Starting phenix.real_space_refine on Tue Sep 15 18:13:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rdx_24426/09_2026/7rdx_24426_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rdx_24426/09_2026/7rdx_24426.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rdx_24426/09_2026/7rdx_24426_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rdx_24426/09_2026/7rdx_24426_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rdx_24426/09_2026/7rdx_24426.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rdx_24426/09_2026/7rdx_24426.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.088 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: 10 Type Number sf(0) Gaussians Zn 8 6.06 5 Al 2 5.89 5 P 86 5.49 5 Mg 3 5.21 5 S 151 5.16 5 C 13534 2.51 5 N 3677 2.21 5 O 4361 1.98 5 F 6 1.80 5 H 20496 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 42324 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 14676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 927, 14676 Classifications: {'peptide': 927} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 896} Chain: "B" Number of atoms: 2823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 2823 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1182 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain: "D" Number of atoms: 2846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 2846 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 178} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 8971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 8971 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 29, 'TRANS': 560} Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 3, 'ARG:plan': 5, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 76 Chain: "F" Number of atoms: 9074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 9074 Classifications: {'peptide': 590} Link IDs: {'CIS': 1, 'PTRANS': 29, 'TRANS': 559} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "P" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 1085 Classifications: {'RNA': 34} Modifications used: {'3*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 15, 'rna3p_pyr': 18} Link IDs: {'rna3p': 33} Chain: "T" Number of atoms: 1470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 1470 Classifications: {'RNA': 46} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 20, 'rna3p_pyr': 20} Link IDs: {'rna2p': 6, 'rna3p': 39} Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 91 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 2, 'ADP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 71 Unusual residues: {' MG': 1, ' ZN': 3, '1N7': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 35 Unusual residues: {' MG': 1, ' ZN': 3, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4797 SG CYS A 301 66.312 49.509 111.475 1.00 30.26 S ATOM 4874 SG CYS A 306 65.751 50.585 115.120 1.00 29.31 S ATOM 4939 SG CYS A 310 67.331 47.211 114.245 1.00 25.49 S ATOM 7696 SG CYS A 487 68.049 64.645 97.698 1.00 34.45 S ATOM 10213 SG CYS A 645 66.847 66.278 100.945 1.00 38.64 S ATOM 10223 SG CYS A 646 66.083 62.639 100.211 1.00 36.10 S ATOM 21576 SG CYS E 5 115.002 67.973 48.825 1.00 81.36 S ATOM 21621 SG CYS E 8 118.118 68.671 50.190 1.00 86.14 S ATOM 21898 SG CYS E 26 116.162 71.934 50.263 1.00 86.37 S ATOM 21941 SG CYS E 29 117.074 70.323 46.949 1.00 90.09 S ATOM 22268 SG CYS E 50 94.043 83.875 45.352 1.00117.14 S ATOM 22323 SG CYS E 55 92.436 83.454 41.913 1.00128.23 S ATOM 22577 SG CYS E 72 94.886 86.351 42.546 1.00122.30 S ATOM 21741 SG CYS E 16 106.086 69.129 42.460 1.00 90.46 S ATOM 21768 SG CYS E 19 106.904 65.609 41.219 1.00 96.53 S ATOM 30547 SG CYS F 5 64.544 69.640 51.555 1.00124.11 S ATOM 30592 SG CYS F 8 66.541 70.229 48.576 1.00128.60 S ATOM 30869 SG CYS F 26 66.366 73.037 51.218 1.00125.16 S ATOM 30912 SG CYS F 29 63.419 72.486 49.171 1.00130.34 S ATOM 31239 SG CYS F 50 57.811 83.622 72.839 1.00138.94 S ATOM 31294 SG CYS F 55 54.075 84.168 73.430 1.00147.33 S ATOM 31548 SG CYS F 72 56.000 86.508 71.062 1.00144.26 S ATOM 30712 SG CYS F 16 55.223 71.754 57.520 1.00121.07 S ATOM 30739 SG CYS F 19 53.782 68.771 55.472 1.00129.58 S Time building chain proxies: 7.08, per 1000 atoms: 0.17 Number of scatterers: 42324 At special positions: 0 Unit cell: (151.94, 154.08, 174.41, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 10 Type Number sf(0) Zn 8 29.99 S 151 16.00 P 86 15.00 Al 2 13.00 Mg 3 11.99 F 6 9.00 O 4361 8.00 N 3677 7.00 C 13534 6.00 H 20496 1.00 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: 4.05 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 8 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 29 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 5 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 26 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 72 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 55 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 50 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 703 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 19 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 16 " pdb=" ZN F1000 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 26 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 8 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 29 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 5 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" NE2 HIS F 75 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 50 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 55 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 72 " pdb=" ZN F1002 " pdb="ZN ZN F1002 " - pdb=" NE2 HIS F 33 " pdb="ZN ZN F1002 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 19 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 16 " Number of angles added : 27 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4874 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 28 sheets defined 44.2% alpha, 13.0% beta 34 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 7.50 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 Processing helix chain 'A' and resid 76 through 91 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 142 through 149 Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 169 through 177 removed outlier: 4.267A pdb=" N ARG A 173 " --> pdb=" O PRO A 169 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN A 177 " --> pdb=" O ARG A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 200 removed outlier: 3.744A pdb=" N GLN A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA A 185 " --> pdb=" O ARG A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.543A pdb=" N SER A 239 " --> pdb=" O ASP A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.900A