Starting phenix.real_space_refine on Mon Oct 26 20:35:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7re1_24430/10_2026/7re1_24430.cif Found real_map, /net/cci-nas-00/data/ceres_data/7re1_24430/10_2026/7re1_24430.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7re1_24430/10_2026/7re1_24430.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7re1_24430/10_2026/7re1_24430.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7re1_24430/10_2026/7re1_24430.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7re1_24430/10_2026/7re1_24430.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7re1_24430/10_2026/7re1_24430.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7re1_24430/10_2026/7re1_24430.cif" } resolution = 2.91 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= 0.031 sd= 1.303 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 13484 2.51 5 N 3657 2.21 5 O 4437 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 29 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: 21825 Number of models: 1 Model: "" Number of chains: 19 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: 4557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4557 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PTRANS': 29, 'TRANS': 559} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "F" Number of atoms: 4557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4557 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 2, 'PTRANS': 29, 'TRANS': 558} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "P" Number of atoms: 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: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 91 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 2, 'ADP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 71 Unusual residues: {' MG': 1, ' ZN': 3, '1N7': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 35 Unusual residues: {' MG': 1, ' ZN': 3, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "A" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 95 Classifications: {'water': 95} Link IDs: {None: 94} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "P" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "T" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2454 SG CYS A 301 62.863 45.535 117.628 1.00 65.71 S ATOM 2495 SG CYS A 306 62.249 46.786 121.192 1.00 65.13 S ATOM 2527 SG CYS A 310 63.846 43.367 120.614 1.00 59.03 S ATOM 3935 SG CYS A 487 64.664 60.713 104.014 1.00 66.11 S ATOM 5188 SG CYS A 645 63.653 62.526 107.227 1.00 71.91 S ATOM 5194 SG CYS A 646 63.003 58.807 106.758 1.00 69.76 S ATOM 10896 SG CYS E 5 112.659 64.168 54.701 1.00 81.99 S ATOM 10917 SG CYS E 8 115.804 64.423 56.437 1.00 83.65 S ATOM 11055 SG CYS E 26 114.029 67.688 55.934 1.00 81.79 S ATOM 11076 SG CYS E 29 115.354 66.267 52.940 1.00 81.74 S ATOM 11241 SG CYS E 50 93.343 81.615 51.188 1.00 86.34 S ATOM 11271 SG CYS E 55 91.833 81.488 47.640 1.00 90.55 S ATOM 11404 SG CYS E 72 94.591 84.127 48.571 1.00 83.16 S ATOM 10978 SG CYS E 16 104.655 66.442 47.289 1.00 81.05 S ATOM 10993 SG CYS E 19 105.305 62.929 45.888 1.00 83.14 S ATOM 15453 SG CYS F 5 61.276 64.849 56.971 1.00 73.73 S ATOM 15474 SG CYS F 8 64.035 65.154 54.533 1.00 77.17 S ATOM 15612 SG CYS F 26 63.417 68.190 56.551 1.00 77.53 S ATOM 15633 SG CYS F 29 60.829 67.489 54.250 1.00 78.77 S ATOM 15798 SG CYS F 50 53.526 79.656 78.077 1.00 82.02 S ATOM 15828 SG CYS F 55 49.946 80.964 78.280 1.00 88.78 S ATOM 15961 SG CYS F 72 52.280 82.603 75.866 1.00 78.64 S ATOM 15535 SG CYS F 16 52.340 67.221 62.583 1.00 72.29 S ATOM 15550 SG CYS F 19 50.379 64.076 61.484 1.00 75.11 S Time building chain proxies: 4.63, per 1000 atoms: 0.21 Number of scatterers: 21825 At special positions: 0 Unit cell: (146.59, 150.87, 181.9, 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 4437 8.00 N 3657 7.00 C 13484 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 8 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 26 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 29 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 5 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 50 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 72 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 55 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E 703 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 19 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 16 " pdb=" ZN F1000 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 26 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 8 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 29 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 5 