Starting phenix.real_space_refine on Tue Sep 15 22:36:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6j4y_0673/09_2026/6j4y_0673.cif Found real_map, /net/cci-nas-00/data/ceres_data/6j4y_0673/09_2026/6j4y_0673.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 { model { file = "/net/cci-nas-00/data/ceres_data/6j4y_0673/09_2026/6j4y_0673.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6j4y_0673/09_2026/6j4y_0673.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6j4y_0673/09_2026/6j4y_0673.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6j4y_0673/09_2026/6j4y_0673.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6j4y_0673/09_2026/6j4y_0673.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6j4y_0673/09_2026/6j4y_0673.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): 0.22s 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 74.349 61.628 141.409 1.00103.22 S ATOM 549 SG CYS A 70 77.838 60.712 142.250 1.00 94.73 S ATOM 594 SG CYS A 77 76.739 64.287 142.859 1.00 74.48 S ATOM 829 SG CYS A 107 78.094 84.444 98.822 1.00142.68 S ATOM 851 SG CYS A 110 79.432 81.098 98.060 1.00152.38 S ATOM 1222 SG CYS A 168 76.130 84.506 95.841 1.00155.44 S ATOM 19876 SG CYS B1163 87.848 61.549 128.436 1.00 76.06 S ATOM 19894 SG CYS B1166 86.006 64.947 127.396 1.00 77.90 S ATOM 20017 SG CYS B1182 84.045 61.436 128.499 1.00108.37 S ATOM 20040 SG CYS B1185 86.183 61.726 125.116 1.00109.59 S ATOM 20985 SG CYS C 85 88.226 75.511 208.113 1.00126.06 S ATOM 21033 SG CYS C 91 84.009 76.384 209.952 1.00108.11 S ATOM 21056 SG CYS C 94 85.456 78.831 206.471 1.00108.09 S ATOM 29164 SG CYS I 78 83.440 167.170 147.709 1.00173.59 S ATOM 29380 SG CYS I 103 83.647 163.547 147.106 1.00166.64 S ATOM 28780 SG CYS I 29 64.394 147.264 107.042 1.00154.71 S ATOM 28805 SG CYS I 32 61.392 149.602 105.503 1.00153.57 S ATOM 29521 SG CYS J 7 89.795 109.246 195.908 1.00 34.60 S ATOM 29544 SG CYS J 10 92.313 108.612 198.493 1.00 33.65 S ATOM 29820 SG CYS J 44 93.240 111.509 196.597 1.00 40.97 S ATOM 29826 SG CYS J 45 90.505 111.436 199.574 1.00 40.49 S ATOM 30988 SG CYS L 33 48.583 94.668 185.578 1.00114.61 S ATOM 31003 SG CYS L 36 46.619 94.984 188.830 1.00124.33 S ATOM 31113 SG CYS L 50 45.948 92.271 185.761 1.00122.63 S ATOM 31137 SG CYS L 53 45.471 96.288 184.731 1.00130.70 S ATOM 36833 SG CYS M 25 52.182 109.264 99.941 1.00198.31 S ATOM 36858 SG CYS M 28 52.384 105.826 99.485 1.00168.76 S ATOM 37016 SG CYS M 49 55.351 107.384 98.535 1.00180.55 S ATOM 37040 SG CYS M 52 52.462 107.692 96.184 1.00191.36 S ATOM 37277 SG CYS V 12 21.102 83.087 121.854 1.00 34.75 S ATOM 37299 SG CYS V 15 22.137 85.968 119.559 1.00 22.76 S ATOM 37401 SG CYS V 29 19.419 86.646 121.615 1.00 18.00 S ATOM 37422 SG CYS V 32 18.925 84.099 118.725 1.00 25.35 S Time building chain proxies: 8.74, per 1000 atoms: 0.19 Number of scatterers: 46185 At special positions: 0 Unit cell: (175.82, 178.8, 233.93, 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: 3.31 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 B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " 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: 4.84 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: 3.623A 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: 3.609A pdb=" N GLU A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) removed outlier: 3.680A 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: 3.719A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 506 removed outlier: 3.502A 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: 3.946A pdb=" N ASN A 549 " --> pdb=" O GLU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 583 removed outlier: 3.957A pdb=" N ALA A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 3.716A 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: 3.753A 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: 3.582A 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: 3.682A 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: 3.590A 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: 3.579A 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: 3.990A 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: 3.593A 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: 3.771A 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: 3.727A 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: 3.632A pdb=" N ALA A1321 " --> pdb=" O ALA A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1334 through 1343 removed outlier: 3.566A pdb=" N SER A1340 " --> pdb=" O VAL A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1362 removed outlier: 3.583A pdb=" N SER A1349 " --> pdb=" O GLU A1345 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP A1362 " --> pdb=" O VAL A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1380 removed outlier: 4.106A 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: 3.664A 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: 3.698A 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: 3.592A 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: 3.714A 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: 4.006A 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: 3.642A pdb=" N ILE B 342 " --> pdb=" O ARG B 338 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N GLN B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) removed outlier: 3.922A 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: 3.562A 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: 3.689A pdb=" N TYR B 562 " --> pdb=" O LEU B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 600 removed outlier: 3.850A pdb=" N LEU B 589 " --> pdb=" O ASP B 585 " (cutoff:3.500A) removed outlier: 3.772A 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: 3.636A 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: 3.700A 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: 3.578A 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: 3.908A 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: 3.740A 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: 3.695A 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: 4.039A 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: 3.507A 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: 3.771A 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: 3.914A pdb=" N ALA D 164 " --> pdb=" O PRO D 161 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ALA D 165 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS D 166 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 4.260A 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: 3.506A pdb=" N ARG E 93 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 3.876A 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: 4.168A 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: 3.510A 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: 3.953A 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: 3.616A 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: 3.805A 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: 3.618A pdb=" N LEU W 309 " --> pdb=" O GLU W 305 " (cutoff:3.500A) removed outlier: 3.831A 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: 3.816A pdb=" N LEU a 48 " --> pdb=" O GLY a 44 " (cutoff:3.500A) Processing helix chain 'a' and resid 63 through 76 removed outlier: 3.978A pdb=" N PHE a 67 " --> pdb=" O ARG a 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 114 removed outlier: 3.735A pdb=" N ILE a 89 " --> pdb=" O GLN a 85 " (cutoff:3.500A) Processing helix chain 'a' and resid 120 through 131 removed outlier: 3.853A 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: 3.606A 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: 3.727A 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: 3.568A pdb=" N VAL g 30 " --> pdb=" O PRO g 26 " (cutoff:3.500A) Processing helix chain 'g' and resid 45 through 72 removed outlier: 4.468A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) removed outlier: 3.738A 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: 3.712A 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: 10.889A 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: 3.762A pdb=" N GLY A 184 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 3.692A 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: 3.590A 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: 3.762A 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: 3.562A pdb=" N SER A 349 " --> pdb=" O ARG B1106 " (cutoff:3.500A) removed outlier: 3.585A 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: 5.550A 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: 3.835A pdb=" N TYR A 405 " --> pdb=" O GLU A 434 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N HIS A 436 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 7.016A 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: 3.756A 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: 6.467A pdb=" N VAL H 95 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE H 29 " --> pdb=" O THR H 11 " (cutoff:3.500A) removed outlier: 6.734A 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: 