REVERT: A 850 MET cc_start: 0.8816 (tpt) cc_final: 0.8576 (tpt) REVERT: A 1065 MET cc_start: 0.9030 (mmm) cc_final: 0.8586 (mmm) REVERT: A 1074 ILE cc_start: 0.9389 (mm) cc_final: 0.9141 (tp) REVERT: B 89 MET cc_start: 0.9186 (tpt) cc_final: 0.8637 (tpp) REVERT: B 164 MET cc_start: 0.8695 (ttp) cc_final: 0.8131 (ttt) REVERT: B 245 MET cc_start: 0.9244 (tmm) cc_final: 0.8962 (tmm) REVERT: B 278 PHE cc_start: 0.9209 (m-80) cc_final: 0.8903 (m-80) REVERT: B 305 MET cc_start: 0.9349 (tpp) cc_final: 0.9049 (mmm) REVERT: B 699 MET cc_start: 0.8481 (tpp) cc_final: 0.7863 (tpp) REVERT: B 773 MET cc_start: 0.9181 (mtm) cc_final: 0.8307 (ptp) REVERT: B 968 MET cc_start: 0.8254 (tmm) cc_final: 0.7736 (tmm) REVERT: B 999 MET cc_start: 0.8711 (ttm) cc_final: 0.8081 (ttp) REVERT: B 1028 GLU cc_start: 0.8778 (tt0) cc_final: 0.8323 (tm-30) REVERT: B 1098 MET cc_start: 0.8285 (mtm) cc_final: 0.7803 (mpp) REVERT: B 1100 ASP cc_start: 0.8974 (p0) cc_final: 0.8635 (p0) REVERT: B 1101 ASP cc_start: 0.9421 (m-30) cc_final: 0.9135 (m-30) REVERT: B 1133 MET cc_start: 0.9270 (mmp) cc_final: 0.8730 (mmp) REVERT: B 1152 MET cc_start: 0.9128 (tpt) cc_final: 0.8797 (tpt) REVERT: B 1208 MET cc_start: 0.9223 (mmt) cc_final: 0.8952 (mmm) REVERT: B 1210 MET cc_start: 0.9346 (mtm) cc_final: 0.8905 (mtm) REVERT: C 32 LEU cc_start: 0.9063 (tp) cc_final: 0.8007 (tp) REVERT: C 36 MET cc_start: 0.9178 (mtm) cc_final: 0.8478 (mtm) REVERT: C 59 ASP cc_start: 0.8873 (p0) cc_final: 0.8614 (p0) REVERT: F 103 MET cc_start: 0.9505 (tpp) cc_final: 0.9279 (tpp) REVERT: G 85 GLU cc_start: 0.6939 (mm-30) cc_final: 0.6016 (mt-10) REVERT: I 33 ASP cc_start: 0.8951 (m-30) cc_final: 0.8215 (p0) REVERT: I 61 ASP cc_start: 0.4867 (m-30) cc_final: 0.4360 (m-30) REVERT: I 64 GLN cc_start: 0.8109 (mp10) cc_final: 0.7791 (mp10) REVERT: J 48 MET cc_start: 0.9575 (mmm) cc_final: 0.9147 (mmm) REVERT: K 35 PHE cc_start: 0.8815 (m-80) cc_final: 0.8595 (m-80) REVERT: a 120 MET cc_start: 0.6017 (mtm) cc_final: 0.5393 (mtt) REVERT: e 120 MET cc_start: 0.8505 (mmm) cc_final: 0.8150 (mmt) REVERT: h 56 MET cc_start: 0.0647 (tmm) cc_final: -0.0177 (tpp) REVERT: h 59 MET cc_start: 0.8712 (mmp) cc_final: 0.8265 (mmm) REVERT: h 76 ARG cc_start: 0.8449 (mpp-170) cc_final: 0.7602 (ttp-170) outliers start: 2 outliers final: 0 residues processed: 295 average time/residue: 0.2248 time to fit residues: 111.9249 Evaluate side-chains 240 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 40 optimal weight: 8.9990 chunk 390 optimal weight: 50.0000 chunk 116 optimal weight: 6.9990 chunk 512 optimal weight: 7.9990 chunk 392 optimal weight: 50.0000 chunk 215 optimal weight: 0.6980 chunk 256 optimal weight: 20.0000 chunk 355 optimal weight: 20.0000 chunk 140 optimal weight: 0.4980 chunk 425 optimal weight: 40.0000 chunk 476 optimal weight: 30.0000 overall best weight: 5.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN A 961 ASN ** A 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 GLN A1435 GLN B 64 HIS ** B 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 GLN ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 78 GLN ** h 81 ASN ** 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 = 0.3741 r_free = 0.3741 target = 0.062845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.042104 restraints weight = 398214.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.043291 restraints weight = 221726.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.044068 restraints weight = 153187.