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" 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=" NE2 HIS F 33 " pdb="ZN ZN F1002 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 16 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 19 " Number of angles added : 26 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4874 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 27 sheets defined 44.5% alpha, 12.3% beta 34 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 2.81 Creating SS restraints... Processing helix chain 'A' and resid 3 through 13 removed outlier: 3.560A pdb=" N PHE A 7 " --> pdb=" O ASP A 3 " (cutoff:3.500A) removed outlier: 3.545A 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 removed outlier: 3.514A pdb=" N LYS A 159 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 177 removed outlier: 4.226A 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: 4.021A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 260 removed outlier: 4.370A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS A 256 " --> pdb=" O ALA A 253 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N VAL A 257 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ASP A 258 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 3.529A 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: 3.569A pdb=" N CYS A 301 " --> pdb=" O CYS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.828A pdb=" N HIS A 309 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.583A 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: 3.703A 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: 4.735A 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: 4.188A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.580A 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: 3.869A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 removed outlier: 3.511A pdb=" N LEU A 527 " --> pdb=" O ASP A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 581 removed outlier: 4.092A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.813A 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 removed outlier: 3.507A pdb=" N MET A 626 " --> pdb=" O CYS A 622 " (cutoff:3.500A) 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: 3.650A 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: 3.503A pdb=" N LYS A 849 " --> pdb=" O ASP A 846 " (cutoff:3.500A) removed outlier: 3.668A 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: 4.003A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 917 removed outlier: 3.928A pdb=" N ARG A 914 " --> pdb=" O ASN A 911 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TRP A 916 " --> pdb=" O SER A 913 " (cutoff:3.500A) removed outlier: 3.719A 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: 4.189A pdb=" N ALA B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 79 Processing helix chain 'B' and resid 79 through 98 removed outlier: 3.641A 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: 4.327A pdb=" N LEU B 122 " --> pdb=" O ASN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 143 removed outlier: 4.094A 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: 3.622A 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: 3.545A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 62 removed outlier: 3.696A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.794A 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: 3.508A pdb=" N GLU D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 99 removed outlier: 3.608A 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: 3.557A pdb=" N ASN D 140 " --> pdb=" O ASN D 136 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR D 141 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 removed outlier: 3.692A 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: 3.817A pdb=" N SER E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 97 removed outlier: 3.898A pdb=" N CYS E 97 " --> pdb=" O LYS E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 112 removed outlier: 3.866A pdb=" N ALA E 108 " --> pdb=" O THR E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 123 Processing helix chain 'E' and resid 127 through 146 removed outlier: 3.503A pdb=" N ALA E 135 " --> pdb=" O LYS E 131 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS E 146 " --> pdb=" O GLU E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 149 No H-bonds generated for 'chain 'E' and resid 147 through 149' Processing helix chain 'E' and resid 265 through 275 Processing helix chain 'E' and resid 290 through 299 removed outlier: 3.686A pdb=" N GLY E 294 " --> pdb=" O HIS E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 325 removed