Starting phenix.real_space_refine on Mon Nov 18 02:20:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j51_0676/11_2024/6j51_0676.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j51_0676/11_2024/6j51_0676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j51_0676/11_2024/6j51_0676.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j51_0676/11_2024/6j51_0676.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j51_0676/11_2024/6j51_0676.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j51_0676/11_2024/6j51_0676.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 336 5.49 5 Mg 1 5.21 5 S 214 5.16 5 C 28970 2.51 5 N 8476 2.21 5 O 9654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 47661 Number of models: 1 Model: "" Number of chains: 36 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: {'RNA': 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: "0" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 739 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "1" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 737 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 527 SG CYS A 67 73.788 61.247 141.221 1.00103.22 S ATOM 549 SG CYS A 70 77.286 60.356 142.049 1.00 94.73 S ATOM 594 SG CYS A 77 76.159 63.918 142.683 1.00 74.48 S ATOM 829 SG CYS A 107 77.246 84.365 98.772 1.00142.68 S ATOM 851 SG CYS A 110 78.610 81.035 97.986 1.00152.38 S ATOM 1222 SG CYS A 168 75.275 84.429 95.796 1.00155.44 S ATOM 19876 SG CYS B1163 87.259 61.365 128.218 1.00 76.06 S ATOM 19894 SG CYS B1166 85.386 64.753 127.204 1.00 77.90 S ATOM 20017 SG CYS B1182 83.456 61.219 128.289 1.00108.37 S ATOM 20040 SG CYS B1185 85.584 61.549 124.904 1.00109.59 S ATOM 20985 SG CYS C 85 87.697 74.823 207.982 1.00126.06 S ATOM 21033 SG CYS C 91 83.478 75.650 209.835 1.00108.11 S ATOM 21056 SG CYS C 94 84.896 78.131 206.366 1.00108.09 S ATOM 29164 SG CYS I 78 82.005 166.820 148.172 1.00173.59 S ATOM 29380 SG CYS I 103 82.241 163.203 147.546 1.00166.64 S ATOM 28780 SG CYS I 29 63.036 147.014 107.420 1.00154.71 S ATOM 28805 SG CYS I 32 60.011 149.335 105.903 1.00153.57 S ATOM 29521 SG CYS J 7 88.956 108.647 195.989 1.00 34.60 S ATOM 29544 SG CYS J 10 91.484 108.018 198.564 1.00 33.65 S ATOM 29820 SG CYS J 44 92.383 110.935 196.683 1.00 40.97 S ATOM 29826 SG CYS J 45 89.654 110.820 199.666 1.00 40.49 S ATOM 30988 SG CYS L 33 47.844 93.790 185.655 1.00114.61 S ATOM 31003 SG CYS L 36 45.885 94.068 188.914 1.00124.33 S ATOM 31113 SG CYS L 50 45.231 91.368 185.829 1.00122.63 S ATOM 31137 SG CYS L 53 44.717 95.388 184.826 1.00130.70 S ATOM 36833 SG CYS M 25 50.964 108.658 100.492 1.00198.31 S ATOM 36858 SG CYS M 28 51.187 105.242 99.898 1.00168.76 S ATOM 37016 SG CYS M 49 54.091 106.874 98.881 1.00180.55 S ATOM 37040 SG CYS M 52 51.099 107.232 96.671 1.00191.36 S ATOM 37277 SG CYS V 12 20.319 82.382 121.919 1.00 34.75 S ATOM 37299 SG CYS V 15 21.325 85.285 119.641 1.00 22.76 S ATOM 37401 SG CYS V 29 18.606 85.928 121.706 1.00 18.00 S ATOM 37422 SG CYS V 32 18.127 83.394 118.802 1.00 25.35 S Time building chain proxies: 23.15, per 1000 atoms: 0.49 Number of scatterers: 47661 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 336 15.00 Mg 1 11.99 O 9654 8.00 N 8476 7.00 C 28970 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: 10.34 Conformation dependent library (CDL) restraints added in 4.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 67 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 168 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 91 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 85 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 78 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 32 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 50 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 53 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 33 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 52 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 25 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 49 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 28 " pdb=" ZN V 300 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 12 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 15 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 29 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 32 " Number of angles added : 33 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9586 Finding SS restraints... Secondary structure from input PDB file: 201 helices and 60 sheets defined 43.1% alpha, 17.3% beta 144 base pairs and 266 stacking pairs defined. Time for finding SS restraints: 16.73 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: 3.604A pdb=" N CYS A 105 " --> pdb=" O LYS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 4.042A 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: 3.700A 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: 3.509A pdb=" N GLN A 278 " --> pdb=" O ASN A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 306 removed outlier: 3.622A pdb=" N MET A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 331 removed outlier: 3.585A pdb=" N LEU A 330 " --> pdb=" O ILE A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 341 Processing helix chain 'A' and resid 369 through 375 Processing helix chain 'A' and resid 385 through 396 removed outlier: 3.609A 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: 3.947A pdb=" N ASN A 549 " --> pdb=" O GLU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 583 removed outlier: 3.958A pdb=" N ALA A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 3.714A 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: 3.512A 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: 3.772A 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: 3.627A pdb=" N VAL A 913 " --> pdb=" O LYS A 910 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 914 " --> pdb=" O PRO A 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 910 through 914' Processing helix chain 'A' and resid 923 through 947 removed outlier: 3.991A pdb=" N GLU A 929 " --> pdb=" O GLU A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 973 Processing helix chain 'A' and resid 984 through 996 Processing helix chain 'A' and resid 1006 through 1017 removed outlier: 3.632A pdb=" N THR A1017 " --> pdb=" O GLN A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1028 Processing helix chain 'A' and resid 1029 through 1035 Processing helix chain 'A' and resid 1040 through 1058 removed outlier: 3.601A pdb=" N GLN A1056 " --> pdb=" O GLU A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1079 Proline residue: A1077 - end of helix Processing helix chain 'A' and resid 1098 through 1108 removed outlier: 3.594A pdb=" N ARG A1102 " --> pdb=" O LEU A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1128 Processing helix chain 'A' and resid 1129 through 1141 Processing helix chain 'A' and resid 1145 through 1148 No H-bonds generated for 'chain 'A' and resid 1145 through 1148' Processing helix chain 'A' and resid 1168 through 1177 removed outlier: 3.547A pdb=" N ALA A1174 " --> pdb=" O ASP A1170 " (cutoff:3.500A) removed outlier: 3.772A 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: 3.725A pdb=" N VAL A1221 " --> pdb=" O LYS A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1272 removed outlier: 3.896A pdb=" N LYS A1264 " --> pdb=" O ASP A1260 " (cutoff:3.500A) Processing helix chain 'A' and resid 1315 through 1321 removed