Starting phenix.real_space_refine on Mon Oct 26 17:49:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7re0_24429/10_2026/7re0_24429.cif Found real_map, /net/cci-nas-00/data/ceres_data/7re0_24429/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/7re0_24429/10_2026/7re0_24429.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7re0_24429/10_2026/7re0_24429.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7re0_24429/10_2026/7re0_24429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7re0_24429/10_2026/7re0_24429.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7re0_24429/10_2026/7re0_24429.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7re0_24429/10_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/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: {'RNAv2': 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: {'RNAv2': 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: 4.55, per 1000 atoms: 0.21 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: 1.75 Conformation dependent library (CDL) restraints added in 800.7 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: 2.85 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: 4.43 Time building geometry restraints manager: 2.21 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: 12727 34.00 - 68.01: 379 68.01 - 102.01: 15 102.01 - 136.02: 6 136.02 - 170.02: 3 Dihedral angle restraints: 13130 sinusoidal: 5575 harmonic: 7555 Sorted by residual: dihedral pdb=" C4' A P 35 " pdb=" C3' A P 35 " pdb=" C2' A P 35 " pdb=" C1' A P 35 " ideal model delta sinusoidal sigma weight residual 36.35 -35.57 71.92 1 3.10e+00 1.04e-01 6.89e+02 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=" O4' A P 35 " pdb=" C4' A P 35 " pdb=" C3' A P 35 " pdb=" C2' A P 35 " ideal model delta sinusoidal sigma weight residual -35.15 23.79 -58.94 1 4.00e+00 6.25e-02 2.90e+02 ... (remaining 13127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2933 0.062 - 0.123: 474 0.123 - 0.185: 47 0.185 - 0.247: 75 0.247 - 0.308: 7 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: 2.220 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 24.460 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.700 ------------------------------------------------------------------------------- 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 : 0.920 59.546 30505 Z= 0.547 Chirality : 0.057 0.308 3536 Planarity : 0.007 0.220 3617 Dihedral : 15.086 170.022 8256 Min Nonbonded Distance : 1.129 Molprobity Statistics. All-atom Clashscore : 13.09 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 0.00942 / 0.59 (22178) covalent geometry : angle 0.90685 / 0.55 (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 : 0.807 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: 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: 0.1476 time to fit residues: 97.9461 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 : 0.786 ------------------------------------------------------------------------------- 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: [197, 215, 20, 132, 248, 207, 155, 244, 183, 111, 258] 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 = 0.4122 r_free = 0.4122 target = 0.093168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.062654 restraints weight = 88559.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.064803 restraints weight = 36168.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.066115 restraints weight = 20450.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.066887 restraints weight = 14183.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.067379 restraints weight = 11370.079| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2282 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= 0.186 Angle : 0.738 14.579 30505 Z= 0.362 Chirality : 0.046 0.356 3536 Planarity : 0.005 0.045 3617 Dihedral : 11.310 171.616 3763 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.12 % Favored : 94.81 % Rotamer: Outliers : 4.69 % Allowed : 14.16 % 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: -1.17 (0.16), residues: 2541 helix: 0.11 (0.16), residues: 1014 sheet: -0.72 (0.31), residues: 269 loop : -1.53 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 80 TYR 0.022 0.002 TYR E 299 PHE 0.026 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 0.00399 / 0.19 (22178) covalent geometry : angle 0.72276 / 0.36 (30478) hydrogen bonds : bond 0.04728 / 3.25 ( 926) hydrogen bonds : angle 4.59318 / 3.19 ( 2544) metal coordination : bond 0.01254 / 0.87 ( 32) metal coordination : angle 5.07727 / 3.26 ( 27) Misc. bond : bond 0.00238 / 0.12 ( 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 238 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 135 time to evaluate : 0.834 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: A 111 VAL cc_start: 0.8458 (t) cc_final: 0.8164 (m) REVERT: A 242 MET cc_start: 0.8433 (mtt) cc_final: 0.8129 (mtt) REVERT: A 855 MET cc_start: 0.8386 (mmt) cc_final: 0.8095 (mmt) REVERT: A 903 TYR cc_start: 0.7538 (m-80) cc_final: 0.6891 (m-80) REVERT: B 65 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8393 (mm-40) REVERT: C 47 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7410 (tm-30) REVERT: D 42 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8477 (tp) REVERT: E 68 MET cc_start: 0.8774 (mmm) cc_final: 0.8367 (mmm) REVERT: E 204 ASP cc_start: 0.3955 (OUTLIER) cc_final: 0.1818 (t0) REVERT: E 441 CYS cc_start: 0.3240 (OUTLIER) cc_final: 0.2684 (t) REVERT: F 258 ILE cc_start: -0.1168 (OUTLIER) cc_final: -0.1530 (tt) REVERT: F 274 MET cc_start: 0.8985 (tmm) cc_final: 0.8658 (mmt) REVERT: F 378 MET cc_start: 0.8348 (tpp) cc_final: 0.8058 (tpp) outliers start: 103 outliers final: 48 residues processed: 232 average time/residue: 0.1486 time to fit residues: 54.9580 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 : 0.595 ------------------------------------------------------------------------------- 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 776 VAL 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 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 340 VAL 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 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: [52, 14, 219, 76, 93, 125, 200, 228, 114, 64, 203] chunk 52 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 219 optimal weight: 0.4980 chunk 76 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 200 optimal weight: 0.0980 chunk 228 optimal weight: 8.9990 chunk 114 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 chunk 203 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 157 GLN E 492 GLN E 531 GLN E 548 GLN E 562 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.091809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.060834 restraints weight = 89376.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.062937 restraints weight = 36950.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.064247 restraints weight = 21076.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.065023 restraints weight = 14616.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.065513 restraints weight = 11636.935| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22214 Z= 0.124 Angle : 0.642 14.345 30505 Z= 0.312 Chirality : 0.044 0.326 3536 Planarity : 0.004 0.042 3617 Dihedral : 10.385 178.130 3721 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.55 % Allowed : 14.98 % Favored : 81.47 % 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: -0.78 (0.16), residues: 2541 helix: 0.49 (0.17), residues: 1014 sheet: -0.38 (0.32), residues: 264 loop : -1.39 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 129 TYR 0.024 0.001 TYR B 135 PHE 0.013 0.001 PHE D 92 TRP 0.016 0.001 TRP F 114 HIS 0.011 0.001 HIS F 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (22178) covalent geometry : angle 0.63104 / 0.31 (30478) hydrogen bonds : bond 0.04067 / 2.88 ( 926) hydrogen bonds : angle 4.33716 / 3.03 ( 2544) metal coordination : bond 0.00799 / 0.57 ( 32) metal coordination : angle 4.08826 / 2.63 ( 27) Misc. bond : bond 0.00124 / 0.07 ( 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 205 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 127 time to evaluate : 0.803 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 111 VAL cc_start: 0.8562 (t) cc_final: 0.8296 (m) REVERT: A 336 ASP cc_start: 0.7646 (t0) cc_final: 0.7372 (t0) REVERT: A 615 MET cc_start: 0.8250 (tmm) cc_final: 0.7982 (tmm) REVERT: A 658 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7923 (mt-10) REVERT: A 855 MET cc_start: 0.8192 (mmt) cc_final: 0.7979 (mmt) REVERT: B 15 PHE cc_start: 0.8322 (t80) cc_final: 0.8101 (t80) REVERT: C 47 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7335 (tm-30) REVERT: C 54 SER cc_start: 0.9242 (m) cc_final: 0.8898 (t) REVERT: E 204 ASP cc_start: 0.3770 (OUTLIER) cc_final: 0.1778 (t0) REVERT: F 258 ILE cc_start: -0.0773 (OUTLIER) cc_final: -0.1134 (tt) REVERT: F 274 MET cc_start: 0.8989 (tmm) cc_final: 0.8671 (mmm) REVERT: F 378 MET cc_start: 0.8195 (tpp) cc_final: 0.7866 (tpp) outliers start: 78 outliers final: 44 residues processed: 199 average time/residue: 0.1395 time to fit residues: 44.6115 Evaluate side-chains 163 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 117 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 544 LEU 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 C residue 57 SER Chi-restraints excluded: chain C residue 68 ILE 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 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 366 THR Chi-restraints excluded: chain E residue 399 ILE 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 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 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 376 ILE Chi-restraints excluded: chain F residue 414 LYS 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: [25, 55, 3, 175, 240, 209, 150, 236, 59, 122, 65] chunk 25 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 chunk 240 optimal weight: 20.0000 chunk 209 optimal weight: 6.9990 chunk 150 optimal weight: 30.0000 chunk 236 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 572 HIS A 791 ASN B 19 GLN D 43 ASN E 554 HIS ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 464 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.086416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.054393 restraints weight = 91222.