Starting phenix.real_space_refine on Tue Aug 26 23:05:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rdx_24426/08_2025/7rdx_24426_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rdx_24426/08_2025/7rdx_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_24426/08_2025/7rdx_24426_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rdx_24426/08_2025/7rdx_24426_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rdx_24426/08_2025/7rdx_24426.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rdx_24426/08_2025/7rdx_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-2.0-5787/lib/python3.9/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: 8.39, per 1000 atoms: 0.20 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: 4.01 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 8.81 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: 12.23 Time building geometry restraints manager: 5.54 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: 76472 1.95 - 3.90: 754 3.90 - 5.85: 82 5.85 - 7.80: 13 7.80 - 9.75: 7 Bond angle restraints: 77328 Sorted by residual: angle pdb=" C VAL E 187 " pdb=" CA VAL E 187 " pdb=" CB VAL E 187 " ideal model delta sigma weight residual 112.19 108.43 3.76 1.15e+00 7.56e-01 1.07e+01 angle pdb=" C23 1N7 A1005 " pdb=" C24 1N7 A1005 " pdb=" N1 1N7 A1005 " ideal model delta sigma weight residual 115.43 125.18 -9.75 3.00e+00 1.11e-01 1.06e+01 angle pdb=" C28 1N7 E 707 " pdb=" N2 1N7 E 707 " pdb=" C30 1N7 E 707 " ideal model delta sigma weight residual 111.22 101.62 9.60 3.00e+00 1.11e-01 1.02e+01 angle pdb=" C23 1N7 E 707 " pdb=" C24 1N7 E 707 " pdb=" N1 1N7 E 707 " ideal model delta sigma weight residual 115.43 124.80 -9.37 3.00e+00 1.11e-01 9.75e+00 angle pdb=" C SER F 80 " pdb=" N PHE F 81 " pdb=" CA PHE F 81 " ideal model delta sigma weight residual 121.70 127.06 -5.36 1.80e+00 3.09e-01 8.87e+00 ... (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: 3410 0.088 - 0.177: 174 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: 3.030 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: 0.270 Extract box with map and model: 0.580 Check model and map are aligned: 0.130 Set scattering table: 0.130 Process input model: 61.270 Find NCS groups from input model: 0.460 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 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= 0.293 Angle : 0.664 24.329 30954 Z= 0.338 Chirality : 0.046 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 aren 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 covalent geometry : bond 0.00604 (22458) covalent geometry : angle 0.63751 (30927) hydrogen bonds : bond 0.15888 ( 931) hydrogen bonds : angle 6.45153 ( 2562) metal coordination : bond 0.01457 ( 32) metal coordination : angle 6.29535 ( 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 : 1.267 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: 0.6959 (m-80) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.4415 time to fit residues: 114.4792 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 : 1.144 ------------------------------------------------------------------------------- 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: 6.9990 overall best weight: 1.3540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 GLN A 573 GLN A 911 ASN D 65 GLN E 354 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.171399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.101989 restraints weight = 86788.719| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.34 r_work: 0.3291 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.0699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 22490 Z= 0.168 Angle : 0.604 25.929 30954 Z= 0.297 Chirality : 0.039 0.289 3613 Planarity : 0.004 0.052 3622 Dihedral : 15.739 169.096 4267 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.02 % Favored : 93.94 % Rotamer: Outliers : 0.27 % Allowed : 3.47 % Favored : 96.25 % 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 aren not related in a simple way. whole: -1.21 (0.17), residues: 2541 helix: 0.35 (0.17), residues: 1009 sheet: -1.18 (0.29), residues: 316 loop : -1.69 (0.17), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 726 TYR 0.013 0.001 TYR A 748 PHE 0.015 0.001 PHE A 652 TRP 0.008 0.001 TRP A 268 HIS 0.005 0.001 HIS F 33 Details of bonding type rmsd covalent geometry : bond 0.00374 (22458) covalent geometry : angle 0.56914 (30927) hydrogen bonds : bond 0.05142 ( 931) hydrogen bonds : angle 4.93628 ( 2562) metal coordination : bond 0.01097 ( 32) metal coordination : angle 6.84068 ( 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 155 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 149 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 