outlier: 3.590A 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: 4.491A pdb=" N ALA E 454 " --> pdb=" O ASP E 450 " (cutoff:3.500A) removed outlier: 3.569A 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: 4.604A pdb=" N SER E 523 " --> pdb=" O ASN E 519 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N LYS E 524 " --> pdb=" O ALA E 520 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE E 525 " --> pdb=" O VAL E 521 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 537 removed outlier: 3.581A 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: 3.728A pdb=" N LEU E 585 " --> pdb=" O LEU E 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 37 removed outlier: 3.678A pdb=" N SER F 36 " --> pdb=" O ASP F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 112 removed outlier: 4.502A pdb=" N ALA F 108 " --> pdb=" O THR F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 123 removed outlier: 3.558A pdb=" N ILE F 121 " --> pdb=" O ALA F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 146 removed outlier: 3.783A 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: 3.818A pdb=" N GLN F 275 " --> pdb=" O LYS F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 299 removed outlier: 4.045A pdb=" N ILE F 293 " --> pdb=" O SER F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 324 removed outlier: 3.603A pdb=" N VAL F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) 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: 3.693A pdb=" N VAL F 456 " --> pdb=" O VAL F 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 499 removed outlier: 3.761A pdb=" N ILE F 493 " --> pdb=" O ASN F 489 " (cutoff:3.500A) Processing helix chain 'F' and resid 515 through 526 removed outlier: 3.566A pdb=" N SER F 523 " --> pdb=" O ASN F 519 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS F 524 " --> pdb=" O ALA F 520 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE F 525 " --> pdb=" O VAL F 521 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU F 526 " --> pdb=" O ALA F 522 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 566 removed outlier: 3.747A 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: 5.328A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ASP A 60 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE A 66 " --> pdb=" O ASP A 60 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N TYR A 69 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 4.316A 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: 6.995A pdb=" N ASP A 29 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 5.105A 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: 6.395A pdb=" N ILE A 201 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.051A 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: 6.454A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 9.477A pdb=" N SER A 363 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 6.607A 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: 6.454A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.517A 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: 6.707A pdb=" N LEU A 673 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU A 387 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL B 131 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU A 389 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.696A 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: 6.471A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 3 through 4 Processing sheet with id=AB4, first strand: chain 'E' and resid 24 through 25 removed outlier: 3.920A pdb=" N LEU E 14 " --> pdb=" O LEU E 25 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 64 through 66 Processing sheet with id=AB6, first strand: chain 'E' and resid 84 through 85 Processing sheet with id=AB7, first strand: chain 'E' and resid 212 through 213 Processing sheet with id=AB8, first strand: chain 'E' and resid 355 through 359 removed outlier: 6.249A pdb=" N VAL E 371 " --> pdb=" O VAL E 397 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ILE E 399 " --> pdb=" O VAL E 371 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N PHE E 373 " --> pdb=" O ILE E 399 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N SER E 278 " --> pdb=" O TYR E 398 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N MET E 436 " --> pdb=" O TYR E 277 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N THR E 279 " --> pdb=" O MET E 436 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 471 through 475 removed outlier: 6.099A pdb=" N PHE E 472 " --> pdb=" O CYS E 574 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N MET E 576 " --> pdb=" O PHE E 472 