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.056308 restraints weight = 39492.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.057489 restraints weight = 23399.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.058239 restraints weight = 16772.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.058656 restraints weight = 13624.392| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 22214 Z= 0.330 Angle : 0.792 14.274 30505 Z= 0.384 Chirality : 0.048 0.379 3536 Planarity : 0.004 0.043 3617 Dihedral : 10.070 150.220 3710 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.92 % Allowed : 15.44 % Favored : 80.65 % 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: -0.81 (0.16), residues: 2541 helix: 0.45 (0.16), residues: 1027 sheet: -0.52 (0.31), residues: 267 loop : -1.38 (0.17), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 51 TYR 0.020 0.002 TYR A 887 PHE 0.021 0.002 PHE D 92 TRP 0.009 0.002 TRP F 114 HIS 0.007 0.001 HIS E 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00733 / 0.33 (22178) covalent geometry : angle 0.76938 / 0.38 (30478) hydrogen bonds : bond 0.04784 / 3.31 ( 926) hydrogen bonds : angle 4.54912 / 3.18 ( 2544) metal coordination : bond 0.03103 / 2.07 ( 32) metal coordination : angle 6.42447 / 3.93 ( 27) Misc. bond : bond 0.00032 / 0.02 ( 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 203 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 117 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: A 855 MET cc_start: 0.8458 (mmt) cc_final: 0.8169 (mmp) REVERT: A 900 LEU cc_start: 0.9081 (tp) cc_final: 0.8800 (tp) REVERT: B 65 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8825 (mm-40) REVERT: B 67 MET cc_start: 0.8820 (mmm) cc_final: 0.8588 (mmm) REVERT: C 47 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7812 (tm-30) REVERT: C 54 SER cc_start: 0.9338 (m) cc_final: 0.8984 (t) REVERT: C 67 ASP cc_start: 0.7891 (t0) cc_final: 0.7401 (t70) REVERT: E 204 ASP cc_start: 0.3914 (OUTLIER) cc_final: 0.1976 (t0) REVERT: E 429 MET cc_start: 0.6187 (mmm) cc_final: 0.5454 (tpp) REVERT: F 204 ASP cc_start: 0.3975 (OUTLIER) cc_final: 0.3710 (t70) REVERT: F 258 ILE cc_start: -0.0272 (OUTLIER) cc_final: -0.0654 (tt) REVERT: F 272 VAL cc_start: 0.8780 (t) cc_final: 0.8442 (p) REVERT: F 274 MET cc_start: 0.9126 (tmm) cc_final: 0.8653 (mmm) REVERT: F 378 MET cc_start: 0.8362 (tpp) cc_final: 0.7971 (tpp) REVERT: F 474 MET cc_start: 0.7677 (mpp) cc_final: 0.7417 (mpp) outliers start: 86 outliers final: 54 residues processed: 190 average time/residue: 0.1416 time to fit residues: 43.6303 Evaluate side-chains 169 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 111 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 206 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 761 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 899 MET 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 B residue 119 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 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 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 410 THR Chi-restraints excluded: chain E residue 436 MET 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 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 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 405 LEU Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 438 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: [84, 187, 92, 180, 145, 200, 202, 143, 149, 53, 247] chunk 84 optimal weight: 0.9990 chunk 187 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 chunk 180 optimal weight: 5.9990 chunk 145 optimal weight: 0.3980 chunk 200 optimal weight: 10.0000 chunk 202 optimal weight: 7.9990 chunk 143 optimal weight: 20.0000 chunk 149 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 247 optimal weight: 9.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 19 GLN C 63 GLN D 176 ASN E 349 ASN ** E 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.086053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.054252 restraints weight = 91312.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.056157 restraints weight = 39644.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.057349 restraints weight = 23497.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.058080 restraints weight = 16831.