152 average time/residue: 0.4352 time to fit residues: 97.8356 Evaluate side-chains 136 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 133 time to evaluate : 1.148 ------------------------------------------------------------------------------- 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: 9.9990 chunk 233 optimal weight: 20.0000 chunk 18 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 215 optimal weight: 7.9990 chunk 79 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 223 optimal weight: 30.0000 chunk 244 optimal weight: 1.9990 chunk 182 optimal weight: 40.0000 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 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 = 0.4370 r_free = 0.4370 target = 0.171445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.103746 restraints weight = 86705.980| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.50 r_work: 0.3285 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.0949 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= 0.160 Angle : 0.576 25.737 30954 Z= 0.279 Chirality : 0.038 0.236 3613 Planarity : 0.003 0.045 3622 Dihedral : 14.700 167.369 4267 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.98 % Favored : 93.98 % Rotamer: Outliers : 0.32 % Allowed : 5.16 % Favored : 94.52 % 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 aren not related in a simple way. whole: -1.09 (0.17), residues: 2541 helix: 0.45 (0.17), residues: 1022 sheet: -1.23 (0.29), residues: 315 loop : -1.61 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 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 C 36 Details of bonding type rmsd covalent geometry : bond 0.00361 (22458) covalent geometry : angle 0.54048 (30927) hydrogen bonds : bond 0.04731 ( 931) hydrogen bonds : angle 4.63799 ( 2562) metal coordination : bond 0.01162 ( 32) metal coordination : angle 6.72513 ( 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 151 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 144 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.8362 (mt0) cc_final: 0.8152 (mt0) REVERT: A 573 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8528 (tt0) outliers start: 7 outliers final: 6 residues processed: 147 average time/residue: 0.4197 time to fit residues: 92.2505 Evaluate side-chains 141 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 134 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain A residue 573 GLN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 113 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 134 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 909 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.171999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.101706 restraints weight = 86568.114| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.33 r_work: 0.3296 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1121 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= 0.139 Angle : 0.557 25.561 30954 Z= 0.270 Chirality : 0.038 0.168 3613 Planarity : 0.003 0.044 3622 Dihedral : 14.474 166.821 4267 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.98 % Favored : 93.98 % Rotamer: Outliers : 0.37 % Allowed : 5.90 % Favored : 93.74 % 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 aren not related in a simple way. whole: -0.95 (0.17), residues: 2541 helix: 0.59 (0.17), residues: 1023 sheet: -1.17 (0.29), residues: 315 loop : -1.55 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 497 TYR 0.011 0.001 TYR A 748 PHE 0.014 0.001 PHE A 652 TRP 0.007 0.001 TRP A 916 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00314 (22458) covalent geometry : angle 0.52054 (30927) hydrogen bonds : bond 0.04429 ( 931) hydrogen bonds : angle 4.50046 ( 2562) metal coordination : bond 0.01132 ( 32) metal coordination : angle 6.72706 ( 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 160 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 152 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.8307 (mt0) cc_final: 0.8099 (mt0) REVERT: A 573 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.7514 (tt0) REVERT: A 648 LEU cc_start: 0.8533 (tt) cc_final: 0.8326 (tp) REVERT: D 157 GLN cc_start: 0.8780 (mm-40) cc_final: 0.8553 (mm110) REVERT: E 497 ARG cc_start: 0.7832 (tpp-160) cc_final: 0.7620 (tpp-160) REVERT: F 306 TYR cc_start: 0.7121 (m-80) cc_final: 0.6057 (m-10) outliers start: 8 outliers final: 5 residues processed: 156 average time/residue: 0.4288 time to fit residues: 99.4597 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 : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain A residue 573 GLN 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 506 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 