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.044586 restraints weight = 121596.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.044805 restraints weight = 105340.242| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 47588 Z= 0.186 Angle : 0.640 19.311 65369 Z= 0.335 Chirality : 0.044 0.270 7326 Planarity : 0.004 0.068 7516 Dihedral : 21.557 173.567 8502 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.51 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % 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: 0.63 (0.12), residues: 5042 helix: 1.46 (0.12), residues: 1935 sheet: -0.28 (0.18), residues: 753 loop : -0.12 (0.13), residues: 2354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG h 76 TYR 0.021 0.001 TYR B 344 PHE 0.022 0.002 PHE H 97 TRP 0.018 0.002 TRP B 678 HIS 0.006 0.001 HIS b 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.19 (47554) covalent geometry : angle 0.62792 / 0.33 (65336) hydrogen bonds : bond 0.04692 / 3.02 ( 2101) hydrogen bonds : angle 4.55927 / 3.19 ( 5691) metal coordination : bond 0.01174 / 0.72 ( 34) metal coordination : angle 5.63998 / 3.16 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 22 LEU cc_start: 0.9146 (mt) cc_final: 0.8520 (mp) REVERT: A 41 MET cc_start: 0.4049 (tpt) cc_final: 0.3643 (tpt) REVERT: A 84 MET cc_start: 0.8802 (tpp) cc_final: 0.8406 (tpp) REVERT: A 108 MET cc_start: 0.8590 (ppp) cc_final: 0.8388 (ppp) REVERT: A 139 TRP cc_start: 0.8828 (t60) cc_final: 0.8622 (t-100) REVERT: A 305 MET cc_start: 0.9504 (mmm) cc_final: 0.9301 (mmm) REVERT: A 457 MET cc_start: 0.8921 (mmp) cc_final: 0.7959 (mmm) REVERT: A 464 MET cc_start: 0.9347 (ptm) cc_final: 0.8957 (ptm) REVERT: A 501 GLU cc_start: 0.9128 (tt0) cc_final: 0.8777 (mt-10) REVERT: A 535 MET cc_start: 0.9289 (ttp) cc_final: 0.8972 (ttp) REVERT: A 651 GLN cc_start: 0.9328 (mm-40) cc_final: 0.8739 (mm-40) REVERT: A 677 MET cc_start: 0.9242 (mmp) cc_final: 0.9040 (mmp) REVERT: A 738 LEU cc_start: 0.9062 (mt) cc_final: 0.8854 (mt) REVERT: A 762 MET cc_start: 0.9250 (mmt) cc_final: 0.8565 (mmt) REVERT: A 819 MET cc_start: 0.9267 (mmm) cc_final: 0.8758 (mmt) REVERT: A 827 ASP cc_start: 0.9255 (m-30) cc_final: 0.8877 (m-30) REVERT: A 1074 ILE cc_start: 0.9411 (mm) cc_final: 0.9144 (tp) REVERT: B 89 MET cc_start: 0.9196 (tpt) cc_final: 0.8607 (tpp) REVERT: B 164 MET cc_start: 0.8590 (ttp) cc_final: 0.8340 (ttp) REVERT: B 190 MET cc_start: 0.8600 (mmp) cc_final: 0.8038 (mtp) REVERT: B 245 MET cc_start: 0.9194 (tmm) cc_final: 0.8868 (tmm) REVERT: B 278 PHE cc_start: 0.9208 (m-80) cc_final: 0.8885 (m-80) REVERT: B 305 MET cc_start: 0.9394 (tpp) cc_final: 0.9072 (mmm) REVERT: B 699 MET cc_start: 0.8470 (tpp) cc_final: 0.7848 (tpp) REVERT: B 773 MET cc_start: 0.9189 (mtm) cc_final: 0.8348 (ptp) REVERT: B 968 MET cc_start: 0.8267 (tmm) cc_final: 0.7764 (tmm) REVERT: B 999 MET cc_start: 0.8722 (ttm) cc_final: 0.8172 (ttm) REVERT: B 1021 MET cc_start: 0.9299 (mmt) cc_final: 0.8426 (mmp) REVERT: B 1028 GLU cc_start: 0.8708 (tt0) cc_final: 0.8325 (tm-30) REVERT: B 1098 MET cc_start: 0.8302 (mtm) cc_final: 0.7797 (mpp) REVERT: B 1100 ASP cc_start: 0.8950 (p0) cc_final: 0.8651 (p0) REVERT: B 1101 ASP cc_start: 0.9295 (m-30) cc_final: 0.8963 (m-30) REVERT: B 1133 MET cc_start: 0.9313 (mmp) cc_final: 0.8759 (mmp) REVERT: B 1138 MET cc_start: 0.9101 (tpp) cc_final: 0.8859 (tpp) REVERT: B 1152 MET cc_start: 0.8969 (tpt) cc_final: 