6.313A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LEU H 121 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LYS H 112 " --> pdb=" O PHE H 103 " (cutoff:3.500A) removed outlier: 4.975A 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: 7.036A 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: 3.562A 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: 7.227A 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: 3.582A 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: 6.929A 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: 4.955A pdb=" N GLU I 47 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR A1152 " --> pdb=" O ARG I 45 " (cutoff:3.500A) removed outlier: 4.646A 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: 7.199A pdb=" N TYR B 116 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LEU B 84 " --> pdb=" O PRO B 114 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY B 159 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 6.671A 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: 4.038A pdb=" N HIS B 227 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.511A 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: 5.766A pdb=" N TRP B 579 " --> pdb=" O VAL B 575 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL B 575 " --> pdb=" O TRP B 579 " (cutoff:3.500A) removed outlier: 3.770A 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: 6.880A 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: 4.468A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 7.004A 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: 8.802A 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: 6.880A 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: 4.468A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 7.004A 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: 8.802A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.339A 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: 7.048A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.322A 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: 3.556A 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: 7.011A pdb=" N GLU C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 3.684A 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: 4.298A pdb=" N ASN C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.805A 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: 5.194A 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: 4.085A 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: 4.778A 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: 3.554A 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: 3.534A 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: 5.220A 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: 4.228A 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: 3.777A 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: 6.588A 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: 3.802A 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: 4.016A 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: 7.011A pdb=" N GLY V 56 " --> pdb=" O VAL V 84 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL V 86 " --> pdb=" O PHE V 54 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N PHE V 54 " --> pdb=" O VAL V 86 " (cutoff:3.500A) removed outlier: 3.623A 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: 6.542A pdb=" N PHE W 413 " --> pdb=" O ASP W 409 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLU W 420 " --> pdb=" O TYR W 427 " (cutoff:3.500A) removed outlier: 6.327A 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: 6.039A 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: 6.671A 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: 7.373A 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: 7.671A 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: 276 hydrogen bonds 548 hydrogen bond angles 0 basepair planarities 108 basepair parallelities 205 stacking parallelities Total time for adding SS restraints: 15.20 Time building geometry restraints manager: 4.69 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: 11079 1.33 - 1.45: 10778 1.45 - 1.57: 24829 1.57 - 1.70: 526 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 1.433 -0.098 1.19e-02 7.06e+03 6.77e+01 bond pdb=" CA ILE W 440 " pdb=" C ILE W 440 " ideal model delta sigma weight residual 1.521 1.432 0.089 1.21e-02 6.83e+03 5.46e+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 5.30e+01 bond pdb=" C1' DG N -37 " pdb=" N9 DG N -37 " ideal model delta sigma weight residual 1.468 1.372 0.096 1.40e-02 5.10e+03 4.73e+01 bond pdb=" C1' DG N -19 " pdb=" N9 DG N -19 " ideal model delta sigma weight residual 1.468 1.375 0.093 1.40e-02 5.10e+03 4.45e+01 ... (remaining 47549 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.00: 64423 4.00 - 8.00: 835 8.00 - 12.00: 68 12.00 - 15.99: 9 15.99 - 19.99: 1 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 92.34 15.92 1.66e+00 3.63e-01 9.19e+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 99.58 12.42 1.40e+00 5.10e-01 7.87e+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 96.78 13.99 1.63e+00 3.76e-01 7.37e+01 angle pdb=" O CYS V 29 " pdb=" C CYS V 29 " pdb=" N PRO V 30 " ideal model delta sigma weight residual 121.31 114.31 7.00 8.50e-01 1.38e+00 6.78e+01 angle pdb=" O4' DT T -26 " pdb=" C4' DT T -26 " pdb=" C3' DT T -26 " ideal model delta sigma weight residual 106.00 101.74 4.26 6.00e-01 2.78e+00 5.04e+01 ... (remaining 65331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.00: 26759 35.00 - 69.99: 1485 69.99 - 104.99: 60 104.99 - 139.99: 4 139.99 - 174.98: 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 -36.68 73.03 1 3.10e+00 1.04e-01 7.07e+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 36.34 -36.12 72.47 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 27.76 -62.91 1 4.00e+00 6.25e-02 3.27e+02 ... (remaining 28306 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 6846 0.129 - 0.258: 464 0.258 - 0.387: 12 0.387 - 0.516: 2 0.516 - 0.646: 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 1.04e+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 8.81e+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 4.53e+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 6.11e-02 3.73e+01 pdb=" C ILE B 336 " 0.106 2.00e-02 2.50e+03 pdb=" O ILE B 336 " -0.040 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 3.72e-02 1.38e+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 3.61e-02 1.31e+01 pdb=" C GLU C 88 " 0.062 2.00e-02 2.50e+03 pdb=" O GLU C 88 " -0.023 2.00e-02 2.50e+03 pdb=" N ASP C 89 " -0.021 2.00e-02 2.50e+03 ... (remaining 7513 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 268 2.55 - 3.14: 34073 3.14 - 3.72: 71607 3.72 - 4.31: 100780 4.31 - 4.90: 159704 Nonbonded interactions: 366432 Sorted by model distance: nonbonded pdb=" NH1 ARG B 328 " pdb=" OD1 ASP M 68 " model vdw 1.962 3.120 nonbonded pdb=" NH1 ARG V 85 " pdb=" OD1 ASP V 87 " model vdw 2.072 3.120 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 nonbonded pdb=" N CYS J 45 " pdb="ZN ZN J 101 " model vdw 2.186 2.310 ... (remaining 366427 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 53.390 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6252 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 0.662 47588 Z= 0.611 Angle : 1.274 27.623 65369 Z= 0.774 Chirality : 0.070 0.646 7326 Planarity : 0.007 0.064 7516 Dihedral : 17.809 174.985 18723 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.65 % Allowed : 4.24 % Favored : 95.10 % Rotamer: Outliers : 0.72 % Allowed : 3.13 % Favored : 96.15 % 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: -1.68 (0.11), residues: 5042 helix: -1.29 (0.10), residues: 1856 sheet: -0.75 (0.18), residues: 715 loop : -0.95 (0.12), residues: 2471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 25 TYR 0.049 0.004 TYR d 80 PHE 0.051 0.004 PHE A1176 TRP 0.037 0.004 TRP G 79 HIS 0.015 0.003 HIS f 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00940 / 0.56 (47554) covalent geometry : angle 1.23594 / 0.77 (65336) hydrogen bonds : bond 0.23097 / 15.32 ( 2102) hydrogen bonds : angle 7.32168 / 5.17 ( 5693) metal coordination : bond 0.26253 / 17.17 ( 34) metal coordination : angle 13.81568 / 9.00 ( 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 737 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 705 time to evaluate : 1.734 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: A 90 VAL cc_start: 0.8336 (m) cc_final: 0.8114 (m) REVERT: A 240 LEU cc_start: 0.9377 (tp) cc_final: 0.8948 (mt) REVERT: A 306 ASP cc_start: 0.8154 (t0) cc_final: 0.7919 (t0) REVERT: A 464 MET cc_start: 0.8334 (mtp) cc_final: 0.8091 (mtm) REVERT: A 535 MET cc_start: 0.8275 (ttp) cc_final: 0.7898 (ttp) REVERT: A 606 MET cc_start: 0.8140 (tpp) cc_final: 0.7924 (tpp) REVERT: A 825 LEU cc_start: 0.9010 (mt) cc_final: 0.8657 (tt) REVERT: A 958 LEU cc_start: 0.8802 (mt) cc_final: 0.8590 (mp) REVERT: A 1378 MET cc_start: 0.7486 (mtp) cc_final: 0.7097 (mtm) REVERT: A 1447 MET cc_start: 0.7547 (mmp) cc_final: 0.7005 (mmm) REVERT: B 71 ILE cc_start: 0.4790 (OUTLIER) cc_final: 0.4433 (mt) REVERT: B 274 ILE cc_start: 0.7976 (mm) cc_final: 0.6948 (mm) REVERT: B 302 MET cc_start: 0.8782 (ttm) cc_final: 0.8546 (ttp) REVERT: B 428 CYS cc_start: 0.6834 (OUTLIER) cc_final: 0.6269 (t) REVERT: B 486 SER cc_start: 0.8749 (m) cc_final: 0.8443 (p) REVERT: B 812 LEU cc_start: 0.8901 (mt) cc_final: 0.8238 (tt) REVERT: B 1101 ASP cc_start: 0.7857 (m-30) cc_final: 0.7552 (t0) REVERT: B 1138 MET cc_start: 0.7942 (mmm) cc_final: 0.7658 (mmm) REVERT: B 1206 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8086 (mt-10) REVERT: C 36 MET cc_start: 0.7756 (mtm) cc_final: 0.7423 (mtm) REVERT: D 91 LYS cc_start: 0.8372 (ttmt) cc_final: 0.8149 (ptpp) REVERT: G 11 LEU cc_start: 0.8764 (mt) cc_final: 0.8375 (mp) REVERT: G 118 ASN cc_start: 0.6832 (p0) cc_final: 0.6548 (p0) REVERT: I 40 ASP cc_start: 0.6195 (t0) cc_final: 0.5891 (p0) REVERT: J 59 PHE cc_start: 0.8083 (m-10) cc_final: 0.7870 (m-10) REVERT: K 18 LYS cc_start: 0.7995 (tptp) cc_final: 0.7373 (tppt) REVERT: K 87 LEU cc_start: 0.8434 (tp) cc_final: 0.8062 (tp) REVERT: M 72 ASP cc_start: 0.7891 (m-30) cc_final: 0.7582 (m-30) REVERT: V 25 MET cc_start: 0.4702 (tpt) cc_final: 0.4496 (ttp) REVERT: b 24 ASP cc_start: 0.7517 (t70) cc_final: 0.7032 (m-30) REVERT: f 68 ASP cc_start: 0.6258 (m-30) cc_final: 0.4347 (p0) outliers start: 32 outliers final: 1 residues processed: 733 average time/residue: 0.3035 time to fit residues: 351.1558 Evaluate side-chains 332 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 329 time to evaluate : 1.728 ------------------------------------------------------------------------------- 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: 50.0000 chunk 430 optimal weight: 0.0570 chunk 41 optimal weight: 8.9990 chunk 265 optimal weight: 8.9990 chunk 523 optimal weight: 6.9990 chunk 497 optimal weight: 10.0000 chunk 414 optimal weight: 30.0000 chunk 310 optimal weight: 10.0000 chunk 488 optimal weight: 8.9990 chunk 366 optimal weight: 20.0000 chunk 223 optimal weight: 4.9990 overall best weight: 6.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 GLN ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN A1190 GLN ** A1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 ASN B 794 ASN B 887 HIS B 996 HIS C 13 GLN E 145 HIS ** E 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 GLN H 13 GLN I 22 ASN I 64 GLN M 53 ASN ** W 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 339 GLN W 434 ASN W 441 ASN ** W 783 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 38 ASN c 84 GLN d 64 ASN ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 68 GLN e 76 GLN f 64 ASN g 31 HIS ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.082536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.058160 restraints weight = 307331.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.059408 restraints weight = 182321.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.059827 restraints weight = 107418.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.059937 restraints weight = 92507.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.059985 restraints weight = 83710.388| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 47588 Z= 0.266 Angle : 0.834 20.533 65369 Z= 0.433 Chirality : 0.053 1.037 7326 Planarity : 0.006 0.107 7516 Dihedral : 21.811 172.105 8502 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.13 % Favored : 96.59 % Rotamer: Outliers : 0.02 % Allowed : 2.35 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.11), residues: 5042 helix: 0.29 (0.11), residues: 1915 sheet: -0.35 (0.18), residues: 724 loop : -0.54 (0.13), residues: 2403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B1220 TYR 0.032 0.002 TYR B 797 PHE 0.027 0.003 PHE D 34 TRP 0.036 0.002 TRP V 67 HIS 0.025 0.002 HIS W 783 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.27 (47554) covalent geometry : angle 0.82275 / 0.43 (65336) hydrogen bonds : bond 0.06926 / 4.51 ( 2102) hydrogen bonds : angle 5.38295 / 3.79 ( 5693) metal coordination : bond 0.02573 / 1.70 ( 34) metal coordination : angle 6.17357 / 3.65 ( 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 399 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 398 time to evaluate : 1.599 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: A 41 MET cc_start: 0.5163 (mtp) cc_final: 0.4770 (mmm) REVERT: A 84 MET cc_start: 0.8043 (tmm) cc_final: 0.7443 (tmm) REVERT: A 454 MET cc_start: 0.9037 (mpp) cc_final: 0.8693 (mpp) REVERT: A 464 MET cc_start: 0.9161 (mtp) cc_final: 0.8857 (mtp) REVERT: A 501 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8248 (mt-10) REVERT: A 958 LEU cc_start: 0.9648 (mt) cc_final: 0.9169 (mp) REVERT: A 1064 GLU cc_start: 0.8440 (mm-30) cc_final: 0.7890 (mm-30) REVERT: B 245 MET cc_start: 0.8436 (tmm) cc_final: 0.8062 (tmm) REVERT: B 519 GLU cc_start: 0.8426 (tm-30) cc_final: 0.7877 (pp20) REVERT: B 588 MET cc_start: 0.8595 (ppp) cc_final: 0.8283 (ppp) REVERT: B 789 MET cc_start: 0.8932 (mmp) cc_final: 0.8716 (mmm) REVERT: B 809 MET cc_start: 0.8910 (mtt) cc_final: 0.8536 (mtt) REVERT: B 812 LEU cc_start: 0.9624 (mt) cc_final: 0.8952 (tt) REVERT: B 864 LYS cc_start: 0.8772 (mmpt) cc_final: 0.8505 (mmmt) REVERT: B 872 GLU cc_start: 0.7386 (mt-10) cc_final: 0.6439 (mt-10) REVERT: B 1021 MET cc_start: 0.9117 (mpp) cc_final: 0.8806 (mpp) REVERT: B 1072 MET cc_start: 0.7744 (ttm) cc_final: 0.7475 (ttm) REVERT: B 1082 MET cc_start: 0.8526 (tpp) cc_final: 0.8274 (tpp) REVERT: B 1128 LEU cc_start: 0.9365 (mt) cc_final: 0.9133 (mt) REVERT: B 1203 LEU cc_start: 0.9661 (tt) cc_final: 0.9426 (tp) REVERT: B 1206 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8128 (mt-10) REVERT: C 20 MET cc_start: 0.8483 (tmm) cc_final: 0.8270 (tmm) REVERT: C 32 LEU cc_start: 0.9512 (tp) cc_final: 0.9299 (tp) REVERT: C 36 MET cc_start: 0.9019 (mtm) cc_final: 0.8731 (mtp) REVERT: D 91 LYS cc_start: 0.8399 (ttmt) cc_final: 0.8091 (ptpp) REVERT: E 57 MET cc_start: 0.8227 (ttm) cc_final: 0.7500 (ttm) REVERT: E 81 PHE cc_start: 0.7408 (m-80) cc_final: 0.7105 (m-80) REVERT: G 11 LEU cc_start: 0.8964 (mt) cc_final: 0.8746 (mp) REVERT: G 28 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8443 (pm20) REVERT: G 55 ASP cc_start: 0.8888 (p0) cc_final: 0.8017 (t70) REVERT: I 64 GLN cc_start: 0.7995 (mt0) cc_final: 0.7554 (mt0) REVERT: I 97 MET cc_start: 0.8329 (mmm) cc_final: 0.8081 (mmm) REVERT: W 409 ASP cc_start: 0.2346 (m-30) cc_final: 0.2057 (m-30) REVERT: W 415 THR cc_start: -0.0278 (m) cc_final: -0.0546 (p) REVERT: W 771 LYS cc_start: 0.8553 (tptt) cc_final: 0.8227 (mtmm) REVERT: c 62 ILE cc_start: 0.5276 (mm) cc_final: 0.5022 (pt) REVERT: f 58 LEU cc_start: 0.7217 (tp) cc_final: 0.6816 (pp) REVERT: f 68 ASP cc_start: 0.4869 (m-30) cc_final: 0.4421 (p0) outliers start: 1 outliers final: 0 residues processed: 399 average time/residue: 0.2773 time to fit residues: 182.8676 Evaluate side-chains 270 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 269 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: 2.9990 chunk 456 optimal weight: 40.0000 chunk 428 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 471 optimal weight: 40.0000 chunk 375 optimal weight: 3.9990 chunk 415 optimal weight: 20.0000 chunk 313 optimal weight: 10.0000 chunk 306 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 737 ASN A 787 HIS A1190 GLN ** A1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 996 HIS ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 ASN H 138 ASN I 22 ASN ** W 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 339 GLN ** W 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 73 ASN ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 125 GLN h 60 ASN ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.082398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.057766 restraints weight = 300635.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.059379 restraints weight = 161259.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.059117 restraints weight = 102629.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.059560 restraints weight = 83347.