Starting phenix.real_space_refine on Sat Jul 4 15:56:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7re0_24429/07_2026/7re0_24429.cif Found real_map, /net/cci-nas-00/data/ceres_data/7re0_24429/07_2026/7re0_24429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7re0_24429/07_2026/7re0_24429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7re0_24429/07_2026/7re0_24429.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7re0_24429/07_2026/7re0_24429.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7re0_24429/07_2026/7re0_24429.cif" model { file = "/net/cci-nas-00/data/ceres_data/7re0_24429/07_2026/7re0_24429.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7re0_24429/07_2026/7re0_24429.cif" } resolution = 3.5 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= 0.011 sd= 1.077 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: 9 Type Number sf(0) Gaussians Zn 8 6.06 5 Al 2 5.89 5 P 77 5.49 5 Mg 3 5.21 5 S 151 5.16 5 C 13390 2.51 5 N 3653 2.21 5 O 4287 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21577 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 7470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 927, 7470 Classifications: {'peptide': 927} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 896} Chain: "B" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1408 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 9} 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: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 576 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain: "D" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1415 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 177} 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: 4550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4550 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'CIS': 1, 'PTRANS': 29, 'TRANS': 559} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 3, 'GLU:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "F" Number of atoms: 4550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4550 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'CIS': 2, 'PTRANS': 29, 'TRANS': 558} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 3, 'GLU:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "P" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 719 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 15, 'rna3p_pyr': 18} Link IDs: {'rna3p': 33} Chain: "T" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 789 Classifications: {'RNA': 37} Modifications used: {'rna3p_pur': 20, 'rna3p_pyr': 17} Link IDs: {'rna3p': 36} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 1, ' ZN': 2, 'ADP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" 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} 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 2454 SG CYS A 301 67.264 45.450 119.235 1.00 66.41 S ATOM 2495 SG CYS A 306 66.670 46.803 122.763 1.00 65.72 S ATOM 2527 SG CYS A 310 68.298 43.392 122.281 1.00 59.62 S ATOM 3935 SG CYS A 487 69.093 60.435 105.395 1.00 66.69 S ATOM 5188 SG CYS A 645 67.891 62.289 108.535 1.00 71.92 S ATOM 5194 SG CYS A 646 67.250 58.546 108.018 1.00 69.89 S ATOM 10896 SG CYS E 5 110.546 65.599 55.107 1.00 81.99 S ATOM 10917 SG CYS E 8 113.550 67.537 55.418 1.00 83.81 S ATOM 11055 SG CYS E 26 110.403 69.419 56.178 1.00 81.91 S ATOM 11076 SG CYS E 29 110.790 68.661 52.763 1.00 82.02 S ATOM 11241 SG CYS E 50 85.966 71.045 62.688 1.00 85.94 S ATOM 11271 SG CYS E 55 83.332 69.827 60.118 1.00 89.95 S ATOM 11404 SG CYS E 72 84.595 73.574 60.136 1.00 82.73 S ATOM 10978 SG CYS E 16 100.009 63.068 52.210 1.00 81.29 S ATOM 10993 SG CYS E 19 101.569 60.239 50.186 1.00 83.44 S ATOM 15446 SG CYS F 5 65.161 64.889 58.228 1.00 74.00 S ATOM 15467 SG CYS F 8 67.970 65.171 55.838 1.00 77.58 S ATOM 15605 SG CYS F 26 67.431 68.139 57.916 1.00 77.71 S ATOM 15626 SG CYS F 29 64.838 67.636 55.596 1.00 79.20 S ATOM 15791 SG CYS F 50 57.936 79.431 79.759 1.00 81.53 S ATOM 15821 SG CYS F 55 54.398 80.847 79.865 1.00 87.91 S ATOM 15954 SG CYS F 72 56.807 82.410 77.540 1.00 77.99 S ATOM 15528 SG CYS F 16 56.279 67.501 63.967 1.00 72.40 S ATOM 15543 SG CYS F 19 54.232 64.466 62.732 1.00 75.25 S Time building chain proxies: 4.13, per 1000 atoms: 0.19 Number of scatterers: 21577 At special positions: 0 Unit cell: (156.22, 150.87, 182.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 8 29.99 S 151 16.00 P 77 15.00 Al 2 13.00 Mg 3 11.99 F 6 9.00 O 4287 8.00 N 3653 7.00 C 13390 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 982.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2000 " pdb="ZN ZN A2000 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 310 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 306 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 301 " pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 487 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 646 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 645 " pdb=" ZN E1000 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 8 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 26 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 5 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 29 " pdb=" ZN E1001 " pdb="ZN ZN E1001 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 50 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 72 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 55 " pdb=" ZN E1002 " pdb="ZN ZN E1002 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E1002 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 19 " pdb="ZN ZN E1002 " - 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=" ND1 HIS F 75 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 55 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 72 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 50 " pdb=" ZN F1002 " pdb="ZN ZN F1002 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F1002 " - pdb=" NE2 HIS F 33 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 19 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 16 " Number of angles added : 27 5078 Ramachandran restraints generated. 2539 Oldfield, 0 Emsley, 2539 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: 100 helices and 28 sheets defined 44.9% alpha, 12.8% beta 34 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 2.50 Creating SS restraints... Processing helix chain 'A' and resid 3 through 13 removed outlier: 3.536A pdb=" N PHE A 7 " --> pdb=" O ASP A 3 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 8 " --> pdb=" O ALA A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 91 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 140 through 149 Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 169 through 177 removed outlier: 4.231A pdb=" N ARG A 173 " --> pdb=" O PRO A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 200 Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 234 through 248 Proline residue: A 243 - end of helix removed outlier: 4.022A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 260 removed outlier: 4.421A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS A 256 " --> pdb=" O ALA A 253 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL A 257 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ASP A 258 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 3.525A 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 removed outlier: 3.566A pdb=" N CYS A 301 " --> pdb=" O CYS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.804A pdb=" N HIS A 309 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.598A 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: 3.753A 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: 4.740A 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 448 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 480 removed outlier: 4.153A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.575A pdb=" N VAL A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.895A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 removed