0.8580 (tpt) REVERT: B 1208 MET cc_start: 0.9177 (mmt) cc_final: 0.8784 (mmm) REVERT: C 32 LEU cc_start: 0.9064 (tp) cc_final: 0.8059 (tp) REVERT: C 36 MET cc_start: 0.9156 (mtm) cc_final: 0.8465 (mtm) REVERT: C 59 ASP cc_start: 0.8860 (p0) cc_final: 0.8605 (p0) REVERT: C 244 PHE cc_start: 0.8897 (t80) cc_final: 0.8160 (t80) REVERT: F 103 MET cc_start: 0.9560 (tpp) cc_final: 0.9295 (tpp) REVERT: G 85 GLU cc_start: 0.6944 (mm-30) cc_final: 0.6028 (mt-10) REVERT: H 96 MET cc_start: 0.8804 (mtm) cc_final: 0.8384 (mtp) REVERT: I 33 ASP cc_start: 0.8919 (m-30) cc_final: 0.8170 (p0) REVERT: I 61 ASP cc_start: 0.4937 (m-30) cc_final: 0.4565 (m-30) REVERT: J 1 MET cc_start: 0.9051 (ptp) cc_final: 0.8606 (pmm) REVERT: J 48 MET cc_start: 0.9590 (mmm) cc_final: 0.9201 (mmm) REVERT: a 120 MET cc_start: 0.6037 (mtm) cc_final: 0.5416 (mtt) REVERT: e 120 MET cc_start: 0.8479 (mmm) cc_final: 0.8142 (mmt) REVERT: h 59 MET cc_start: 0.8718 (mmp) cc_final: 0.8312 (mmp) outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.2042 time to fit residues: 100.8412 Evaluate side-chains 235 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 80 optimal weight: 9.9990 chunk 518 optimal weight: 0.0030 chunk 401 optimal weight: 40.0000 chunk 150 optimal weight: 9.9990 chunk 118 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 193 optimal weight: 2.9990 chunk 131 optimal weight: 8.9990 chunk 301 optimal weight: 4.9990 chunk 44 optimal weight: 20.0000 chunk 63 optimal weight: 7.9990 overall best weight: 4.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN A 882 GLN A 961 ASN ** A 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 GLN ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 GLN W 786 ASN c 84 GLN d 64 ASN ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.063722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.043827 restraints weight = 434995.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.045049 restraints weight = 235004.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.045837 restraints weight = 159377.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.046288 restraints weight = 125945.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.046641 restraints weight = 109690.008| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 47588 Z= 0.164 Angle : 0.620 19.071 65369 Z= 0.325 Chirality : 0.044 0.273 7326 Planarity : 0.004 0.122 7516 Dihedral : 21.522 173.675 8502 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.35 % Favored : 96.59 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.12), residues: 5042 helix: 1.54 (0.12), residues: 1936 sheet: -0.33 (0.19), residues: 744 loop : -0.07 (0.14), residues: 2362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 97 TYR 0.035 0.001 TYR B1092 PHE 0.026 0.001 PHE A 445 TRP 0.013 0.001 TRP A 956 HIS 0.012 0.001 HIS C 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (47554) covalent geometry : angle 0.60870 / 0.32 (65336) hydrogen bonds : bond 0.04457 / 2.88 ( 2101) hydrogen bonds : angle 4.50026 / 3.15 ( 5691) metal coordination : bond 0.00933 / 0.55 ( 34) metal coordination : angle 5.33654 / 2.98 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LEU cc_start: 0.9145 (mt) cc_final: 0.8211 (mp) REVERT: A 41 MET cc_start: 0.3984 (tpt) cc_final: 0.3631 (tpt) REVERT: A 108 MET cc_start: 0.8543 (ppp) cc_final: 0.8318 (ppp) REVERT: A 139 TRP cc_start: 0.8738 (t60) cc_final: 0.8399 (t-100) REVERT: A 305 MET cc_start: 