101 optimal weight: 0.7980 chunk 140 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 249 optimal weight: 20.0000 chunk 149 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 222 optimal weight: 30.0000 chunk 12 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4354 r_free = 0.4354 target = 0.169731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.099618 restraints weight = 86472.477| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.29 r_work: 0.3252 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 22490 Z= 0.225 Angle : 0.589 25.881 30954 Z= 0.290 Chirality : 0.039 0.158 3613 Planarity : 0.003 0.045 3622 Dihedral : 14.426 179.202 4267 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.77 % Favored : 93.19 % Rotamer: Outliers : 0.37 % Allowed : 7.08 % Favored : 92.55 % 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 aren not related in a simple way. whole: -1.02 (0.17), residues: 2541 helix: 0.56 (0.17), residues: 1022 sheet: -1.28 (0.29), residues: 320 loop : -1.60 (0.18), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 507 TYR 0.014 0.001 TYR A 748 PHE 0.018 0.001 PHE A 652 TRP 0.008 0.001 TRP A 916 HIS 0.006 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00518 (22458) covalent geometry : angle 0.55355 (30927) hydrogen bonds : bond 0.04694 ( 931) hydrogen bonds : angle 4.51397 ( 2562) metal coordination : bond 0.01273 ( 32) metal coordination : angle 6.79375 ( 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 146 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 138 time to evaluate : 1.122 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: D 157 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8538 (mm110) REVERT: E 497 ARG cc_start: 0.7868 (tpp-160) cc_final: 0.7651 (tpp-160) REVERT: F 306 TYR cc_start: 0.7109 (m-80) cc_final: 0.6060 (m-10) outliers start: 8 outliers final: 7 residues processed: 142 average time/residue: 0.4422 time to fit residues: 92.2721 Evaluate side-chains 140 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 133 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 184 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 150 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 254 optimal weight: 9.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 573 GLN A 909 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.170760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.097961 restraints weight = 86464.877| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.85 r_work: 0.3301 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 22490 Z= 0.169 Angle : 0.561 25.635 30954 Z= 0.272 Chirality : 0.038 0.145 3613 Planarity : 0.003 0.041 3622 Dihedral : 14.328 177.722 4267 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.02 % Favored : 93.94 % Rotamer: Outliers : 0.55 % Allowed : 7.82 % Favored : 91.64 % 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 aren not related in a simple way. whole: -0.91 (0.17), residues: 2541 helix: 0.66 (0.17), residues: 1023 sheet: -1.24 (0.29), residues: 321 loop : -1.53 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 22 TYR 0.013 0.001 TYR E 541 PHE 0.014 0.001 PHE A 652 TRP 0.008 0.001 TRP A 916 HIS 0.004 0.001 HIS A 650 Details of bonding type rmsd covalent geometry : bond 0.00389 (22458) covalent geometry : angle 0.52444 (30927) hydrogen bonds : bond 0.04390 ( 931) hydrogen bonds : angle 4.39858 ( 2562) metal coordination : bond 0.01143 ( 32) metal coordination : angle 6.74513 ( 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 155 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 1.168 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 573 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8488 (tt0) REVERT: D 157 GLN cc_start: 0.8753 (mm-40) cc_final: 0.8495 (mm110) REVERT: F 306 TYR cc_start: 0.7029 (m-80) cc_final: 0.5897 (m-10) outliers start: 12 outliers final: 8 residues processed: 151 average time/residue: 0.4649 time to fit residues: 102.0742 Evaluate side-chains 143 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 ASN Chi-restraints excluded: chain A residue 573 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 19 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 chunk 208 optimal weight: 8.9990 chunk 123 optimal weight: 2.9990 chunk 186 optimal weight: 10.0000 chunk 240 optimal weight: 30.0000 chunk 246 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 157 optimal weight: 9.9990 chunk 176 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.169657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.100068 restraints weight = 86386.446| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.25 r_work: 0.3252 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 