outlier: 3.630A pdb=" N ALA A1321 " --> pdb=" O ALA A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1334 through 1343 removed outlier: 3.565A pdb=" N SER A1340 " --> pdb=" O VAL A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1362 removed outlier: 3.582A pdb=" N SER A1349 " --> pdb=" O GLU A1345 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP A1362 " --> pdb=" O VAL A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1380 removed outlier: 4.107A pdb=" N MET A1371 " --> pdb=" O ASN A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1393 Processing helix chain 'A' and resid 1398 through 1404 Processing helix chain 'A' and resid 1407 through 1418 Processing helix chain 'A' and resid 1426 through 1433 removed outlier: 3.664A 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: 3.591A pdb=" N TYR A1460 " --> pdb=" O PRO A1457 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 29 Processing helix chain 'B' and resid 31 through 44 removed outlier: 3.713A pdb=" N SER B 37 " --> pdb=" O GLN B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 51 Processing helix chain 'B' and resid 100 through 107 Processing helix chain 'B' and resid 176 through 183 removed outlier: 3.602A pdb=" N LEU B 180 " --> pdb=" O ASP B 176 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS B 182 " --> pdb=" O VAL B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 280 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 299 through 312 Proline residue: B 308 - end of helix Processing helix chain 'B' and resid 318 through 328 Processing helix chain 'B' and resid 337 through 351 removed outlier: 3.643A pdb=" N ILE B 342 " --> pdb=" O ARG B 338 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N GLN B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP B 347 " --> pdb=" O GLN B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 383 removed outlier: 4.262A pdb=" N LYS B 367 " --> pdb=" O PHE B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 395 No H-bonds generated for 'chain 'B' and resid 393 through 395' Processing helix chain 'B' and resid 401 through 429 removed outlier: 3.907A 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: 3.564A 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: 3.774A pdb=" N SER B 591 " --> pdb=" O SER B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 658 Processing helix chain 'B' and resid 677 through 683 removed outlier: 3.637A pdb=" N LEU B 681 " --> pdb=" O GLY B 677 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 682 " --> pdb=" O TRP B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 696 removed outlier: 3.699A pdb=" N GLU B 696 " --> pdb=" O GLY B 692 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 692 through 696' Processing helix chain 'B' and resid 703 through 708 removed outlier: 3.576A 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: 3.909A pdb=" N ASN B 767 " --> pdb=" O GLN B 763 " (cutoff:3.500A) removed outlier: 3.516A 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: 3.916A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1061 removed outlier: 3.508A 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: 3.741A 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: 3.578A 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: 3.521A pdb=" N VAL D 101 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 129 Processing helix chain 'D' and resid 138 through 148 removed outlier: 3.508A pdb=" N ILE D 142 " --> pdb=" O HIS D 138 " (cutoff:3.500A) removed outlier: 3.870A 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: 3.938A pdb=" N LYS D 166 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS D 167 " --> pdb=" O ALA D 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 161 through 167' Processing helix chain 'D' and resid 170 through 182 Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 37 through 46 Processing helix chain 'E' and resid 53 through 57 Processing helix chain 'E' and resid 64 through 71 Processing helix chain 'E' and resid 88 through 102 removed outlier: 3.505A 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: 3.722A 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: 3.508A 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: 3.715A 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: 3.617A pdb=" N ILE K 111 " --> pdb=" O GLU K 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 78 removed outlier: 3.658A pdb=" N ILE M 69 " --> pdb=" O GLN M 65 " (cutoff:3.500A) Processing helix chain 'V' and resid 20 through 27 removed outlier: 3.724A pdb=" N PHE V 24 " --> pdb=" O PRO V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 32 through 37 Processing helix chain 'V' and resid 42 through 49 Processing helix chain 'V' and resid 66 through 72 Processing helix chain 'V' and resid 91 through 101 Processing helix chain 'W' and resid 213 through 218 removed outlier: 3.884A pdb=" N ILE W 218 " --> pdb=" O ARG W 215 " (cutoff:3.500A) Processing helix chain 'W' and resid 235 through 251 Processing helix chain 'W' and resid 278 through 287 removed outlier: 3.804A pdb=" N ILE W 282 " --> pdb=" O LYS W 278 " (cutoff:3.500A) Processing helix chain 'W' and resid 302 through 304 No H-bonds generated for 'chain 'W' and resid 302 through 304' Processing helix chain 'W' and resid 305 through 310 removed outlier: 3.619A pdb=" N LEU W 309 " --> pdb=" O GLU W 305 " (cutoff:3.500A) removed outlier: 3.831A 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: 3.976A pdb=" N PHE a 67 " --> pdb=" O ARG a 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 114 removed outlier: 3.736A pdb=" N ILE a 89 " --> pdb=" O GLN a 85 " (cutoff:3.500A) Processing helix chain 'a' and resid 120 through 131 removed outlier: 3.856A 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: 3.604A 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: 3.726A pdb=" N LEU c 83 " --> pdb=" O ILE c 79 " (cutoff:3.500A) removed outlier: 3.765A 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: 3.667A pdb=" N ILE d 91 " --> pdb=" O THR d 87 " (cutoff:3.500A) Processing helix chain 'd' and resid 100 through 121 removed outlier: 3.900A 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: 3.825A 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: 3.653A 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: 3.566A pdb=" N VAL g 30 " --> pdb=" O PRO g 26 " (cutoff:3.500A) Processing helix chain 'g' and resid 45 through 72 removed outlier: 4.466A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) removed outlier: 3.736A 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: 3.710A pdb=" N ILE h 91 " --> pdb=" O THR h 87 " (cutoff:3.500A) Processing helix chain 'h' and resid 100 through 121 Processing sheet with id=AA1, first strand: chain 'A' and resid 1421 through 1422 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 91 removed outlier: 6.892A pdb=" N THR A 238 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 10.888A pdb=" N LYS A 88 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 10.403A 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: 3.691A pdb=" N LYS A 201 " --> pdb=" O GLY A 184 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N TRP A 186 " --> pdb=" O GLU A 199 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU A 199 " --> pdb=" O TRP A 186 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 251 through 252 removed outlier: 3.589A pdb=" N ILE A 251 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 