outlier: 3.522A pdb=" N LEU A 527 " --> pdb=" O ASP A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 580 removed outlier: 4.110A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 640 through 642 No H-bonds generated for 'chain 'A' and resid 640 through 642' 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 773 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.610A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 808 Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 846 through 851 removed outlier: 3.534A pdb=" N LYS A 849 " --> pdb=" O ASP A 846 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP A 851 " --> pdb=" O VAL A 848 " (cutoff:3.500A) 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 903 removed outlier: 3.986A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 917 removed outlier: 3.925A pdb=" N ARG A 914 " --> pdb=" O ASN A 911 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TRP A 916 " --> pdb=" O SER A 913 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU A 917 " --> pdb=" O ARG A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 923 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 28 removed outlier: 4.186A pdb=" N ALA B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 79 removed outlier: 4.047A pdb=" N ALA B 54 " --> pdb=" O ASP B 50 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N MET B 55 " --> pdb=" O ARG B 51 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLN B 56 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 98 removed outlier: 3.643A pdb=" N LEU B 98 " --> pdb=" O MET B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 109 Processing helix chain 'B' and resid 118 through 125 removed outlier: 4.338A pdb=" N LEU B 122 " --> pdb=" O ASN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 143 removed outlier: 4.083A pdb=" N ASP B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 2 through 20 removed outlier: 3.653A pdb=" N LYS C 7 " --> pdb=" O MET C 3 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N CYS C 8 " --> pdb=" O SER C 4 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL C 11 " --> pdb=" O LYS C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 24 Processing helix chain 'C' and resid 25 through 41 removed outlier: 3.588A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 62 removed outlier: 3.712A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'D' and resid 9 through 29 Processing helix chain 'D' and resid 32 through 82 removed outlier: 3.570A pdb=" N GLN D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 99 removed outlier: 3.634A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 134 through 141 removed outlier: 3.579A pdb=" N ASN D 140 " --> pdb=" O ASN D 136 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR D 141 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 removed outlier: 3.686A pdb=" N ILE D 172 " --> pdb=" O LEU D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 180 Processing helix chain 'E' and resid 26 through 37 removed outlier: 3.824A pdb=" N SER E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 63 Processing helix chain 'E' and resid 93 through 97 removed outlier: 3.885A pdb=" N CYS E 97 " --> pdb=" O LYS E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 112 removed outlier: 3.894A pdb=" N ALA E 108 " --> pdb=" O THR E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 123 removed outlier: 3.507A pdb=" N ILE E 121 " --> pdb=" O ALA E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 145 removed outlier: 3.526A pdb=" N ALA E 135 " --> pdb=" O LYS E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 149 Processing helix chain 'E' and resid 265 through 275 Processing helix chain 'E' and resid 287 through 299 removed outlier: 3.504A pdb=" N ALA E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE E 293 " --> pdb=" O SER E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 325 removed outlier: 3.655A pdb=" N ALA E 316 " --> pdb=" O ALA E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 391 Processing helix chain 'E' and resid 418 through 422 Processing helix chain 'E' and resid 423 through 432 Processing helix chain 'E' and resid 445 through 456 removed outlier: 4.556A pdb=" N ALA E 454 " --> pdb=" O ASP E 450 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL E 456 " --> pdb=" O VAL E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 499 Processing helix chain 'E' and resid 515 through 526 removed outlier: 4.491A pdb=" N SER E 523 " --> pdb=" O ASN E 519 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LYS E 524 " --> pdb=" O ALA E 520 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE E 525 " --> pdb=" O VAL E 521 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 537 removed outlier: 3.563A pdb=" N GLN E 537 " --> pdb=" O VAL E 533 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 533 through 537' Processing helix chain 'E' and resid 557 through 566 Processing helix chain 'E' and resid 580 through 585 removed outlier: 3.713A pdb=" N LEU E 585 " --> pdb=" O LEU E 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 37 removed outlier: 3.641A pdb=" N SER F 36 " --> pdb=" O ASP F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 112 removed outlier: 4.538A pdb=" N ALA F 108 " --> pdb=" O THR F 104 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS F 112 " --> pdb=" O ALA F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 123 removed outlier: 3.596A pdb=" N ILE F 121 " --> pdb=" O ALA F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 146 removed outlier: 3.755A pdb=" N PHE F 133 " --> pdb=" O ARG F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 264 No H-bonds generated for 'chain 'F' and resid 262 through 264' Processing helix chain 'F' and resid 265 through 275 removed outlier: 3.904A pdb=" N GLN F 275 " --> pdb=" O LYS F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 299 removed outlier: 4.047A pdb=" N ILE F 293 " --> pdb=" O SER F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 324 removed outlier: 3.570A pdb=" N VAL F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) 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 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: 3.675A pdb=" N VAL F 456 " --> pdb=" O VAL F 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 499 removed outlier: 3.755A pdb=" N ILE F 493 " --> pdb=" O ASN F 489 " (cutoff:3.500A) Processing helix chain 'F' and resid 515 through 526 removed outlier: 3.515A pdb=" N SER F 523 " --> pdb=" O ASN F 519 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS F 524 " --> pdb=" O ALA F 520 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE F 525 " --> pdb=" O VAL F 521 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU F 526 " --> pdb=" O ALA F 522 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 566 removed outlier: 3.765A pdb=" N THR F 566 " --> pdb=" O ASN F 562 " (cutoff:3.500A) Processing helix chain 'F' and resid 578 through 584 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 5.326A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASP A 60 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ILE A 66 " --> pdb=" O ASP A 60 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N TYR A 69 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LYS A 98 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 33 removed outlier: 6.980A pdb=" N ASP A 29 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ASN A 52 " --> pdb=" O ASP A 29 " (cutoff:3.500A) 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: 6.416A pdb=" N ILE A 201 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.433A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 9.468A pdb=" N SER A 363 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N PHE A 334 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.433A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.696A pdb=" N LEU A 673 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU A 387 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL B 131 