22490 Z= 0.225 Angle : 0.582 25.659 30954 Z= 0.286 Chirality : 0.039 0.156 3613 Planarity : 0.003 0.040 3622 Dihedral : 14.339 177.568 4267 Min Nonbonded Distance : 1.698 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.93 % Favored : 93.03 % Rotamer: Outliers : 0.46 % Allowed : 8.41 % Favored : 91.13 % 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 aren not related in a simple way. whole: -0.95 (0.17), residues: 2541 helix: 0.63 (0.17), residues: 1023 sheet: -1.27 (0.29), residues: 320 loop : -1.55 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 427 TYR 0.024 0.001 TYR F 421 PHE 0.015 0.001 PHE A 652 TRP 0.008 0.001 TRP A 916 HIS 0.006 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00518 (22458) covalent geometry : angle 0.54700 (30927) hydrogen bonds : bond 0.04567 ( 931) hydrogen bonds : angle 4.43776 ( 2562) metal coordination : bond 0.01254 ( 32) metal coordination : angle 6.75242 ( 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 147 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 157 GLN cc_start: 0.8782 (mm-40) cc_final: 0.8508 (mm110) REVERT: F 306 TYR cc_start: 0.7090 (m-80) cc_final: 0.6051 (m-10) outliers start: 10 outliers final: 10 residues processed: 142 average time/residue: 0.4335 time to fit residues: 91.4948 Evaluate side-chains 144 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 E residue 290 HIS Chi-restraints excluded: chain E residue 380 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 123 optimal weight: 2.9990 chunk 255 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 161 optimal weight: 0.7980 chunk 243 optimal weight: 0.8980 chunk 218 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 chunk 119 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.171920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.098704 restraints weight = 86191.382| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.93 r_work: 0.3321 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 22490 Z= 0.116 Angle : 0.544 25.375 30954 Z= 0.262 Chirality : 0.037 0.145 3613 Planarity : 0.003 0.042 3622 Dihedral : 14.243 169.580 4267 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.59 % Favored : 94.37 % Rotamer: Outliers : 0.41 % Allowed : 8.68 % Favored : 90.90 % 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 aren not related in a simple way. whole: -0.73 (0.17), residues: 2541 helix: 0.78 (0.17), residues: 1024 sheet: -1.14 (0.29), residues: 324 loop : -1.42 (0.18), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 427 TYR 0.022 0.001 TYR F 421 PHE 0.013 0.001 PHE A 652 TRP 0.008 0.001 TRP A 916 HIS 0.005 0.001 HIS A 572 Details of bonding type rmsd covalent geometry : bond 0.00260 (22458) covalent geometry : angle 0.50748 (30927) hydrogen bonds : bond 0.04170 ( 931) hydrogen bonds : angle 4.29231 ( 2562) metal coordination : bond 0.01120 ( 32) metal coordination : angle 6.70135 ( 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 147 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 138 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 648 LEU cc_start: 0.8537 (tt) cc_final: 0.8327 (tp) REVERT: D 157 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8476 (mm110) REVERT: E 497 ARG cc_start: 0.7657 (tpp-160) cc_final: 0.7409 (tpp-160) REVERT: F 306 TYR cc_start: 0.7048 (m-80) cc_final: 0.5929 (m-10) outliers start: 9 outliers final: 8 residues processed: 143 average time/residue: 0.4284 time to fit residues: 91.3384 Evaluate side-chains 142 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 1.164 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 87 optimal weight: 1.9990 chunk 210 optimal weight: 20.0000 chunk 7 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 140 optimal weight: 10.0000 chunk 254 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.171297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.101041 restraints weight = 86177.693| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.31 r_work: 0.3281 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1574 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= 0.158 Angle : 0.552 25.369 30954 Z= 0.267 Chirality : 0.038 0.145 3613 Planarity : 0.003 0.041 3622 Dihedral : 14.210 168.360 4267 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.45 % Favored : 93.51 % Rotamer: Outliers : 0.41 % Allowed : 8.91 % Favored : 90.68 % 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 aren not related in a simple way. whole: -0.72 (0.17), residues: 2541 helix: 0.80 (0.17), residues: 1026 sheet: -1.19 (0.29), residues: 320 loop : -1.39 (0.18), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 155 TYR 0.018 0.001 TYR F 421 PHE 0.014 0.001 PHE A 652 TRP 0.009 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00361 (22458) covalent geometry : angle 0.51592 (30927) hydrogen bonds : bond 0.04267 ( 931) hydrogen bonds : angle 4.28922 ( 2562) metal coordination : bond 0.01173 ( 32) metal coordination : angle 6.66840 ( 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 151 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 1.220 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: A 648 LEU cc_start: 0.8550 (tt) cc_final: 0.8332 (tp) REVERT: D 157 GLN cc_start: 0.8764 (mm-40) cc_final: 0.8464 (mm110) REVERT: E 497 ARG cc_start: 0.7766 (tpp-160) cc_final: 0.7533 (tpp-160) REVERT: F 169 VAL cc_start: 0.7504 (t) cc_final: 0.7186 (p) REVERT: F 306 TYR cc_start: 0.7069 (m-80) cc_final: 0.6009 (m-10) outliers start: 9 outliers final: 9 residues processed: 147 average time/residue: 0.4254 time to fit residues: 93.1863 Evaluate side-chains 148 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 139 time to evaluate : 1.245 ------------------------------------------------------------------------------- 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 E residue 380 THR 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 64 optimal weight: 8.9990 chunk 226 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 39 optimal weight: 0.4980 chunk 136 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.172009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.099093 restraints weight = 86324.396| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.85 r_work: 0.3321 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1646 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= 0.131 Angle : 0.542 25.124 30954 Z= 0.260 Chirality : 0.037 0.145 3613 Planarity : 0.003 0.057 3622 Dihedral : 14.146 172.296 4267 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.90 % Favored : 94.06 % Rotamer: Outliers : 0.41 % Allowed : 8.87 % Favored : 90.72 % 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 aren not related in a simple way. whole: -0.63 (0.17), residues: 2541 helix: 0.89 (0.17), residues: 1020 sheet: -1.17 (0.29), residues: 324 loop : -1.34 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 105 TYR 0.016 0.001 TYR F 421 PHE 0.013 0.001 PHE A 652 TRP 0.009 0.001 TRP A 916 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00297 (22458) covalent geometry : angle 0.50608 (30927) hydrogen bonds : bond 0.04146 ( 931) hydrogen bonds : angle 4.22800 ( 2562) metal coordination : bond 0.01134 ( 32) metal coordination : angle 6.63217 ( 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 148 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 139 time to evaluate : 1.336 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 648 LEU cc_start: 0.8485 (tt) cc_final: 0.8278 (tp) REVERT: E 497 ARG cc_start: 0.7703 (tpp-160) cc_final: 0.7495 (tpp-160) REVERT: F 169 VAL cc_start: 0.7569 (t) cc_final: 0.7229 (p) REVERT: F 306 TYR cc_start: 0.7076 (m-80) cc_final: 0.5874 (m-10) outliers start: 9 outliers final: 9 residues processed: 144 average time/residue: 0.4356 time to fit residues: 93.5823 Evaluate side-chains 145 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 136 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 E residue 380 THR 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: 0.3980 chunk 74 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 222 optimal weight: 20.0000 chunk 109 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 230 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.172760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.103818 restraints weight = 86293.212| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.29 r_work: 0.3281 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 22490 Z= 0.114 Angle : 0.540 24.951 30954 Z= 0.258 Chirality : 0.037 0.145 3613 Planarity : 0.003 0.102 3622 Dihedral : 14.050 176.147 4267 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.18 % Favored : 93.78 % Rotamer: Outliers : 0.41 % Allowed : 8.82 % Favored : 90.77 % 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 aren not related in a simple way. whole: -0.51 (0.17), residues: 2541 helix: 0.99 (0.17), residues: 1016 sheet: -1.07 (0.29), residues: 326 loop : -1.29 (0.18), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 105 TYR 0.011 0.001 TYR F 421 PHE 0.013 0.001 PHE A 104 TRP 0.009 0.001 TRP A 916 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00257 (22458) covalent geometry : angle 0.50391 (30927) hydrogen bonds : bond 0.04035 ( 931) hydrogen bonds : angle 4.16534 ( 2562) metal coordination : bond 0.01135 ( 32) metal coordination : angle 6.55904 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13801.93 seconds wall clock time: 235 minutes 3.51 seconds (14103.51 seconds total)