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.059697 restraints weight = 74283.301| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 47588 Z= 0.174 Angle : 0.681 17.539 65369 Z= 0.361 Chirality : 0.048 0.735 7326 Planarity : 0.005 0.129 7516 Dihedral : 21.609 171.271 8502 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.15 % Favored : 96.61 % Rotamer: Outliers : 0.09 % Allowed : 2.02 % Favored : 97.90 % 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: 0.20 (0.12), residues: 5042 helix: 0.89 (0.12), residues: 1918 sheet: -0.26 (0.18), residues: 709 loop : -0.26 (0.13), residues: 2415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 173 TYR 0.022 0.002 TYR A 37 PHE 0.030 0.002 PHE B 394 TRP 0.035 0.002 TRP V 67 HIS 0.007 0.001 HIS C 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.17 (47554) covalent geometry : angle 0.67101 / 0.36 (65336) hydrogen bonds : bond 0.05240 / 3.38 ( 2102) hydrogen bonds : angle 4.87996 / 3.44 ( 5693) metal coordination : bond 0.00783 / 0.46 ( 34) metal coordination : angle 5.27085 / 3.03 ( 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 362 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 358 time to evaluate : 1.732 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: A 41 MET cc_start: 0.5097 (mtp) cc_final: 0.4711 (mmm) REVERT: A 84 MET cc_start: 0.8125 (tmm) cc_final: 0.7661 (tmm) REVERT: A 240 LEU cc_start: 0.9484 (tp) cc_final: 0.9035 (mt) REVERT: A 342 MET cc_start: 0.9325 (mmm) cc_final: 0.9070 (mmp) REVERT: A 456 MET cc_start: 0.8707 (ttm) cc_final: 0.7814 (ttp) REVERT: A 464 MET cc_start: 0.9122 (mtp) cc_final: 0.8766 (mtp) REVERT: A 487 GLU cc_start: 0.7339 (tt0) cc_final: 0.7096 (tt0) REVERT: A 501 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8264 (mt-10) REVERT: A 635 MET cc_start: 0.9001 (tpt) cc_final: 0.8727 (tpt) REVERT: A 677 MET cc_start: 0.8627 (mmp) cc_final: 0.8347 (mmp) REVERT: A 844 LYS cc_start: 0.8736 (mmmm) cc_final: 0.8346 (mttm) REVERT: A 850 MET cc_start: 0.8501 (ttt) cc_final: 0.7933 (tpp) REVERT: A 958 LEU cc_start: 0.9594 (mt) cc_final: 0.9366 (mp) REVERT: A 1064 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8002 (mm-30) REVERT: A 1065 MET cc_start: 0.9010 (mmp) cc_final: 0.8741 (mmp) REVERT: A 1439 MET cc_start: 0.8765 (tmm) cc_final: 0.8300 (tmm) REVERT: B 245 MET cc_start: 0.8665 (tmm) cc_final: 0.8189 (tmm) REVERT: B 469 ARG cc_start: 0.8144 (ptp-170) cc_final: 0.7859 (ptt180) REVERT: B 588 MET cc_start: 0.8587 (ppp) cc_final: 0.8309 (ppp) REVERT: B 699 MET cc_start: 0.8609 (tpt) cc_final: 0.7865 (ttt) REVERT: B 789 MET cc_start: 0.8990 (mmp) cc_final: 0.8757 (mmm) REVERT: B 809 MET cc_start: 0.8751 (mtt) cc_final: 0.8434 (mtp) REVERT: B 812 LEU cc_start: 0.9621 (mt) cc_final: 0.8931 (tt) REVERT: B 864 LYS cc_start: 0.8865 (mmpt) cc_final: 0.8547 (mmmt) REVERT: B 872 GLU cc_start: 0.7388 (mt-10) cc_final: 0.6166 (mt-10) REVERT: B 1021 MET cc_start: 0.9179 (mpp) cc_final: 0.8899 (mpp) REVERT: B 1072 MET cc_start: 0.7642 (ttm) cc_final: 0.7328 (ttm) REVERT: B 1098 MET cc_start: 0.8202 (mpp) cc_final: 0.7842 (mpp) REVERT: B 1203 LEU cc_start: 0.9638 (tt) cc_final: 0.9124 (tt) REVERT: B 1206 GLU cc_start: 0.8660 (mt-10) cc_final: 0.7604 (mt-10) REVERT: C 20 MET cc_start: 0.8526 (tmm) cc_final: 0.8083 (tmm) REVERT: C 32 LEU cc_start: 0.9537 (tp) cc_final: 0.9139 (tp) REVERT: C 36 MET cc_start: 0.8964 (mtm) cc_final: 0.7858 (mtm) REVERT: D 91 LYS cc_start: 0.8377 (ttmt) cc_final: 0.8060 (ptpp) REVERT: E 57 MET cc_start: 0.8305 (ttm) cc_final: 0.6973 (ttp) REVERT: G 11 LEU cc_start: 0.9035 (mt) cc_final: 0.8835 (mp) REVERT: G 55 ASP cc_start: 0.8955 (p0) cc_final: 0.8067 (t70) REVERT: G 113 ARG cc_start: 0.5221 (ttt-90) cc_final: 0.4428 (ptp-170) REVERT: I 64 GLN cc_start: 0.8064 (mt0) cc_final: 0.7298 (tt0) REVERT: I 97 MET cc_start: 0.8298 (mmm) cc_final: 0.8046 (mmm) REVERT: J 1 MET cc_start: 0.8799 (ttm) cc_final: 0.8579 (ttm) REVERT: J 48 MET cc_start: 0.9081 (mmm) cc_final: 0.8545 (mmm) REVERT: W 763 TYR cc_start: 0.9128 (m-10) cc_final: 0.8805 (m-80) REVERT: W 771 LYS cc_start: 0.8538 (tptt) cc_final: 0.8292 (ptmm) REVERT: c 62 ILE cc_start: 0.5430 (mm) cc_final: 0.5228 (pt) REVERT: c 74 LYS cc_start: 0.7884 (mmpt) cc_final: 0.7234 (pttp) outliers start: 4 outliers final: 0 residues processed: 362 average time/residue: 0.2733 time to fit residues: 162.9447 Evaluate side-chains 264 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 1.450 ------------------------------------------------------------------------------- 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: 50.0000 chunk 331 optimal weight: 30.0000 chunk 93 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 222 optimal weight: 9.9990 chunk 364 optimal weight: 9.9990 chunk 191 optimal weight: 9.9990 chunk 210 optimal weight: 5.9990 chunk 408 optimal weight: 50.0000 chunk 6 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 GLN ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 GLN ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN ** A 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 GLN ** A1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 ASN ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 12 ASN I 22 ASN I 31 ASN V 31 ASN ** W 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 783 HIS ** W 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 44 GLN ** d 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 79 HIS ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 68 GLN f 93 GLN h 79 HIS ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.079343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.054520 restraints weight = 301958.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.055329 restraints weight = 178817.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.055623 restraints weight = 115431.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.055736 restraints weight = 90305.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.055815 restraints weight = 85982.851| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 47588 Z= 0.290 Angle : 0.799 21.280 65369 Z= 0.408 Chirality : 0.048 0.419 7326 Planarity : 0.005 0.061 7516 Dihedral : 21.677 169.888 8502 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.57 % Favored : 96.21 % Rotamer: Outliers : 0.04 % Allowed : 3.05 % Favored : 96.91 % 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: 0.19 (0.12), residues: 5042 helix: 0.92 (0.12), residues: 1928 sheet: -0.34 (0.18), residues: 732 loop : -0.28 (0.13), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A1381 TYR 0.027 0.002 TYR A 37 PHE 0.030 0.002 PHE B 100 TRP 0.024 0.003 TRP A 139 HIS 0.016 0.002 HIS B 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.29 (47554) covalent geometry : angle 0.78610 / 0.41 (65336) hydrogen bonds : bond 0.05729 / 3.70 ( 2102) hydrogen bonds : angle 4.95284 / 3.51 ( 5693) metal coordination : bond 0.01909 / 1.02 ( 34) metal coordination : angle 6.49871 / 3.80 ( 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 314 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 312 time to evaluate : 1.612 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: A 41 MET cc_start: 0.5555 (mtp) cc_final: 0.5210 (mmm) REVERT: A 84 MET cc_start: 0.8102 (tmm) cc_final: 0.7516 (tmm) REVERT: A 122 MET cc_start: -0.2111 (tpt) cc_final: -0.2365 (tpt) REVERT: A 240 LEU cc_start: 0.9549 (tp) cc_final: 0.9171 (tp) REVERT: A 454 MET cc_start: 0.8844 (mpp) cc_final: 0.8501 (mpp) REVERT: A 456 MET cc_start: 0.8681 (ttm) cc_final: 0.7696 (ttp) REVERT: A 464 MET cc_start: 0.8898 (mtp) cc_final: 0.8666 (mtp) REVERT: A 501 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8310 (mt-10) REVERT: A 548 MET cc_start: 0.8918 (mtm) cc_final: 0.8118 (mpp) REVERT: A 635 MET cc_start: 0.9127 (tpt) cc_final: 0.8916 (tpt) REVERT: A 677 MET cc_start: 0.8696 (mmp) cc_final: 0.8356 (mmp) REVERT: A 958 LEU cc_start: 0.9664 (mt) cc_final: 0.9278 (mp) REVERT: A 1064 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8223 (mm-30) REVERT: A 1065 MET cc_start: 0.9246 (mmp) cc_final: 0.9004 (mmp) REVERT: A 1412 LEU cc_start: 0.9445 (mt) cc_final: 0.9222 (mt) REVERT: A 1432 MET cc_start: 0.9344 (mtp) cc_final: 0.9130 (mtt) REVERT: A 1439 MET cc_start: 0.8671 (tmm) cc_final: 0.8256 (tmm) REVERT: B 245 MET cc_start: 0.8631 (tmm) cc_final: 0.8379 (tmm) REVERT: B 588 MET cc_start: 0.8640 (ppp) cc_final: 0.8313 (ppp) REVERT: B 593 MET cc_start: 0.8996 (mmt) cc_final: 0.8683 (tpp) REVERT: B 789 MET cc_start: 0.9087 (mmp) cc_final: 0.8878 (mmm) REVERT: B 809 MET cc_start: 0.8898 (mtt) cc_final: 0.8584 (mtt) REVERT: B 812 LEU cc_start: 0.9678 (mt) cc_final: 0.9060 (tt) REVERT: B 1021 MET cc_start: 0.9276 (mpp) cc_final: 0.9039 (mpp) REVERT: B 1072 MET cc_start: 0.7642 (ttm) cc_final: 0.7376 (ttm) REVERT: B 1082 MET cc_start: 0.8545 (tpp) cc_final: 0.8234 (tpp) REVERT: B 1101 ASP cc_start: 0.8929 (m-30) cc_final: 0.8202 (t0) REVERT: B 1124 ARG cc_start: 0.9129 (mpp80) cc_final: 0.8908 (mpp80) REVERT: B 1138 MET cc_start: 0.9096 (mmm) cc_final: 0.8805 (mmm) REVERT: B 1203 LEU cc_start: 0.9662 (tt) cc_final: 0.9128 (tt) REVERT: B 1206 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8236 (mt-10) REVERT: C 36 MET cc_start: 0.8891 (mtm) cc_final: 0.8600 (mtp) REVERT: D 176 ASP cc_start: 0.8632 (m-30) cc_final: 0.8432 (m-30) REVERT: E 21 MET cc_start: 0.8941 (tmm) cc_final: 0.8677 (tmm) REVERT: E 34 MET cc_start: 0.8353 (tpp) cc_final: 0.8149 (tpp) REVERT: F 89 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8747 (mt-10) REVERT: G 44 TYR cc_start: 0.7670 (m-80) cc_final: 0.7219 (m-80) REVERT: G 48 VAL cc_start: 0.8369 (t) cc_final: 0.7999 (p) REVERT: G 113 ARG cc_start: 0.5193 (ttt-90) cc_final: 0.4415 (ptp-170) REVERT: G 118 ASN cc_start: 0.8029 (p0) cc_final: 0.7786 (p0) REVERT: I 40 ASP cc_start: 0.7132 (t0) cc_final: 0.6849 (t0) REVERT: I 64 GLN cc_start: 0.8184 (mt0) cc_final: 0.7475 (tt0) REVERT: W 763 TYR cc_start: 0.9162 (m-10) cc_final: 0.8820 (m-80) REVERT: W 771 LYS cc_start: 0.8568 (tptt) cc_final: 0.8265 (ptpp) REVERT: W 782 LEU cc_start: 0.8434 (mt) cc_final: 0.8213 (mm) outliers start: 2 outliers final: 1 residues processed: 314 average time/residue: 0.2646 time to fit residues: 137.0182 Evaluate side-chains 248 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 247 time to evaluate : 1.414 ------------------------------------------------------------------------------- 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: 5.9990 chunk 409 optimal weight: 50.0000 chunk 119 optimal weight: 10.0000 chunk 248 optimal weight: 2.9990 chunk 512 optimal weight: 20.0000 chunk 438 optimal weight: 30.0000 chunk 267 optimal weight: 10.0000 chunk 275 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 274 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN ** A 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1056 GLN A1190 GLN ** A1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN ** W 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 60 ASN ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3907 r_free = 0.3907 target = 0.079159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.054612 restraints weight = 300173.