344 through 346 removed outlier: 3.761A pdb=" N LEU B1128 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.561A pdb=" N SER A 349 " --> pdb=" O ARG B1106 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR A 352 " --> pdb=" O MET A 488 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL A 365 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N MET A 464 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL A 367 " --> pdb=" O MET A 464 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 376 through 380 removed outlier: 3.835A pdb=" N TYR A 405 " --> pdb=" O GLU A 434 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N HIS A 436 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ALA A 403 " --> pdb=" O HIS A 436 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 406 " --> pdb=" O ILE A 414 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 513 through 514 removed outlier: 3.755A pdb=" N LYS A 519 " --> pdb=" O SER A 514 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 541 through 543 Processing sheet with id=AB1, first strand: chain 'A' and resid 566 through 568 removed outlier: 6.465A 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: 6.314A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU H 121 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LYS H 112 " --> pdb=" O PHE H 103 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N PHE H 103 " --> pdb=" O LYS H 112 " (cutoff:3.500A) removed outlier: 6.742A 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: 3.581A pdb=" N ARG A1243 " --> pdb=" O PHE A1227 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU A1238 " --> pdb=" O LEU A1199 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL A1244 " --> pdb=" O TRP A1193 " (cutoff:3.500A) removed outlier: 6.929A 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: 4.645A pdb=" N ARG I 45 " --> pdb=" O THR A1152 " (cutoff:3.500A) removed outlier: 6.807A 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: 4.928A pdb=" N ILE B 82 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N TYR B 116 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 5.322A 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: 6.672A pdb=" N LEU B 117 " --> pdb=" O HIS B 157 " (cutoff:3.500A) removed outlier: 5.382A 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: 3.513A pdb=" N ALA B 205 " --> pdb=" O ARG B 490 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 215 through 218 removed outlier: 4.037A pdb=" N HIS B 227 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.511A 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: 3.771A pdb=" N GLY B 581 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 792 through 796 removed outlier: 6.880A 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: 6.417A 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: 6.170A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 792 through 796 removed outlier: 6.880A 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: 6.417A 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: 6.170A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL B 952 " --> pdb=" O LYS L 60 " (cutoff:3.500A) removed outlier: 3.812A 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: 6.670A 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: 6.869A pdb=" N GLU C 18 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 4.714A 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: 4.923A 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: 6.928A 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: 6.804A pdb=" N ASN C 154 " --> pdb=" O LYS C 51 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LYS C 160 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ILE C 45 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLY C 162 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LEU C 43 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE L 67 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 71 through 73 removed outlier: 4.780A pdb=" N GLU C 131 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 111 through 114 removed outlier: 3.553A pdb=" N CYS C 145 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 4 through 6 removed outlier: 4.644A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TRP G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.220A 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: 5.865A pdb=" N VAL G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 7.013A 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: 7.937A pdb=" N GLY G 161 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 6.754A 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: 7.010A pdb=" N GLY G 98 " --> pdb=" O VAL G 94 " (cutoff:3.500A) removed outlier: 4.963A 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: 3.921A 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: 4.481A pdb=" N VAL G 120 " --> pdb=" O MET G 131 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET G 131 " --> pdb=" O VAL G 120 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA G 129 " --> pdb=" O ASN G 122 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 15 through 19 Processing sheet with id=AF4, first strand: chain 'I' and resid 70 through 71 removed outlier: 3.524A pdb=" N SER I 71 " --> pdb=" O CYS I 83 " (cutoff:3.500A) removed outlier: 4.017A 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: 6.858A pdb=" N VAL V 86 " --> pdb=" O PHE V 54 " (cutoff:3.500A) removed outlier: 6.898A 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: 3.757A pdb=" N SER W 261 " --> pdb=" O GLU W 275 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'W' and resid 407 through 410 removed outlier: 6.541A pdb=" N PHE W 413 " --> pdb=" O ASP W 409 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU W 420 " --> pdb=" O TYR W 427 " (cutoff:3.500A) removed outlier: 6.327A 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: 6.038A 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: 6.674A 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: 7.458A 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: 7.669A 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: 363 hydrogen bonds 722 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 266 stacking parallelities Total time for adding SS restraints: 30.92 Time building geometry restraints manager: 12.23 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: 10794 1.33 - 1.45: 11873 1.45 - 1.57: 25531 1.57 - 1.70: 668 1.70 - 1.82: 342 Bond restraints: 49208 Sorted by residual: bond pdb=" C CYS V 29 " pdb=" N PRO V 30 " ideal model delta sigma weight residual 1.335 1.433 -0.099 1.19e-02 7.06e+03 6.86e+01 bond pdb=" C1' G P -2 " pdb=" N9 G P -2 " ideal model delta sigma weight residual 1.475 1.362 0.113 1.50e-02 4.44e+03 5.65e+01 bond pdb=" C1' G P -1 " pdb=" N9 G P -1 " ideal model delta sigma weight residual 1.475 1.362 0.113 1.50e-02 4.44e+03 5.65e+01 bond pdb=" CA ILE W 440 " pdb=" C ILE W 440 " ideal model delta sigma weight residual 1.521 1.431 0.090 1.21e-02 6.83e+03 5.50e+01 bond pdb=" C1' U P 4 " pdb=" N1 U P 4 " ideal model delta sigma weight residual 1.480 1.584 -0.104 1.50e-02 4.44e+03 4.79e+01 ... (remaining 49203 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.99: 67001 3.99 - 7.97: 804 7.97 - 11.96: 69 11.96 - 15.94: 9 15.94 - 19.93: 1 Bond angle restraints: 67884 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 