pdb=" N SER A 255 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N HIS A 256 " --> pdb=" O ALA A 253 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N VAL A 257 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ASP A 258 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP A 260 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.718A pdb=" N LEU A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N HIS A 309 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.790A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 377 through 385 removed outlier: 4.757A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 480 removed outlier: 4.285A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 519 removed outlier: 4.036A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 532 removed outlier: 3.508A pdb=" N LEU A 527 " --> pdb=" O ASP A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 580 removed outlier: 4.231A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 580 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 removed outlier: 3.653A pdb=" N ASN A 600 " --> pdb=" O GLY A 596 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR A 606 " --> pdb=" O LEU A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 627 through 638 Processing helix chain 'A' and resid 647 through 662 Processing helix chain 'A' and resid 687 through 710 Processing helix chain 'A' and resid 717 through 733 Processing helix chain 'A' and resid 738 through 753 Processing helix chain 'A' and resid 768 through 774 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.515A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 808 removed outlier: 3.541A pdb=" N LYS A 807 " --> pdb=" O ASP A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 856 through 867 Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 874 through 902 removed outlier: 4.258A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 915 removed outlier: 4.189A pdb=" N ARG A 914 " --> pdb=" O ASN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 923 removed outlier: 4.351A pdb=" N TYR A 921 " --> pdb=" O GLU A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'B' and resid 9 through 29 Processing helix chain 'B' and resid 31 through 53 Processing helix chain 'B' and resid 55 through 98 removed outlier: 3.844A pdb=" N ALA B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 110 removed outlier: 3.649A pdb=" N ASN B 109 " --> pdb=" O ASN B 105 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA B 110 " --> pdb=" O ILE B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 125 removed outlier: 4.343A pdb=" N LEU B 122 " --> pdb=" O ASN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 142 Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.728A pdb=" N ILE B 172 " --> pdb=" O LEU B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 2 through 20 removed outlier: 3.641A pdb=" N LYS C 7 " --> pdb=" O MET C 3 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N CYS C 8 " --> pdb=" O SER C 4 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL C 11 " --> pdb=" O LYS C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 41 removed outlier: 3.962A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 62 removed outlier: 3.783A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 75 removed outlier: 3.530A pdb=" N GLU C 74 " --> pdb=" O LYS C 70 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N MET C 75 " --> pdb=" O LEU C 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 29 Processing helix chain 'D' and resid 31 through 82 Processing helix chain 'D' and resid 83 through 99 removed outlier: 3.949A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 113 removed outlier: 3.556A pdb=" N ASP D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 141 Processing helix chain 'D' and resid 176 through 180 Processing helix chain 'E' and resid 26 through 37 removed outlier: 3.519A pdb=" N SER E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 112 removed outlier: 3.962A pdb=" N ALA E 108 " --> pdb=" O THR E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 123 Processing helix chain 'E' and resid 127 through 146 Processing helix chain 'E' and resid 262 through 264 No H-bonds generated for 'chain 'E' and resid 262 through 264' Processing helix chain 'E' and resid 265 through 274 Processing helix chain 'E' and resid 287 through 299 removed outlier: 4.210A pdb=" N ILE E 293 " --> pdb=" O SER E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 325 Processing helix chain 'E' and resid 361 through 363 No H-bonds generated for 'chain 'E' and resid 361 through 363' Processing helix chain 'E' and resid 376 through 379 Processing helix chain 'E' and resid 380 through 390 Processing helix chain 'E' and resid 418 through 422 Processing helix chain 'E' and resid 423 through 433 Processing helix chain 'E' and resid 445 through 456 removed outlier: 4.220A pdb=" N ALA E 454 " --> pdb=" O ASP E 450 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU E 455 " --> pdb=" O THR E 451 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL E 456 " --> pdb=" O VAL E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 501 Processing helix chain 'E' and resid 503 through 507 removed outlier: 3.815A pdb=" N ARG E 507 " --> pdb=" O PRO E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 515 through 527 removed outlier: 3.603A pdb=" N SER E 523 " --> pdb=" O ASN E 519 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS E 524 " --> pdb=" O ALA E 520 " (cutoff:3.500A) Processing helix chain 'E' and resid 557 through 566 Processing helix chain 'E' and resid 578 through 585 removed outlier: 3.961A pdb=" N LYS E 584 " --> pdb=" O ASP E 580 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU E 585 " --> pdb=" O LEU E 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 37 Processing helix chain 'F' and resid 59 through 61 No H-bonds generated for 'chain 'F' and resid 59 through 61' Processing helix chain 'F' and resid 102 through 112 removed outlier: 3.622A pdb=" N CYS F 112 " --> pdb=" O ALA F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 125 removed outlier: 4.351A pdb=" N TYR F 120 " --> pdb=" O ASN F 116 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR F 125 " --> pdb=" O ILE F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 148 removed outlier: 3.720A pdb=" N PHE F 133 " --> pdb=" O ARG F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 273 Processing helix chain 'F' and resid 287 through 299 Processing helix chain 'F' and resid 310 through 324 Processing helix chain 'F' and resid 361 through 363 No H-bonds generated for 'chain 'F' and resid 361 through 363' Processing helix chain 'F' and