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.055122 restraints weight = 177338.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.055556 restraints weight = 123707.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.055953 restraints weight = 87779.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.055932 restraints weight = 85722.071| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 47588 Z= 0.230 Angle : 0.685 19.428 65369 Z= 0.358 Chirality : 0.046 0.325 7326 Planarity : 0.004 0.047 7516 Dihedral : 21.666 169.316 8502 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.79 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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: 0.35 (0.12), residues: 5042 helix: 1.09 (0.12), residues: 1928 sheet: -0.39 (0.18), residues: 711 loop : -0.17 (0.13), residues: 2403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG H 145 TYR 0.032 0.002 TYR h 80 PHE 0.041 0.002 PHE B 394 TRP 0.020 0.002 TRP V 67 HIS 0.008 0.001 HIS f 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.23 (47554) covalent geometry : angle 0.67245 / 0.36 (65336) hydrogen bonds : bond 0.04662 / 3.00 ( 2102) hydrogen bonds : angle 4.78411 / 3.37 ( 5693) metal coordination : bond 0.01364 / 0.76 ( 34) metal coordination : angle 5.90424 / 3.66 ( 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 315 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 1.421 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: A 41 MET cc_start: 0.5492 (mtp) cc_final: 0.5137 (mmm) REVERT: A 84 MET cc_start: 0.8208 (tmm) cc_final: 0.7650 (tmm) REVERT: A 122 MET cc_start: -0.1932 (tpt) cc_final: -0.2216 (tpt) REVERT: A 178 ASP cc_start: 0.8307 (m-30) cc_final: 0.7994 (p0) REVERT: A 240 LEU cc_start: 0.9531 (tp) cc_final: 0.9106 (tp) REVERT: A 305 MET cc_start: 0.9049 (mtp) cc_final: 0.8845 (mtp) REVERT: A 464 MET cc_start: 0.8888 (mtp) cc_final: 0.8560 (mtp) REVERT: A 501 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8402 (mt-10) REVERT: A 522 MET cc_start: 0.8850 (mtm) cc_final: 0.8517 (pmm) REVERT: A 635 MET cc_start: 0.9101 (tpt) cc_final: 0.8670 (tpt) REVERT: A 677 MET cc_start: 0.8607 (mmp) cc_final: 0.8406 (mmp) REVERT: A 958 LEU cc_start: 0.9653 (mt) cc_final: 0.9200 (mp) REVERT: A 1064 GLU cc_start: 0.8432 (mm-30) cc_final: 0.7895 (mm-30) REVERT: A 1412 LEU cc_start: 0.9416 (mt) cc_final: 0.9184 (mt) REVERT: A 1439 MET cc_start: 0.8778 (tmm) cc_final: 0.8390 (tmm) REVERT: A 1447 MET cc_start: 0.8289 (mmp) cc_final: 0.7492 (mmm) REVERT: B 119 MET cc_start: 0.8642 (mpp) cc_final: 0.8366 (mpp) REVERT: B 245 MET cc_start: 0.8650 (tmm) cc_final: 0.8152 (tmm) REVERT: B 305 MET cc_start: 0.9582 (mmm) cc_final: 0.9187 (mmm) REVERT: B 593 MET cc_start: 0.8987 (mmt) cc_final: 0.8614 (tpp) REVERT: B 699 MET cc_start: 0.8787 (tpt) cc_final: 0.7890 (ttt) REVERT: B 789 MET cc_start: 0.9086 (mmp) cc_final: 0.8748 (mmp) REVERT: B 809 MET cc_start: 0.8847 (mtt) cc_final: 0.8531 (mtt) REVERT: B 812 LEU cc_start: 0.9658 (mt) cc_final: 0.8952 (tt) REVERT: B 864 LYS cc_start: 0.8802 (mmpt) cc_final: 0.8589 (mmtm) REVERT: B 872 GLU cc_start: 0.7370 (mt-10) cc_final: 0.6735 (mt-10) REVERT: B 1021 MET cc_start: 0.9270 (mpp) cc_final: 0.8990 (mpp) REVERT: B 1133 MET cc_start: 0.8969 (mmm) cc_final: 0.8175 (mmp) REVERT: B 1152 MET cc_start: 0.8829 (tpt) cc_final: 0.8336 (tpp) REVERT: B 1203 LEU cc_start: 0.9695 (tt) cc_final: 0.9437 (tt) REVERT: B 1207 LEU cc_start: 0.9630 (mt) cc_final: 0.9249 (mt) REVERT: C 20 MET cc_start: 0.8575 (tmm) cc_final: 0.8070 (tmm) REVERT: C 36 MET cc_start: 0.8810 (mtm) cc_final: 0.8152 (mtm) REVERT: E 34 MET cc_start: 0.8320 (tpp) cc_final: 0.8118 (tpp) REVERT: E 57 MET cc_start: 0.8166 (ttp) cc_final: 0.6917 (ttp) REVERT: F 89 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8698 (mt-10) REVERT: G 44 TYR cc_start: 0.7594 (m-80) cc_final: 0.7192 (m-80) REVERT: I 39 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8767 (mp0) REVERT: I 40 ASP cc_start: 0.7227 (t0) cc_final: 0.6879 (t0) REVERT: I 64 GLN cc_start: 0.8189 (mt0) cc_final: 0.7603 (tt0) REVERT: L 70 ASP cc_start: 0.8297 (t0) cc_final: 0.8009 (t70) REVERT: W 763 TYR cc_start: 0.9189 (m-10) cc_final: 0.8884 (m-80) REVERT: h 113 LYS cc_start: 0.6288 (mtmm) cc_final: 0.5596 (ptmm) outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 0.2500 time to fit residues: 130.8616 Evaluate side-chains 245 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 1.397 ------------------------------------------------------------------------------- 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: 5.9990 chunk 397 optimal weight: 50.0000 chunk 412 optimal weight: 50.0000 chunk 486 optimal weight: 3.9990 chunk 263 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 353 optimal weight: 5.9990 chunk 379 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 212 optimal weight: 0.9990 chunk 464 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN ** A 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 GLN ** A1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN ** W 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 783 HIS ** W 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 64 ASN ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3921 r_free = 0.3921 target = 0.079755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.054686 restraints weight = 304990.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.056171 restraints weight = 175800.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.056071 restraints weight = 105401.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.056378 restraints weight = 94056.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.056449 restraints weight = 83104.583| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 47588 Z= 0.151 Angle : 0.625 17.392 65369 Z= 0.328 Chirality : 0.044 0.306 7326 Planarity : 0.004 0.070 7516 Dihedral : 21.579 167.001 8502 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.39 % Favored : 96.47 % Rotamer: Outliers : 0.02 % Allowed : 1.14 % Favored : 98.84 % 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: 0.59 (0.12), residues: 5042 helix: 1.34 (0.12), residues: 1921 sheet: -0.29 (0.19), residues: 715 loop : -0.07 (0.13), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG f 95 TYR 0.055 0.001 TYR h 80 PHE 0.024 0.001 PHE D 115 TRP 0.018 0.001 TRP A 139 HIS 0.021 0.001 HIS B 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (47554) covalent geometry : angle 0.61524 / 0.33 (65336) hydrogen bonds : bond 0.04234 / 2.71 ( 2102) hydrogen bonds : angle 4.56719 / 3.23 ( 5693) metal coordination : bond 0.00831 / 0.48 ( 34) metal coordination : angle 4.92804 / 2.96 ( 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 307 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 306 time to evaluate : 1.539 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 41 MET cc_start: 0.5486 (mtp) cc_final: 0.5145 (mmm) REVERT: A 84 MET cc_start: 0.8177 (tmm) cc_final: 0.7601 (tmm) REVERT: A 178 ASP cc_start: 0.8435 (m-30) cc_final: 0.8100 (p0) REVERT: A 182 LEU cc_start: 0.9313 (tp) cc_final: 0.9013 (tp) REVERT: A 240 LEU cc_start: 0.9425 (tp) cc_final: 0.9003 (tp) REVERT: A 456 MET cc_start: 0.8998 (ttm) cc_final: 0.8612 (ttp) REVERT: A 464 MET cc_start: 0.8836 (mtp) cc_final: 0.8541 (mtm) REVERT: A 501 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8285 (mt-10) REVERT: A 535 MET cc_start: 0.8974 (ttp) cc_final: 0.8445 (mtp) REVERT: A 635 MET cc_start: 0.9023 (tpt) cc_final: 0.8560 (tpt) REVERT: A 677 MET cc_start: 0.8664 (mmp) cc_final: 0.8442 (mmp) REVERT: A 770 MET cc_start: 0.8754 (mmp) cc_final: 0.8465 (tpp) REVERT: A 827 ASP cc_start: 0.9031 (m-30) cc_final: 0.8755 (m-30) REVERT: A 844 LYS cc_start: 0.8834 (mppt) cc_final: 0.8507 (mppt) REVERT: A 850 MET cc_start: 0.8220 (tpp) cc_final: 0.7471 (tpp) REVERT: A 958 LEU cc_start: 0.9657 (mt) cc_final: 0.9226 (mp) REVERT: A 1064 GLU cc_start: 0.8318 (mm-30) cc_final: 0.8033 (mm-30) REVERT: A 1065 MET cc_start: 0.9291 (mmm) cc_final: 0.8942 (mmp) REVERT: A 1439 MET cc_start: 0.8574 (tmm) cc_final: 0.8276 (tmm) REVERT: B 106 LEU cc_start: 0.9704 (mt) cc_final: 0.9443 (mt) REVERT: B 245 MET cc_start: 0.8597 (tmm) cc_final: 0.8073 (tmm) REVERT: B 305 MET