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.058558 restraints weight = 13649.948| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 22214 Z= 0.259 Angle : 0.714 14.219 30505 Z= 0.343 Chirality : 0.047 0.362 3536 Planarity : 0.004 0.048 3617 Dihedral : 9.843 147.868 3708 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.51 % Allowed : 16.35 % Favored : 80.15 % 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: -0.66 (0.17), residues: 2541 helix: 0.61 (0.16), residues: 1026 sheet: -0.64 (0.31), residues: 275 loop : -1.28 (0.18), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 560 TYR 0.027 0.002 TYR E 93 PHE 0.019 0.002 PHE D 92 TRP 0.016 0.001 TRP E 114 HIS 0.007 0.001 HIS E 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.26 (22178) covalent geometry : angle 0.69370 / 0.34 (30478) hydrogen bonds : bond 0.04301 / 3.04 ( 926) hydrogen bonds : angle 4.39741 / 3.07 ( 2544) metal coordination : bond 0.02274 / 1.47 ( 32) metal coordination : angle 5.67880 / 3.51 ( 27) Misc. bond : bond 0.00032 / 0.02 ( 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 196 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 119 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 TRP cc_start: 0.8651 (OUTLIER) cc_final: 0.7144 (m-90) REVERT: A 615 MET cc_start: 0.8295 (tmm) cc_final: 0.7706 (ttt) REVERT: A 855 MET cc_start: 0.8441 (mmt) cc_final: 0.8180 (mmp) REVERT: B 94 MET cc_start: 0.8454 (mtp) cc_final: 0.8186 (mtp) REVERT: C 47 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7785 (tm-30) REVERT: C 54 SER cc_start: 0.9286 (m) cc_final: 0.8939 (t) REVERT: C 67 ASP cc_start: 0.7855 (t0) cc_final: 0.7327 (t70) REVERT: D 52 ASP cc_start: 0.9171 (t0) cc_final: 0.8703 (m-30) REVERT: D 60 GLU cc_start: 0.8934 (pp20) cc_final: 0.8665 (pp20) REVERT: D 94 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8347 (mtm) REVERT: E 204 ASP cc_start: 0.4034 (OUTLIER) cc_final: 0.2101 (t0) REVERT: E 324 TYR cc_start: 0.3893 (m-10) cc_final: 0.3501 (m-10) REVERT: E 429 MET cc_start: 0.6204 (mmm) cc_final: 0.5496 (tpp) REVERT: F 258 ILE cc_start: 0.0219 (OUTLIER) cc_final: -0.0134 (tt) REVERT: F 378 MET cc_start: 0.8300 (tpp) cc_final: 0.7894 (tpp) REVERT: F 474 MET cc_start: 0.7559 (mpp) cc_final: 0.7329 (mpp) outliers start: 77 outliers final: 53 residues processed: 188 average time/residue: 0.1414 time to fit residues: 43.0903 Evaluate side-chains 173 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 116 time to evaluate : 0.763 ------------------------------------------------------------------------------- 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 231 VAL Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain B residue 106 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 90 MET Chi-restraints excluded: chain D residue 94 MET Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 130 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 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 436 MET Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 561 PHE 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 209 VAL Chi-restraints excluded: chain F residue 219 LEU 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 347 LYS 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 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 588 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: [175, 125, 33, 176, 85, 95, 134, 64, 109, 180, 82] chunk 175 optimal weight: 9.9990 chunk 125 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 176 optimal weight: 0.0170 chunk 85 optimal weight: 0.9990 chunk 95 optimal weight: 9.9990 chunk 134 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 180 optimal weight: 5.9990 chunk 82 optimal weight: 0.6980 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 19 GLN D 168 GLN ** E 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.087968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.056583 restraints weight = 91255.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.058595 restraints weight = 38582.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.059835 restraints weight = 22379.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.060581 restraints weight = 15856.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.061056 restraints weight = 12778.327| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22214 Z= 0.113 Angle : 0.634 14.118 30505 Z= 0.302 Chirality : 0.043 0.327 3536 Planarity : 0.003 0.040 3617 Dihedral : 9.222 148.322 3694 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.87 % Allowed : 17.49 % 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: -0.32 (0.17), residues: 2541 helix: 0.95 (0.17), residues: 1015 sheet: -0.27 (0.31), residues: 274 loop : -1.19 (0.18), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 51 TYR 0.015 0.001 TYR F 224 PHE 0.017 0.001 PHE F 437 TRP 0.015 0.001 TRP A 916 HIS 0.006 0.001 HIS F 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (22178) covalent geometry : angle 0.62030 / 0.30 (30478) hydrogen bonds : bond 0.03645 / 2.62 ( 926) hydrogen bonds : angle 4.14426 / 2.91 ( 2544) metal coordination : bond 0.00697 / 0.48 ( 32) metal coordination : angle 4.43765 / 2.81 ( 27) Misc. bond : bond 0.00289 / 0.15 ( 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 191 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 128 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8265 (mmm) cc_final: 0.7991 (mmm) REVERT: A 268 TRP cc_start: 0.8575 (OUTLIER) cc_final: 