0.9494 (mmm) cc_final: 0.9111 (mmm) REVERT: A 456 MET cc_start: 0.8836 (ttp) cc_final: 0.8468 (ttp) REVERT: A 457 MET cc_start: 0.8920 (mmp) cc_final: 0.7948 (mmm) REVERT: A 464 MET cc_start: 0.9413 (ptm) cc_final: 0.8865 (ptm) REVERT: A 501 GLU cc_start: 0.9103 (tt0) cc_final: 0.8623 (mt-10) REVERT: A 535 MET cc_start: 0.9288 (ttp) cc_final: 0.8961 (ttp) REVERT: A 677 MET cc_start: 0.9239 (mmp) cc_final: 0.9037 (mmp) REVERT: A 762 MET cc_start: 0.9249 (mmt) cc_final: 0.8092 (mmt) REVERT: A 819 MET cc_start: 0.9270 (mmm) cc_final: 0.8758 (mmt) REVERT: A 827 ASP cc_start: 0.9259 (m-30) cc_final: 0.8882 (m-30) REVERT: A 1074 ILE cc_start: 0.9429 (mm) cc_final: 0.9166 (tp) REVERT: A 1414 GLU cc_start: 0.9552 (mm-30) cc_final: 0.9320 (mm-30) REVERT: B 89 MET cc_start: 0.9076 (tpt) cc_final: 0.8478 (tpp) REVERT: B 164 MET cc_start: 0.8616 (ttp) cc_final: 0.8392 (ttp) REVERT: B 190 MET cc_start: 0.8711 (mmp) cc_final: 0.8116 (mtp) REVERT: B 245 MET cc_start: 0.9238 (tmm) cc_final: 0.8922 (tmm) REVERT: B 278 PHE cc_start: 0.9231 (m-80) cc_final: 0.8907 (m-80) REVERT: B 305 MET cc_start: 0.9392 (tpp) cc_final: 0.9090 (mmm) REVERT: B 699 MET cc_start: 0.8479 (tpp) cc_final: 0.7834 (tpp) REVERT: B 773 MET cc_start: 0.9298 (mtm) cc_final: 0.8362 (ptp) REVERT: B 789 MET cc_start: 0.8998 (mmm) cc_final: 0.8492 (mmp) REVERT: B 839 MET cc_start: 0.8904 (pmm) cc_final: 0.8702 (pmm) REVERT: B 968 MET cc_start: 0.8284 (tmm) cc_final: 0.7787 (tmm) REVERT: B 999 MET cc_start: 0.8725 (ttm) cc_final: 0.8083 (ttm) REVERT: B 1021 MET cc_start: 0.9412 (mmt) cc_final: 0.8299 (mmp) REVERT: B 1028 GLU cc_start: 0.8785 (tt0) cc_final: 0.8340 (tm-30) REVERT: B 1098 MET cc_start: 0.8269 (mtm) cc_final: 0.7776 (mpp) REVERT: B 1100 ASP cc_start: 0.8906 (p0) cc_final: 0.8645 (p0) REVERT: B 1101 ASP cc_start: 0.9288 (m-30) cc_final: 0.8960 (m-30) REVERT: B 1133 MET cc_start: 0.9351 (mmp) cc_final: 0.8781 (mmp) REVERT: B 1138 MET cc_start: 0.9144 (tpp) cc_final: 0.8908 (tpp) REVERT: B 1152 MET cc_start: 0.9041 (tpt) cc_final: 0.8662 (tpt) REVERT: B 1208 MET cc_start: 0.9220 (mmt) cc_final: 0.8942 (mmm) REVERT: B 1210 MET cc_start: 0.9155 (mtm) cc_final: 0.8883 (mtm) REVERT: C 32 LEU cc_start: 0.9078 (tp) cc_final: 0.8087 (tp) REVERT: C 36 MET cc_start: 0.9180 (mtm) cc_final: 0.8512 (mtm) REVERT: C 59 ASP cc_start: 0.8814 (p0) cc_final: 0.8464 (p0) REVERT: C 244 PHE cc_start: 0.8848 (t80) cc_final: 0.8052 (t80) REVERT: F 103 MET cc_start: 0.9561 (tpp) cc_final: 0.9153 (tpp) REVERT: G 85 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6003 (mt-10) REVERT: H 96 MET cc_start: 0.8786 (mtm) cc_final: 0.8381 (mtp) REVERT: I 33 ASP cc_start: 0.8870 (m-30) cc_final: 0.8166 (p0) REVERT: I 94 ASP cc_start: 0.7809 (t0) cc_final: 0.7582 (t70) REVERT: J 1 MET cc_start: 0.9050 (ptp) cc_final: 0.8538 (pmm) REVERT: J 48 MET cc_start: 0.9606 (mmm) cc_final: 0.9230 (mmm) REVERT: L 70 ASP cc_start: 0.8612 (t70) cc_final: 0.8378 (t0) REVERT: a 120 MET cc_start: 0.6045 (mtm) cc_final: 0.5430 (mtt) REVERT: e 120 MET cc_start: 0.8404 (mmm) cc_final: 0.8095 (mmt) REVERT: h 56 MET cc_start: 0.1321 (tmm) cc_final: 0.0742 (tpp) REVERT: h 59 MET cc_start: 0.8742 (mmp) cc_final: 0.8300 (mmp) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.1875 time to fit residues: 93.3516 Evaluate side-chains 238 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 129 optimal weight: 9.9990 chunk 463 optimal weight: 20.0000 chunk 275 optimal weight: 10.0000 chunk 119 optimal weight: 20.0000 chunk 27 optimal weight: 30.0000 chunk 490 optimal weight: 0.8980 chunk 238 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 188 optimal weight: 9.9990 chunk 290 optimal weight: 40.0000 chunk 120 optimal weight: 7.