resid 375 through 379 Processing helix chain 'F' and resid 380 through 390 Processing helix chain 'F' and resid 418 through 422 Processing helix chain 'F' and resid 423 through 432 Processing helix chain 'F' and resid 445 through 456 removed outlier: 3.716A pdb=" N VAL F 456 " --> pdb=" O VAL F 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 499 removed outlier: 3.795A pdb=" N ILE F 493 " --> pdb=" O ASN F 489 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE F 499 " --> pdb=" O VAL F 495 " (cutoff:3.500A) Processing helix chain 'F' and resid 515 through 526 removed outlier: 4.340A pdb=" N SER F 523 " --> pdb=" O ASN F 519 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LYS F 524 " --> pdb=" O ALA F 520 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE F 525 " --> pdb=" O VAL F 521 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU F 526 " --> pdb=" O ALA F 522 " (cutoff:3.500A) Processing helix chain 'F' and resid 534 through 536 No H-bonds generated for 'chain 'F' and resid 534 through 536' Processing helix chain 'F' and resid 553 through 556 Processing helix chain 'F' and resid 557 through 566 removed outlier: 3.725A pdb=" N THR F 566 " --> pdb=" O ASN F 562 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 3.527A pdb=" N PHE A 56 " --> pdb=" O PHE A 70 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL A 71 " --> pdb=" O GLN A 117 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N GLN A 117 " --> pdb=" O VAL A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 33 Processing sheet with id=AA3, first strand: chain 'A' and resid 36 through 38 Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 224 removed outlier: 6.501A pdb=" N ILE A 201 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 338 through 343 removed outlier: 9.481A pdb=" N SER A 363 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N PHE A 334 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 338 through 343 Processing sheet with id=AA7, first strand: chain 'A' and resid 345 through 348 Processing sheet with id=AA8, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.492A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AB1, first strand: chain 'A' and resid 755 through 758 Processing sheet with id=AB2, first strand: chain 'A' and resid 816 through 822 Processing sheet with id=AB3, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.421A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.421A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL D 159 " --> pdb=" O VAL D 167 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 3 through 4 Processing sheet with id=AB6, first strand: chain 'E' and resid 24 through 25 removed outlier: 3.645A pdb=" N LEU E 14 " --> pdb=" O LEU E 25 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 69 through 71 removed outlier: 3.529A pdb=" N PHE E 81 " --> pdb=" O LEU E 65 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 152 through 153 removed outlier: 4.100A pdb=" N THR E 228 " --> pdb=" O VAL E 181 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N VAL E 181 " --> pdb=" O THR E 228 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR E 198 " --> pdb=" O PHE E 182 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 355 through 359 removed outlier: 6.806A pdb=" N THR E 367 " --> pdb=" O LEU E 391 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ALA E 393 " --> pdb=" O THR E 367 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASP E 369 " --> pdb=" O ALA E 393 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N SER E 278 " --> pdb=" O TYR E 398 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 440 through 441 Processing sheet with id=AC2, first strand: chain 'E' and resid 471 through 475 removed outlier: 6.452A pdb=" N PHE E 472 " --> pdb=" O CYS E 574 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N MET E 576 " --> pdb=" O PHE E 472 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N MET E 474 " --> pdb=" O MET E 576 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N TYR E 541 " --> pdb=" O LYS E 569 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N GLY E 571 " --> pdb=" O TYR E 541 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N TYR E 543 " --> pdb=" O GLY E 571 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LEU E 573 " --> pdb=" O TYR E 543 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE E 545 " --> pdb=" O LEU E 573 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ILE E 575 " --> pdb=" O ILE E 545 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR E 547 " --> pdb=" O ILE E 575 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL E 510 " --> pdb=" O ILE E 545 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N THR E 547 " --> pdb=" O VAL E 510 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ILE E 512 " --> pdb=" O THR E 547 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 481 through 482 Processing sheet with id=AC4, first strand: chain 'F' and resid 3 through 4 Processing sheet with id=AC5, first strand: chain 'F' and resid 14 through 15 removed outlier: 3.838A pdb=" N LEU F 14 " --> pdb=" O LEU F 25 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 63 through 66 Processing sheet with id=AC7, first strand: chain 'F' and resid 84 through 85 Processing sheet with id=AC8, first strand: chain 'F' and resid 165 through 167 Processing sheet with id=AC9, first strand: chain 'F' and resid 330 through 332 removed outlier: 6.707A pdb=" N ILE F 304 " --> pdb=" O VAL F 356 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N CYS F 358 " --> pdb=" O ILE F 304 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TYR F 306 " --> pdb=" O CYS F 358 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL F 305 " --> pdb=" O VAL F 372 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ASP F 374 " --> pdb=" O VAL F 305 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N THR F 307 " --> pdb=" O ASP F 374 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N THR F 367 " --> pdb=" O ALA F 393 " (cutoff:3.500A) removed outlier: 10.201A pdb=" N HIS F 395 " --> pdb=" O THR F 367 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASP F 369 " --> pdb=" O HIS F 395 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N VAL F 397 " --> pdb=" O ASP F 369 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL F 371 " --> pdb=" O VAL F 397 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ILE F 399 " --> pdb=" O VAL F 371 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N PHE F 373 " --> pdb=" O ILE F 399 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 471 through 475 removed outlier: 5.845A pdb=" N PHE F 472 " --> pdb=" O CYS F 574 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N MET F 576 " --> pdb=" O PHE F 472 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N MET F 474 " --> pdb=" O MET F 576 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL F 510 " --> pdb=" O ILE F 545 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N THR F 547 " --> pdb=" O VAL F 510 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ILE F 512 " --> pdb=" O THR F 547 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N PHE F 511 " --> pdb=" O GLN F 531 " (cutoff:3.500A) 863 hydrogen bonds defined for protein. 