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU A 389 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA9, first strand: chain 'A' and resid 755 through 758 Processing sheet with id=AB1, first strand: chain 'A' and resid 816 through 822 Processing sheet with id=AB2, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.453A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.453A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N VAL D 159 " --> pdb=" O VAL D 167 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 3 through 4 Processing sheet with id=AB5, first strand: chain 'E' and resid 24 through 25 removed outlier: 3.907A pdb=" N LEU E 14 " --> pdb=" O LEU E 25 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 64 through 66 Processing sheet with id=AB7, first strand: chain 'E' and resid 84 through 85 Processing sheet with id=AB8, first strand: chain 'E' and resid 212 through 213 Processing sheet with id=AB9, first strand: chain 'E' and resid 355 through 359 removed outlier: 6.714A pdb=" N ILE E 304 " --> pdb=" O VAL E 356 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N CYS E 358 " --> pdb=" O ILE E 304 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N TYR E 306 " --> pdb=" O CYS E 358 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL E 371 " --> pdb=" O VAL E 397 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ILE E 399 " --> pdb=" O VAL E 371 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N PHE E 373 " --> pdb=" O ILE E 399 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N SER E 278 " --> pdb=" O TYR E 398 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N MET E 436 " --> pdb=" O TYR E 277 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N THR E 279 " --> pdb=" O MET E 436 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 471 through 475 removed outlier: 6.127A pdb=" N PHE E 472 " --> pdb=" O CYS E 574 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N MET E 576 " --> pdb=" O PHE E 472 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N MET E 474 " --> pdb=" O MET E 576 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASP E 542 " --> pdb=" O GLY E 571 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N LEU E 573 " --> pdb=" O ASP E 542 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL E 544 " --> pdb=" O LEU E 573 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ILE E 575 " --> pdb=" O VAL E 544 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE E 546 " --> pdb=" O ILE E 575 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N PHE E 511 " --> pdb=" O GLN E 531 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 481 through 482 Processing sheet with id=AC3, first strand: chain 'F' and resid 3 through 4 Processing sheet with id=AC4, first strand: chain 'F' and resid 64 through 66 Processing sheet with id=AC5, first strand: chain 'F' and resid 84 through 85 Processing sheet with id=AC6, first strand: chain 'F' and resid 152 through 153 Processing sheet with id=AC7, first strand: chain 'F' and resid 162 through 163 Processing sheet with id=AC8, first strand: chain 'F' and resid 277 through 280 removed outlier: 6.384A pdb=" N SER F 278 " --> pdb=" O TYR F 398 " (cutoff:3.500A) removed outlier: 9.197A pdb=" N THR F 367 " --> pdb=" O ALA F 393 " (cutoff:3.500A) removed outlier: 9.971A pdb=" N HIS F 395 " --> pdb=" O THR F 367 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ASP F 369 " --> pdb=" O HIS F 395 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N VAL F 397 " --> pdb=" O ASP F 369 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL F 371 " --> pdb=" O VAL F 397 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ILE F 399 " --> pdb=" O VAL F 371 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N PHE F 373 " --> pdb=" O ILE F 399 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ILE F 304 " --> pdb=" O VAL F 356 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N CYS F 358 " --> pdb=" O ILE F 304 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N TYR F 306 " --> pdb=" O CYS F 358 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 440 through 441 Processing sheet with id=AD1, first strand: chain 'F' and resid 510 through 512 863 hydrogen bonds defined for protein. 2382 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 83 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 3.81 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.41: 9075 1.41 - 1.61: 12879 1.61 - 1.81: 222 1.81 - 2.02: 1 2.02 - 2.22: 1 Bond restraints: 22178 Sorted by residual: bond pdb=" C ALA B 74 " pdb=" N ARG B 75 " ideal model delta sigma weight residual 1.332 2.222 -0.889 1.40e-02 5.10e+03 4.04e+03 bond pdb=" C ALA B 53 " pdb=" N ALA B 54 " ideal model delta sigma weight residual 1.332 1.789 -0.457 1.40e-02 5.10e+03 1.06e+03 bond pdb=" C PRO F 234 " pdb=" N LEU F 235 " ideal model delta sigma weight residual 1.329 1.621 -0.292 1.43e-02 4.89e+03 4.17e+02 bond pdb=" F1 AF3 F1005 " pdb="AL AF3 F1005 " ideal model delta sigma weight residual 1.637 1.801 -0.164 2.00e-02 2.50e+03 6.70e+01 bond pdb=" F2 AF3 F1005 " pdb="AL AF3 F1005 " ideal model delta sigma weight residual 1.637 1.801 -0.164 2.00e-02 2.50e+03 6.69e+01 ... (remaining 22173 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.91: 30468 11.91 - 23.82: 9 23.82 - 35.73: 0 35.73 - 47.64: 0 47.64 - 59.55: 1 Bond angle restraints: 30478 Sorted by residual: angle pdb=" O ALA B 53 " pdb=" C ALA B 53 " pdb=" N ALA B 54 " ideal model delta sigma weight residual 122.59 63.04 59.55 1.33e+00 5.65e-01 2.00e+03 angle pdb=" O PRO F 234 " pdb=" C PRO F 234 " pdb=" N LEU F 235 " ideal model delta sigma weight residual 123.10 106.18 16.92 1.20e+00 6.94e-01 1.99e+02 angle pdb=" CA PRO F 234 " pdb=" C PRO F 234 " pdb=" N LEU F 235 " ideal model delta sigma weight residual 115.50 130.25 -14.75 1.27e+00 6.20e-01 1.35e+02 angle pdb=" C PRO F 234 " pdb=" N LEU F 235 " pdb=" CA LEU F 235 " ideal model delta sigma weight residual 122.65 139.75 -17.10 1.49e+00 4.50e-01 1.32e+02 angle pdb=" CA ALA B 53 " pdb=" C ALA B 53 " pdb=" N ALA B 54 " ideal model delta sigma weight residual 116.84 135.68 -18.84 1.71e+00 3.42e-01 1.21e+02 ... (remaining 30473 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.00: 12800 34.00 - 68.01: 307 68.01 - 102.01: 14 102.01 - 136.02: 6 136.02 - 170.02: 3 Dihedral angle restraints: 13130 sinusoidal: 5575 harmonic: 7555 Sorted by residual: dihedral pdb=" CA SER E 80 " pdb=" C SER E 80 " pdb=" N PHE E 81 " pdb=" CA PHE E 81 " ideal model delta harmonic sigma weight residual 180.00 48.83 131.17 0 5.00e+00 4.00e-02 6.88e+02 dihedral pdb=" CA LYS E 189 " pdb=" C LYS E 189 " pdb=" N ASN E 190 " pdb=" CA ASN E 190 " ideal model delta harmonic sigma weight residual 0.00 42.52 -42.52 0 5.00e+00 4.00e-02 7.23e+01 dihedral pdb=" CA ASN F 190 " pdb=" C ASN F 190 " pdb=" N SER F 191 " pdb=" CA SER F 191 " ideal model delta harmonic sigma weight residual 180.00 139.31 40.69 0 5.00e+00 4.00e-02 6.62e+01 ... (remaining 13127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 3008 0.062 - 0.123: 472 0.123 - 0.185: 47 0.185 - 0.247: 6 0.247 - 0.308: 3 Chirality restraints: 3536 Sorted by residual: chirality pdb=" CA TYR F 149 " pdb=" N TYR F 149 " pdb=" C TYR F 149 " pdb=" CB TYR F 149 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA VAL E 2 " pdb=" N VAL E 2 " pdb=" C VAL E 2 " pdb=" CB VAL E 2 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA ASN F 190 " pdb=" N ASN F 190 " pdb=" C ASN F 190 " pdb=" CB ASN F 190 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 3533 not shown) Planarity restraints: 3617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 53 " 0.174 2.00e-02 2.50e+03 2.20e-01 4.83e+02 pdb=" C ALA B 53 " -0.377 2.00e-02 2.50e+03 pdb=" O ALA B 53 " 0.100 2.00e-02 2.50e+03 pdb=" N ALA B 54 " 0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 74 " -0.088 2.00e-02 2.50e+03 1.45e-01 2.10e+02 pdb=" C ALA B 74 " 0.248 2.00e-02 2.50e+03 pdb=" O ALA B 74 " -0.108 2.00e-02 2.50e+03 pdb=" N ARG B 75 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET E 233 " 0.077 5.00e-02 