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN ** A 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 GLN ** B 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 ASN D 172 GLN I 31 ASN V 31 ASN W 264 GLN ** h 81 ASN ** 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 = 0.3724 r_free = 0.3724 target = 0.061811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.041086 restraints weight = 393475.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.042270 restraints weight = 217480.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.043040 restraints weight = 149907.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.043548 restraints weight = 119286.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.043772 restraints weight = 103218.481| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 47588 Z= 0.201 Angle : 0.653 18.994 65369 Z= 0.340 Chirality : 0.044 0.277 7326 Planarity : 0.004 0.063 7516 Dihedral : 21.553 174.737 8502 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.01 % Favored : 95.93 % Rotamer: Outliers : 0.02 % Allowed : 0.40 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % 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: 0.65 (0.12), residues: 5042 helix: 1.52 (0.12), residues: 1934 sheet: -0.43 (0.19), residues: 743 loop : -0.11 (0.13), residues: 2365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG L 72 TYR 0.019 0.002 TYR a 41 PHE 0.020 0.002 PHE B 100 TRP 0.015 0.002 TRP A 956 HIS 0.007 0.001 HIS f 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.20 (47554) covalent geometry : angle 0.64054 / 0.34 (65336) hydrogen bonds : bond 0.05057 / 3.27 ( 2101) hydrogen bonds : angle 4.59415 / 3.23 ( 5691) metal coordination : bond 0.01150 / 0.66 ( 34) metal coordination : angle 5.63684 / 3.19 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 278 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LEU cc_start: 0.9206 (mt) cc_final: 0.8307 (mp) REVERT: A 41 MET cc_start: 0.3784 (tpt) cc_final: 0.3371 (tpt) REVERT: A 108 MET cc_start: 0.8549 (ppp) cc_final: 0.8250 (ppp) REVERT: A 139 TRP cc_start: 0.8878 (t60) cc_final: 0.8593 (t-100) REVERT: A 305 MET cc_start: 0.9520 (mmm) cc_final: 0.9134 (mmm) REVERT: A 457 MET cc_start: 0.8798 (mmp) cc_final: 0.8010 (mmm) REVERT: A 464 MET cc_start: 0.9383 (ptm) cc_final: 0.8628 (ptm) REVERT: A 487 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8114 (mm-30) REVERT: A 501 GLU cc_start: 0.9149 (tt0) cc_final: 0.8763 (mt-10) REVERT: A 535 MET cc_start: 0.9269 (ttp) cc_final: 0.8976 (ttp) REVERT: A 709 MET cc_start: 0.7040 (mmm) cc_final: 0.6340 (ttm) REVERT: A 738 LEU cc_start: 0.9077 (mt) cc_final: 0.8854 (mt) REVERT: A 819 MET cc_start: 0.9234 (mmm) cc_final: 0.8679 (mmt) REVERT: A 827 ASP cc_start: 0.9254 (m-30) cc_final: 0.8880 (m-30) REVERT: A 1074 ILE cc_start: 0.9468 (mm) cc_final: 0.9169 (tp) REVERT: A 1432 MET cc_start: 0.9310 (ptm) cc_final: 0.9074 (ptm) REVERT: B 89 MET cc_start: 0.8919 (tpt) cc_final: 0.8210 (tpp) REVERT: B 99 MET cc_start: 0.6552 (mmp) cc_final: 0.6283 (mmm) REVERT: B 164 MET cc_start: 0.8587 (ttp) cc_final: 0.8370 (ttp) REVERT: B 245 MET cc_start: 0.9198 (tmm) cc_final: 0.8966 (tmm) REVERT: B 278 PHE