92.36 15.90 1.66e+00 3.63e-01 9.18e+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 99.49 12.51 1.40e+00 5.10e-01 7.99e+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 96.75 14.02 1.63e+00 3.76e-01 7.40e+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 6.77e+01 angle pdb=" C ARG W 388 " pdb=" N PRO W 389 " pdb=" CA PRO W 389 " ideal model delta sigma weight residual 119.84 128.73 -8.89 1.25e+00 6.40e-01 5.06e+01 ... (remaining 67879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.00: 27210 35.00 - 70.01: 1887 70.01 - 105.01: 69 105.01 - 140.01: 9 140.01 - 175.02: 2 Dihedral angle restraints: 29177 sinusoidal: 14337 harmonic: 14840 Sorted by residual: dihedral pdb=" N GLN B 63 " pdb=" C GLN B 63 " pdb=" CA GLN B 63 " pdb=" CB GLN B 63 " ideal model delta harmonic sigma weight residual 122.80 98.07 24.73 0 2.50e+00 1.60e-01 9.79e+01 dihedral pdb=" CA ARG e 63 " pdb=" C ARG e 63 " pdb=" N LYS e 64 " pdb=" CA LYS e 64 " ideal model delta harmonic sigma weight residual -180.00 -142.28 -37.72 0 5.00e+00 4.00e-02 5.69e+01 dihedral pdb=" CA ARG a 63 " pdb=" C ARG a 63 " pdb=" N LYS a 64 " pdb=" CA LYS a 64 " ideal model delta harmonic sigma weight residual -180.00 -143.69 -36.31 0 5.00e+00 4.00e-02 5.27e+01 ... (remaining 29174 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 7180 0.130 - 0.260: 418 0.260 - 0.390: 12 0.390 - 0.520: 2 0.520 - 0.650: 2 Chirality restraints: 7614 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 1.06e+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 2.06 0.59 2.00e-01 2.50e+01 8.69e+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 4.59e+00 ... (remaining 7611 not shown) Planarity restraints: 7588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 336 " -0.030 2.00e-02 2.50e+03 6.05e-02 3.66e+01 pdb=" C ILE B 336 " 0.105 2.00e-02 2.50e+03 pdb=" O ILE B 336 " -0.039 2.00e-02 2.50e+03 pdb=" N ARG B 337 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 89 " -0.019 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C ASP C 89 " 0.064 2.00e-02 2.50e+03 pdb=" O ASP C 89 " -0.023 2.00e-02 2.50e+03 pdb=" N TYR C 90 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 88 " -0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+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 7585 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.31: 29 2.31 - 2.96: 20371 2.96 - 3.60: 69623 3.60 - 4.25: 111816 4.25 - 4.90: 178608 Nonbonded interactions: 380447 Sorted by model distance: nonbonded pdb=" N3 DC T 22 " pdb=" N2 DG N -22 " model vdw 1.661 2.560 nonbonded pdb=" O2 DC T 18 " pdb=" N2 DG N -18 " model vdw 1.793 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 2.147 2.170 nonbonded pdb=" O3' G P 10 " pdb="MG MG A1803 " model vdw 2.157 2.170 ... (remaining 380442 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.570 Check model and map are aligned: 0.300 Set scattering table: 0.400 Process input model: 122.150 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.190 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6183 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 : 0.009 0.113 49208 Z= 0.586 Angle : 1.209 19.928 67884 Z= 0.699 Chirality : 0.068 0.650 7614 Planarity : 0.007 0.064 7588 Dihedral : 19.226 175.017 19591 Min Nonbonded Distance : 1.661 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.65 % Allowed : 4.34 % Favored : 95.00 % Rotamer: Outliers : 0.74 % Allowed : 3.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.10), residues: 5042 helix: -1.29 (0.10), residues: 1856 sheet: -0.74 (0.18), residues: 716 loop : -0.96 (0.12), residues: 2470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP G 79 HIS 0.015 0.003 HIS f 75 PHE 0.051 0.005 PHE A1176 TYR 0.050 0.004 TYR d 80 ARG 0.016 0.001 ARG L 62 *********************** 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 763 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 730 time to evaluate : 4.818 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: A 122 MET cc_start: 0.3330 (tpt) cc_final: 0.2386 (tpp) REVERT: A 305 MET cc_start: 0.8579 (mtt) cc_final: 0.8309 (mtt) REVERT: A 437 LEU cc_start: 0.8582 (tp) cc_final: 0.8113 (tp) REVERT: A 457 MET cc_start: 0.7290 (mtm) cc_final: 0.7089 (mtp) REVERT: A 535 MET cc_start: 0.7618 (ttp) cc_final: 0.7352 (ttm) REVERT: A 548 MET cc_start: 0.7349 (mtm) cc_final: 0.7013 (mtp) REVERT: A 1072 GLN cc_start: 0.8528 (mt0) cc_final: 0.8309 (mt0) REVERT: B 473 SER cc_start: 0.9034 (t) cc_final: 0.8789 (p) REVERT: B 771 SER cc_start: 0.9330 (m) cc_final: 0.8649 (p) REVERT: B 846 ILE cc_start: 0.8938 (mt) cc_final: 0.8732 (mm) REVERT: B 1100 ASP cc_start: 0.8170 (m-30) cc_final: 0.7520 (t0) REVERT: B 1124 ARG cc_start: 0.8108 (mtm-85) cc_final: 0.7804 (mpp80) REVERT: B 1202 LEU cc_start: 0.9130 (tp) cc_final: 0.8928 (tp) REVERT: B 1208 MET cc_start: 0.7705 (mtp) cc_final: 0.7464 (mtm) REVERT: E 73 ASP cc_start: 0.7738 (p0) cc_final: 0.7420 (p0) REVERT: G 39 THR cc_start: 0.9032 (p) cc_final: 0.8235 (p) REVERT: I 65 ASP cc_start: 0.5265 (t0) cc_final: 0.4765 (t0) REVERT: J 16 ASP cc_start: 0.7721 (p0) cc_final: 0.7494 (p0) REVERT: J 59 PHE cc_start: 0.7600 (m-10) cc_final: 0.7330 (m-10) REVERT: K 6 ARG cc_start: 0.7688 (mmm-85) cc_final: 0.6642 (mtp180) REVERT: K 7 PHE cc_start: 0.7678 (p90) cc_final: 0.7008 (p90) REVERT: W 438 ASN cc_start: 0.2221 (m-40) cc_final: 0.1945 (t0) REVERT: a 120 MET cc_start: 0.1097 (mtp) cc_final: 0.0511 (tpt) REVERT: d 65 ASP cc_start: 0.5365 (t0) cc_final: 0.5115 (t70) REVERT: e 78 PHE cc_start: 0.1952 (m-80) cc_final: 0.1750 (t80) outliers start: 33 outliers final: 4 residues processed: 758 average time/residue: 0.6667 time to fit residues: 799.0509 Evaluate side-chains 347 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 343 time to evaluate : 4.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 450 optimal weight: 10.0000 chunk 404 optimal weight: 8.9990 chunk 224 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 273 optimal weight: 0.9990 chunk 216 optimal weight: 1.9990 chunk 418 optimal weight: 40.0000 chunk 161 optimal weight: 9.9990 chunk 254 optimal weight: 1.9990 chunk 311 optimal weight: 9.9990 chunk 484 optimal weight: 30.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 737 ASN A 839 GLN A1190 GLN A1435 GLN B 359 GLN B 438 ASN B 887 HIS B 996 HIS C 13 GLN C 188 HIS E 36 GLN E 145 HIS ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN M 53 ASN ** W 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 434 ASN W 783 HIS W 784 ASN c 38 ASN c 73 ASN c 82 HIS ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 68 GLN g 31 HIS ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6338 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 49208 Z= 0.249 Angle : 0.689 10.242 67884 Z= 0.376 Chirality : 0.044 0.252 7614 Planarity : 0.005 0.071 7588 Dihedral : 23.675 174.567 9370 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.62 % Favored : 97.16 % Rotamer: Outliers : 0.07 % Allowed : 1.84 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.11), residues: 5042 helix: 0.49 (0.11), residues: 1918 sheet: -0.36 (0.18), residues: 715 loop : -0.40 (0.13), residues: 2409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 459 HIS 0.008 0.001 HIS W 783 PHE 0.024 0.002 PHE e 104 TYR 0.023 0.002 TYR B 811 ARG 0.025 0.001 ARG B 469 *********************** 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 434 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 431 