0.7128 (m-90) REVERT: A 615 MET cc_start: 0.8063 (tmm) cc_final: 0.7715 (ttt) REVERT: A 665 GLU cc_start: 0.7217 (pm20) cc_final: 0.6975 (pm20) REVERT: A 855 MET cc_start: 0.8291 (mmt) cc_final: 0.8088 (mmp) REVERT: B 15 PHE cc_start: 0.8299 (t80) cc_final: 0.7924 (t80) REVERT: B 94 MET cc_start: 0.8292 (mtp) cc_final: 0.7897 (mtp) REVERT: C 34 GLN cc_start: 0.8245 (tp40) cc_final: 0.7882 (tm-30) REVERT: C 38 ASP cc_start: 0.8397 (m-30) cc_final: 0.7740 (m-30) REVERT: C 47 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7626 (tm-30) REVERT: C 54 SER cc_start: 0.9187 (m) cc_final: 0.8872 (t) REVERT: D 48 GLU cc_start: 0.9184 (tp30) cc_final: 0.8857 (tp30) REVERT: D 60 GLU cc_start: 0.8821 (pp20) cc_final: 0.8551 (pp20) REVERT: E 68 MET cc_start: 0.8889 (mmm) cc_final: 0.7035 (mmp) REVERT: E 204 ASP cc_start: 0.4279 (OUTLIER) cc_final: 0.2777 (t0) REVERT: E 280 LEU cc_start: 0.8830 (tp) cc_final: 0.8614 (mt) REVERT: E 429 MET cc_start: 0.6165 (mmm) cc_final: 0.5479 (tpp) REVERT: E 462 LYS cc_start: 0.5834 (mmpt) cc_final: 0.5474 (mmmt) REVERT: F 258 ILE cc_start: 0.0442 (OUTLIER) cc_final: 0.0188 (tt) REVERT: F 272 VAL cc_start: 0.8646 (t) cc_final: 0.8421 (p) REVERT: F 274 MET cc_start: 0.8814 (tmm) cc_final: 0.8408 (mmm) REVERT: F 378 MET cc_start: 0.8144 (tpp) cc_final: 0.7692 (tpp) outliers start: 63 outliers final: 44 residues processed: 185 average time/residue: 0.1371 time to fit residues: 41.7341 Evaluate side-chains 164 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 117 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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 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 776 VAL Chi-restraints excluded: chain C residue 4 SER 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 366 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 398 TYR 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 166 SER Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 219 LEU 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 506 TRP 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: [67, 150, 16, 198, 241, 127, 157, 83, 187, 100, 94] chunk 67 optimal weight: 0.2980 chunk 150 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 198 optimal weight: 7.9990 chunk 241 optimal weight: 5.9990 chunk 127 optimal weight: 0.7980 chunk 157 optimal weight: 7.9990 chunk 83 optimal weight: 0.8980 chunk 187 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 94 optimal weight: 20.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 703 ASN B 19 GLN ** E 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.087979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.056953 restraints weight = 90631.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.058960 restraints weight = 38098.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.060209 restraints weight = 22109.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.060972 restraints weight = 15632.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.061359 restraints weight = 12575.140| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22214 Z= 0.110 Angle : 0.624 14.020 30505 Z= 0.295 Chirality : 0.043 0.323 3536 Planarity : 0.003 0.039 3617 Dihedral : 8.930 150.100 3690 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.69 % Allowed : 17.85 % Favored : 79.46 % 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: -0.12 (0.17), residues: 2541 helix: 1.14 (0.17), residues: 1012 sheet: -0.16 (0.32), residues: 279 loop : -1.09 (0.18), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 365 TYR 0.015 0.001 TYR E 324 PHE 0.019 0.001 PHE F 90 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 0.00236 / 0.11 (22178) covalent geometry : angle 0.61164 / 0.29 (30478) hydrogen bonds : bond 0.03544 / 2.57 ( 926) hydrogen bonds : angle 4.05239 / 2.86 ( 2544) metal coordination : bond 0.00720 / 0.50 ( 32) metal coordination : angle 4.19793 / 2.65 ( 27) Misc. bond : bond 0.00043 / 0.02 ( 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 184 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 125 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 615 MET cc_start: 0.8099 (tmm) cc_final: 0.7716 (ttm) REVERT: B 15 PHE cc_start: 0.8274 (t80) cc_final: 0.7920 (t80) REVERT: B 94 MET cc_start: 0.8354 (mtp) cc_final: 0.8154 (mtp) REVERT: C 34 GLN cc_start: 0.8239 (tp40) cc_final: 0.7935 (tm-30) REVERT: C 47 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7570 (tm-30) REVERT: C 54 SER cc_start: 0.9190 (m) cc_final: 0.8877 (t) REVERT: C 75 MET cc_start: 0.6842 (ttm) cc_final: 0.6513 (mtp) REVERT: D 48 GLU cc_start: 0.9145 (tp30) cc_final: 0.8825 (tp30) REVERT: D 60 GLU cc_start: 0.8834 (pp20) cc_final: 0.8518 (pp20) REVERT: E 165 LEU cc_start: 0.4522 (OUTLIER) cc_final: 0.2705 (tp) REVERT: E 204 ASP cc_start: 0.4335 (OUTLIER) cc_final: 0.2969 (t0) REVERT: E 429 MET cc_start: 0.6087 (mmm) cc_final: 0.5405 (tpp) REVERT: F 258 ILE cc_start: 0.0790 (OUTLIER) cc_final: 0.0547 (tt) REVERT: F 272 VAL cc_start: 0.8575 (t) cc_final: 0.8371 (p) REVERT: F 274 MET