4.00e+02 1.17e-01 2.20e+01 pdb=" N PRO E 234 " -0.203 5.00e-02 4.00e+02 pdb=" CA PRO E 234 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO E 234 " 0.062 5.00e-02 4.00e+02 ... (remaining 3614 not shown) Histogram of nonbonded interaction distances: 1.13 - 1.88: 8 1.88 - 2.64: 409 2.64 - 3.39: 28828 3.39 - 4.15: 53558 4.15 - 4.90: 96158 Nonbonded interactions: 178961 Sorted by model distance: nonbonded pdb=" O ASP E 101 " pdb=" N VAL E 103 " model vdw 1.129 3.120 nonbonded pdb=" O ASP F 204 " pdb=" CE LYS F 524 " model vdw 1.226 3.440 nonbonded pdb=" NZ LYS B 61 " pdb=" OP1 G T 113 " model vdw 1.429 3.120 nonbonded pdb=" O ASP F 101 " pdb=" N VAL F 103 " model vdw 1.432 3.120 nonbonded pdb=" N SER A 904 " pdb=" OD1 ASN E 95 " model vdw 1.764 3.120 ... (remaining 178956 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 through 22 or (resid 23 through 25 and (name N or name C \ A or name C or name O or name CB )) or resid 26 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 resid 33 through 35 or (resid 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 38 or (resid 39 and (n \ ame N or name CA or name C or name O or name CB )) or resid 40 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB )) or resid 49 thro \ ugh 191)) } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.200 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: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.970 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.897 22214 Z= 0.901 Angle : 0.896 59.546 30505 Z= 0.544 Chirality : 0.046 0.308 3536 Planarity : 0.007 0.220 3617 Dihedral : 14.429 170.022 8256 Min Nonbonded Distance : 1.129 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.66 % Favored : 93.15 % Rotamer: Outliers : 9.24 % Allowed : 9.11 % Favored : 81.65 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.16), residues: 2539 helix: -0.60 (0.16), residues: 1004 sheet: -1.02 (0.29), residues: 299 loop : -1.71 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 443 TYR 0.020 0.002 TYR F 224 PHE 0.019 0.002 PHE A 102 TRP 0.016 0.002 TRP A 916 HIS 0.012 0.001 HIS F 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00940 / 0.59 (22178) covalent geometry : angle 0.88231 / 0.54 (30478) hydrogen bonds : bond 0.16456 / 10.62 ( 926) hydrogen bonds : angle 6.35842 / 4.37 ( 2544) metal coordination : bond 0.01486 / 0.97 ( 32) metal coordination : angle 5.34919 / 3.52 ( 27) Misc. bond : bond 0.50867 / 25.37 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5078 Ramachandran restraints generated. 2539 Oldfield, 0 Emsley, 2539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5078 Ramachandran restraints generated. 2539 Oldfield, 0 Emsley, 2539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 241 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 VAL cc_start: 0.8228 (t) cc_final: 0.7942 (m) REVERT: A 758 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8815 (tt) REVERT: A 761 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7177 (m-30) REVERT: B 15 PHE cc_start: 0.8373 (t80) cc_final: 0.7768 (t80) REVERT: B 94 MET cc_start: 0.8404 (mtm) cc_final: 0.8190 (mtt) REVERT: D 42 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8288 (tp) REVERT: D 48 GLU cc_start: 0.9093 (tp30) cc_final: 0.8883 (tp30) REVERT: E 204 ASP cc_start: 0.3220 (OUTLIER) cc_final: 0.1975 (t0) REVERT: E 441 CYS cc_start: 0.2933 (OUTLIER) cc_final: 0.2605 (t) REVERT: E 548 GLN cc_start: -0.0621 (OUTLIER) cc_final: -0.0848 (tt0) REVERT: F 210 VAL cc_start: 0.4201 (OUTLIER) cc_final: 0.3574 (m) REVERT: F 258 ILE cc_start: -0.0112 (OUTLIER) cc_final: -0.0494 (tt) REVERT: F 376 ILE cc_start: 0.7459 (OUTLIER) cc_final: 0.7100 (mp) REVERT: F 455 LEU cc_start: 0.6824 (OUTLIER) cc_final: 0.6124 (tp) outliers start: 203 outliers final: 43 residues processed: 426 average time/residue: 0.1429 time to fit residues: 94.7586 Evaluate side-chains 180 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 127 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 525 ILE Chi-restraints excluded: chain E residue 548 GLN Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain F residue 177 ASN Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 262 PHE Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 525 ILE Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain F residue 588 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 30.0000 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 30.0000 chunk 111 optimal weight: 0.9980 chunk 258 optimal weight: 10.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 497 ASN B 43 ASN B 56 GLN C 19 GLN D 176 ASN F 354 GLN F 518 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.091306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.059745 restraints weight = 91432.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.061914 restraints weight = 37795.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.063256 restraints weight = 21559.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.064048 restraints weight = 15004.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.064547 restraints weight = 11996.925| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22214 Z= 0.184 Angle : 0.696 14.542 30505 Z= 0.350 Chirality : 0.043 0.268 3536 Planarity : 0.005 0.044 3617 Dihedral : 9.814 172.159 3763 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.04 % Favored : 94.88 % Rotamer: Outliers : 4.78 % Allowed : 14.07 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.16), residues: 2541 helix: 0.08 (0.16), residues: 1012 sheet: -0.70 (0.31), residues: 271 loop : -1.53 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 80 TYR 0.020 0.002 TYR E 382 PHE 0.022 0.002 PHE B 15 TRP 0.008 0.001 TRP A 916 HIS 0.007 0.001 HIS E 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (22178) covalent geometry : angle 0.68004 / 0.35 (30478) hydrogen bonds : bond 0.04777 / 3.29 ( 926) hydrogen bonds : angle 4.58272 / 3.18 ( 2544) metal coordination : bond 0.01246 / 0.86 ( 32) metal coordination : angle 5.01868 / 3.24 ( 27) Misc. bond : bond 0.00126 / 0.06 ( 4) *********************** 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 **************************** Evaluate side-chains 240 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 135 time to evaluate : 0.762 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 111 VAL cc_start: 0.8483 (t) cc_final: 0.8201 (m) REVERT: A 855 MET cc_start: 0.8337 (mmt) cc_final: 0.8011 (mmt) REVERT: A 903 TYR cc_start: 0.7691 (m-80) cc_final: 0.7024 (m-80) REVERT: B 65 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8371 (mm-40) REVERT: C 47 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7323 (tm-30) REVERT: E 68 MET cc_start: 0.8760 (mmm) cc_final: 0.8496 (mmm) REVERT: E 204 ASP cc_start: 0.3952 (OUTLIER) cc_final: 0.1816 (t0) REVERT: E 441 CYS cc_start: 0.3269 (OUTLIER) cc_final: 0.2691 (t) REVERT: F 258 ILE cc_start: -0.1133 (OUTLIER) cc_final: -0.1548 (tt) REVERT: F 274 MET cc_start: 0.8917 (tmm) cc_final: 0.8561 (mmt) REVERT: F 378 MET cc_start: 0.8266 (tpp) cc_final: 0.7975 (tpp) outliers start: 105 outliers final: 49 residues processed: 234 average time/residue: 0.1315 time to fit residues: 48.7397 Evaluate side-chains 167 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 114 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 525 ILE Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 572 ILE Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 460 LYS Chi-restraints excluded: chain F residue 525 ILE Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 588 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 52 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 219 optimal weight: 0.0370 chunk 76 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 200 optimal weight: 7.9990 chunk 228 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 203 optimal weight: 1.9990 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 791 ASN D 157 GLN E 492 GLN E 531 GLN E 548 GLN E 554 HIS E 562 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.089962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.058843 restraints weight = 88734.