time to evaluate : 5.006 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: A 74 MET cc_start: 0.7309 (pmm) cc_final: 0.6522 (ptm) REVERT: A 106 ILE cc_start: 0.8652 (pt) cc_final: 0.8404 (pt) REVERT: A 122 MET cc_start: 0.3362 (tpt) cc_final: 0.2465 (tpp) REVERT: A 437 LEU cc_start: 0.8552 (tp) cc_final: 0.7939 (tp) REVERT: A 464 MET cc_start: 0.8354 (mtp) cc_final: 0.8140 (mtm) REVERT: A 488 MET cc_start: 0.8496 (mmm) cc_final: 0.8183 (tpp) REVERT: A 1065 MET cc_start: 0.8553 (mmm) cc_final: 0.7772 (mmm) REVERT: A 1405 PHE cc_start: 0.6991 (t80) cc_final: 0.6747 (t80) REVERT: B 771 SER cc_start: 0.9461 (m) cc_final: 0.9119 (p) REVERT: B 846 ILE cc_start: 0.9370 (mt) cc_final: 0.9128 (mm) REVERT: B 1021 MET cc_start: 0.8373 (mpp) cc_final: 0.8004 (mpp) REVERT: B 1082 MET cc_start: 0.7983 (tpt) cc_final: 0.7024 (tpt) REVERT: B 1152 MET cc_start: 0.7677 (mmt) cc_final: 0.7211 (tpt) REVERT: B 1210 MET cc_start: 0.7549 (ttm) cc_final: 0.7330 (ttm) REVERT: C 32 LEU cc_start: 0.8500 (tp) cc_final: 0.8015 (tp) REVERT: C 36 MET cc_start: 0.7989 (mtm) cc_final: 0.7604 (mtm) REVERT: C 244 PHE cc_start: 0.8124 (t80) cc_final: 0.7869 (t80) REVERT: E 73 ASP cc_start: 0.7919 (p0) cc_final: 0.7538 (p0) REVERT: E 92 MET cc_start: 0.8497 (tmm) cc_final: 0.8236 (tmm) REVERT: I 97 MET cc_start: 0.8426 (mmm) cc_final: 0.7953 (mmm) REVERT: J 1 MET cc_start: 0.6440 (ttm) cc_final: 0.6113 (mtp) REVERT: K 7 PHE cc_start: 0.8128 (p90) cc_final: 0.7334 (p90) REVERT: K 94 ILE cc_start: 0.8992 (mt) cc_final: 0.8653 (tp) REVERT: W 438 ASN cc_start: 0.2240 (m-40) cc_final: 0.2009 (t0) REVERT: d 56 MET cc_start: 0.4181 (mtm) cc_final: 0.2513 (mmt) REVERT: d 59 MET cc_start: 0.4954 (tpp) cc_final: 0.2111 (mmt) REVERT: h 70 ILE cc_start: 0.5210 (mt) cc_final: 0.4891 (tp) REVERT: h 116 THR cc_start: 0.5182 (m) cc_final: 0.4918 (t) outliers start: 3 outliers final: 0 residues processed: 433 average time/residue: 0.6013 time to fit residues: 429.7466 Evaluate side-chains 270 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 4.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 269 optimal weight: 9.9990 chunk 150 optimal weight: 10.0000 chunk 403 optimal weight: 10.0000 chunk 330 optimal weight: 5.9990 chunk 133 optimal weight: 9.9990 chunk 485 optimal weight: 40.0000 chunk 524 optimal weight: 0.7980 chunk 432 optimal weight: 40.0000 chunk 481 optimal weight: 50.0000 chunk 165 optimal weight: 10.0000 chunk 389 optimal weight: 20.0000 overall best weight: 7.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN A 291 ASN ** A 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 446 ASN ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN A 787 HIS ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 ASN ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 958 GLN B 996 HIS C 13 GLN ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS E 53 GLN G 122 ASN H 138 ASN I 79 HIS ** W 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 346 ASN W 441 ASN c 38 ASN c 68 ASN d 79 HIS ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 79 HIS ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6568 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 49208 Z= 0.409 Angle : 0.766 11.880 67884 Z= 0.408 Chirality : 0.045 0.232 7614 Planarity : 0.006 0.062 7588 Dihedral : 23.588 173.293 9370 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.75 % Favored : 96.01 % Rotamer: Outliers : 0.07 % Allowed : 2.66 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.12), residues: 5042 helix: 0.73 (0.11), residues: 1929 sheet: -0.44 (0.18), residues: 747 loop : -0.31 (0.13), residues: 2366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 18 HIS 0.009 0.002 HIS b 75 PHE 0.028 0.003 PHE e 104 TYR 0.031 0.002 TYR B1092 ARG 0.011 0.001 ARG A 329 *********************** 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 321 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 318 time to evaluate : 4.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.7529 (pmm) cc_final: 0.6827 (ptm) REVERT: A 84 MET cc_start: 0.7765 (ttp) cc_final: 0.7037 (ppp) REVERT: A 122 MET cc_start: 0.4172 (tpt) cc_final: 0.3378 (tpp) REVERT: A 306 ASP cc_start: 0.8343 (t0) cc_final: 0.8017 (t0) REVERT: A 437 LEU cc_start: 0.8857 (tp) cc_final: 0.8199 (tp) REVERT: A 1072 GLN cc_start: 0.8360 (mt0) cc_final: 0.8099 (mt0) REVERT: A 1103 LEU cc_start: 0.9488 (pp) cc_final: 0.9036 (tt) REVERT: A 1405 PHE cc_start: 0.7211 (t80) cc_final: 0.6791 (t80) REVERT: A 1439 MET cc_start: 0.7782 (ttp) cc_final: 0.7312 (ttt) REVERT: B 302 MET cc_start: 0.8881 (ppp) cc_final: 0.8553 (ppp) REVERT: B 839 MET cc_start: 0.9052 (pmm) cc_final: 0.8829 (pmm) REVERT: B 944 THR cc_start: 0.8443 (p) cc_final: 0.8161 (p) REVERT: B 950 ASP cc_start: 0.8366 (p0) cc_final: 0.8063 (p0) REVERT: B 1021 MET cc_start: 0.8702 (mpp) cc_final: 0.8359 (mpp) REVERT: B 1139 ILE cc_start: 0.9463 (mt) cc_final: 0.9160 (mt) REVERT: C 32 LEU cc_start: 0.8692 (tp) cc_final: 0.8315 (tp) REVERT: C 36 MET cc_start: 0.7853 (mtm) cc_final: 0.7286 (mtm) REVERT: C 59 ASP cc_start: 0.7447 (m-30) cc_final: 0.7043 (m-30) REVERT: E 57 MET cc_start: 0.8082 (tpp) cc_final: 0.7765 (tpp) REVERT: E 73 ASP cc_start: 0.8205 (p0) cc_final: 0.7919 (p0) REVERT: E 92 MET cc_start: 0.8317 (tmm) cc_final: 0.7144 (tmm) REVERT: E 138 ASP cc_start: 0.8538 (p0) cc_final: 0.8062 (p0) REVERT: G 1 MET cc_start: 0.7675 (ptm) cc_final: 0.7453 (ptt) REVERT: G 35 GLU cc_start: 0.7163 (pt0) cc_final: 0.6882 (pt0) REVERT: G 53 ASN cc_start: 0.8257 (t0) cc_final: 0.7940 (t0) REVERT: I 97 MET cc_start: 0.8437 (mmm) cc_final: 0.7858 (mmm) REVERT: J 1 MET cc_start: 0.6804 (ttm) cc_final: 0.6506 (mtp) REVERT: W 438 ASN cc_start: 0.2487 (m-40) cc_final: 0.2162 (t0) REVERT: d 56 MET cc_start: 0.4284 (mtm) cc_final: 0.2538 (mmt) REVERT: d 59 MET cc_start: 0.4862 (tpp) cc_final: 0.2297 (mmt) REVERT: h 70 ILE cc_start: 0.5528 (mt) cc_final: 0.4845 (tp) REVERT: h 116 THR cc_start: 0.5682 (m) cc_final: 0.5350 (t) outliers start: 3 outliers final: 2 residues processed: 321 average time/residue: 0.5976 time to fit residues: 325.3023 Evaluate side-chains 236 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 234 time to evaluate : 5.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 479 optimal weight: 8.9990 chunk 365 optimal weight: 40.0000 chunk 252 optimal weight: 20.0000 chunk 53 optimal weight: 0.9990 chunk 231 optimal weight: 8.9990 chunk 326 optimal weight: 2.9990 chunk 487 optimal weight: 9.9990 chunk 516 optimal weight: 10.0000 chunk 254 optimal weight: 3.9990 chunk 462 optimal weight: 6.9990 chunk 139 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 GLN A 737 ASN B 63 GLN ** B 426 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** C 13 GLN E 94 ASN F 119 GLN G 122 ASN V 31 ASN ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 106 HIS ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 49208 Z= 0.214 Angle : 0.592 11.390 67884 Z= 0.324 Chirality : 0.041 0.232 7614 Planarity : 0.004 0.059 7588 Dihedral : 23.465 174.132 9370 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.76 % Favored : 97.02 % Rotamer: Outliers : 0.02 % Allowed : 1.88 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.12), residues: 5042 helix: 1.21 (0.12), residues: 1940 sheet: -0.40 (0.18), residues: 725 loop : -0.15 (0.13), residues: 2377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 201 HIS 0.008 0.001 HIS b 75 PHE 0.024 0.001 PHE e 104 TYR 0.017 0.001 TYR B 811 ARG 0.005 0.000 ARG B 469 *********************** 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 330 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 329 time to evaluate : 5.