2400 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 83 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 11.51 Time building geometry restraints manager: 5.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 20432 1.03 - 1.23: 155 1.23 - 1.42: 9571 1.42 - 1.62: 12570 1.62 - 1.81: 226 Bond restraints: 42954 Sorted by residual: bond pdb=" F3 AF3 E 706 " pdb="AL AF3 E 706 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.67e+01 bond pdb=" F2 AF3 F1005 " pdb="AL AF3 F1005 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" F3 AF3 F1005 " pdb="AL AF3 F1005 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.64e+01 bond pdb=" F1 AF3 F1005 " pdb="AL AF3 F1005 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.63e+01 bond pdb=" F2 AF3 E 706 " pdb="AL AF3 E 706 " ideal model delta sigma weight residual 1.637 1.799 -0.162 2.00e-02 2.50e+03 6.53e+01 ... (remaining 42949 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 76310 1.95 - 3.90: 915 3.90 - 5.85: 83 5.85 - 7.80: 13 7.80 - 9.75: 7 Bond angle restraints: 77328 Sorted by residual: angle pdb=" O5' C P 25 " pdb=" C5' C P 25 " pdb=" C4' C P 25 " ideal model delta sigma weight residual 109.40 112.79 -3.39 8.00e-01 1.56e+00 1.80e+01 angle pdb=" O4' G T 11 " pdb=" C1' G T 11 " pdb=" N9 G T 11 " ideal model delta sigma weight residual 108.20 105.21 2.99 8.00e-01 1.56e+00 1.39e+01 angle pdb=" O5' U P 26 " pdb=" C5' U P 26 " pdb=" C4' U P 26 " ideal model delta sigma weight residual 109.40 112.26 -2.86 8.00e-01 1.56e+00 1.28e+01 angle pdb=" O5' A T 43 " pdb=" C5' A T 43 " pdb=" C4' A T 43 " ideal model delta sigma weight residual 109.40 112.21 -2.81 8.00e-01 1.56e+00 1.23e+01 angle pdb=" O5' C P 24 " pdb=" C5' C P 24 " pdb=" C4' C P 24 " ideal model delta sigma weight residual 109.40 112.20 -2.80 8.00e-01 1.56e+00 1.23e+01 ... (remaining 77323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 20061 35.84 - 71.68: 529 71.68 - 107.52: 48 107.52 - 143.36: 17 143.36 - 179.20: 21 Dihedral angle restraints: 20676 sinusoidal: 11757 harmonic: 8919 Sorted by residual: dihedral pdb=" C5' ADP A1004 " pdb=" O5' ADP A1004 " pdb=" PA ADP A1004 " pdb=" O2A ADP A1004 " ideal model delta sinusoidal sigma weight residual 300.00 121.31 178.69 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP A1004 " pdb=" O3A ADP A1004 " pdb=" PA ADP A1004 " pdb=" PB ADP A1004 " ideal model delta sinusoidal sigma weight residual 300.00 134.13 165.87 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" CA SER A 759 " pdb=" C SER A 759 " pdb=" N ASP A 760 " pdb=" CA ASP A 760 " ideal model delta harmonic sigma weight residual 180.00 147.83 32.17 0 5.00e+00 4.00e-02 4.14e+01 ... (remaining 20673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 3334 0.088 - 0.177: 250 0.177 - 0.265: 18 0.265 - 0.353: 6 0.353 - 0.442: 5 Chirality restraints: 3613 Sorted by residual: chirality pdb=" C17 1N7 A1005 " pdb=" C16 1N7 A1005 " pdb=" C18 1N7 A1005 " pdb=" O3 1N7 A1005 " both_signs ideal model delta sigma weight residual False 2.40 2.84 -0.44 2.00e-01 2.50e+01 4.88e+00 chirality pdb=" C15 1N7 A1006 " pdb=" C14 1N7 A1006 " pdb=" C16 1N7 A1006 " pdb=" C2 1N7 A1006 " both_signs ideal model delta sigma weight residual False -2.47 -2.89 0.42 2.00e-01 2.50e+01 4.37e+00 chirality pdb=" C17 1N7 A1006 " pdb=" C16 1N7 A1006 " pdb=" C18 1N7 A1006 " pdb=" O3 1N7 A1006 " both_signs ideal model delta sigma weight residual False 2.40 2.82 -0.42 2.00e-01 2.50e+01 4.31e+00 ... (remaining 3610 not shown) Planarity restraints: 6124 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 52 " -0.041 5.00e-02 4.00e+02 6.27e-02 6.29e+00 pdb=" N PRO E 53 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO E 53 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 53 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G T 11 " -0.026 2.00e-02 2.50e+03 1.09e-02 4.18e+00 pdb=" N9 G T 11 " 0.030 2.00e-02 2.50e+03 pdb=" C8 G T 11 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G T 11 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G T 11 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G T 11 " -0.002 2.00e-02 2.50e+03 pdb=" O6 G T 11 " -0.005 2.00e-02 2.50e+03 pdb=" N1 G T 11 " -0.001 2.00e-02 2.50e+03 pdb=" C2 G T 11 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G T 11 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G T 11 " 0.006 2.00e-02 2.50e+03 pdb=" C4 G T 11 " -0.004 2.00e-02 2.50e+03 pdb=" H8 G T 11 " 0.001 2.00e-02 2.50e+03 pdb=" H1 G T 11 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS F 444 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO F 445 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO F 445 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 445 " -0.021 5.00e-02 4.00e+02 ... (remaining 6121 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.87: 150 1.87 - 2.55: 38189 2.55 - 3.24: 129279 3.24 - 3.92: 164178 3.92 - 4.60: 258859 Nonbonded interactions: 590655 Sorted by model distance: nonbonded pdb=" HE1 PHE A 77 " pdb="HE21 GLN A 81 " model vdw 1.190 2.100 nonbonded pdb=" HE1 HIS F 75 " pdb="ZN ZN F1001 " model vdw 1.213 1.408 nonbonded pdb=" HB3 CYS E 26 " pdb="ZN ZN E 701 " model vdw 1.320 1.544 nonbonded pdb=" H THR E 286 " pdb=" O1B ADP E 704 " model vdw 1.557 2.450 nonbonded pdb=" HG SER D 11 " pdb=" OD2 ASP D 52 " model vdw 1.585 2.450 ... (remaining 590650 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 'B' and ((resid 7 and (name N or name CA or name C or name O or name CB o \ r name OG or name HA or name HB2 or name HB3 or name HG )) or resid 8 through 22 \ or (resid 23 through 24 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 25 through 191)) selection = (chain 'D' and (resid 7 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 33 \ through 35 or (resid 36 and (name N or name CA or name C or name O or name CB o \ r name H or name HA or name HB2 or name HB3)) or resid 37 through 38 or (resid 3 \ 9 and (name N or name CA or name C or name O or name CB or name H or name HA or \ name HB2 or name HB3)) or resid 40 through 47 or (resid 48 and (name N or name C \ A or name C or name O or name CB or name H or name HA or name HB2 or name HB3)) \ or resid 49 through 191)) } ncs_group { reference = (chain 'E' and (resid 1 through 288 or (resid 289 and (name N or name CA or name \ C or name O or name CB or name OG or name HA or name HB2 or name HB3)) or resid \ 290 through 706)) selection = (chain 'F' and (resid 1 through 145 or (resid 146 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid \ 147 through 148 or (resid 149 and (name N or name CA or name C or name O or name \ CB or name H or name HA or name HB2 or name HB3)) or resid 150 through 172 or ( \ resid 173 and (name N or name CA or name C or name O or name CB or name H or nam \ e HA or name HB2 or name HB3)) or resid 174 through 177 or (resid 178 through 17 \ 9 and (name N or name CA or name C or name O or name CB or name H or name HA or \ name HB2 or name HB3)) or resid 180 through 222 or (resid 223 through 225 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA or name HB2 \ or name HB3)) or resid 226 or (resid 227 and (name N or name CA or name C or na \ me O or name CB or name H or name HA or name HB2 or name HB3)) or resid 228 thro \ ugh 229 or (resid 230 and (name N or name CA or name C or name O or name CB or n \ ame H or name HA or name HB2 or name HB3)) or resid 231 through 1005)) } 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 individual isotropic 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: 2.100 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: 0.260 Extract box with map and model: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 56.460 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 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 : 0.006 0.163 22490 Z= 0.305 Angle : 0.688 24.329 30954 Z= 0.396 Chirality : 0.048 0.442 3613 Planarity : 0.003 0.063 3622 Dihedral : 16.418 178.691 8833 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.30 % Favored : 93.66 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.16), residues: 2541 helix: 0.21 (0.17), residues: 972 sheet: -1.38 (0.28), residues: 323 loop : -1.77 (0.17), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 497 TYR 0.015 0.001 TYR A 483 PHE 0.016 0.001 PHE A 652 TRP 0.013 0.001 TRP D 154 HIS 0.006 0.001 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.30 (22458) covalent geometry : angle 0.66280 / 0.39 (30927) hydrogen bonds : bond 0.15888 / 10.44 ( 931) hydrogen bonds : angle 6.45153 / 4.46 ( 2562) metal coordination : bond 0.01457 / 1.02 ( 32) metal coordination : angle 6.29535 / 5.11 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 149 is missing expected H atoms. Skipping. Residue TYR 224 is missing expected H atoms. Skipping. Residue LEU 227 is missing expected H atoms. Skipping. Residue SER 289 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue TYR 476 is missing expected H atoms. Skipping. Residue ILE 575 is missing expected H atoms. Skipping. Residue SER 289 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue TYR 476 is missing expected H atoms. Skipping. Residue ILE 575 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 1.148 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: F 421 TYR cc_start: 0.7249 (m-80) cc_final: 0.6958 (m-80) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.3923 time to fit residues: 104.1263 Evaluate side-chains 137 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 197 optimal weight: 0.0770 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 20.0000 chunk 111 optimal weight: 0.9980 chunk 258 optimal weight: 9.9990 overall best weight: 1.3540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 GLN A 573 GLN A 911 ASN E 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.171333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.105660 restraints weight = 86831.492| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.54 r_work: 0.3270 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.0594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 22490 Z= 0.174 Angle : 0.611 25.617 30954 Z= 0.306 Chirality : 0.040 0.323 3613 Planarity : 0.004 0.054 3622 Dihedral : 16.119 171.729 4267 Min Nonbonded Distance : 1.696 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.94 % Favored : 94.02 % Rotamer: Outliers : 0.23 % Allowed : 3.20 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.16), residues: 2541 helix: 0.30 (0.17), residues: 1002 sheet: -1.16 (0.29), residues: 315 loop : -1.72 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 96 TYR 0.015 0.001 TYR B 135 PHE 0.016 0.001 PHE A 652 TRP 0.008 0.001 TRP A 268 HIS 0.004 0.001 HIS E 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (22458) covalent geometry : angle 0.57777 / 0.30 (30927) hydrogen bonds : bond 0.05710 / 3.88 ( 931) hydrogen bonds : angle 5.07687 / 3.50 ( 2562) metal coordination : bond 0.01240 / 0.84 ( 32) metal coordination : angle 6.77255 / 5.52 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 149 is missing expected H atoms. Skipping. Residue TYR 224 is missing expected H atoms. Skipping. Residue LEU 227 is missing expected H atoms. Skipping. Residue SER 289 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue TYR 476 is missing expected H atoms. Skipping. Residue ILE 575 is missing expected H atoms. Skipping. Residue SER 289 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue TYR 476 is missing expected H atoms. Skipping. Residue ILE 575 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 146 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 148 average time/residue: 0.4059 time to fit residues: 91.0856 Evaluate side-chains 137 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 134 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 506 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 61 optimal weight: 1.9990 chunk 199 optimal weight: 10.0000 chunk 233 optimal weight: 20.0000 chunk 18 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 79 optimal weight: 0.4980 chunk 81 optimal weight: 0.9990 chunk 223 optimal weight: 20.0000 chunk 244 optimal weight: 9.9990 chunk 182 optimal weight: 40.0000 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 GLN E 270 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.171509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.098427 restraints weight = 86559.269| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.87 r_work: 0.3318 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 22490 Z= 0.154 Angle : 0.580 25.878 30954 Z= 0.284 Chirality : 0.039 0.256 3613 Planarity : 0.004 0.053 3622 Dihedral : 15.098 169.379 4267 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.94 % Favored : 94.02 % Rotamer: Outliers : 0.27 % Allowed : 4.62 % Favored : 95.