cc_start: 0.9588 (mmm) cc_final: 0.9197 (mmm) REVERT: B 588 MET cc_start: 0.8562 (ppp) cc_final: 0.8323 (ppp) REVERT: B 593 MET cc_start: 0.8999 (mmt) cc_final: 0.8656 (tpp) REVERT: B 789 MET cc_start: 0.9107 (mmp) cc_final: 0.8772 (mmp) REVERT: B 809 MET cc_start: 0.8821 (mtt) cc_final: 0.8473 (mtt) REVERT: B 812 LEU cc_start: 0.9651 (mt) cc_final: 0.8949 (tt) REVERT: B 1021 MET cc_start: 0.9282 (mpp) cc_final: 0.8952 (mpp) REVERT: B 1098 MET cc_start: 0.8196 (mpp) cc_final: 0.7837 (mpp) REVERT: B 1133 MET cc_start: 0.9088 (mmm) cc_final: 0.8504 (mmp) REVERT: B 1203 LEU cc_start: 0.9683 (tt) cc_final: 0.9467 (tt) REVERT: B 1207 LEU cc_start: 0.9632 (mt) cc_final: 0.9277 (mt) REVERT: C 20 MET cc_start: 0.8721 (tmm) cc_final: 0.8184 (tmm) REVERT: C 36 MET cc_start: 0.8818 (mtm) cc_final: 0.8117 (mtm) REVERT: E 21 MET cc_start: 0.9091 (tmm) cc_final: 0.8885 (tmm) REVERT: E 34 MET cc_start: 0.8318 (tpp) cc_final: 0.8056 (tpp) REVERT: E 57 MET cc_start: 0.7942 (ttp) cc_final: 0.7594 (ttp) REVERT: F 89 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8567 (mt-10) REVERT: G 113 ARG cc_start: 0.5250 (ttt-90) cc_final: 0.4513 (ptp-170) REVERT: I 39 GLU cc_start: 0.9099 (mm-30) cc_final: 0.8801 (mp0) REVERT: I 40 ASP cc_start: 0.7272 (t0) cc_final: 0.6845 (t0) REVERT: I 64 GLN cc_start: 0.8195 (mt0) cc_final: 0.7770 (tt0) REVERT: W 763 TYR cc_start: 0.9200 (m-10) cc_final: 0.8831 (m-80) REVERT: h 113 LYS cc_start: 0.6170 (mtmm) cc_final: 0.5467 (ptmm) outliers start: 1 outliers final: 1 residues processed: 307 average time/residue: 0.2201 time to fit residues: 114.1692 Evaluate side-chains 250 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 249 time to evaluate : 1.334 ------------------------------------------------------------------------------- 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: 10.0000 chunk 390 optimal weight: 50.0000 chunk 116 optimal weight: 0.0670 chunk 512 optimal weight: 20.0000 chunk 392 optimal weight: 40.0000 chunk 215 optimal weight: 6.9990 chunk 256 optimal weight: 10.0000 chunk 355 optimal weight: 20.0000 chunk 140 optimal weight: 8.9990 chunk 425 optimal weight: 9.9990 chunk 476 optimal weight: 50.0000 overall best weight: 7.2128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 136 ASN ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 GLN ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN ** A 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 GLN ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS B 761 HIS B 843 GLN ** B 932 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN M 53 ASN ** W 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 784 ASN ** d 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.077646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.052808 restraints weight = 307336.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.053504 restraints weight = 170437.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.053574 restraints weight = 121986.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.053845 restraints weight = 93458.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.054075 restraints weight = 81730.329| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 47588 Z= 0.288 Angle : 0.754 19.723 65369 Z= 0.387 Chirality : 0.046 0.289 7326 Planarity : 0.005 0.094 7516 Dihedral : 21.667 167.790 8502 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.58 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % 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: 0.30 (0.12), residues: 5042 helix: 1.06 (0.12), residues: 1936 sheet: -0.44 (0.19), residues: 700 loop : -0.20 (0.13), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG h 76 TYR 0.064 0.002 TYR h 80 PHE 0.031 0.002 PHE B 394 TRP 0.025 0.002 TRP A 139 HIS 0.018 0.002 HIS B 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.29 (47554) covalent geometry : angle 0.74223 / 0.39 (65336) hydrogen bonds : bond 0.05306 / 3.43 ( 2102) hydrogen bonds : angle 4.85032 / 3.42 ( 5693) metal coordination : bond 0.01793 / 0.96 ( 34) metal coordination : angle 6.00985 / 3.52 ( 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 278 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 1.285 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 41 MET cc_start: 0.5585 (mtp) cc_final: 0.5228 (mmm) REVERT: A 84 MET cc_start: 0.8240 (tmm) cc_final: 0.7646 (ppp) REVERT: A 178 ASP cc_start: 0.8342 (m-30) cc_final: 0.8083 (p0) REVERT: A 182 LEU cc_start: 0.9347 (tp) cc_final: 0.9038 (tp) REVERT: A 240 LEU cc_start: 0.9534 (tp) cc_final: 0.9269 (tp) REVERT: A 305 MET cc_start: 0.9337 (mmm) cc_final: 0.8855 (mmm) REVERT: A 456 MET cc_start: 0.8878 (ttm) cc_final: 0.8450 (ttp) REVERT: A 501 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8311 (mt-10) REVERT: A 522 MET cc_start: 0.9071 (mtm) cc_final: 0.8694 (pmm) REVERT: A 635 MET cc_start: 0.9038 (tpt) cc_final: 0.8736 (tpt) REVERT: A 677 MET cc_start: 0.8742 (mmp) cc_final: 0.8373 (mmp) REVERT: A 827 ASP cc_start: 0.9066 (m-30) cc_final: 0.8778 (m-30) REVERT: A 844 LYS cc_start: 0.9297 (mptt) cc_final: 0.8888 (mttp) REVERT: A 850 MET cc_start: 0.8073 (tpp) cc_final: 0.7539 (tpp) REVERT: A 1064 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7830 (mm-30) REVERT: A 1270 MET cc_start: 0.9361 (pmm) cc_final: 0.8957 (pmm) REVERT: A 1378 MET cc_start: 0.8607 (mtp) cc_final: 0.8237 (ttm) REVERT: A 1447 MET cc_start: 0.8010 (mmp) cc_final: 0.7669 (mmp) REVERT: B 245 MET cc_start: 0.8657 (tmm) cc_final: 0.8181 (tmm) REVERT: B 302 MET cc_start: 0.9239 (ptm) cc_final: 0.8983 (ptm) REVERT: B 305 MET cc_start: 0.9596 (mmm) cc_final: 0.9207 (mmm) REVERT: B 588 MET cc_start: 0.8603 (ppp) cc_final: 0.8314 (ppp) REVERT: B 593 MET cc_start: 0.8931 (mmt) cc_final: 0.8581 (tpp) REVERT: B 699 MET cc_start: 0.8783 (tpt) cc_final: 0.7882 (ttt) REVERT: B 747 MET cc_start: 0.8809 (mmm) cc_final: 0.8304 (mmm) REVERT: B 789 MET cc_start: 0.9084 (mmp) cc_final: 0.8769 (mmp) REVERT: B 809 MET cc_start: 0.8783 (mtt) cc_final: 0.8452 (mtt) REVERT: B 812 LEU cc_start: 0.9645 (mt) cc_final: 0.9044 (tt) REVERT: B 1021 MET cc_start: 0.9284 (mpp) cc_final: 0.8930 (mpp) REVERT: B 1072 MET cc_start: 0.8018 (mmm) cc_final: 0.7634 (mmm) REVERT: B 1098 MET cc_start: 0.8109 (mpp) cc_final: 0.7744 (mpp) REVERT: B 1133 MET cc_start: 0.9083 (mmm) cc_final: 0.8324 (mmp) REVERT: B 1152 MET cc_start: 0.8774 (tpt) cc_final: 0.8311 (tpp) REVERT: B 1206 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8344 (mp0) REVERT: B 1210 MET cc_start: 0.9377 (tpp) cc_final: 0.9092 (mmm) REVERT: C 20 MET cc_start: 0.8736 (tmm) cc_final: 0.8288 (tmm) REVERT: C 36 MET cc_start: 0.8802 (mtm) cc_final: 0.8148 (mtm) REVERT: C 79 MET cc_start: 0.8712 (tpp) cc_final: 0.8410 (tpt) REVERT: D 91 LYS cc_start: 0.8442 (ttmt) cc_final: 0.8110 (ptpp) REVERT: E 21 MET cc_start: 0.8964 (tmm) cc_final: 0.8750 (tmm) REVERT: E 34 MET cc_start: 0.8367 (tpp) cc_final: 0.8053 (tpp) REVERT: F 89 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8610 (mt-10) REVERT: G 44 TYR cc_start: 0.7509 (m-80) cc_final: 0.7134 (m-80) REVERT: G 113 ARG cc_start: 0.5248 (ttt-90) cc_final: 0.4505 (ptp-170) REVERT: I 39 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8902 (mp0) REVERT: I 40 ASP cc_start: 0.7446 (t0) cc_final: 0.7121 (t0) REVERT: I 64 GLN cc_start: 0.8300 (mt0) cc_final: 0.7899 (tt0) REVERT: J 1 MET cc_start: 0.8833 (ttm) cc_final: 0.7879 (ttp) REVERT: W 763 TYR cc_start: 0.9212 (m-10) cc_final: 0.8326 (m-80) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.2238 time to fit residues: 104.6119 Evaluate side-chains 229 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 1.292 ------------------------------------------------------------------------------- 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: 7.9990 chunk 518 optimal weight: 9.9990 chunk 401 optimal weight: 30.0000 chunk 150 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 193 optimal weight: 9.9990 chunk 131 optimal weight: 0.0870 chunk 301 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 overall best weight: 2.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN ** A 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 GLN ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 HIS B 932 HIS I 22 ASN ** W 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 783 HIS ** b 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 38 ASN ** d 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 81 ASN ** 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 = 0.3909 r_free = 0.3909 target = 0.079156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.054290 restraints weight = 300726.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.055351 restraints weight = 162825.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.055425 restraints weight = 113670.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.055913 restraints weight = 84866.