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.4194 (tpt) cc_final: 0.3919 (tpp) REVERT: A 254 ASP cc_start: 0.6700 (p0) cc_final: 0.6437 (m-30) REVERT: A 306 ASP cc_start: 0.8391 (t0) cc_final: 0.8014 (t0) REVERT: A 490 LEU cc_start: 0.9168 (tp) cc_final: 0.8835 (tp) REVERT: A 827 ASP cc_start: 0.8394 (m-30) cc_final: 0.8054 (m-30) REVERT: A 1114 LYS cc_start: 0.8738 (tptp) cc_final: 0.8531 (tppt) REVERT: A 1405 PHE cc_start: 0.7026 (t80) cc_final: 0.6775 (t80) REVERT: A 1409 VAL cc_start: 0.9358 (t) cc_final: 0.9070 (m) REVERT: B 302 MET cc_start: 0.8853 (ppp) cc_final: 0.8646 (ppp) REVERT: B 839 MET cc_start: 0.8976 (pmm) cc_final: 0.8763 (pmm) REVERT: B 944 THR cc_start: 0.8344 (p) cc_final: 0.8124 (p) REVERT: B 950 ASP cc_start: 0.8235 (p0) cc_final: 0.7924 (p0) REVERT: B 1021 MET cc_start: 0.8614 (mpp) cc_final: 0.8177 (mpp) REVERT: B 1098 MET cc_start: 0.8403 (mtm) cc_final: 0.7553 (mtp) REVERT: B 1120 GLU cc_start: 0.7390 (pp20) cc_final: 0.7163 (pp20) REVERT: C 32 LEU cc_start: 0.8544 (tp) cc_final: 0.8087 (tp) REVERT: C 36 MET cc_start: 0.7710 (mtm) cc_final: 0.7185 (mtm) REVERT: C 59 ASP cc_start: 0.7170 (m-30) cc_final: 0.6885 (m-30) REVERT: E 73 ASP cc_start: 0.7925 (p0) cc_final: 0.7677 (p0) REVERT: E 92 MET cc_start: 0.8310 (tmm) cc_final: 0.7844 (tmm) REVERT: E 138 ASP cc_start: 0.8538 (p0) cc_final: 0.8055 (p0) REVERT: G 35 GLU cc_start: 0.7118 (pt0) cc_final: 0.6849 (pt0) REVERT: G 53 ASN cc_start: 0.8173 (t0) cc_final: 0.7887 (t0) REVERT: J 1 MET cc_start: 0.6664 (ttm) cc_final: 0.6387 (mtp) REVERT: K 7 PHE cc_start: 0.8239 (p90) cc_final: 0.7296 (p90) REVERT: W 438 ASN cc_start: 0.2136 (m-40) cc_final: 0.1694 (t0) REVERT: c 118 LYS cc_start: 0.5529 (tppt) cc_final: 0.3554 (mttp) REVERT: d 56 MET cc_start: 0.4123 (mtm) cc_final: 0.2526 (mmt) REVERT: d 59 MET cc_start: 0.4221 (tpp) cc_final: 0.2507 (tpp) REVERT: h 70 ILE cc_start: 0.5187 (mt) cc_final: 0.4781 (tp) REVERT: h 116 THR cc_start: 0.5671 (m) cc_final: 0.5369 (t) outliers start: 1 outliers final: 0 residues processed: 330 average time/residue: 0.5830 time to fit residues: 326.2745 Evaluate side-chains 248 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 5.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 429 optimal weight: 8.9990 chunk 293 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 384 optimal weight: 9.9990 chunk 212 optimal weight: 0.8980 chunk 440 optimal weight: 50.0000 chunk 356 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 263 optimal weight: 9.9990 chunk 463 optimal weight: 40.0000 chunk 130 optimal weight: 0.7980 overall best weight: 5.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 HIS A 737 ASN ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 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 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN C 149 ASN G 122 ASN c 82 HIS d 46 HIS ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6569 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 49208 Z= 0.303 Angle : 0.634 10.247 67884 Z= 0.342 Chirality : 0.042 0.210 7614 Planarity : 0.004 0.089 7588 Dihedral : 23.393 174.142 9370 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.91 % Favored : 95.93 % Rotamer: Outliers : 0.02 % Allowed : 1.52 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.12), residues: 5042 helix: 1.29 (0.12), residues: 1935 sheet: -0.42 (0.18), residues: 712 loop : -0.18 (0.13), residues: 2395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP V 67 HIS 0.009 0.001 HIS B 97 PHE 0.019 0.002 PHE K 71 TYR 0.029 0.002 TYR h 80 ARG 0.017 0.001 ARG A 435 *********************** 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 306 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 305 time to evaluate : 5.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.4367 (tpt) cc_final: 0.3980 (tpp) REVERT: A 180 MET cc_start: 0.7281 (tmm) cc_final: 0.6969 (tmm) REVERT: A 282 MET cc_start: 0.8587 (ppp) cc_final: 0.8290 (ppp) REVERT: A 305 MET cc_start: 0.8856 (mmt) cc_final: 0.7315 (mmt) REVERT: A 306 ASP cc_start: 0.8539 (t0) cc_final: 0.8148 (t0) REVERT: A 314 GLN cc_start: 0.7801 (mm-40) cc_final: 0.7484 (mm-40) REVERT: A 342 MET cc_start: 0.7969 (mmp) cc_final: 0.7587 (mmp) REVERT: A 437 LEU cc_start: 0.9001 (tp) cc_final: 0.8266 (tp) REVERT: A 1114 LYS cc_start: 0.8739 (tptp) cc_final: 0.8513 (tppt) REVERT: B 302 MET cc_start: 0.8901 (ppp) cc_final: 0.8683 (ppp) REVERT: B 839 MET cc_start: 0.8998 (pmm) cc_final: 0.8541 (pmm) REVERT: B 944 THR cc_start: 0.8339 (p) cc_final: 0.8114 (p) REVERT: B 950 ASP cc_start: 0.8202 (p0) cc_final: 0.7878 (p0) REVERT: B 1098 MET cc_start: 0.8399 (mtm) cc_final: 0.7448 (mtt) REVERT: C 32 LEU cc_start: 0.8614 (tp) cc_final: 0.8266 (tp) REVERT: C 36 MET cc_start: 0.7750 (mtm) cc_final: 0.7260 (mtm) REVERT: C 59 ASP cc_start: 0.7289 (m-30) cc_final: 0.6934 (m-30) REVERT: C 79 MET cc_start: 0.8342 (tpp) cc_final: 0.7992 (tpp) REVERT: D 176 ASP cc_start: 0.8158 (t70) cc_final: 0.7918 (t70) REVERT: E 73 ASP cc_start: 0.7882 (p0) cc_final: 0.7640 (p0) REVERT: E 92 MET cc_start: 0.8485 (tmm) cc_final: 0.8269 (tmm) REVERT: E 138 ASP cc_start: 0.8788 (p0) cc_final: 0.8478 (p0) REVERT: G 53 ASN cc_start: 0.8238 (t0) cc_final: 0.7894 (t0) REVERT: W 438 ASN cc_start: 0.2175 (m-40) cc_final: 0.1707 (t0) REVERT: c 118 LYS cc_start: 0.6261 (tppt) cc_final: 0.4330 (mttp) REVERT: d 59 MET cc_start: 0.4322 (tpp) cc_final: 0.2674 (tpp) REVERT: h 70 ILE cc_start: 0.5293 (mt) cc_final: 0.4925 (tp) REVERT: h 116 THR cc_start: 0.5806 (m) cc_final: 0.5490 (t) outliers start: 1 outliers final: 0 residues processed: 306 average time/residue: 0.5846 time to fit residues: 304.0283 Evaluate side-chains 237 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 4.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 173 optimal weight: 10.0000 chunk 464 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 303 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 chunk 516 optimal weight: 6.9990 chunk 428 optimal weight: 6.9990 chunk 239 optimal weight: 0.0980 chunk 42 optimal weight: 6.9990 chunk 170 optimal weight: 30.0000 chunk 271 optimal weight: 6.9990 overall best weight: 5.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 ASN B 932 HIS ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN G 122 ASN ** W 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 125 GLN ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 49208 Z= 0.308 Angle : 0.631 9.955 67884 Z= 0.340 Chirality : 0.042 0.288 7614 Planarity : 0.004 0.066 7588 Dihedral : 23.415 174.340 9370 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.73 % Favored : 96.19 % Rotamer: Outliers : 0.04 % Allowed : 1.41 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.12), residues: 5042 helix: 1.30 (0.12), residues: 1938 sheet: -0.55 (0.18), residues: 720 loop : -0.21 (0.13), residues: 2384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 579 HIS 0.009 0.001 HIS b 75 PHE 0.040 0.002 PHE e 104 TYR 0.021 0.002 TYR B 797 ARG 0.020 0.001 ARG A 721 *********************** 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 303 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 301 time to evaluate : 5.