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N MET E 474 " --> pdb=" O MET E 576 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASP E 542 " --> pdb=" O GLY E 571 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N LEU E 573 " --> pdb=" O ASP E 542 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL E 544 " --> pdb=" O LEU E 573 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ILE E 575 " --> pdb=" O VAL E 544 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N PHE E 546 " --> pdb=" O ILE E 575 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N PHE E 511 " --> pdb=" O GLN E 531 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 481 through 482 Processing sheet with id=AC2, first strand: chain 'F' and resid 3 through 4 Processing sheet with id=AC3, first strand: chain 'F' and resid 64 through 66 Processing sheet with id=AC4, first strand: chain 'F' and resid 84 through 85 Processing sheet with id=AC5, first strand: chain 'F' and resid 166 through 167 removed outlier: 3.681A pdb=" N GLY F 184 " --> pdb=" O GLY F 196 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N GLY F 196 " --> pdb=" O GLY F 184 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 162 through 163 Processing sheet with id=AC7, first strand: chain 'F' and resid 277 through 280 removed outlier: 6.392A pdb=" N SER F 278 " --> pdb=" O TYR F 398 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N THR F 367 " --> pdb=" O ALA F 393 " (cutoff:3.500A) removed outlier: 10.002A pdb=" N HIS F 395 " --> pdb=" O THR F 367 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ASP F 369 " --> pdb=" O HIS F 395 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N VAL F 397 " --> pdb=" O ASP F 369 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL F 371 " --> pdb=" O VAL F 397 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE F 399 " --> pdb=" O VAL F 371 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE F 373 " --> pdb=" O ILE F 399 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA F 308 " --> pdb=" O CYS F 358 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N SER F 331 " --> pdb=" O PHE F 357 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N THR F 359 " --> pdb=" O SER F 331 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 440 through 441 Processing sheet with id=AC9, first strand: chain 'F' and resid 510 through 512 removed outlier: 3.590A pdb=" N VAL F 544 " --> pdb=" O GLY F 571 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU F 573 " --> pdb=" O VAL F 544 " (cutoff:3.500A) 863 hydrogen bonds defined for protein. 2391 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 83 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 5.04 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 3343 1.28 - 1.42: 5982 1.42 - 1.55: 12521 1.55 - 1.68: 234 1.68 - 1.82: 220 Bond restraints: 22300 Sorted by residual: bond pdb=" F1 AF3 F1005 " pdb="AL AF3 F1005 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" F1 AF3 E 706 " pdb="AL AF3 E 706 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" F3 AF3 F1005 " pdb="AL AF3 F1005 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.62e+01 bond pdb=" F2 AF3 F1005 " pdb="AL AF3 F1005 " ideal model delta sigma weight residual 1.637 1.799 -0.162 2.00e-02 2.50e+03 6.60e+01 bond pdb=" F3 AF3 E 706 " pdb="AL AF3 E 706 " ideal model delta sigma weight residual 1.637 1.799 -0.162 2.00e-02 2.50e+03 6.54e+01 ... (remaining 22295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.10: 30398 3.10 - 6.19: 227 6.19 - 9.29: 33 9.29 - 12.38: 6 12.38 - 15.48: 2 Bond angle restraints: 30666 Sorted by residual: angle pdb=" C LYS F 189 " pdb=" N ASN F 190 " pdb=" CA ASN F 190 " ideal model delta sigma weight residual 121.70 137.18 -15.48 1.80e+00 3.09e-01 7.39e+01 angle pdb=" C LYS E 189 " pdb=" N ASN E 190 " pdb=" CA ASN E 190 " ideal model delta sigma weight residual 121.70 135.25 -13.55 1.80e+00 3.09e-01 5.67e+01 angle pdb=" N HIS E 290 " pdb=" CA HIS E 290 " pdb=" C HIS E 290 " ideal model delta sigma weight residual 113.30 104.73 8.57 1.34e+00 5.57e-01 4.09e+01 angle pdb=" C SER F 80 " pdb=" N PHE F 81 " pdb=" CA PHE F 81 " ideal model delta sigma weight residual 121.70 130.47 -8.77 1.80e+00 3.09e-01 2.37e+01 angle pdb=" CA SER E 80 " pdb=" C SER E 80 " pdb=" N PHE E 81 " ideal model delta sigma weight residual 116.50 123.62 -7.12 1.63e+00 3.76e-01 1.91e+01 ... (remaining 30661 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.94: 12775 34.94 - 69.89: 349 69.89 - 104.83: 19 104.83 - 139.77: 7 139.77 - 174.72: 4 Dihedral angle restraints: 13154 sinusoidal: 5597 harmonic: 7557 Sorted by residual: dihedral pdb=" CA SER E 80 " pdb=" C