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.060902 restraints weight = 36409.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.062182 restraints weight = 20790.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.062961 restraints weight = 14459.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.063428 restraints weight = 11524.631| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22214 Z= 0.176 Angle : 0.644 14.305 30505 Z= 0.322 Chirality : 0.042 0.227 3536 Planarity : 0.004 0.042 3617 Dihedral : 8.859 174.970 3719 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.87 % Allowed : 15.12 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.16), residues: 2541 helix: 0.49 (0.16), residues: 1020 sheet: -0.26 (0.33), residues: 247 loop : -1.42 (0.17), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 129 TYR 0.023 0.002 TYR B 135 PHE 0.016 0.002 PHE D 92 TRP 0.010 0.001 TRP A 916 HIS 0.012 0.001 HIS F 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 (22178) covalent geometry : angle 0.62877 / 0.32 (30478) hydrogen bonds : bond 0.04199 / 2.94 ( 926) hydrogen bonds : angle 4.37585 / 3.06 ( 2544) metal coordination : bond 0.01585 / 1.10 ( 32) metal coordination : angle 4.75887 / 3.00 ( 27) Misc. bond : bond 0.00044 / 0.02 ( 4) *********************** 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 **************************** Evaluate side-chains 211 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 126 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 VAL cc_start: 0.8667 (t) cc_final: 0.8368 (m) REVERT: A 132 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8794 (mtp180) REVERT: A 242 MET cc_start: 0.8683 (mtt) cc_final: 0.8316 (mtt) REVERT: A 336 ASP cc_start: 0.7780 (t0) cc_final: 0.7512 (t0) REVERT: A 658 GLU cc_start: 0.8334 (mm-30) cc_final: 0.8028 (mt-10) REVERT: A 855 MET cc_start: 0.8298 (mmt) cc_final: 0.8013 (mmp) REVERT: A 924 MET cc_start: 0.9211 (mmm) cc_final: 0.8913 (mmt) REVERT: B 15 PHE cc_start: 0.8361 (t80) cc_final: 0.7997 (t80) REVERT: B 65 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8503 (mm-40) REVERT: C 47 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7551 (tm-30) REVERT: C 54 SER cc_start: 0.9257 (m) cc_final: 0.8953 (t) REVERT: E 204 ASP cc_start: 0.3822 (OUTLIER) cc_final: 0.1836 (t0) REVERT: F 258 ILE cc_start: -0.0543 (OUTLIER) cc_final: -0.0919 (tt) REVERT: F 274 MET cc_start: 0.9031 (tmm) cc_final: 0.8642 (mmm) REVERT: F 378 MET cc_start: 0.8247 (tpp) cc_final: 0.7910 (tpp) outliers start: 85 outliers final: 50 residues processed: 204 average time/residue: 0.1273 time to fit residues: 41.4618 Evaluate side-chains 172 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 118 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 525 ILE Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 525 ILE Chi-restraints excluded: chain F residue 530 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 25 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 3 optimal weight: 0.0980 chunk 175 optimal weight: 0.2980 chunk 240 optimal weight: 7.9990 chunk 209 optimal weight: 9.9990 chunk 150 optimal weight: 8.9990 chunk 236 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 19 GLN D 43 ASN D 176 ASN ** E 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.089390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.058006 restraints weight = 88278.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.060031 restraints weight = 36546.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.061296 restraints weight = 20949.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.062036 restraints weight = 14622.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.062507 restraints weight = 11752.046| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22214 Z= 0.151 Angle : 0.607 14.220 30505 Z= 0.302 Chirality : 0.040 0.222 3536 Planarity : 0.003 0.042 3617 Dihedral : 8.391 152.208 3712 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.23 % Allowed : 16.39 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.17), residues: 2541 helix: 0.69 (0.17), residues: 1025 sheet: -0.10 (0.33), residues: 247 loop : -1.32 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 51 TYR 0.014 0.001 TYR E 277 PHE 0.014 0.001 PHE D 92 TRP 0.013 0.001 TRP A 916 HIS 0.006 0.001 HIS A 892 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (22178) covalent geometry : angle 0.59192 / 0.30 (30478) hydrogen bonds : bond 0.03882 / 2.75 ( 926) hydrogen bonds : angle 4.23648 / 2.97 ( 2544) metal coordination : bond 0.01237 / 0.85 ( 32) metal coordination : angle 4.49439 / 2.83 ( 27) Misc. bond : bond 0.00021 / 0.01 ( 4) *********************** 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 **************************** Evaluate side-chains 196 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 125 time to evaluate : 0.807 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 132 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8820 (mtp180) REVERT: A 242 MET cc_start: 0.8528 (mtt) cc_final: 0.8010 (mtt) REVERT: A 615 MET cc_start: 0.8256 (tmm) cc_final: 0.7832 (ttm) REVERT: A 658 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8011 (mt-10) REVERT: A 855 MET cc_start: 0.8319 (mmt) cc_final: 0.8057 (mmp) REVERT: B 65 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8477 (mm-40) REVERT: B 67 MET cc_start: 0.8694 (mmm) cc_final: 0.8480 (mmm) REVERT: C 47 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7544 (tm-30) REVERT: C 54 SER cc_start: 0.9250 (m) cc_final: 0.8945 (t) REVERT: E 68 MET cc_start: 0.8558 (mmm) cc_final: 0.8238 (mmm) REVERT: E 204 ASP cc_start: 0.3774 (OUTLIER) cc_final: 0.1930 (t0) REVERT: E 429 MET cc_start: 0.6047 (mmm) cc_final: 0.5192 (tpp) REVERT: F 204 ASP cc_start: 0.4029 (OUTLIER) cc_final: 0.3769 (t70) REVERT: F 258 ILE cc_start: -0.0239 (OUTLIER) cc_final: -0.0612 (tt) REVERT: F 272 VAL cc_start: 0.8688 (t) cc_final: 0.8351 (p) REVERT: F 274 MET cc_start: 0.9035 (tmm) cc_final: 0.8661 (mmm) REVERT: F 378 MET cc_start: 0.8259 (tpp) cc_final: 0.7893 (tpp) outliers start: 71 outliers final: 49 residues processed: 188 average time/residue: 0.1361 time to fit residues: 41.2225 Evaluate side-chains 169 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 115 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 572 ILE Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 492 GLN Chi-restraints excluded: chain F residue 525 ILE Chi-restraints excluded: chain F residue 530 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 84 optimal weight: 4.9990 chunk 187 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 145 optimal weight: 0.0870 chunk 200 optimal weight: 0.0970 chunk 202 optimal weight: 0.9980 chunk 143 optimal weight: 0.0060 chunk 149 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 247 optimal weight: 8.9990 overall best weight: 0.4374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 464 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.090269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.059315 restraints weight = 87042.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.061368 restraints weight = 35575.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.062616 restraints weight = 20193.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.063400 restraints weight = 14072.