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.055856 restraints weight = 76918.565| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 47588 Z= 0.140 Angle : 0.617 17.099 65369 Z= 0.323 Chirality : 0.044 0.296 7326 Planarity : 0.004 0.072 7516 Dihedral : 21.580 166.818 8502 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.57 % Favored : 96.35 % Rotamer: Outliers : 0.02 % Allowed : 0.69 % Favored : 99.28 % 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: 0.58 (0.12), residues: 5042 helix: 1.32 (0.12), residues: 1938 sheet: -0.27 (0.19), residues: 711 loop : -0.09 (0.13), residues: 2393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG a 116 TYR 0.023 0.001 TYR A 544 PHE 0.023 0.001 PHE D 115 TRP 0.024 0.002 TRP A 139 HIS 0.011 0.001 HIS W 783 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (47554) covalent geometry : angle 0.60674 / 0.32 (65336) hydrogen bonds : bond 0.04039 / 2.60 ( 2102) hydrogen bonds : angle 4.52967 / 3.20 ( 5693) metal coordination : bond 0.00835 / 0.47 ( 34) metal coordination : angle 5.08906 / 3.10 ( 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 303 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 302 time to evaluate : 1.386 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: A 41 MET cc_start: 0.5593 (mtp) cc_final: 0.5233 (mmm) REVERT: A 84 MET cc_start: 0.8137 (tmm) cc_final: 0.7465 (ppp) REVERT: A 178 ASP cc_start: 0.8387 (m-30) cc_final: 0.7974 (p0) REVERT: A 182 LEU cc_start: 0.9319 (tp) cc_final: 0.8992 (tp) REVERT: A 240 LEU cc_start: 0.9479 (tp) cc_final: 0.9202 (tp) REVERT: A 305 MET cc_start: 0.9313 (mmm) cc_final: 0.8642 (mmm) REVERT: A 456 MET cc_start: 0.9027 (ttm) cc_final: 0.8483 (ttp) REVERT: A 464 MET cc_start: 0.9016 (mtp) cc_final: 0.8741 (mtm) REVERT: A 522 MET cc_start: 0.8898 (mtm) cc_final: 0.8631 (pmm) REVERT: A 635 MET cc_start: 0.8995 (tpt) cc_final: 0.8495 (tpt) REVERT: A 677 MET cc_start: 0.8893 (mmp) cc_final: 0.8315 (mmp) REVERT: A 770 MET cc_start: 0.9004 (mmp) cc_final: 0.8628 (mmp) REVERT: A 827 ASP cc_start: 0.8950 (m-30) cc_final: 0.8636 (m-30) REVERT: A 844 LYS cc_start: 0.9343 (mptt) cc_final: 0.8892 (mppt) REVERT: A 958 LEU cc_start: 0.9650 (mt) cc_final: 0.9157 (mp) REVERT: A 1064 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7852 (mm-30) REVERT: A 1378 MET cc_start: 0.8657 (mtp) cc_final: 0.8270 (ttm) REVERT: A 1412 LEU cc_start: 0.9415 (mt) cc_final: 0.9176 (mt) REVERT: A 1447 MET cc_start: 0.8131 (mmp) cc_final: 0.7659 (mmm) REVERT: B 106 LEU cc_start: 0.9684 (mt) cc_final: 0.9474 (mt) REVERT: B 245 MET cc_start: 0.8585 (tmm) cc_final: 0.8062 (tmm) REVERT: B 302 MET cc_start: 0.9208 (ptm) cc_final: 0.8970 (ptm) REVERT: B 305 MET cc_start: 0.9601 (mmm) cc_final: 0.9218 (mmm) REVERT: B 593 MET cc_start: 0.9065 (mmt) cc_final: 0.8722 (tpp) REVERT: B 699 MET cc_start: 0.8836 (tpt) cc_final: 0.7950 (ttt) REVERT: B 789 MET cc_start: 0.9126 (mmp) cc_final: 0.8821 (mmp) REVERT: B 809 MET cc_start: 0.8820 (mtt) cc_final: 0.8466 (mtt) REVERT: B 812 LEU cc_start: 0.9597 (mt) cc_final: 0.8923 (tt) REVERT: B 1021 MET cc_start: 0.9282 (mpp) cc_final: 0.9039 (mpp) REVERT: B 1072 MET cc_start: 0.7902 (mmm) cc_final: 0.7549 (mmm) REVERT: B 1098 MET cc_start: 0.8182 (mpp) cc_final: 0.7813 (mpp) REVERT: B 1133 MET cc_start: 0.9098 (mmm) cc_final: 0.8355 (mmp) REVERT: B 1152 MET cc_start: 0.8707 (tpt) cc_final: 0.8281 (tpp) REVERT: B 1203 LEU cc_start: 0.9678 (tt) cc_final: 0.9452 (tt) REVERT: B 1207 LEU cc_start: 0.9729 (mm) cc_final: 0.9427 (mm) REVERT: B 1210 MET cc_start: 0.9400 (tpp) cc_final: 0.9160 (mmm) REVERT: C 20 MET cc_start: 0.8679 (tmm) cc_final: 0.8171 (tmm) REVERT: C 36 MET cc_start: 0.8830 (mtm) cc_final: 0.8108 (mtm) REVERT: C 79 MET cc_start: 0.8760 (tpp) cc_final: 0.8422 (tpt) REVERT: D 91 LYS cc_start: 0.8411 (ttmt) cc_final: 0.8085 (ptpt) REVERT: E 21 MET cc_start: 0.8992 (tmm) cc_final: 0.8697 (tmm) REVERT: E 57 MET cc_start: 0.7358 (ttp) cc_final: 0.6815 (ttp) REVERT: G 22 MET cc_start: 0.9368 (ptt) cc_final: 0.8757 (ptt) REVERT: G 35 GLU cc_start: 0.6667 (mm-30) cc_final: 0.6221 (tp30) REVERT: G 113 ARG cc_start: 0.5235 (ttt-90) cc_final: 0.4520 (ptp-170) REVERT: I 39 GLU cc_start: 0.9139 (mm-30) cc_final: 0.8877 (mp0) REVERT: I 40 ASP cc_start: 0.7475 (t0) cc_final: 0.7154 (t0) REVERT: I 64 GLN cc_start: 0.8253 (mt0) cc_final: 0.7844 (tt0) REVERT: J 1 MET cc_start: 0.8892 (ttm) cc_final: 0.8130 (ttp) REVERT: J 48 MET cc_start: 0.9241 (mmm) cc_final: 0.8875 (mmm) REVERT: M 73 TRP cc_start: 0.5922 (t60) cc_final: 0.5627 (t60) REVERT: a 120 MET cc_start: 0.2379 (mpp) cc_final: 0.2018 (mmt) outliers start: 1 outliers final: 0 residues processed: 303 average time/residue: 0.2374 time to fit residues: 121.2967 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 : 1.116 ------------------------------------------------------------------------------- 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: 7.9990 chunk 463 optimal weight: 20.0000 chunk 275 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 490 optimal weight: 8.9990 chunk 238 optimal weight: 7.9990 chunk 109 optimal weight: 7.9990 chunk 188 optimal weight: 1.9990 chunk 290 optimal weight: 30.0000 chunk 120 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 GLN ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN ** A 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 GLN ** A1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS I 22 ASN ** W 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3876 r_free = 0.3876 target = 0.077685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.054315 restraints weight = 332535.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.054792 restraints weight = 190785.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.055047 restraints weight = 140243.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.055138 restraints weight = 111505.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.055162 restraints weight = 109122.628| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.5404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 47588 Z= 0.276 Angle : 0.740 19.608 65369 Z= 0.378 Chirality : 0.045 0.299 7326 Planarity : 0.005 0.080 7516 Dihedral : 21.628 167.440 8502 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.76 % Favored : 95.16 % 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: 0.35 (0.12), residues: 5042 helix: 1.08 (0.12), residues: 1954 sheet: -0.29 (0.19), residues: 698 loop : -0.22 (0.13), residues: 2390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG a 116 TYR 0.020 0.002 TYR B 811 PHE 0.036 0.002 PHE B 394 TRP 0.025 0.002 TRP A 139 HIS 0.011 0.002 HIS A 660 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.28 (47554) covalent geometry : angle 0.72883 / 0.38 (65336) hydrogen bonds : bond 0.05219 / 3.38 ( 2102) hydrogen bonds : angle 4.80113 / 3.38 ( 5693) metal coordination : bond 0.01431 / 0.78 ( 34) metal coordination : angle 5.70636 / 3.35 ( 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 286 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 1.126 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 41 MET cc_start: 0.5569 (mtp) cc_final: 0.5093 (mmm) REVERT: A 84 MET cc_start: 0.8278 (tmm) cc_final: 0.7654 (ppp) REVERT: A 178 ASP cc_start: 0.8442 (m-30) cc_final: 0.8131 (p0) REVERT: A 182 LEU cc_start: 0.9348 (tp) cc_final: 0.9029 (tp) REVERT: A 324 LYS cc_start: 0.9537 (tppt) cc_final: 0.8975 (tptp) REVERT: A 456 MET cc_start: 0.8920 (ttm) cc_final: 0.8607 (ttp) REVERT: A 464 MET cc_start: 0.8909 (mtp) cc_final: 0.8631 (mtp) REVERT: A 522 MET cc_start: 0.9202 (mtm) cc_final: 0.8677 (pmm) REVERT: A 548 MET cc_start: 0.8600 (mmt) cc_final: 0.7946 (mmm) REVERT: A 635 MET cc_start: 0.9060 (tpt) cc_final: 0.8738 (tpt) REVERT: A 677 MET cc_start: 0.8934 (mmp) cc_final: 0.8342 (mmp) REVERT: A 770 MET cc_start: 0.9033 (mmp) cc_final: 0.8673 (mmp) REVERT: A 827 ASP cc_start: 0.9091 (m-30) cc_final: 0.8797 (m-30) REVERT: A 844 LYS cc_start: 0.9349 (mptt) cc_final: 0.8817 (mppt) REVERT: A 1064 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7864 (mm-30) REVERT: A 1378 MET cc_start: 0.8641 (mtp) cc_final: 0.8270 (ttm) REVERT: A 1439 MET cc_start: 0.8510 (tmm) cc_final: 0.8211 (tmm) REVERT: B 245 MET cc_start: 0.8608 (tmm) cc_final: 0.8274 (tmm) REVERT: B 302 MET cc_start: 0.9225 (ptm) cc_final: 0.8991 (ptm) REVERT: B 305 MET cc_start: 0.9627 (mmm) cc_final: 0.9276 (mmm) REVERT: B 374 MET cc_start: 0.8967 (ptp) cc_final: 0.8764 (ptp) REVERT: B 593 MET cc_start: 0.9028 (mmt) cc_final: 0.8689 (tpp) REVERT: B 789 MET cc_start: 0.9063 (mmp) cc_final: 0.8762 (mmp) REVERT: B 809 MET cc_start: 0.8753 (mtt) cc_final: 0.8411 (mtt) REVERT: B 812 LEU cc_start: 0.9653 (mt) cc_final: 0.9051 (tt) REVERT: B 1021 MET cc_start: 0.9289 (mpp) cc_final: 0.8907 (mpp) REVERT: B 1072 MET cc_start: 0.7976 (mmm) cc_final: 0.7595 (mmm) REVERT: B 1098 MET cc_start: 0.8192 (mpp) cc_final: 0.7755 (mpp) REVERT: B 1133 MET cc_start: 0.9119 (mmm) cc_final: 0.8564 (mmp) REVERT: B 1138 MET cc_start: 0.9124 (tpt) cc_final: 0.8912 (tpp) REVERT: B 1152 MET cc_start: 0.8655 (tpt) cc_final: 0.8296 (tpp) REVERT: B 1206 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8307 (mt-10) REVERT: C 20 MET cc_start: 0.8698 (tmm) cc_final: 0.8265 (tmm) REVERT: D 91 LYS cc_start: 0.8471 (ttmt) cc_final: 0.8107 (ptpt) REVERT: E 34 MET cc_start: 0.8501 (tpp) cc_final: 0.8153 (tpp) REVERT: G 22 MET