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.17), residues: 2541 helix: 0.42 (0.17), residues: 1016 sheet: -1.22 (0.28), residues: 320 loop : -1.62 (0.17), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 105 TYR 0.016 0.001 TYR F 269 PHE 0.015 0.001 PHE A 652 TRP 0.007 0.001 TRP A 268 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (22458) covalent geometry : angle 0.54467 / 0.28 (30927) hydrogen bonds : bond 0.05042 / 3.42 ( 931) hydrogen bonds : angle 4.73704 / 3.27 ( 2562) metal coordination : bond 0.01166 / 0.82 ( 32) metal coordination : angle 6.76555 / 5.57 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 149 is missing expected H atoms. Skipping. Residue TYR 224 is missing expected H atoms. Skipping. Residue LEU 227 is missing expected H atoms. Skipping. Residue SER 289 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue TYR 476 is missing expected H atoms. Skipping. Residue ILE 575 is missing expected H atoms. Skipping. Residue SER 289 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue TYR 476 is missing expected H atoms. Skipping. Residue ILE 575 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 146 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.8312 (mt0) cc_final: 0.8023 (mt0) REVERT: B 57 ARG cc_start: 0.7754 (mtm-85) cc_final: 0.7527 (mtm-85) outliers start: 6 outliers final: 5 residues processed: 148 average time/residue: 0.4063 time to fit residues: 91.5412 Evaluate side-chains 137 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 132 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 506 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 113 optimal weight: 0.5980 chunk 131 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 111 optimal weight: 0.3980 chunk 54 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 909 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.171614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.098867 restraints weight = 86302.532| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.85 r_work: 0.3283 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 22490 Z= 0.145 Angle : 0.564 25.730 30954 Z= 0.276 Chirality : 0.038 0.228 3613 Planarity : 0.003 0.067 3622 Dihedral : 14.593 168.549 4267 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.14 % Favored : 93.82 % Rotamer: Outliers : 0.27 % Allowed : 6.08 % Favored : 93.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.17), residues: 2541 helix: 0.50 (0.17), residues: 1023 sheet: -1.22 (0.29), residues: 316 loop : -1.60 (0.18), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 105 TYR 0.011 0.001 TYR A 515 PHE 0.014 0.001 PHE A 652 TRP 0.007 0.001 TRP A 916 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (22458) covalent geometry : angle 0.52762 / 0.27 (30927) hydrogen bonds : bond 0.04719 / 3.18 ( 931) hydrogen bonds : angle 4.58475 / 3.16 ( 2562) metal coordination : bond 0.01159 / 0.81 ( 32) metal coordination : angle 6.72631 / 5.51 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 149 is missing expected H atoms. Skipping. Residue TYR 224 is missing expected H atoms. Skipping. Residue LEU 227 is missing expected H atoms. Skipping. Residue SER 289 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue TYR 476 is missing expected H atoms. Skipping. Residue ILE 575 is missing expected H atoms. Skipping. Residue SER 289 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue TYR 476 is missing expected H atoms. Skipping. Residue ILE 575 is missing expected H atoms. Skipping. Evaluate side-chains 148 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 142 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 648 LEU cc_start: 0.8509 (tt) cc_final: 0.8306 (tp) REVERT: C 3 MET cc_start: 0.8512 (tpp) cc_final: 0.8295 (tpp) outliers start: 6 outliers final: 4 residues processed: 144 average time/residue: 0.4048 time to fit residues: 88.3418 Evaluate side-chains 137 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 133 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 506 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 101 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 249 optimal weight: 20.0000 chunk 149 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 222 optimal weight: 30.0000 chunk 12 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 GLN A 909 ASN D 19 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.170071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.099820 restraints weight = 86401.377| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.26 r_work: 0.3263 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 22490 Z= 0.224 Angle : 0.585 25.754 30954 Z= 0.290 Chirality : 0.040 0.229 3613 Planarity : 0.004 0.062 3622 Dihedral : 14.526 171.195 4267 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.41 % Favored : 93.55 % Rotamer: Outliers : 0.41 % Allowed : 6.76 % Favored : 92.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.17), residues: 2541 helix: 0.50 (0.17), residues: 1022 sheet: -1.28 (0.29), residues: 315 loop : -1.65 (0.17), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 105 TYR 0.014 0.001 TYR A 748 PHE 0.016 0.001 PHE A 652 TRP 0.008 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.22 (22458) covalent geometry : angle 0.55048 / 0.29 (30927) hydrogen bonds : bond 0.04850 / 3.27 ( 931) hydrogen bonds : angle 4.57412 / 3.16 ( 2562) metal coordination : bond 0.01249 / 0.88 ( 32) metal coordination : angle 6.72369 / 5.51 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 149 is missing expected H atoms. Skipping. Residue TYR 224 is missing expected H atoms. Skipping. Residue LEU 227 is missing expected H atoms. Skipping. Residue SER 289 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue TYR 476 is missing expected H atoms. Skipping. Residue ILE 575 is missing expected H atoms. Skipping. Residue SER 289 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue TYR 476 is missing expected H atoms. Skipping. Residue ILE 575 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 141 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.8351 (mt0) cc_final: 0.8085 (mt0) outliers start: 9 outliers final: 8 residues processed: 145 average time/residue: 0.4063 time to fit residues: 89.0990 Evaluate side-chains 143 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 506 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 184 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 150 optimal weight: 7.9990 chunk 0 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 254 optimal weight: 20.0000 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 GLN A 909 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.170632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.100522 restraints weight = 86352.322| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.31 r_work: 0.3267 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 