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.063835 restraints weight = 11211.751| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22214 Z= 0.104 Angle : 0.584 14.150 30505 Z= 0.287 Chirality : 0.040 0.214 3536 Planarity : 0.003 0.039 3617 Dihedral : 8.094 153.337 3704 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.10 % Allowed : 16.53 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.17), residues: 2541 helix: 0.88 (0.17), residues: 1024 sheet: -0.02 (0.33), residues: 258 loop : -1.21 (0.17), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 21 TYR 0.019 0.001 TYR A 831 PHE 0.017 0.001 PHE B 15 TRP 0.013 0.001 TRP A 916 HIS 0.006 0.001 HIS F 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (22178) covalent geometry : angle 0.57269 / 0.29 (30478) hydrogen bonds : bond 0.03592 / 2.60 ( 926) hydrogen bonds : angle 4.09711 / 2.88 ( 2544) metal coordination : bond 0.00554 / 0.39 ( 32) metal coordination : angle 3.83064 / 2.46 ( 27) Misc. bond : bond 0.00021 / 0.01 ( 4) *********************** 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 **************************** Evaluate side-chains 202 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 134 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 ASP cc_start: 0.7257 (p0) cc_final: 0.6902 (p0) REVERT: A 242 MET cc_start: 0.8655 (mtt) cc_final: 0.8088 (mtt) REVERT: A 336 ASP cc_start: 0.7762 (t0) cc_final: 0.7343 (t0) REVERT: A 615 MET cc_start: 0.8194 (tmm) cc_final: 0.7770 (ttm) REVERT: A 658 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8011 (mt-10) REVERT: A 855 MET cc_start: 0.8320 (mmt) cc_final: 0.8103 (mmp) REVERT: B 15 PHE cc_start: 0.8362 (t80) cc_final: 0.8017 (t80) REVERT: B 51 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8747 (tpp80) REVERT: B 67 MET cc_start: 0.8701 (mmm) cc_final: 0.8489 (mmm) REVERT: B 90 MET cc_start: 0.8505 (tmm) cc_final: 0.8093 (tmm) REVERT: B 94 MET cc_start: 0.8405 (mtp) cc_final: 0.7808 (mtp) REVERT: C 34 GLN cc_start: 0.8274 (tp40) cc_final: 0.7723 (tm-30) REVERT: C 47 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7500 (tm-30) REVERT: C 54 SER cc_start: 0.9233 (m) cc_final: 0.8841 (t) REVERT: D 52 ASP cc_start: 0.9034 (t0) cc_final: 0.8566 (m-30) REVERT: D 62 MET cc_start: 0.8730 (tpp) cc_final: 0.8475 (tpp) REVERT: E 68 MET cc_start: 0.8554 (mmm) cc_final: 0.6943 (mmp) REVERT: E 204 ASP cc_start: 0.3969 (OUTLIER) cc_final: 0.2404 (t0) REVERT: E 280 LEU cc_start: 0.8722 (tp) cc_final: 0.8486 (mt) REVERT: E 429 MET cc_start: 0.5909 (mmm) cc_final: 0.5115 (tpp) REVERT: F 258 ILE cc_start: 0.0340 (OUTLIER) cc_final: -0.0021 (tt) REVERT: F 274 MET cc_start: 0.9014 (tmm) cc_final: 0.8649 (mmm) REVERT: F 378 MET cc_start: 0.8153 (tpp) cc_final: 0.7799 (tpp) REVERT: F 474 MET cc_start: 0.6233 (tpt) cc_final: 0.5940 (mpp) outliers start: 68 outliers final: 49 residues processed: 196 average time/residue: 0.1380 time to fit residues: 43.4847 Evaluate side-chains 174 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 122 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 572 ILE Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 177 ASN Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 492 GLN Chi-restraints excluded: chain F residue 506 TRP Chi-restraints excluded: chain F residue 507 ARG Chi-restraints excluded: chain F residue 525 ILE Chi-restraints excluded: chain F residue 530 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 175 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 176 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 109 optimal weight: 0.0980 chunk 180 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 HIS ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN D 168 GLN ** E 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.088010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.056377 restraints weight = 91019.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.058358 restraints weight = 38697.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.059622 restraints weight = 22715.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.060361 restraints weight = 16044.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.060791 restraints weight = 12971.038| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22214 Z= 0.171 Angle : 0.611 14.071 30505 Z= 0.302 Chirality : 0.041 0.223 3536 Planarity : 0.003 0.039 3617 Dihedral : 7.799 151.629 3697 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.28 % Allowed : 16.76 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.17), residues: 2541 helix: 0.92 (0.17), residues: 1030 sheet: 0.17 (0.35), residues: 240 loop : -1.17 (0.17), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 567 TYR 0.014 0.001 TYR B 135 PHE 0.014 0.001 PHE D 92 TRP 0.009 0.001 TRP A 916 HIS 0.006 0.001 HIS E 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (22178) covalent geometry : angle 0.59523 / 0.30 (30478) hydrogen bonds : bond 0.03852 / 2.73 ( 926) hydrogen bonds : angle 4.09676 / 2.88 ( 2544) metal coordination : bond 0.01550 / 1.05 ( 32) metal coordination : angle 4.65299 / 2.91 ( 27) Misc. bond : bond 0.00144 / 0.08 ( 4) *********************** 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 **************************** Evaluate side-chains 197 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 125 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 ASP cc_start: 0.7359 (p0) cc_final: 0.6987 (p0) REVERT: A 242 MET cc_start: 0.8776 (mtt) cc_final: 0.8232 (mtt) REVERT: A 615 MET cc_start: 0.8250 (tmm) cc_final: 0.7783 (ttm) REVERT: A 658 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8000 (mt-10) REVERT: A 668 MET cc_start: 0.7802 (ttm) cc_final: 0.7599 (ttm) REVERT: A 855 MET cc_start: 0.8388 (mmt) cc_final: 0.8155 (mmp) REVERT: B 65 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8638 (mm-40) REVERT: B 67 MET cc_start: 0.8789 (mmm) cc_final: 0.8522 (mmm) REVERT: B 94 MET cc_start: 0.8526 (mtp) cc_final: 0.8066 (mtp) REVERT: C 34 GLN cc_start: 0.8369 (tp40) cc_final: 0.7851 (tm-30) REVERT: C 47 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7703 (tm-30) REVERT: D 52 ASP cc_start: 0.9129 (t0) cc_final: 0.8732 (m-30) REVERT: E 204 ASP cc_start: 0.4196 (OUTLIER) cc_final: 0.2681 (t0) REVERT: E 429 MET cc_start: 0.6030 (mmm) cc_final: 0.5260 (tpp) REVERT: F 204 ASP cc_start: 0.4008 (OUTLIER) cc_final: 0.3729 (t70) REVERT: F 258 ILE cc_start: 0.0584 (OUTLIER) cc_final: 0.0354 (tt) REVERT: F 274 MET cc_start: 0.9073 (tmm) cc_final: 0.8663 (mmm) REVERT: F 378 MET cc_start: 0.8195 (tpp) cc_final: 0.7800 (tpp) REVERT: F 474 MET cc_start: 0.6317 (tpt) cc_final: 0.5918 (mpp) outliers start: 72 outliers final: 52 residues processed: 190 average time/residue: 0.1347 time to fit residues: 41.4863 Evaluate side-chains 169 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 113 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 572 ILE Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 177 ASN Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 492 GLN Chi-restraints excluded: chain F residue 506 TRP Chi-restraints excluded: chain F residue 507 ARG Chi-restraints excluded: chain F residue 525 ILE Chi-restraints excluded: chain F residue 530 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 67 optimal weight: 0.9980 chunk 150 optimal weight: 20.0000 chunk 16 optimal weight: 4.9990 chunk 198 optimal weight: 10.0000 chunk 241 optimal weight: 7.9990 chunk 127 optimal weight: 0.7980 chunk 157 optimal weight: 20.0000 chunk 83 optimal weight: 0.0170 chunk 187 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 94 optimal weight: 8.9990 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 19 GLN ** E 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.088851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.057689 restraints weight = 90433.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.059709 restraints weight = 37915.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.060977 restraints weight = 21939.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.061751 restraints weight = 15424.