cc_start: 0.8809 (tmm) cc_final: 0.8290 (tpp) REVERT: F 378 MET cc_start: 0.8052 (tpp) cc_final: 0.7579 (tpp) outliers start: 59 outliers final: 44 residues processed: 179 average time/residue: 0.1342 time to fit residues: 39.4512 Evaluate side-chains 160 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 113 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 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 C residue 4 SER Chi-restraints excluded: chain D residue 35 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 E residue 127 THR Chi-restraints excluded: chain E residue 165 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 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 166 SER Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 219 LEU 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 391 LEU Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 506 TRP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: [17, 165, 197, 32, 101, 224, 194, 244, 10, 45, 5] chunk 17 optimal weight: 0.9990 chunk 165 optimal weight: 6.9990 chunk 197 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 101 optimal weight: 4.9990 chunk 224 optimal weight: 6.9990 chunk 194 optimal weight: 0.0970 chunk 244 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 19 GLN ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 HIS ** E 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.087684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.056988 restraints weight = 88921.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.058983 restraints weight = 36776.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.060222 restraints weight = 21106.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.060960 restraints weight = 14801.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.061433 restraints weight = 11864.356| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22214 Z= 0.142 Angle : 0.632 13.929 30505 Z= 0.299 Chirality : 0.043 0.331 3536 Planarity : 0.003 0.038 3617 Dihedral : 8.760 148.563 3688 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.64 % Allowed : 18.21 % Favored : 79.14 % 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: -0.12 (0.17), residues: 2541 helix: 1.12 (0.17), residues: 1014 sheet: -0.25 (0.32), residues: 280 loop : -1.04 (0.18), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 579 TYR 0.013 0.001 TYR F 224 PHE 0.018 0.001 PHE F 90 TRP 0.010 0.001 TRP A 916 HIS 0.008 0.001 HIS E 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (22178) covalent geometry : angle 0.61892 / 0.30 (30478) hydrogen bonds : bond 0.03643 / 2.61 ( 926) hydrogen bonds : angle 4.06344 / 2.87 ( 2544) metal coordination : bond 0.01114 / 0.74 ( 32) metal coordination : angle 4.41328 / 2.76 ( 27) Misc. bond : bond 0.00033 / 0.02 ( 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 172 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 114 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8080 (mmm) cc_final: 0.7730 (tpt) REVERT: A 268 TRP cc_start: 0.8589 (OUTLIER) cc_final: 0.7039 (m-90) REVERT: A 615 MET cc_start: 0.8136 (tmm) cc_final: 0.7726 (ttt) REVERT: B 15 PHE cc_start: 0.8276 (t80) cc_final: 0.7958 (t80) REVERT: B 94 MET cc_start: 0.8496 (mtp) cc_final: 0.8192 (mtp) REVERT: B 135 TYR cc_start: 0.8485 (t80) cc_final: 0.8280 (t80) REVERT: C 34 GLN cc_start: 0.8271 (tp40) cc_final: 0.8044 (tm-30) REVERT: C 47 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7633 (tm-30) REVERT: C 54 SER cc_start: 0.9221 (m) cc_final: 0.8896 (t) REVERT: D 48 GLU cc_start: 0.9116 (tp30) cc_final: 0.8817 (tp30) REVERT: D 60 GLU cc_start: 0.8868 (pp20) cc_final: 0.8529 (pp20) REVERT: E 204 ASP cc_start: 0.4060 (OUTLIER) cc_final: 0.2921 (t0) REVERT: E 429 MET cc_start: 0.6106 (mmm) cc_final: 0.5480 (tpp) REVERT: F 258 ILE cc_start: 0.0903 (OUTLIER) cc_final: 0.0662 (tt) REVERT: F 272 VAL cc_start: 0.8497 (t) cc_final: 0.8264 (p) REVERT: F 274 MET cc_start: 0.8789 (tmm) cc_final: 0.8321 (tpp) REVERT: F 378 MET cc_start: 0.8052 (tpp) cc_final: 0.7601 (tpp) outliers start: 58 outliers final: 41 residues processed: 168 average time/residue: 0.1300 time to fit residues: 36.1842 Evaluate side-chains 155 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 111 time to evaluate : 0.798 ------------------------------------------------------------------------------- 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 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 776 VAL Chi-restraints excluded: chain C residue 10 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 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 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 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 183 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 219 LEU 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 391 LEU Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 506 TRP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: [99, 134, 93, 75, 40, 155, 149, 15, 169, 71, 1] chunk 99 optimal weight: 6.9990 chunk 134 optimal weight: 0.0670 chunk 93 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 155 optimal weight: 50.0000 chunk 149 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 169 optimal weight: 20.0000 chunk 71 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.087991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.057481 restraints weight = 91676.