SER E 80 " pdb=" N PHE E 81 " pdb=" CA PHE E 81 " ideal model delta harmonic sigma weight residual 180.00 47.31 132.69 0 5.00e+00 4.00e-02 7.04e+02 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 36.34 -35.76 72.10 1 3.10e+00 1.04e-01 6.92e+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 23.64 -58.79 1 4.00e+00 6.25e-02 2.89e+02 ... (remaining 13151 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.030: 3567 1.030 - 2.059: 0 2.059 - 3.089: 0 3.089 - 4.119: 0 4.119 - 5.148: 2 Chirality restraints: 3569 Sorted by residual: chirality pdb=" C18 1N7 A1005 " pdb=" C17 1N7 A1005 " pdb=" C19 1N7 A1005 " pdb=" C6 1N7 A1005 " both_signs ideal model delta sigma weight residual False 2.53 -2.62 5.15 2.00e-01 2.50e+01 6.63e+02 chirality pdb=" C6 1N7 A1005 " pdb=" C18 1N7 A1005 " pdb=" C5 1N7 A1005 " pdb=" C7 1N7 A1005 " both_signs ideal model delta sigma weight residual False -2.43 2.67 -5.10 2.00e-01 2.50e+01 6.49e+02 chirality pdb=" C17 1N7 A1006 " pdb=" C16 1N7 A1006 " pdb=" C18 1N7 A1006 " pdb=" O3 1N7 A1006 " both_signs ideal model delta sigma weight residual False 2.40 2.81 -0.41 2.00e-01 2.50e+01 4.16e+00 ... (remaining 3566 not shown) Planarity restraints: 3621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 52 " 0.035 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO E 53 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO E 53 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 53 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS F 444 " -0.034 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO F 445 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO F 445 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 445 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 288 " -0.010 2.00e-02 2.50e+03 1.92e-02 3.68e+00 pdb=" C LYS E 288 " 0.033 2.00e-02 2.50e+03 pdb=" O LYS E 288 " -0.012 2.00e-02 2.50e+03 pdb=" N SER E 289 " -0.011 2.00e-02 2.50e+03 ... (remaining 3618 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 95 2.41 - 3.03: 12820 3.03 - 3.65: 33725 3.65 - 4.28: 51575 4.28 - 4.90: 84824 Nonbonded interactions: 183039 Sorted by model distance: nonbonded pdb="MG MG A1003 " pdb=" O1A ADP A1004 " model vdw 1.787 2.170 nonbonded pdb="MG MG E 705 " pdb=" F3 AF3 E 706 " model vdw 1.881 2.120 nonbonded pdb=" OD1 ASN A 209 " pdb="MG MG A1003 " model vdw 1.982 2.170 nonbonded pdb=" O2B ADP F1003 " pdb="MG MG F1004 " model vdw 1.985 2.170 nonbonded pdb="MG MG F1004 " pdb=" F3 AF3 F1005 " model vdw 2.032 2.120 ... (remaining 183034 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' and resid 1 through 706) 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.430 Check model and map are aligned: 0.100 Set scattering table: 0.040 Process input model: 26.040 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 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:9.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.899 22333 Z= 0.675 Angle : 0.776 15.478 30692 Z= 0.395 Chirality : 0.135 5.148 3569 Planarity : 0.004 0.052 3621 Dihedral : 15.089 174.718 8280 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 8.69 % Allowed : 8.83 % Favored : 82.48 % Cbeta Deviations : 0.00 % 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: -1.74 (0.16), residues: 2541 helix: -0.47 (0.16), residues: 999 sheet: -1.00 (0.29), residues: 295 loop : -1.74 (0.17), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 155 TYR 0.020 0.002 TYR F 224 PHE 0.017 0.002 PHE A 652 TRP 0.015 0.002 TRP A 916 HIS 0.010 0.001 HIS E 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00614 / 0.31 (22300) covalent geometry : angle 0.76271 / 0.39 (30666) hydrogen bonds : bond 0.15980 / 10.60 ( 935) hydrogen bonds : angle 6.04284 / 4.25 ( 2553) metal coordination : bond 0.01047 / 0.70 ( 32) metal coordination : angle 4.99589 / 3.45 ( 26) Misc. bond : bond 0.89949 / 47.34 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 278 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.7048 (mtp85) cc_final: 0.6504 (mtp-110) REVERT: A 31 VAL cc_start: 0.8497 (OUTLIER) cc_final: 0.8274 (m) REVERT: A 105 ARG cc_start: 0.7698 (ttm-80) cc_final: 0.7440 (ttm-80) REVERT: A 138 ASN cc_start: 0.8242 (t0) cc_final: 0.7949 (t0) REVERT: A 431 GLU cc_start: 0.7423 (tt0) cc_final: 0.7059 (mm-30) REVERT: A 553 ARG cc_start: 0.7975 (ptp-110) cc_final: 0.7438 (ttm-80) REVERT: A 807 LYS cc_start: 0.8494 (mtpp) cc_final: 0.8209 (mtpp) REVERT: A 811 GLU cc_start: 0.8107 (tt0) cc_final: 0.7703 (tt0) REVERT: A 818 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.8434 (ptp) REVERT: A 922 GLU cc_start: 0.7290 (tt0) cc_final: 0.6817 (tm-30) REVERT: B 51 ARG cc_start: 0.6043 (OUTLIER) cc_final: 0.5636 (tpm-80) REVERT: B 55 MET cc_start: 0.2588 (OUTLIER) cc_final: 0.1587 (mpp) REVERT: B 65 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7704 (mp10) REVERT: B 96 ARG cc_start: 0.6840 (mtp-110) cc_final: 0.6480 (mtm-85) REVERT: B 108 ASN cc_start: 0.7403 (m-40) cc_final: 0.6858 (m110) REVERT: B 112 ASP cc_start: 0.6932 (t0) cc_final: 0.6581 (t0) REVERT: B 155 GLU cc_start: 0.7435 (pt0) cc_final: 0.7077 (pt0) REVERT: C 38 ASP cc_start: 0.8059 (m-30) cc_final: 0.7722 (m-30) REVERT: D 43 ASN cc_start: 0.5684 (m-40) cc_final: 0.5179 (t0) REVERT: D 47 SER cc_start: 0.5592 (m) cc_final: 0.5387 (m) REVERT: D 56 GLN cc_start: 0.6222 (OUTLIER) cc_final: 0.5858 (pt0) REVERT: D 69 GLN cc_start: 0.7588 (tt0) cc_final: 0.6891 (tp40) REVERT: D 87 MET cc_start: 0.8144 (tpp) cc_final: 0.7923 (tpp) REVERT: D 155 GLU cc_start: 0.7522 (pt0) cc_final: 0.7232 (pt0) REVERT: D 189 LEU cc_start: 0.7866 (mt) cc_final: 0.7421 (mm) REVERT: E 156 GLU cc_start: 0.4251 (OUTLIER) cc_final: 0.3307 (tp30) REVERT: E 173 ARG cc_start: 0.7911 (mtm180) cc_final: 0.7506 (mpt90) REVERT: E 212 ARG cc_start: 0.6333 (ttp80) cc_final: 0.5536 (mmp80) REVERT: E 274 MET cc_start: 0.7145 (tpp) cc_final: 0.6926 (tpp) REVERT: E 349 ASN cc_start: 0.6424 (t0) cc_final: 0.6116 (p0) REVERT: E 359 THR cc_start: 0.8129 (OUTLIER) cc_final: 0.7883 (t) REVERT: E 365 GLU cc_start: 0.8246 (mt-10) cc_final: 0.8034 (mt-10) REVERT: E 394 LYS cc_start: 0.8426 (mptt) cc_final: 0.7901 (mtpp) REVERT: E 464 HIS cc_start: 0.5812 (t70) cc_final: 0.5467 (t-170) REVERT: E 480 ILE cc_start: 0.8319 (mt) cc_final: 0.8052 (pt) REVERT: E 497 ARG cc_start: 0.5861 (OUTLIER) cc_final: 0.4366 (ttt-90) REVERT: E 548 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7474 (tt0) REVERT: F 122 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7470 (pt) REVERT: F 129 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8460 (tpt90) REVERT: F 180 TYR cc_start: 0.6285 (m-80) cc_final: 0.5719 (m-10) REVERT: F 195 ILE cc_start: 0.1306 (OUTLIER) cc_final: 0.1087 (tt) REVERT: F 207 ASP cc_start: 0.4877 (OUTLIER) cc_final: 0.4629 (OUTLIER) REVERT: F 347 LYS cc_start: 0.3733 (OUTLIER) cc_final: 0.2691 (tppp) REVERT: F 360 VAL cc_start: 0.9123 (t) cc_final: 0.8921 (m) REVERT: F 437 PHE cc_start: 0.7076 (OUTLIER) cc_final: 0.6647 (t80) REVERT: F 546 PHE cc_start: 0.4379 (t80) cc_final: 0.4177 (t80) REVERT: F 584 LYS cc_start: 0.3857 (mmtt) cc_final: 0.3547 (mmtm) outliers start: 191 outliers final: 80 residues processed: 455 average time/residue: 0.4595 time to fit residues: 245.6242 Evaluate side-chains 322 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 227 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL 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 259 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 759 SER 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 A residue 870 THR Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 56 GLN 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 163 ASP Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 164 HIS Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 493 ILE Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain E residue 498 GLU Chi-restraints excluded: chain E residue 501 THR Chi-restraints excluded: chain E residue 525 ILE Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 548 GLN Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 129 ARG Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 177 ASN Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 460 LYS Chi-restraints excluded: chain F residue 499 PHE Chi-restraints excluded: chain F residue 526 LEU 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: 0.4980 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 258 optimal weight: 10.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 698 GLN A 789 GLN B 43 ASN D 65 GLN D 105 ASN E 404 GLN ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 537 GLN F 518 GLN F 531 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.165905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.134591 restraints weight = 33004.654| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.99 r_work: 0.3543 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22333 Z= 0.149 Angle : 0.665 14.332 30692 Z= 0.325 Chirality : 0.044 0.333 3569 Planarity : 0.004 0.054 3621 Dihedral : 12.658 167.945 3851 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 6.73 % Allowed : 13.15 % Favored : 80.12 % 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: -1.21 (0.16), residues: 2541 helix: 0.11 (0.16), residues: 1019 sheet: -0.79 (0.29), residues: 289 loop : -1.59 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 442 