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.062225 restraints weight = 12418.848| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22214 Z= 0.112 Angle : 0.583 14.035 30505 Z= 0.287 Chirality : 0.040 0.216 3536 Planarity : 0.003 0.039 3617 Dihedral : 7.490 150.071 3688 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.69 % Allowed : 17.67 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.17), residues: 2541 helix: 1.02 (0.17), residues: 1025 sheet: 0.02 (0.34), residues: 254 loop : -1.07 (0.17), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 365 TYR 0.014 0.001 TYR E 324 PHE 0.018 0.001 PHE F 437 TRP 0.012 0.001 TRP A 916 HIS 0.005 0.001 HIS F 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (22178) covalent geometry : angle 0.57153 / 0.29 (30478) hydrogen bonds : bond 0.03503 / 2.49 ( 926) hydrogen bonds : angle 4.03993 / 2.84 ( 2544) metal coordination : bond 0.00763 / 0.51 ( 32) metal coordination : angle 3.86817 / 2.46 ( 27) Misc. bond : bond 0.00052 / 0.03 ( 4) *********************** 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 **************************** Evaluate side-chains 182 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 123 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 ASP cc_start: 0.7271 (p0) cc_final: 0.6890 (p0) REVERT: A 242 MET cc_start: 0.8776 (mtt) cc_final: 0.8262 (mtt) REVERT: A 336 ASP cc_start: 0.7764 (t0) cc_final: 0.7524 (t0) REVERT: A 615 MET cc_start: 0.8185 (tmm) cc_final: 0.7773 (ttm) REVERT: A 658 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7867 (mt-10) REVERT: A 855 MET cc_start: 0.8342 (mmt) cc_final: 0.8134 (mmp) REVERT: B 65 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.8628 (mm-40) REVERT: B 67 MET cc_start: 0.8672 (mmm) cc_final: 0.8469 (mmm) REVERT: B 94 MET cc_start: 0.8469 (mtp) cc_final: 0.8069 (mtp) REVERT: C 34 GLN cc_start: 0.8231 (tp40) cc_final: 0.7903 (tm-30) REVERT: C 47 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7471 (tm-30) REVERT: C 54 SER cc_start: 0.9247 (m) cc_final: 0.8906 (t) REVERT: C 75 MET cc_start: 0.6827 (ttm) cc_final: 0.6487 (ttm) REVERT: D 48 GLU cc_start: 0.9191 (tp30) cc_final: 0.7964 (tp30) REVERT: D 52 ASP cc_start: 0.9107 (t0) cc_final: 0.8723 (m-30) REVERT: D 62 MET cc_start: 0.8972 (tpp) cc_final: 0.8743 (tpp) REVERT: E 204 ASP cc_start: 0.4279 (OUTLIER) cc_final: 0.2967 (t0) REVERT: E 429 MET cc_start: 0.5931 (mmm) cc_final: 0.5174 (tpp) REVERT: E 462 LYS cc_start: 0.5957 (mmpt) cc_final: 0.5616 (mmmt) REVERT: F 204 ASP cc_start: 0.3938 (OUTLIER) cc_final: 0.3700 (t70) REVERT: F 258 ILE cc_start: 0.0639 (OUTLIER) cc_final: 0.0415 (tt) REVERT: F 274 MET cc_start: 0.9047 (tmm) cc_final: 0.8688 (mmm) REVERT: F 378 MET cc_start: 0.8166 (tpp) cc_final: 0.7745 (tpp) outliers start: 59 outliers final: 49 residues processed: 179 average time/residue: 0.1468 time to fit residues: 42.4221 Evaluate side-chains 170 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 117 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 572 ILE Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 177 ASN Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 492 GLN Chi-restraints excluded: chain F residue 506 TRP Chi-restraints excluded: chain F residue 507 ARG Chi-restraints excluded: chain F residue 525 ILE Chi-restraints excluded: chain F residue 530 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 17 optimal weight: 0.0980 chunk 165 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 244 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 45 optimal weight: 0.6980 chunk 5 optimal weight: 7.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 349 ASN ** E 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.088900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.057818 restraints weight = 91032.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.059834 restraints weight = 38084.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.061096 restraints weight = 22070.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.061859 restraints weight = 15566.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.062314 restraints weight = 12479.951| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22214 Z= 0.114 Angle : 0.586 13.965 30505 Z= 0.286 Chirality : 0.039 0.215 3536 Planarity : 0.003 0.039 3617 Dihedral : 7.257 150.766 3686 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.96 % Allowed : 17.67 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.17), residues: 2541 helix: 1.15 (0.17), residues: 1016 sheet: 0.08 (0.33), residues: 259 loop : -1.01 (0.18), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 365 TYR 0.012 0.001 TYR B 135 PHE 0.017 0.001 PHE B 15 TRP 0.012 0.001 TRP A 916 HIS 0.006 0.001 HIS F 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (22178) covalent geometry : angle 0.57540 / 0.29 (30478) hydrogen bonds : bond 0.03475 / 2.49 ( 926) hydrogen bonds : angle 3.99366 / 2.83 ( 2544) metal coordination : bond 0.00799 / 0.53 ( 32) metal coordination : angle 3.85333 / 2.44 ( 27) Misc. bond : bond 0.00027 / 0.01 ( 4) *********************** 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 **************************** Evaluate side-chains 190 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 125 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8196 (mmm) cc_final: 0.7552 (tpt) REVERT: A 153 ASP cc_start: 0.7238 (p0) cc_final: 0.6880 (p0) REVERT: A 242 MET cc_start: 0.8740 (mtt) cc_final: 0.8243 (mtt) REVERT: A 268 TRP cc_start: 0.8590 (OUTLIER) cc_final: 0.7141 (m-90) REVERT: A 615 MET cc_start: 0.8185 (tmm) cc_final: 0.7765 (ttm) REVERT: A 658 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7962 (mt-10) REVERT: A 903 TYR cc_start: 0.7613 (m-80) cc_final: 0.7218 (m-80) REVERT: B 15 PHE cc_start: 0.8434 (t80) cc_final: 0.8058 (t80) REVERT: B 65 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.8562 (mm-40) REVERT: B 67 MET cc_start: 0.8678 (mmm) cc_final: 0.8475 (mmm) REVERT: B 94 MET cc_start: 0.8472 (mtp) cc_final: 0.8049 (mtp) REVERT: C 34 GLN cc_start: 0.8210 (tp40) cc_final: 0.7920 (tm-30) REVERT: C 47 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7452 (tm-30) REVERT: C 54 SER cc_start: 0.9229 (m) cc_final: 0.8905 (t) REVERT: C 75 MET cc_start: 0.6828 (ttm) cc_final: 0.6525 (ttm) REVERT: D 48 GLU cc_start: 0.9181 (tp30) cc_final: 0.7885 (tp30) REVERT: D 52 ASP cc_start: 0.9114 (t0) cc_final: 0.8732 (m-30) REVERT: E 204 ASP cc_start: 0.4219 (OUTLIER) cc_final: 0.3017 (t0) REVERT: E 429 MET cc_start: 0.5918 (mmm) cc_final: 0.5497 (tpp) REVERT: F 204 ASP cc_start: 0.3904 (OUTLIER) cc_final: 0.3646 (t70) REVERT: F 258 ILE cc_start: 0.0741 (OUTLIER) cc_final: 0.0519 (tt) REVERT: F 274 MET cc_start: 0.9024 (tmm) cc_final: 0.8670 (mmm) REVERT: F 378 MET cc_start: 0.8122 (tpp) cc_final: 0.7676 (tpp) REVERT: F 576 MET cc_start: 0.5055 (OUTLIER) cc_final: 0.4790 (ppp) outliers start: 65 outliers final: 51 residues processed: 183 average time/residue: 0.1328 time to fit residues: 39.6540 Evaluate side-chains 174 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 117 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 94 MET Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 572 ILE Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 177 ASN Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 492 GLN Chi-restraints excluded: chain F residue 506 TRP Chi-restraints excluded: chain F residue 507 ARG Chi-restraints excluded: chain F residue 525 ILE Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 576 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 99 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 169 optimal weight: 4.9990 chunk 71 optimal weight: 0.0020 chunk 1 optimal weight: 1.9990 overall best weight: 3.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 572 HIS B 19 GLN E 354 GLN ** E 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 557 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.085770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.054189 restraints weight = 90631.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.056075 restraints weight = 39244.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.057263 restraints weight = 23254.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.057980 restraints weight = 16616.