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.059423 restraints weight = 39980.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.060624 restraints weight = 23569.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.061377 restraints weight = 16776.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.061768 restraints weight = 13558.350| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22214 Z= 0.116 Angle : 0.627 13.890 30505 Z= 0.296 Chirality : 0.043 0.323 3536 Planarity : 0.003 0.037 3617 Dihedral : 8.622 148.918 3686 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.32 % Allowed : 18.35 % Favored : 79.33 % 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: -0.03 (0.17), residues: 2541 helix: 1.19 (0.17), residues: 1010 sheet: -0.19 (0.32), residues: 282 loop : -0.99 (0.18), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 51 TYR 0.031 0.001 TYR F 541 PHE 0.014 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 0.00252 / 0.12 (22178) covalent geometry : angle 0.61663 / 0.30 (30478) hydrogen bonds : bond 0.03516 / 2.55 ( 926) hydrogen bonds : angle 4.03984 / 2.86 ( 2544) metal coordination : bond 0.00719 / 0.48 ( 32) metal coordination : angle 3.95640 / 2.49 ( 27) Misc. bond : bond 0.00031 / 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 167 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 116 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.7986 (mmm) cc_final: 0.7663 (tpt) REVERT: A 268 TRP cc_start: 0.8548 (OUTLIER) cc_final: 0.7039 (m-90) REVERT: A 615 MET cc_start: 0.7997 (tmm) cc_final: 0.7606 (ttm) REVERT: A 855 MET cc_start: 0.8384 (mmt) cc_final: 0.8167 (mmp) REVERT: B 15 PHE cc_start: 0.8394 (t80) cc_final: 0.8007 (t80) REVERT: B 51 ARG cc_start: 0.9157 (tpp80) cc_final: 0.8927 (tpp80) REVERT: B 94 MET cc_start: 0.8360 (mtp) cc_final: 0.8067 (mtp) REVERT: C 47 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7509 (tm-30) REVERT: C 54 SER cc_start: 0.9179 (m) cc_final: 0.8894 (t) REVERT: D 48 GLU cc_start: 0.9094 (tp30) cc_final: 0.8803 (tp30) REVERT: D 60 GLU cc_start: 0.8776 (pp20) cc_final: 0.8464 (pp20) REVERT: D 67 MET cc_start: 0.8151 (tmm) cc_final: 0.7692 (tmm) REVERT: D 185 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8159 (mp) REVERT: E 429 MET cc_start: 0.6058 (mmm) cc_final: 0.5412 (tpp) REVERT: F 258 ILE cc_start: 0.1116 (OUTLIER) cc_final: 0.0901 (tt) REVERT: F 272 VAL cc_start: 0.8511 (t) cc_final: 0.8083 (p) REVERT: F 274 MET cc_start: 0.8796 (tmm) cc_final: 0.8363 (tpp) REVERT: F 378 MET cc_start: 0.7987 (tpp) cc_final: 0.7505 (tpp) REVERT: F 436 MET cc_start: 0.2839 (tpp) cc_final: 0.2246 (tmm) outliers start: 51 outliers final: 44 residues processed: 164 average time/residue: 0.1287 time to fit residues: 34.6793 Evaluate side-chains 156 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 109 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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 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 680 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 10 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 185 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 127 THR 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 348 VAL 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 410 THR 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 183 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 219 LEU 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 391 LEU Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 506 TRP 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: [139, 6, 134, 80, 175, 220, 66, 230, 142, 258, 141] chunk 139 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 175 optimal weight: 2.9990 chunk 220 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 230 optimal weight: 1.9990 chunk 142 optimal weight: 40.0000 chunk 258 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 19 GLN ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 GLN ** E 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.085058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.053742 restraints weight = 91310.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.055626 restraints weight = 39414.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.056793 restraints weight = 23357.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.057527 restraints weight = 16769.