TYR 0.018 0.001 TYR F 224 PHE 0.018 0.002 PHE F 472 TRP 0.016 0.001 TRP F 506 HIS 0.007 0.001 HIS F 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (22300) covalent geometry : angle 0.65013 / 0.32 (30666) hydrogen bonds : bond 0.04474 / 3.04 ( 935) hydrogen bonds : angle 4.61773 / 3.31 ( 2553) metal coordination : bond 0.01092 / 0.70 ( 32) metal coordination : angle 4.83518 / 3.42 ( 26) Misc. bond : bond 0.00188 / 0.10 ( 1) *********************** 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 383 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 235 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: A 18 ARG cc_start: 0.6927 (mtp85) cc_final: 0.6456 (mtp-110) REVERT: A 31 VAL cc_start: 0.8456 (OUTLIER) cc_final: 0.8192 (m) REVERT: A 74 ARG cc_start: 0.8494 (ptp-170) cc_final: 0.8189 (ptp-170) REVERT: A 138 ASN cc_start: 0.8241 (t0) cc_final: 0.7929 (t0) REVERT: A 161 ASP cc_start: 0.8220 (p0) cc_final: 0.7597 (p0) REVERT: A 431 GLU cc_start: 0.7810 (tt0) cc_final: 0.7064 (mm-30) REVERT: A 451 SER cc_start: 0.8615 (m) cc_final: 0.8175 (p) REVERT: A 553 ARG cc_start: 0.8044 (ptp-110) cc_final: 0.7530 (ttm-80) REVERT: A 761 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.7745 (m-30) REVERT: A 773 GLN cc_start: 0.8419 (mt0) cc_final: 0.8141 (mt0) REVERT: A 807 LYS cc_start: 0.8155 (mtpp) cc_final: 0.7790 (mttm) REVERT: A 811 GLU cc_start: 0.8760 (tt0) cc_final: 0.8447 (tt0) REVERT: A 818 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.8604 (ptp) REVERT: A 922 GLU cc_start: 0.7775 (tt0) cc_final: 0.7227 (tm-30) REVERT: B 50 ASP cc_start: 0.6788 (p0) cc_final: 0.5728 (p0) REVERT: B 51 ARG cc_start: 0.5891 (OUTLIER) cc_final: 0.5677 (tpm-80) REVERT: B 56 GLN cc_start: 0.4057 (OUTLIER) cc_final: 0.3614 (tm-30) REVERT: B 96 ARG cc_start: 0.7287 (mtp-110) cc_final: 0.6732 (mtm-85) REVERT: B 108 ASN cc_start: 0.7334 (m-40) cc_final: 0.6852 (m110) REVERT: B 112 ASP cc_start: 0.7045 (t0) cc_final: 0.6595 (t0) REVERT: B 155 GLU cc_start: 0.7929 (pt0) cc_final: 0.7581 (pt0) REVERT: C 38 ASP cc_start: 0.8407 (m-30) cc_final: 0.8102 (m-30) REVERT: D 56 GLN cc_start: 0.6243 (OUTLIER) cc_final: 0.5969 (pt0) REVERT: D 69 GLN cc_start: 0.7868 (tt0) cc_final: 0.7089 (tp40) REVERT: D 87 MET cc_start: 0.8305 (tpp) cc_final: 0.7986 (tpp) REVERT: D 94 MET cc_start: 0.7761 (mtp) cc_final: 0.7506 (mtp) REVERT: D 155 GLU cc_start: 0.7545 (pt0) cc_final: 0.7209 (pt0) REVERT: D 189 LEU cc_start: 0.7628 (mt) cc_final: 0.7124 (mm) REVERT: E 155 ARG cc_start: 0.5867 (mmt90) cc_final: 0.4918 (mmm160) REVERT: E 156 GLU cc_start: 0.4621 (OUTLIER) cc_final: 0.3523 (tp30) REVERT: E 168 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6480 (tt0) REVERT: E 173 ARG cc_start: 0.8011 (mtm180) cc_final: 0.7285 (mpt90) REVERT: E 212 ARG cc_start: 0.6508 (ttp80) cc_final: 0.5539 (mmp80) REVERT: E 253 TYR cc_start: 0.8415 (m-80) cc_final: 0.8009 (m-10) REVERT: E 274 MET cc_start: 0.7757 (tpp) cc_final: 0.7471 (tpp) REVERT: E 349 ASN cc_start: 0.6773 (t0) cc_final: 0.6289 (p0) REVERT: E 365 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8375 (mt-10) REVERT: E 394 LYS cc_start: 0.8648 (mptt) cc_final: 0.8043 (mtpp) REVERT: E 464 HIS cc_start: 0.5719 (t70) cc_final: 0.5432 (t-170) REVERT: E 480 ILE cc_start: 0.8494 (mt) cc_final: 0.8115 (pt) REVERT: E 497 ARG cc_start: 0.5870 (OUTLIER) cc_final: 0.4293 (ttt-90) REVERT: F 122 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7584 (pt) REVERT: F 129 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8522 (tpt90) REVERT: F 180 TYR cc_start: 0.6012 (m-80) cc_final: 0.5407 (m-10) REVERT: F 195 ILE cc_start: 0.1409 (OUTLIER) cc_final: 0.1128 (tt) REVERT: F 232 VAL cc_start: 0.9361 (OUTLIER) cc_final: 0.9131 (m) REVERT: F 333 ILE cc_start: 0.8205 (mm) cc_final: 0.7964 (tp) REVERT: F 347 LYS cc_start: 0.4086 (OUTLIER) cc_final: 0.2984 (ttmt) REVERT: F 437 PHE cc_start: 0.7180 (OUTLIER) cc_final: 0.6770 (t80) REVERT: F 464 HIS cc_start: 0.5652 (OUTLIER) cc_final: 0.5342 (m-70) REVERT: F 492 GLN cc_start: 0.5536 (OUTLIER) cc_final: 0.5018 (tp-100) REVERT: F 549 THR cc_start: 0.4898 (m) cc_final: 0.4556 (m) outliers start: 148 outliers final: 74 residues processed: 358 average time/residue: 0.5129 time to fit residues: 214.0097 Evaluate side-chains 306 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 215 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 538 THR 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 818 MET Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 164 HIS Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 493 ILE Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain E residue 525 ILE Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 