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.7369 (tmm) cc_final: 0.6747 (tmm) REVERT: A 282 MET cc_start: 0.8575 (ppp) cc_final: 0.8203 (ppp) REVERT: A 305 MET cc_start: 0.8550 (mmt) cc_final: 0.7139 (mmt) REVERT: A 314 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7451 (mm-40) REVERT: A 456 MET cc_start: 0.7577 (ttp) cc_final: 0.7338 (ttm) REVERT: A 1114 LYS cc_start: 0.8767 (tptp) cc_final: 0.8548 (tppt) REVERT: A 1439 MET cc_start: 0.7322 (tmm) cc_final: 0.6937 (tmm) REVERT: B 839 MET cc_start: 0.9080 (pmm) cc_final: 0.8713 (pmm) REVERT: B 950 ASP cc_start: 0.8336 (p0) cc_final: 0.8037 (p0) REVERT: B 1098 MET cc_start: 0.8337 (mtm) cc_final: 0.7343 (mtt) REVERT: B 1210 MET cc_start: 0.7338 (tpp) cc_final: 0.6181 (tpp) REVERT: C 32 LEU cc_start: 0.8617 (tp) cc_final: 0.8274 (tp) REVERT: C 36 MET cc_start: 0.7746 (mtm) cc_final: 0.7273 (mtm) REVERT: C 59 ASP cc_start: 0.7201 (m-30) cc_final: 0.6915 (m-30) REVERT: C 79 MET cc_start: 0.8223 (tpp) cc_final: 0.7932 (tpp) REVERT: D 176 ASP cc_start: 0.8237 (t70) cc_final: 0.7997 (t70) REVERT: E 73 ASP cc_start: 0.7993 (p0) cc_final: 0.7740 (p0) REVERT: E 122 MET cc_start: 0.5878 (tmm) cc_final: 0.5470 (ppp) REVERT: E 138 ASP cc_start: 0.8796 (p0) cc_final: 0.8500 (p0) REVERT: G 53 ASN cc_start: 0.8256 (t0) cc_final: 0.7876 (t0) REVERT: I 77 GLU cc_start: 0.8015 (tt0) cc_final: 0.6990 (mp0) REVERT: W 438 ASN cc_start: 0.2538 (m-40) cc_final: 0.2076 (t0) REVERT: c 118 LYS cc_start: 0.6665 (tppt) cc_final: 0.4538 (mttp) REVERT: d 56 MET cc_start: 0.4014 (mtm) cc_final: 0.2696 (mmt) REVERT: d 59 MET cc_start: 0.4630 (tpp) cc_final: 0.2821 (tpp) REVERT: h 70 ILE cc_start: 0.5770 (mt) cc_final: 0.5189 (tp) outliers start: 2 outliers final: 1 residues processed: 303 average time/residue: 0.5822 time to fit residues: 297.9356 Evaluate side-chains 237 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 236 time to evaluate : 5.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 498 optimal weight: 8.9990 chunk 58 optimal weight: 0.9980 chunk 294 optimal weight: 30.0000 chunk 377 optimal weight: 5.9990 chunk 292 optimal weight: 10.0000 chunk 434 optimal weight: 50.0000 chunk 288 optimal weight: 20.0000 chunk 514 optimal weight: 30.0000 chunk 322 optimal weight: 3.9990 chunk 313 optimal weight: 8.9990 chunk 237 optimal weight: 0.9980 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN A 839 GLN ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 HIS ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN C 188 HIS V 31 ASN ** W 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 68 ASN ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 38 ASN ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6582 moved from start: 0.5306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 49208 Z= 0.249 Angle : 0.596 11.134 67884 Z= 0.323 Chirality : 0.041 0.207 7614 Planarity : 0.004 0.049 7588 Dihedral : 23.357 174.582 9370 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.87 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.12), residues: 5042 helix: 1.44 (0.12), residues: 1938 sheet: -0.52 (0.18), residues: 740 loop : -0.15 (0.14), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 579 HIS 0.009 0.001 HIS b 75 PHE 0.019 0.002 PHE K 7 TYR 0.029 0.001 TYR h 80 ARG 0.009 0.000 ARG A 721 *********************** 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 303 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 5.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.3989 (tpt) cc_final: 0.3721 (tpp) REVERT: A 180 MET cc_start: 0.7606 (tmm) cc_final: 0.7059 (tmm) REVERT: A 202 LEU cc_start: 0.8523 (tp) cc_final: 0.7846 (tt) REVERT: A 282 MET cc_start: 0.8586 (ppp) cc_final: 0.8198 (ppp) REVERT: A 305 MET cc_start: 0.8462 (mmt) cc_final: 0.7198 (mmt) REVERT: A 314 GLN cc_start: 0.7883 (mm-40) cc_final: 0.7593 (mm-40) REVERT: A 437 LEU cc_start: 0.9033 (tp) cc_final: 0.8520 (tp) REVERT: A 456 MET cc_start: 0.7142 (ttp) cc_final: 0.6798 (ttm) REVERT: A 490 LEU cc_start: 0.9150 (tp) cc_final: 0.8858 (tp) REVERT: A 1114 LYS cc_start: 0.8681 (tptp) cc_final: 0.8470 (tppt) REVERT: B 302 MET cc_start: 0.8883 (ppp) cc_final: 0.8524 (ppp) REVERT: B 944 THR cc_start: 0.8406 (p) cc_final: 0.8201 (p) REVERT: B 950 ASP cc_start: 0.8314 (p0) cc_final: 0.8085 (p0) REVERT: B 1098 MET cc_start: 0.8252 (mtm) cc_final: 0.7346 (mtt) REVERT: B 1210 MET cc_start: 0.7072 (tpp) cc_final: 0.6163 (tpp) REVERT: C 32 LEU cc_start: 0.8612 (tp) cc_final: 0.8282 (tp) REVERT: C 36 MET cc_start: 0.7821 (mtm) cc_final: 0.7367 (mtm) REVERT: C 59 ASP cc_start: 0.7081 (m-30) cc_final: 0.6817 (m-30) REVERT: C 79 MET cc_start: 0.8236 (tpp) cc_final: 0.7956 (tpp) REVERT: D 176 ASP cc_start: 0.8299 (t70) cc_final: 0.8031 (t70) REVERT: E 21 MET cc_start: 0.7833 (tmm) cc_final: 0.7612 (tmm) REVERT: E 73 ASP cc_start: 0.7952 (p0) cc_final: 0.7724 (p0) REVERT: E 138 ASP cc_start: 0.8683 (p0) cc_final: 0.8332 (p0) REVERT: I 77 GLU cc_start: 0.7957 (tt0) cc_final: 0.6950 (mp0) REVERT: K 7 PHE cc_start: 0.8360 (p90) cc_final: 0.6811 (p90) REVERT: W 438 ASN cc_start: 0.2452 (m-40) cc_final: 0.2002 (t0) REVERT: c 118 LYS cc_start: 0.6831 (tppt) cc_final: 0.4617 (mttp) REVERT: d 56 MET cc_start: 0.4121 (mtm) cc_final: 0.2662 (mmt) REVERT: d 59 MET cc_start: 0.4515 (tpp) cc_final: 0.2749 (tpp) REVERT: h 70 ILE cc_start: 0.5975 (mt) cc_final: 0.5484 (tp) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.5925 time to fit residues: 305.3071 Evaluate side-chains 239 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 5.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 318 optimal weight: 10.0000 chunk 205 optimal weight: 9.9990 chunk 307 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 327 optimal weight: 30.0000 chunk 350 optimal weight: 8.9990 chunk 254 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 404 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 GLN ** A 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 ASN A 927 GLN ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN H 44 ASN V 43 GLN ** W 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 moved from start: 0.5681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 49208 Z= 0.315 Angle : 0.645 12.097 67884 Z= 0.345 Chirality : 0.042 0.213 7614 Planarity : 0.004 0.048 7588 Dihedral : 23.367 174.555 9370 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.54 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.12), residues: 5042 helix: 1.33 (0.12), residues: 1935 sheet: -0.65 (0.18), residues: 731 loop : -0.26 (0.13), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 579 HIS 0.011 0.001 HIS A 300 PHE 0.020 0.002 PHE A1227 TYR 0.027 0.002 TYR A 544 ARG 0.010 0.001 ARG B 469 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10084 Ramachandran restraints generated. 5042 Oldfield, 0 Emsley, 5042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 4.