cc_start: 0.9245 (m-80) cc_final: 0.8922 (m-80) REVERT: B 305 MET cc_start: 0.9391 (tpp) cc_final: 0.9056 (mmm) REVERT: B 699 MET cc_start: 0.8352 (tpp) cc_final: 0.7756 (tpp) REVERT: B 773 MET cc_start: 0.9195 (mtm) cc_final: 0.8327 (ptp) REVERT: B 789 MET cc_start: 0.8920 (mmm) cc_final: 0.8341 (mmp) REVERT: B 812 LEU cc_start: 0.9581 (mt) cc_final: 0.9330 (tt) REVERT: B 968 MET cc_start: 0.8328 (tmm) cc_final: 0.7862 (tmm) REVERT: B 999 MET cc_start: 0.8650 (ttm) cc_final: 0.8079 (ttm) REVERT: B 1021 MET cc_start: 0.9428 (mmt) cc_final: 0.9059 (mmp) REVERT: B 1028 GLU cc_start: 0.8761 (tt0) cc_final: 0.8329 (tm-30) REVERT: B 1100 ASP cc_start: 0.8886 (p0) cc_final: 0.8683 (p0) REVERT: B 1101 ASP cc_start: 0.9239 (m-30) cc_final: 0.8984 (m-30) REVERT: B 1133 MET cc_start: 0.9327 (mmp) cc_final: 0.8709 (mmp) REVERT: B 1202 LEU cc_start: 0.9292 (tp) cc_final: 0.8939 (tp) REVERT: B 1206 GLU cc_start: 0.8950 (pt0) cc_final: 0.8736 (pt0) REVERT: B 1208 MET cc_start: 0.9269 (mmt) cc_final: 0.8940 (mmm) REVERT: B 1210 MET cc_start: 0.9186 (mtm) cc_final: 0.8816 (mtm) REVERT: C 59 ASP cc_start: 0.8806 (p0) cc_final: 0.8492 (p0) REVERT: C 244 PHE cc_start: 0.8754 (t80) cc_final: 0.7997 (t80) REVERT: E 57 MET cc_start: 0.8035 (tpp) cc_final: 0.7800 (tpp) REVERT: F 103 MET cc_start: 0.9535 (tpp) cc_final: 0.9143 (tpp) REVERT: G 23 ASN cc_start: 0.9085 (m110) cc_final: 0.8724 (t0) REVERT: G 85 GLU cc_start: 0.7015 (mm-30) cc_final: 0.6110 (mt-10) REVERT: H 96 MET cc_start: 0.8698 (mtm) cc_final: 0.8290 (mtp) REVERT: I 33 ASP cc_start: 0.8951 (m-30) cc_final: 0.8139 (p0) REVERT: I 61 ASP cc_start: 0.5438 (m-30) cc_final: 0.5085 (m-30) REVERT: I 64 GLN cc_start: 0.8131 (mp10) cc_final: 0.7855 (mp10) REVERT: J 1 MET cc_start: 0.8915 (ptp) cc_final: 0.8512 (pmm) REVERT: J 48 MET cc_start: 0.9611 (mmm) cc_final: 0.9200 (mmm) REVERT: a 120 MET cc_start: 0.6232 (mtm) cc_final: 0.5664 (mtt) REVERT: e 120 MET cc_start: 0.8477 (mmm) cc_final: 0.8114 (mmt) REVERT: h 56 MET cc_start: 0.1445 (tmm) cc_final: 0.0637 (tpp) REVERT: h 59 MET cc_start: 0.8775 (mmp) cc_final: 0.8341 (mmp) outliers start: 1 outliers final: 0 residues processed: 279 average time/residue: 0.1600 time to fit residues: 76.7646 Evaluate side-chains 233 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 502 optimal weight: 30.0000 chunk 90 optimal weight: 7.9990 chunk 491 optimal weight: 9.9990 chunk 57 optimal weight: 0.4980 chunk 247 optimal weight: 10.0000 chunk 189 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 228 optimal weight: 20.0000 chunk 499 optimal weight: 5.9990 chunk 255 optimal weight: 0.7980 overall best weight: 4.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN ** A 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 GLN ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 GLN D 172 GLN ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN ** h 81 ASN ** 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 = 0.3733 r_free = 0.3733 target = 0.062213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.041404 restraints weight = 399651.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.042636 restraints weight = 219863.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.043419 restraints weight = 150573.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.043814 restraints weight = 119825.