22490 Z= 0.178 Angle : 0.568 25.783 30954 Z= 0.279 Chirality : 0.039 0.227 3613 Planarity : 0.003 0.062 3622 Dihedral : 14.430 175.091 4267 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.30 % Favored : 93.66 % Rotamer: Outliers : 0.32 % Allowed : 7.18 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.17), residues: 2541 helix: 0.56 (0.17), residues: 1022 sheet: -1.23 (0.29), residues: 319 loop : -1.62 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 105 TYR 0.012 0.001 TYR A 788 PHE 0.015 0.001 PHE A 652 TRP 0.008 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (22458) covalent geometry : angle 0.53132 / 0.28 (30927) hydrogen bonds : bond 0.04675 / 3.14 ( 931) hydrogen bonds : angle 4.49485 / 3.11 ( 2562) metal coordination : bond 0.01194 / 0.84 ( 32) metal coordination : angle 6.77210 / 5.55 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 149 is missing expected H atoms. Skipping. Residue TYR 224 is missing expected H atoms. Skipping. Residue LEU 227 is missing expected H atoms. Skipping. Residue SER 289 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue TYR 476 is missing expected H atoms. Skipping. Residue ILE 575 is missing expected H atoms. Skipping. Residue SER 289 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue TYR 476 is missing expected H atoms. Skipping. Residue ILE 575 is missing expected H atoms. Skipping. Evaluate side-chains 148 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 141 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 648 LEU cc_start: 0.8592 (tt) cc_final: 0.8379 (tp) REVERT: F 306 TYR cc_start: 0.7152 (m-80) cc_final: 0.6165 (m-10) outliers start: 7 outliers final: 6 residues processed: 144 average time/residue: 0.3995 time to fit residues: 87.1728 Evaluate side-chains 140 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 134 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 506 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 19 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 208 optimal weight: 10.0000 chunk 123 optimal weight: 2.9990 chunk 186 optimal weight: 10.0000 chunk 240 optimal weight: 20.0000 chunk 246 optimal weight: 20.0000 chunk 39 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 909 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.168584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.098692 restraints weight = 86588.118| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.26 r_work: 0.3233 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 22490 Z= 0.301 Angle : 0.621 25.772 30954 Z= 0.312 Chirality : 0.042 0.230 3613 Planarity : 0.004 0.074 3622 Dihedral : 14.431 175.300 4267 Min Nonbonded Distance : 1.656 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.36 % Favored : 92.60 % Rotamer: Outliers : 0.50 % Allowed : 7.50 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.17), residues: 2541 helix: 0.45 (0.16), residues: 1022 sheet: -1.39 (0.28), residues: 325 loop : -1.69 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 105 TYR 0.015 0.001 TYR A 748 PHE 0.018 0.002 PHE A 652 TRP 0.008 0.001 TRP A 916 HIS 0.007 0.001 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00694 / 0.30 (22458) covalent geometry : angle 0.58807 / 0.31 (30927) hydrogen bonds : bond 0.05057 / 3.42 ( 931) hydrogen bonds : angle 4.60424 / 3.19 ( 2562) metal coordination : bond 0.01428 / 1.01 ( 32) metal coordination : angle 6.78942 / 5.54 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 149 is missing expected H atoms. Skipping. Residue TYR 224 is missing expected H atoms. Skipping. Residue LEU 227 is missing expected H atoms. Skipping. Residue SER 289 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue TYR 476 is missing expected H atoms. Skipping. Residue ILE 575 is missing expected H atoms. Skipping. Residue SER 289 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue TYR 476 is missing expected H atoms. Skipping. Residue ILE 575 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.8379 (mt0) cc_final: 0.8068 (mt0) REVERT: F 306 TYR cc_start: 0.7125 (m-80) cc_final: 0.6083 (m-10) outliers start: 11 outliers final: 9 residues processed: 139 average time/residue: 0.3976 time to fit residues: 83.9041 Evaluate side-chains 140 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 131 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 506 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 123 optimal weight: 1.9990 chunk 255 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 161 optimal weight: 0.7980 chunk 243 optimal weight: 1.9990 chunk 218 optimal weight: 5.9990 chunk 59 optimal weight: 0.5980 chunk 163 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 127 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 124 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.171201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.098506 restraints weight = 86099.181| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.84 r_work: 0.3310 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 22490 Z= 0.113 Angle : 0.558 25.916 30954 Z= 0.273 Chirality : 0.038 0.227 3613 Planarity : 0.004 0.083 3622 Dihedral : 14.374 174.854 4267 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.86 % Favored : 94.10 % Rotamer: Outliers : 0.37 % Allowed : 7.86 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.17), residues: 2541 helix: 0.62 (0.17), residues: 1023 sheet: -1.26 (0.29), residues: 320 loop : -1.55 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 105 TYR 0.011 0.001 TYR A 831 PHE 0.016 0.001 PHE A 652 TRP 0.008 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (22458) covalent geometry : angle 0.52009 / 0.27 (30927) hydrogen bonds : bond 0.04526 / 3.02 ( 931) hydrogen bonds : angle 4.44536 / 3.07 ( 2562) metal coordination : bond 0.01155 / 0.81 ( 32) metal coordination : angle 6.82021 / 5.57 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 149 is missing expected H atoms. Skipping. Residue TYR 224 is missing expected H atoms. Skipping. Residue LEU 227 is missing expected H atoms. Skipping. Residue SER 289 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue TYR 476 is missing expected H atoms. Skipping. Residue ILE 575 is missing expected H atoms. Skipping. Residue SER 289 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue TYR 476 is missing expected H atoms. Skipping. Residue ILE 575 is missing expected H atoms. Skipping. Evaluate side-chains 145 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 137 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.8271 (mt0) cc_final: 0.8000 (mt0) REVERT: F 306 TYR cc_start: 0.7092 (m-80) cc_final: 0.5989 (m-10) outliers start: 8 outliers final: 7 residues processed: 141 average time/residue: 0.4057 