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.3734 (tpt) cc_final: 0.3466 (tpp) REVERT: A 180 MET cc_start: 0.7631 (tmm) cc_final: 0.7321 (tmm) REVERT: A 202 LEU cc_start: 0.8649 (tp) cc_final: 0.8031 (tt) REVERT: A 282 MET cc_start: 0.8422 (ppp) cc_final: 0.8070 (ppp) REVERT: A 305 MET cc_start: 0.8484 (mmt) cc_final: 0.7196 (mmt) REVERT: A 437 LEU cc_start: 0.9023 (tp) cc_final: 0.8775 (tp) REVERT: A 456 MET cc_start: 0.7246 (ttp) cc_final: 0.6941 (ttm) REVERT: A 677 MET cc_start: 0.6628 (tmm) cc_final: 0.6411 (tmm) REVERT: A 1114 LYS cc_start: 0.8717 (tptp) cc_final: 0.8506 (tppt) REVERT: A 1371 MET cc_start: 0.8727 (pmm) cc_final: 0.8526 (pmm) REVERT: A 1439 MET cc_start: 0.7568 (tmm) cc_final: 0.7173 (tmm) REVERT: B 302 MET cc_start: 0.8873 (ppp) cc_final: 0.8426 (ppp) REVERT: B 839 MET cc_start: 0.8982 (pmm) cc_final: 0.8457 (pmm) REVERT: B 944 THR cc_start: 0.8410 (p) cc_final: 0.8200 (p) REVERT: B 950 ASP cc_start: 0.8365 (p0) cc_final: 0.8112 (p0) REVERT: B 1098 MET cc_start: 0.8292 (mtm) cc_final: 0.7383 (mtt) REVERT: B 1210 MET cc_start: 0.6845 (tpp) cc_final: 0.5955 (tpp) REVERT: C 32 LEU cc_start: 0.8647 (tp) cc_final: 0.8303 (tp) REVERT: C 36 MET cc_start: 0.7855 (mtm) cc_final: 0.7398 (mtm) REVERT: C 59 ASP cc_start: 0.7062 (m-30) cc_final: 0.6802 (m-30) REVERT: C 79 MET cc_start: 0.8335 (tpp) cc_final: 0.8058 (tpp) REVERT: D 176 ASP cc_start: 0.8397 (t70) cc_final: 0.8123 (t70) REVERT: E 73 ASP cc_start: 0.8021 (p0) cc_final: 0.7786 (p0) REVERT: E 138 ASP cc_start: 0.8776 (p0) cc_final: 0.8441 (p0) REVERT: I 77 GLU cc_start: 0.8094 (tt0) cc_final: 0.7162 (mp0) REVERT: K 7 PHE cc_start: 0.8246 (p90) cc_final: 0.6727 (p90) REVERT: W 438 ASN cc_start: 0.2408 (m-40) cc_final: 0.1958 (t0) REVERT: c 118 LYS cc_start: 0.7124 (tppt) cc_final: 0.5503 (pttp) REVERT: d 56 MET cc_start: 0.4250 (mtm) cc_final: 0.2655 (mmt) REVERT: d 59 MET cc_start: 0.4501 (tpp) cc_final: 0.2727 (tpp) REVERT: h 70 ILE cc_start: 0.5828 (mt) cc_final: 0.5298 (tp) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.5765 time to fit residues: 289.5639 Evaluate side-chains 230 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 4.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 468 optimal weight: 30.0000 chunk 493 optimal weight: 30.0000 chunk 449 optimal weight: 20.0000 chunk 479 optimal weight: 0.9980 chunk 492 optimal weight: 10.0000 chunk 288 optimal weight: 0.8980 chunk 208 optimal weight: 6.9990 chunk 376 optimal weight: 0.7980 chunk 147 optimal weight: 9.9990 chunk 433 optimal weight: 5.9990 chunk 453 optimal weight: 20.0000 overall best weight: 3.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 HIS A 489 ASN A 511 GLN A 651 GLN A 737 ASN A 839 GLN ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN ** W 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.5788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 49208 Z= 0.213 Angle : 0.586 15.818 67884 Z= 0.317 Chirality : 0.041 0.285 7614 Planarity : 0.004 0.043 7588 Dihedral : 23.308 174.819 9370 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.75 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.25 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.12), residues: 5042 helix: 1.48 (0.12), residues: 1940 sheet: -0.63 (0.18), residues: 740 loop : -0.12 (0.13), residues: 2362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1230 HIS 0.009 0.001 HIS b 75 PHE 0.039 0.001 PHE e 104 TYR 0.036 0.001 TYR h 80 ARG 0.008 0.000 ARG A1389 *********************** 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 304 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 5.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.3951 (tpt) cc_final: 0.3621 (tpp) REVERT: A 180 MET cc_start: 0.7698 (tmm) cc_final: 0.7374 (tmm) REVERT: A 202 LEU cc_start: 0.8485 (tp) cc_final: 0.7963 (tt) REVERT: A 282 MET cc_start: 0.8592 (ppp) cc_final: 0.8207 (ppp) REVERT: A 305 MET cc_start: 0.8477 (mmt) cc_final: 0.7008 (mmt) REVERT: A 314 GLN cc_start: 0.7714 (mm-40) cc_final: 0.7440 (mm-40) REVERT: A 490 LEU cc_start: 0.9144 (tp) cc_final: 0.8914 (tp) REVERT: A 1114 LYS cc_start: 0.8714 (tptp) cc_final: 0.8492 (tppt) REVERT: A 1439 MET cc_start: 0.7417 (tmm) cc_final: 0.6797 (tmm) REVERT: B 302 MET cc_start: 0.8859 (ppp) cc_final: 0.8518 (ppp) REVERT: B 839 MET cc_start: 0.8913 (pmm) cc_final: 0.8624 (pmm) REVERT: B 950 ASP cc_start: 0.8322 (p0) cc_final: 0.8053 (p0) REVERT: B 1098 MET cc_start: 0.8155 (mtm) cc_final: 0.7333 (mtt) REVERT: B 1152 MET cc_start: 0.7747 (mmt) cc_final: 0.7169 (tpt) REVERT: B 1210 MET cc_start: 0.6795 (tpp) cc_final: 0.6251 (tpp) REVERT: C 36 MET cc_start: 0.7835 (mtm) cc_final: 0.7423 (mtm) REVERT: C 59 ASP cc_start: 0.7075 (m-30) cc_final: 0.6853 (m-30) REVERT: C 79 MET cc_start: 0.8262 (tpp) cc_final: 0.7957 (tpp) REVERT: D 176 ASP cc_start: 0.8368 (t70) cc_final: 0.8106 (t70) REVERT: E 73 ASP cc_start: 0.7863 (p0) cc_final: 0.7615 (p0) REVERT: E 122 MET cc_start: 0.3256 (ppp) cc_final: 0.2958 (ppp) REVERT: E 138 ASP cc_start: 0.8655 (p0) cc_final: 0.8317 (p0) REVERT: I 77 GLU cc_start: 0.8053 (tt0) cc_final: 0.7124 (mp0) REVERT: K 7 PHE cc_start: 0.8245 (p90) cc_final: 0.6691 (p90) REVERT: W 438 ASN cc_start: 0.2375 (m-40) cc_final: 0.1928 (t0) REVERT: c 118 LYS cc_start: 0.7178 (tppt) cc_final: 0.5514 (pttp) REVERT: d 56 MET cc_start: 0.4229 (mtm) cc_final: 0.2635 (mmt) REVERT: d 59 MET cc_start: 0.4509 (tpp) cc_final: 0.2719 (tpp) REVERT: h 70 ILE cc_start: 0.5779 (mt) cc_final: 0.5252 (tp) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.5771 time to fit residues: 303.3467 Evaluate side-chains 236 residues out of total 4466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 4.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.4096 > 50: distance: 8 - 14: 25.281 distance: 14 - 15: 13.423 distance: 14 - 117: 28.103 distance: 15 - 16: 29.308 distance: 15 - 18: 3.527 distance: 16 - 17: 34.342 distance: 16 - 25: 34.956 distance: 17 - 114: 21.210 distance: 18 - 19: 24.948 distance: 19 - 20: 14.112 distance: 19 - 21: 20.071 distance: 20 - 22: 44.926 distance: 21 - 23: 7.984 distance: 22 - 24: 39.321 distance: 23 - 24: 39.015 distance: 25 - 26: 6.584 distance: 25 - 173: 4.142 distance: 26 - 27: 15.215 distance: 26 - 29: 28.893 distance: 27 - 28: 19.269 distance: 27 - 33: 10.407 distance: 28 - 170: 23.631 distance: 29 - 30: 16.430 distance: 30 - 31: 28.381 distance: 30 - 32: 24.683 distance: 33 - 34: 8.812 distance: 34 - 35: 16.377 distance: 34 - 37: 11.934 distance: 35 - 36: 10.822 distance: 35 - 44: 16.985 distance: 37 - 38: 19.887 distance: 38 - 39: 13.975 distance: 39 - 40: 6.759 distance: 40 - 41: 7.172 distance: 41 - 42: 10.204 distance: 41 - 43: 14.168 distance: 44 - 45: 7.386 distance: 45 - 46: 19.520 distance: 45 - 48: 14.710 distance: 46 - 53: 56.827 distance: 48 - 49: 29.841 distance: 49 - 50: 30.200 distance: 50 - 51: 36.878 distance: 50 - 52: 18.980 distance: 53 - 54: 3.084 distance: 53 - 59: 22.013 distance: 54 - 55: 43.780 distance: 54 - 57: 36.191 distance: 55 - 56: 9.764 distance: 55 - 60: 15.450 distance: 57 - 58: 17.050 distance: 58 - 59: 16.478 distance: 60 - 61: 27.952 distance: 61 - 62: 15.249 distance: 61 - 64: 30.031 distance: 62 - 63: 13.049 distance: 62 - 66: 18.815 distance: 64 - 65: 6.194 distance: 66 - 67: 10.175 distance: 67 - 68: 12.430 distance: 67 - 70: 9.534 distance: 68 - 69: 5.464 distance: 68 - 74: 8.557 distance: 70 - 71: 22.583 distance: 71 - 72: 12.430 distance: 71 - 73: 16.406 distance: 74 - 75: 5.448 distance: 75 - 76: 9.019 distance: 75 - 78: 25.930 distance: 76 - 77: 3.917 distance: 76 - 84: 20.475 distance: 78 - 79: 16.361 distance: 79 - 80: 21.245 distance: 79 - 81: 20.711 distance: 80 - 82: 25.350 distance: 81 - 83: 14.027 distance: 82 - 83: 18.346 distance: 84 - 85: 11.771 distance: 85 - 86: 9.318 distance: 85 - 88: 28.177 distance: 86 - 87: 12.886 distance: 86 - 93: 7.505 distance: 88 - 89: 12.150 distance: 89 - 90: 7.474 distance: 90 - 91: 9.386 distance: 91 - 92: 20.827 distance: 93 - 94: 7.665 distance: 94 - 97: 7.610 distance: 95 - 96: 10.478 distance: 95 - 101: 10.628 distance: 97 - 98: 7.425 distance: 99 - 100: 10.069