cc_start: 0.9363 (ptt) cc_final: 0.8774 (ptt) REVERT: G 35 GLU cc_start: 0.6790 (mm-30) cc_final: 0.6386 (tp30) REVERT: G 44 TYR cc_start: 0.7425 (m-80) cc_final: 0.7109 (m-80) REVERT: G 113 ARG cc_start: 0.5288 (ttt-90) cc_final: 0.4567 (ptp-170) REVERT: I 39 GLU cc_start: 0.9279 (mm-30) cc_final: 0.8936 (mp0) REVERT: I 40 ASP cc_start: 0.7871 (t0) cc_final: 0.7557 (t0) REVERT: I 64 GLN cc_start: 0.8353 (mt0) cc_final: 0.8043 (tt0) REVERT: J 66 GLU cc_start: 0.4331 (tp30) cc_final: 0.4085 (tp30) REVERT: M 47 LEU cc_start: 0.6457 (tt) cc_final: 0.6234 (tt) REVERT: W 409 ASP cc_start: -0.0267 (m-30) cc_final: -0.0482 (m-30) REVERT: W 763 TYR cc_start: 0.9212 (m-10) cc_final: 0.8848 (m-80) REVERT: a 120 MET cc_start: 0.2818 (mpp) cc_final: 0.2170 (mmt) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.2198 time to fit residues: 106.3891 Evaluate side-chains 232 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 1.368 ------------------------------------------------------------------------------- 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: 6.9990 chunk 90 optimal weight: 7.9990 chunk 491 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 247 optimal weight: 5.9990 chunk 189 optimal weight: 0.2980 chunk 19 optimal weight: 9.9990 chunk 135 optimal weight: 8.9990 chunk 228 optimal weight: 10.0000 chunk 499 optimal weight: 30.0000 chunk 255 optimal weight: 0.9980 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN ** A 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 GLN ** A1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN W 783 HIS ** b 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.079134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.055933 restraints weight = 329293.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.056261 restraints weight = 189246.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.056704 restraints weight = 126899.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.056785 restraints weight = 103777.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.056818 restraints weight = 97045.236| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.5426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 47588 Z= 0.140 Angle : 0.625 17.297 65369 Z= 0.327 Chirality : 0.044 0.306 7326 Planarity : 0.004 0.104 7516 Dihedral : 21.520 167.096 8502 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.73 % Favored : 96.23 % Rotamer: Outliers : 0.02 % Allowed : 0.16 % Favored : 99.82 % 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: 0.56 (0.12), residues: 5042 helix: 1.33 (0.12), residues: 1939 sheet: -0.29 (0.19), residues: 694 loop : -0.12 (0.13), residues: 2409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 336 TYR 0.040 0.001 TYR h 80 PHE 0.027 0.001 PHE M 56 TRP 0.048 0.002 TRP M 73 HIS 0.012 0.001 HIS W 783 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (47554) covalent geometry : angle 0.61505 / 0.33 (65336) hydrogen bonds : bond 0.04016 / 2.60 ( 2102) hydrogen bonds : angle 4.54140 / 3.21 ( 5693) metal coordination : bond 0.00813 / 0.45 ( 34) metal coordination : angle 4.93415 / 3.04 ( 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 302 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 301 time to evaluate : 1.055 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 41 MET cc_start: 0.5548 (mtp) cc_final: 0.5053 (tmm) REVERT: A 84 MET cc_start: 0.8118 (tmm) cc_final: 0.7454 (tmm) REVERT: A 178 ASP cc_start: 0.8381 (m-30) cc_final: 0.8118 (p0) REVERT: A 180 MET cc_start: 0.7146 (tmm) cc_final: 0.6916 (tmm) REVERT: A 182 LEU cc_start: 0.9316 (tp) cc_final: 0.9005 (tp) REVERT: A 240 LEU cc_start: 0.9495 (tp) cc_final: 0.9154 (tp) REVERT: A 324 LYS cc_start: 0.9618 (tppt) cc_final: 0.8907 (tptp) REVERT: A 342 MET cc_start: 0.9175 (mmm) cc_final: 0.8906 (mmm) REVERT: A 456 MET cc_start: 0.8763 (ttm) cc_final: 0.8394 (ttp) REVERT: A 464 MET cc_start: 0.8957 (mtp) cc_final: 0.8657 (mtm) REVERT: A 501 GLU cc_start: 0.8562 (mt-10) cc_final: 0.7827 (mt-10) REVERT: A 548 MET cc_start: 0.8653 (mmt) cc_final: 0.7860 (mmm) REVERT: A 635 MET cc_start: 0.8970 (tpt) cc_final: 0.8517 (tpt) REVERT: A 677 MET cc_start: 0.8947 (mmp) cc_final: 0.8356 (mmp) REVERT: A 770 MET cc_start: 0.8992 (mmp) cc_final: 0.8772 (mmp) REVERT: A 827 ASP cc_start: 0.9025 (m-30) cc_final: 0.8718 (m-30) REVERT: A 844 LYS cc_start: 0.9233 (mptt) cc_final: 0.8765 (mppt) REVERT: A 958 LEU cc_start: 0.9625 (mt) cc_final: 0.9140 (mp) REVERT: A 1064 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7981 (mm-30) REVERT: A 1211 MET cc_start: 0.8542 (tpp) cc_final: 0.8263 (tmm) REVERT: A 1378 MET cc_start: 0.8634 (mtp) cc_final: 0.8266 (ttm) REVERT: A 1439 MET cc_start: 0.8439 (tmm) cc_final: 0.8154 (tmm) REVERT: B 245 MET cc_start: 0.8582 (tmm) cc_final: 0.8233 (tmm) REVERT: B 302 MET cc_start: 0.9215 (ptm) cc_final: 0.8972 (ptm) REVERT: B 305 MET cc_start: 0.9601 (mmm) cc_final: 0.9247 (mmm) REVERT: B 374 MET cc_start: 0.8997 (ptp) cc_final: 0.8780 (ptp) REVERT: B 593 MET cc_start: 0.9091 (mmt) cc_final: 0.8731 (tpp) REVERT: B 789 MET cc_start: 0.9094 (mmp) cc_final: 0.8830 (mmp) REVERT: B 809 MET cc_start: 0.8805 (mtt) cc_final: 0.8464 (mtt) REVERT: B 812 LEU cc_start: 0.9594 (mt) cc_final: 0.8943 (tt) REVERT: B 1021 MET cc_start: 0.9307 (mpp) cc_final: 0.8860 (mpp) REVERT: B 1101 ASP cc_start: 0.8808 (m-30) cc_final: 0.8466 (t0) REVERT: B 1132 GLU cc_start: 0.8062 (pm20) cc_final: 0.7702 (pm20) REVERT: B 1133 MET cc_start: 0.9061 (mmm) cc_final: 0.8624 (mmm) REVERT: B 1152 MET cc_start: 0.8706 (tpt) cc_final: 0.8387 (tpp) REVERT: B 1203 LEU cc_start: 0.9618 (tt) cc_final: 0.9038 (tt) REVERT: B 1206 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8198 (mt-10) REVERT: B 1207 LEU cc_start: 0.9725 (mm) cc_final: 0.9411 (mm) REVERT: C 20 MET cc_start: 0.8686 (tmm) cc_final: 0.8042 (tmm) REVERT: C 32 LEU cc_start: 0.9578 (tp) cc_final: 0.8973 (tp) REVERT: D 91 LYS cc_start: 0.8383 (ttmt) cc_final: 0.8027 (ptpp) REVERT: E 21 MET cc_start: 0.9028 (tmm) cc_final: 0.8774 (tmm) REVERT: E 34 MET cc_start: 0.8360 (tpp) cc_final: 0.8146 (tpp) REVERT: G 22 MET cc_start: 0.9441 (ptt) cc_final: 0.8876 (ptt) REVERT: G 44 TYR cc_start: 0.7489 (m-80) cc_final: 0.7116 (m-80) REVERT: G 113 ARG cc_start: 0.5228 (ttt-90) cc_final: 0.4582 (ptp-170) REVERT: I 39 GLU cc_start: 0.9272 (mm-30) cc_final: 0.8908 (mp0) REVERT: I 40 ASP cc_start: 0.7812 (t0) cc_final: 0.7507 (t0) REVERT: I 64 GLN cc_start: 0.8316 (mt0) cc_final: 0.7945 (tt0) REVERT: J 48 MET cc_start: 0.9207 (mmm) cc_final: 0.8724 (mmm) REVERT: K 33 ILE cc_start: 0.9127 (pt) cc_final: 0.8921 (pt) REVERT: W 409 ASP cc_start: -0.0265 (m-30) cc_final: -0.0477 (m-30) REVERT: W 763 TYR cc_start: 0.9230 (m-10) cc_final: 0.8873 (m-80) REVERT: a 120 MET cc_start: 0.2795 (mpp) cc_final: 0.2210 (mmt) outliers start: 1 outliers final: 0 residues processed: 302 average time/residue: 0.1969 time to fit residues: 101.0800 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 : 1.220 ------------------------------------------------------------------------------- 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: 2.9990 chunk 207 optimal weight: 0.1980 chunk 267 optimal weight: 6.9990 chunk 525 optimal weight: 30.0000 chunk 1 optimal weight: 9.9990 chunk 106 optimal weight: 0.0980 chunk 480 optimal weight: 20.0000 chunk 398 optimal weight: 50.0000 chunk 417 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 308 optimal weight: 4.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN ** A 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 GLN ** A1435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN ** b 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.079059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.056614 restraints weight = 324867.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.056384 restraints weight = 208733.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.056987 restraints weight = 139094.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.057156 restraints weight = 107326.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.057161 restraints weight = 100402.844| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.5513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 47588 Z= 0.137 Angle : 0.603 14.781 65369 Z= 0.315 Chirality : 0.043 0.315 7326 Planarity : 0.004 0.087 7516 Dihedral : 21.350 167.586 8502 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.91 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: 1.41 (0.12), residues: 1941 sheet: -0.22 (0.19), residues: 695 loop : -0.06 (0.13), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 336 TYR 0.018 0.001 TYR A 544 PHE 0.022 0.001 PHE D 115 TRP 0.022 0.001 TRP M 73 HIS 0.009 0.001 HIS f 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (47554) covalent geometry : angle 0.59570 / 0.31 (65336) hydrogen bonds : bond 0.03900 / 2.52 ( 2102) hydrogen bonds : angle 4.42551 / 3.12 ( 5693) metal coordination : bond 0.00634 / 0.35 ( 34) metal coordination : angle 4.19676 / 2.49 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6316.29 seconds wall clock time: 110 minutes 7.41 seconds (6607.41 seconds total)