time to fit residues: 86.4415 Evaluate side-chains 142 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 135 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 506 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 87 optimal weight: 1.9990 chunk 210 optimal weight: 30.0000 chunk 7 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 117 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 140 optimal weight: 9.9990 chunk 254 optimal weight: 20.0000 chunk 103 optimal weight: 0.2980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.171030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.098457 restraints weight = 86023.780| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.84 r_work: 0.3308 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 22490 Z= 0.141 Angle : 0.554 25.636 30954 Z= 0.270 Chirality : 0.038 0.227 3613 Planarity : 0.003 0.087 3622 Dihedral : 14.307 176.601 4267 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.45 % Favored : 93.51 % Rotamer: Outliers : 0.32 % Allowed : 8.09 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.17), residues: 2541 helix: 0.69 (0.17), residues: 1023 sheet: -1.25 (0.29), residues: 321 loop : -1.51 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 105 TYR 0.012 0.001 TYR A 748 PHE 0.015 0.001 PHE A 652 TRP 0.008 0.001 TRP A 916 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (22458) covalent geometry : angle 0.51728 / 0.27 (30927) hydrogen bonds : bond 0.04478 / 2.98 ( 931) hydrogen bonds : angle 4.38313 / 3.03 ( 2562) metal coordination : bond 0.01147 / 0.82 ( 32) metal coordination : angle 6.72984 / 5.52 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 149 is missing expected H atoms. Skipping. Residue TYR 224 is missing expected H atoms. Skipping. Residue LEU 227 is missing expected H atoms. Skipping. Residue SER 289 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue TYR 476 is missing expected H atoms. Skipping. Residue ILE 575 is missing expected H atoms. Skipping. Residue SER 289 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue TYR 476 is missing expected H atoms. Skipping. Residue ILE 575 is missing expected H atoms. Skipping. Evaluate side-chains 145 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 138 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.8276 (mt0) cc_final: 0.7995 (mt0) REVERT: D 157 GLN cc_start: 0.8755 (mm-40) cc_final: 0.8507 (mm110) REVERT: F 306 TYR cc_start: 0.7093 (m-80) cc_final: 0.6039 (m-10) outliers start: 7 outliers final: 7 residues processed: 141 average time/residue: 0.3971 time to fit residues: 85.1531 Evaluate side-chains 143 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 136 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 506 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 64 optimal weight: 0.0970 chunk 226 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.171805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.099109 restraints weight = 86231.355| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.85 r_work: 0.3318 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 22490 Z= 0.120 Angle : 0.544 25.433 30954 Z= 0.264 Chirality : 0.038 0.227 3613 Planarity : 0.003 0.100 3622 Dihedral : 14.251 173.382 4267 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.82 % Favored : 94.14 % Rotamer: Outliers : 0.37 % Allowed : 8.09 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.17), residues: 2541 helix: 0.76 (0.17), residues: 1023 sheet: -1.25 (0.29), residues: 323 loop : -1.46 (0.18), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 105 TYR 0.017 0.001 TYR E 541 PHE 0.014 0.001 PHE A 652 TRP 0.009 0.001 TRP A 916 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (22458) covalent geometry : angle 0.50715 / 0.26 (30927) hydrogen bonds : bond 0.04355 / 2.89 ( 931) hydrogen bonds : angle 4.31870 / 2.98 ( 2562) metal coordination : bond 0.01155 / 0.81 ( 32) metal coordination : angle 6.71451 / 5.51 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue TYR 149 is missing expected H atoms. Skipping. Residue TYR 224 is missing expected H atoms. Skipping. Residue LEU 227 is missing expected H atoms. Skipping. Residue SER 289 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue TYR 476 is missing expected H atoms. Skipping. Residue ILE 575 is missing expected H atoms. Skipping. Residue SER 289 is missing expected H atoms. Skipping. Residue LYS 473 is missing expected H atoms. Skipping. Residue TYR 476 is missing expected H atoms. Skipping. Residue ILE 575 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 138 time to evaluate : 1.139 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: A 81 GLN cc_start: 0.8296 (mt0) cc_final: 0.8012 (mt0) REVERT: D 157 GLN cc_start: 0.8740 (mm-40) cc_final: 0.8491 (mm110) REVERT: F 306 TYR cc_start: 0.7038 (m-80) cc_final: 0.5944 (m-10) outliers start: 8 outliers final: 8 residues processed: 142 average time/residue: 0.4133 time to fit residues: 88.8400 Evaluate side-chains 144 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 136 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 506 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 15 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 208 optimal weight: 8.9990 chunk 108 optimal weight: 0.0470 chunk 74 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 222 optimal weight: 20.0000 chunk 109 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 230 optimal weight: 2.9990 overall best weight: 1.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.171704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.101373 restraints weight = 86638.485| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.27 r_work: 0.3284 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 22490 Z= 0.139 Angle : 0.554 25.353 30954 Z= 0.267 Chirality : 0.038 0.227 3613 Planarity : 0.004 0.097 3622 Dihedral : 14.212 172.322 4267 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.26 % Favored : 93.70 % Rotamer: Outliers : 0.41 % Allowed : 8.27 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.17), residues: 2541 helix: 0.79 (0.17), residues: 1024 sheet: -1.24 (0.29), residues: 323 loop : -1.43 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 105 TYR 0.012 0.001 TYR E 541 PHE 0.014 0.001 PHE A 652 TRP 0.009 0.001 TRP A 916 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (22458) covalent geometry : angle 0.51790 / 0.26 (30927) hydrogen bonds : bond 0.04364 / 2.90 ( 931) hydrogen bonds : angle 4.30400 / 2.98 ( 2562) metal coordination : bond 0.01140 / 0.81 ( 32) metal coordination : angle 6.65792 / 5.48 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13870.09 seconds wall clock time: 235 minutes 26.04 seconds (14126.04 seconds total)