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.044118 restraints weight = 105112.092| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 47588 Z= 0.159 Angle : 0.618 17.829 65369 Z= 0.324 Chirality : 0.043 0.278 7326 Planarity : 0.004 0.072 7516 Dihedral : 21.533 174.412 8502 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.51 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.12), residues: 5042 helix: 1.55 (0.12), residues: 1940 sheet: -0.47 (0.18), residues: 749 loop : -0.09 (0.14), residues: 2353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 904 TYR 0.028 0.001 TYR B1040 PHE 0.023 0.001 PHE A 445 TRP 0.017 0.002 TRP B 554 HIS 0.007 0.001 HIS B 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 (47554) covalent geometry : angle 0.60741 / 0.32 (65336) hydrogen bonds : bond 0.04353 / 2.83 ( 2101) hydrogen bonds : angle 4.52237 / 3.17 ( 5691) metal coordination : bond 0.00880 / 0.51 ( 34) metal coordination : angle 5.22302 / 3.00 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.947 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 22 LEU cc_start: 0.9181 (mt) cc_final: 0.8581 (mp) REVERT: A 41 MET cc_start: 0.3883 (tpt) cc_final: 0.3509 (tpt) REVERT: A 108 MET cc_start: 0.8578 (ppp) cc_final: 0.8317 (ppp) REVERT: A 139 TRP cc_start: 0.8871 (t60) cc_final: 0.8569 (t-100) REVERT: A 305 MET cc_start: 0.9504 (mmm) cc_final: 0.9109 (mmm) REVERT: A 446 ASN cc_start: 0.8984 (t0) cc_final: 0.8620 (t0) REVERT: A 457 MET cc_start: 0.8862 (mmp) cc_final: 0.8054 (mmm) REVERT: A 464 MET cc_start: 0.9355 (ptm) cc_final: 0.8930 (ptm) REVERT: A 488 MET cc_start: 0.8609 (mmm) cc_final: 0.7931 (mmm) REVERT: A 501 GLU cc_start: 0.9049 (tt0) cc_final: 0.8757 (mt-10) REVERT: A 535 MET cc_start: 0.9266 (ttp) cc_final: 0.8948 (ttp) REVERT: A 651 GLN cc_start: 0.9215 (mm-40) cc_final: 0.8754 (mm-40) REVERT: A 709 MET cc_start: 0.6922 (mmm) cc_final: 0.6238 (ttm) REVERT: A 738 LEU cc_start: 0.9070 (mt) cc_final: 0.8863 (mt) REVERT: A 762 MET cc_start: 0.9005 (mmt) cc_final: 0.8664 (mmt) REVERT: A 819 MET cc_start: 0.9237 (mmm) cc_final: 0.8708 (mmt) REVERT: A 827 ASP cc_start: 0.9257 (m-30) cc_final: 0.8852 (m-30) REVERT: A 1074 ILE cc_start: 0.9458 (mm) cc_final: 0.9174 (tp) REVERT: A 1414 GLU cc_start: 0.9535 (mm-30) cc_final: 0.9286 (mm-30) REVERT: A 1432 MET cc_start: 0.9280 (ptm) cc_final: 0.9055 (ptm) REVERT: B 89 MET cc_start: 0.8899 (tpt) cc_final: 0.8560 (tpp) REVERT: B 164 MET cc_start: 0.8594 (ttp) cc_final: 0.8382 (ttp) REVERT: B 190 MET cc_start: 0.8802 (mmp) cc_final: 0.8299 (mtp) REVERT: B 245 MET cc_start: 0.9202 (tmm) cc_final: 0.8968 (tmm) REVERT: B 278 PHE cc_start: 0.9254 (m-80) cc_final: 0.8865 (m-10) REVERT: B 305 MET cc_start: 0.9395 (tpp) cc_final: 0.9080 (mmm) REVERT: B 699 MET cc_start: 0.8366 (tpp) cc_final: 0.7742 (tpp) REVERT: B 773 MET cc_start: 0.9306 (mtm) cc_final: 0.8394 (ptp) REVERT: B 789 MET cc_start: 0.9015 (mmm) cc_final: 0.8442 (mmp) REVERT: B 839 MET cc_start: 0.8883 (pmm) cc_final: 0.8605 (pmm) REVERT: B 968 MET cc_start: 0.8357 (tmm) cc_final: 0.7893 (tmm) REVERT: B 999 MET cc_start: 0.8706 (ttm) cc_final: 0.8223 (ttm) REVERT: B 1028 GLU cc_start: 0.8747 (tt0) cc_final: 0.8325 (tm-30) REVERT: B 1098 MET cc_start: 0.8215 (mtm) cc_final: 0.7681 (mpp) REVERT: B 1100 ASP cc_start: 0.8844 (p0) cc_final: 0.8625 (p0) REVERT: B 1101 ASP cc_start: 0.9275 (m-30) cc_final: 0.8824 (m-30) REVERT: B 1133 MET cc_start: 0.9377 (mmp) cc_final: 0.8739 (mmp) REVERT: B 1152 MET cc_start: 0.9124 (tpt) cc_final: 0.8829 (tpt) REVERT: B 1202 LEU cc_start: 0.9265 (tp) cc_final: 0.9053 (tp) REVERT: B 1210 MET cc_start: 0.9246 (mtm) cc_final: 0.8950 (mtm) REVERT: C 59 ASP cc_start: 0.8753 (p0) cc_final: 0.8445 (p0) REVERT: C 244 PHE cc_start: 0.8795 (t80) cc_final: 0.7988 (t80) REVERT: E 57 MET cc_start: 0.7971 (tpp) cc_final: 0.7698 (tpp) REVERT: F 103 MET cc_start: 0.9542 (tpp) cc_final: 0.9097 (tpp) REVERT: G 23 ASN cc_start: 0.8970 (m110) cc_final: 0.8574 (t0) REVERT: G 85 GLU cc_start: 0.6975 (mm-30) cc_final: 0.6082 (mt-10) REVERT: H 96 MET cc_start: 0.8711 (mtm) cc_final: 0.8323 (mtp) REVERT: I 61 ASP cc_start: 0.5424 (m-30) cc_final: 0.5080 (m-30) REVERT: I 64 GLN cc_start: 0.8116 (mp10) cc_final: 0.7807 (mp10) REVERT: J 1 MET cc_start: 0.9011 (ptp) cc_final: 0.8560 (pmm) REVERT: J 48 MET cc_start: 0.9588 (mmm) cc_final: 0.9046 (mmm) REVERT: a 120 MET cc_start: 0.6237 (mtm) cc_final: 0.5672 (mtt) REVERT: e 120 MET cc_start: 0.8406 (mmm) cc_final: 0.8065 (mmt) REVERT: h 56 MET cc_start: 0.1421 (tmm) cc_final: 0.0642 (tpp) REVERT: h 59 MET cc_start: 0.8771 (mmp) cc_final: 0.8375 (mmm) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.1585 time to fit residues: 76.0158 Evaluate side-chains 235 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 190 optimal weight: 8.9990 chunk 207 optimal weight: 40.0000 chunk 267 optimal weight: 1.9990 chunk 525 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 106 optimal weight: 0.8980 chunk 480 optimal weight: 2.9990 chunk 398 optimal weight: 50.0000 chunk 417 optimal weight: 9.9990 chunk 146 optimal weight: 0.3980 chunk 308 optimal weight: 10.0000 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN A 787 HIS ** A 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 GLN ** B 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 GLN D 172 GLN ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.062534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.041910 restraints weight = 386240.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.043098 restraints weight = 213018.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.043879 restraints weight = 146524.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.044260 restraints weight = 116312.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.044643 restraints weight = 102134.299| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.5285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 47588 Z= 0.140 Angle : 0.606 16.085 65369 Z= 0.317 Chirality : 0.043 0.284 7326 Planarity : 0.004 0.057 7516 Dihedral : 21.464 174.432 8502 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.75 % Favored : 96.19 % Rotamer: Outliers : 0.02 % Allowed : 0.13 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % 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: 0.73 (0.12), residues: 5042 helix: 1.62 (0.12), residues: 1942 sheet: -0.44 (0.18), residues: 754 loop : -0.07 (0.14), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 351 TYR 0.018 0.001 TYR B 344 PHE 0.026 0.001 PHE A 445 TRP 0.014 0.001 TRP B 554 HIS 0.006 0.001 HIS b 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (47554) covalent geometry : angle 0.59654 / 0.32 (65336) hydrogen bonds : bond 0.04186 / 2.73 ( 2101) hydrogen bonds : angle 4.45513 / 3.13 ( 5691) metal coordination : bond 0.00736 / 0.42 ( 34) metal coordination : angle 4.75940 / 2.70 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7370.74 seconds wall clock time: 127 minutes 42.22 seconds (7662.22 seconds total)