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.058408 restraints weight = 13511.898| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 22214 Z= 0.262 Angle : 0.697 13.812 30505 Z= 0.343 Chirality : 0.044 0.234 3536 Planarity : 0.004 0.038 3617 Dihedral : 7.382 143.926 3685 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.73 % Allowed : 18.49 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.17), residues: 2541 helix: 0.92 (0.16), residues: 1021 sheet: -0.45 (0.31), residues: 297 loop : -1.04 (0.18), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 365 TYR 0.020 0.002 TYR A 887 PHE 0.020 0.002 PHE D 92 TRP 0.010 0.002 TRP F 506 HIS 0.007 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.26 (22178) covalent geometry : angle 0.67771 / 0.34 (30478) hydrogen bonds : bond 0.04279 / 2.97 ( 926) hydrogen bonds : angle 4.24265 / 2.99 ( 2544) metal coordination : bond 0.02430 / 1.55 ( 32) metal coordination : angle 5.48192 / 3.33 ( 27) Misc. bond : bond 0.00034 / 0.02 ( 4) *********************** 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 **************************** Evaluate side-chains 173 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 113 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 TRP cc_start: 0.8657 (OUTLIER) cc_final: 0.7213 (m-90) REVERT: A 855 MET cc_start: 0.8216 (mmp) cc_final: 0.7797 (mmt) REVERT: B 15 PHE cc_start: 0.8252 (t80) cc_final: 0.7965 (t80) REVERT: B 65 GLN cc_start: 0.9152 (OUTLIER) cc_final: 0.8908 (mm-40) REVERT: B 67 MET cc_start: 0.8802 (mmm) cc_final: 0.8571 (mmm) REVERT: B 94 MET cc_start: 0.8536 (mtp) cc_final: 0.7907 (mtp) REVERT: C 34 GLN cc_start: 0.8402 (tp40) cc_final: 0.8019 (tm-30) REVERT: C 47 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7830 (tm-30) REVERT: C 54 SER cc_start: 0.9350 (m) cc_final: 0.8985 (t) REVERT: C 75 MET cc_start: 0.6864 (ttm) cc_final: 0.6580 (ttm) REVERT: D 48 GLU cc_start: 0.9161 (tp30) cc_final: 0.8875 (tp30) REVERT: E 204 ASP cc_start: 0.4313 (OUTLIER) cc_final: 0.2971 (t0) REVERT: E 429 MET cc_start: 0.6222 (mmm) cc_final: 0.5858 (tpp) REVERT: F 204 ASP cc_start: 0.4340 (OUTLIER) cc_final: 0.4084 (t70) REVERT: F 258 ILE cc_start: 0.1100 (OUTLIER) cc_final: 0.0874 (tt) REVERT: F 378 MET cc_start: 0.8133 (tpp) cc_final: 0.7624 (tpp) outliers start: 60 outliers final: 43 residues processed: 167 average time/residue: 0.1364 time to fit residues: 37.1574 Evaluate side-chains 156 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 108 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 572 ILE Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 177 ASN Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 492 GLN Chi-restraints excluded: chain F residue 506 TRP Chi-restraints excluded: chain F residue 507 ARG Chi-restraints excluded: chain F residue 525 ILE Chi-restraints excluded: chain F residue 530 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 139 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 175 optimal weight: 9.9990 chunk 220 optimal weight: 5.9990 chunk 66 optimal weight: 0.0670 chunk 230 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 258 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 overall best weight: 1.4922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 395 HIS F 557 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.087213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.056523 restraints weight = 91316.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.058435 restraints weight = 39846.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.059634 restraints weight = 23522.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.060319 restraints weight = 16756.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.060776 restraints weight = 13604.077| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22214 Z= 0.142 Angle : 0.623 13.884 30505 Z= 0.303 Chirality : 0.041 0.242 3536 Planarity : 0.003 0.038 3617 Dihedral : 7.229 142.736 3684 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.14 % Allowed : 19.03 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.17), residues: 2541 helix: 1.05 (0.17), residues: 1015 sheet: -0.44 (0.32), residues: 297 loop : -0.97 (0.18), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 248 TYR 0.014 0.001 TYR B 135 PHE 0.015 0.001 PHE D 92 TRP 0.011 0.001 TRP A 916 HIS 0.006 0.001 HIS F 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (22178) covalent geometry : angle 0.60968 / 0.30 (30478) hydrogen bonds : bond 0.03707 / 2.63 ( 926) hydrogen bonds : angle 4.07374 / 2.87 ( 2544) metal coordination : bond 0.01098 / 0.72 ( 32) metal coordination : angle 4.35230 / 2.69 ( 27) Misc. bond : bond 0.00023 / 0.01 ( 4) ********************** 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 **************************** Evaluate side-chains 162 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 115 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8170 (mmm) cc_final: 0.7727 (tpt) REVERT: A 268 TRP cc_start: 0.8580 (OUTLIER) cc_final: 0.7114 (m-90) REVERT: A 615 MET cc_start: 0.8129 (tmm) cc_final: 0.7483 (ttt) REVERT: B 15 PHE cc_start: 0.8379 (t80) cc_final: 0.8073 (t80) REVERT: B 65 GLN cc_start: 0.9096 (OUTLIER) cc_final: 0.8834 (mm-40) REVERT: B 94 MET cc_start: 0.8424 (mtp) cc_final: 0.8124 (mtp) REVERT: C 47 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7532 (tm-30) REVERT: C 54 SER cc_start: 0.9232 (m) cc_final: 0.8882 (t) REVERT: C 75 MET cc_start: 0.6881 (ttm) cc_final: 0.6630 (ttm) REVERT: D 48 GLU cc_start: 0.9091 (tp30) cc_final: 0.8810 (tp30) REVERT: E 429 MET cc_start: 0.6153 (mmm) cc_final: 0.5476 (tpp) REVERT: F 114 TRP cc_start: 0.7623 (m100) cc_final: 0.7234 (m100) REVERT: F 204 ASP cc_start: 0.4198 (OUTLIER) cc_final: 0.3973 (t70) REVERT: F 258 ILE cc_start: 0.1049 (OUTLIER) cc_final: 0.0835 (tt) REVERT: F 274 MET cc_start: 0.8702 (tmm) cc_final: 0.8337 (mmm) REVERT: F 378 MET cc_start: 0.7976 (tpp) cc_final: 0.7446 (tpp) REVERT: F 438 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7877 (pt) outliers start: 47 outliers final: 38 residues processed: 157 average time/residue: 0.1445 time to fit residues: 36.8648 Evaluate side-chains 152 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 109 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 572 ILE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 204 ASP Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 492 GLN Chi-restraints excluded: chain F residue 506 TRP Chi-restraints excluded: chain F residue 507 ARG Chi-restraints excluded: chain F residue 525 ILE Chi-restraints excluded: chain F residue 530 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 31 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 203 optimal weight: 6.9990 chunk 207 optimal weight: 0.6980 chunk 213 optimal weight: 8.9990 chunk 202 optimal weight: 0.1980 chunk 34 optimal weight: 3.9990 chunk 187 optimal weight: 20.0000 chunk 197 optimal weight: 4.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.088295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.057688 restraints weight = 91861.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.059748 restraints weight = 38010.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.061005 restraints weight = 21789.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.061770 restraints weight = 15308.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.062240 restraints weight = 12266.538| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 22214 Z= 0.109 Angle : 0.607 13.879 30505 Z= 0.293 Chirality : 0.040 0.214 3536 Planarity : 0.003 0.039 3617 Dihedral : 7.077 142.733 3682 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.82 % Allowed : 19.26 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.17), residues: 2541 helix: 1.17 (0.17), residues: 1013 sheet: -0.31 (0.31), residues: 298 loop : -0.93 (0.18), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 365 TYR 0.014 0.001 TYR E 324 PHE 0.018 0.001 PHE F 90 TRP 0.013 0.001 TRP A 916 HIS 0.007 0.001 HIS F 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (22178) covalent geometry : angle 0.59586 / 0.29 (30478) hydrogen bonds : bond 0.03494 / 2.52 ( 926) hydrogen bonds : angle 4.02740 / 2.86 ( 2544) metal coordination : bond 0.00633 / 0.42 ( 32) metal coordination : angle 3.84976 / 2.43 ( 27) Misc. bond : bond 0.00034 / 0.02 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4769.70 seconds wall clock time: 82 minutes 47.92 seconds (4967.92 seconds total)