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.057953 restraints weight = 13591.691| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 22214 Z= 0.285 Angle : 0.729 13.946 30505 Z= 0.349 Chirality : 0.047 0.356 3536 Planarity : 0.004 0.037 3617 Dihedral : 8.708 144.172 3684 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.28 % Allowed : 18.67 % Favored : 79.05 % 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: -0.25 (0.17), residues: 2541 helix: 0.99 (0.17), residues: 1018 sheet: -0.40 (0.32), residues: 286 loop : -1.08 (0.18), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 96 TYR 0.019 0.002 TYR B 135 PHE 0.019 0.002 PHE D 92 TRP 0.010 0.001 TRP F 506 HIS 0.006 0.001 HIS F 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.28 (22178) covalent geometry : angle 0.71078 / 0.35 (30478) hydrogen bonds : bond 0.04197 / 2.95 ( 926) hydrogen bonds : angle 4.26169 / 3.01 ( 2544) metal coordination : bond 0.02356 / 1.49 ( 32) metal coordination : angle 5.52463 / 3.36 ( 27) Misc. bond : bond 0.00038 / 0.02 ( 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 161 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 111 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: A 268 TRP cc_start: 0.8659 (OUTLIER) cc_final: 0.7126 (m-90) REVERT: A 615 MET cc_start: 0.8271 (tmm) cc_final: 0.7861 (ttt) REVERT: A 665 GLU cc_start: 0.7263 (pm20) cc_final: 0.7004 (pm20) REVERT: A 855 MET cc_start: 0.8426 (mmt) cc_final: 0.8196 (mmp) REVERT: A 924 MET cc_start: 0.8841 (mmm) cc_final: 0.8619 (mtp) REVERT: B 15 PHE cc_start: 0.8256 (t80) cc_final: 0.7890 (t80) REVERT: B 94 MET cc_start: 0.8653 (mtp) cc_final: 0.8308 (mtp) REVERT: C 47 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7741 (tm-30) REVERT: C 54 SER cc_start: 0.9267 (m) cc_final: 0.8948 (t) REVERT: D 48 GLU cc_start: 0.9057 (tp30) cc_final: 0.8761 (tp30) REVERT: D 185 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8218 (mp) REVERT: E 429 MET cc_start: 0.6245 (mmm) cc_final: 0.5593 (tpp) REVERT: F 258 ILE cc_start: 0.1110 (OUTLIER) cc_final: 0.0892 (tt) REVERT: F 274 MET cc_start: 0.8904 (tmm) cc_final: 0.8233 (tpp) REVERT: F 378 MET cc_start: 0.8094 (tpp) cc_final: 0.7574 (tpp) outliers start: 50 outliers final: 43 residues processed: 158 average time/residue: 0.1285 time to fit residues: 34.0158 Evaluate side-chains 152 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 106 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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 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 A residue 926 THR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 10 SER 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 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 127 THR 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 348 VAL 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 410 THR Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 561 PHE Chi-restraints excluded: chain E residue 572 ILE Chi-restraints excluded: chain F residue 70 TYR 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 209 VAL Chi-restraints excluded: chain F residue 219 LEU 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 391 LEU Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 506 TRP Chi-restraints excluded: chain F residue 525 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: [31, 87, 30, 23, 203, 207, 213, 202, 34, 187, 197] chunk 31 optimal weight: 0.8980 chunk 87 optimal weight: 0.0870 chunk 30 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 203 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 213 optimal weight: 10.0000 chunk 202 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 187 optimal weight: 20.0000 chunk 197 optimal weight: 3.9990 overall best weight: 1.0760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 557 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.086757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.055739 restraints weight = 91139.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.057698 restraints weight = 38440.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.058927 restraints weight = 22469.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.059643 restraints weight = 15921.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.060102 restraints weight = 12908.066| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22214 Z= 0.124 Angle : 0.643 13.908 30505 Z= 0.304 Chirality : 0.044 0.330 3536 Planarity : 0.003 0.038 3617 Dihedral : 8.566 144.350 3683 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.91 % Allowed : 19.17 % 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: -0.15 (0.17), residues: 2541 helix: 1.10 (0.17), residues: 1015 sheet: -0.53 (0.31), residues: 311 loop : -0.99 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 51 TYR 0.019 0.001 TYR B 135 PHE 0.019 0.001 PHE B 49 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 0.00271 / 0.12 (22178) covalent geometry : angle 0.63107 / 0.30 (30478) hydrogen bonds : bond 0.03636 / 2.62 ( 926) hydrogen bonds : angle 4.09546 / 2.90 ( 2544) metal coordination : bond 0.00810 / 0.53 ( 32) metal coordination : angle 4.23614 / 2.65 ( 27) Misc. bond : bond 0.00028 / 0.01 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4972.27 seconds wall clock time: 86 minutes 7.78 seconds (5167.78 seconds total)