129 ARG Chi-restraints excluded: chain F residue 130 LEU 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 193 VAL Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 262 PHE Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 464 HIS Chi-restraints excluded: chain F residue 492 GLN Chi-restraints excluded: chain F residue 499 PHE Chi-restraints excluded: chain F residue 526 LEU 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: [5, 6, 12, 126, 30, 127, 233, 144, 232, 97, 104] chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 127 optimal weight: 0.9980 chunk 233 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 chunk 232 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 104 optimal weight: 0.0770 overall best weight: 1.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 497 ASN C 18 GLN E 9 ASN E 492 GLN F 265 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.165090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.133678 restraints weight = 33057.802| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.00 r_work: 0.3519 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22333 Z= 0.171 Angle : 0.660 14.659 30692 Z= 0.322 Chirality : 0.044 0.324 3569 Planarity : 0.004 0.052 3621 Dihedral : 11.892 154.739 3798 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 7.14 % Allowed : 14.47 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.08 (0.16), residues: 2541 helix: 0.28 (0.17), residues: 1021 sheet: -0.79 (0.29), residues: 292 loop : -1.56 (0.17), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 57 TYR 0.032 0.001 TYR F 543 PHE 0.017 0.002 PHE A 741 TRP 0.016 0.002 TRP F 167 HIS 0.008 0.001 HIS F 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (22300) covalent geometry : angle 0.64607 / 0.32 (30666) hydrogen bonds : bond 0.04394 / 2.97 ( 935) hydrogen bonds : angle 4.48064 / 3.23 ( 2553) metal coordination : bond 0.00993 / 0.64 ( 32) metal coordination : angle 4.73196 / 3.35 ( 26) Misc. bond : bond 0.00068 / 0.04 ( 1) *********************** 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 402 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 245 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.7044 (mtp85) cc_final: 0.6574 (mtp-110) REVERT: A 31 VAL cc_start: 0.8503 (OUTLIER) cc_final: 0.8252 (m) REVERT: A 74 ARG cc_start: 0.8582 (ptp-170) cc_final: 0.8193 (ptp-170) REVERT: A 138 ASN cc_start: 0.8260 (t0) cc_final: 0.7920 (t0) REVERT: A 431 GLU cc_start: 0.7830 (tt0) cc_final: 0.7093 (mm-30) REVERT: A 451 SER cc_start: 0.8594 (m) cc_final: 0.8181 (p) REVERT: A 553 ARG cc_start: 0.8068 (ptp-110) cc_final: 0.7551 (ttm-80) REVERT: A 658 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7509 (tt0) REVERT: A 668 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8477 (tpt) REVERT: A 761 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.7881 (m-30) REVERT: A 773 GLN cc_start: 0.8340 (mt0) cc_final: 0.8076 (mt0) REVERT: A 807 LYS cc_start: 0.8234 (mtpp) cc_final: 0.7952 (mttm) REVERT: A 811 GLU cc_start: 0.8759 (tt0) cc_final: 0.8448 (tt0) REVERT: A 922 GLU cc_start: 0.7844 (tt0) cc_final: 0.7334 (tt0) REVERT: B 50 ASP cc_start: 0.6664 (p0) cc_final: 0.6462 (t0) REVERT: B 51 ARG cc_start: 0.6112 (OUTLIER) cc_final: 0.5681 (tpm-80) REVERT: B 55 MET cc_start: 0.2553 (tpp) cc_final: 0.2212 (mpp) REVERT: B 56 GLN cc_start: 0.4225 (OUTLIER) cc_final: 0.3766 (tm-30) REVERT: B 96 ARG cc_start: 0.7346 (mtp-110) cc_final: 0.6807 (mtm-85) REVERT: B 108 ASN cc_start: 0.7363 (m-40) cc_final: 0.6891 (m110) REVERT: B 112 ASP cc_start: 0.7070 (t0) cc_final: 0.6628 (t0) REVERT: B 155 GLU cc_start: 0.8018 (pt0) cc_final: 0.7685 (pt0) REVERT: C 38 ASP cc_start: 0.8453 (m-30) cc_final: 0.8147 (m-30) REVERT: D 43 ASN cc_start: 0.5638 (m-40) cc_final: 0.5156 (t0) REVERT: D 56 GLN cc_start: 0.6316 (OUTLIER) cc_final: 0.6041 (pt0) REVERT: D 69 GLN cc_start: 0.7923 (tt0) cc_final: 0.7128 (tp40) REVERT: D 70 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.7940 (ttm) REVERT: D 87 MET cc_start: 0.8392 (tpp) cc_final: 0.8019 (tpp) REVERT: D 94 MET cc_start: 0.7875 (mtp) cc_final: 0.7572 (mtp) REVERT: D 155 GLU cc_start: 0.7593 (pt0) cc_final: 0.7237 (pt0) REVERT: D 189 LEU cc_start: 0.7702 (mt) cc_final: 0.7182 (mm) REVERT: E 156 GLU cc_start: 0.4714 (OUTLIER) cc_final: 0.3599 (tp30) REVERT: E 168 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.6470 (tt0) REVERT: E 173 ARG cc_start: 0.8008 (mtm180) cc_final: 0.7284 (mpt90) REVERT: E 212 ARG cc_start: 0.6584 (ttp80) cc_final: 0.5526 (mmp80) REVERT: E 253 TYR cc_start: 0.8491 (m-80) cc_final: 0.8090 (m-10) REVERT: E 274 MET cc_start: 0.7863 (tpp) cc_final: 0.7555 (tpp) REVERT: E 349 ASN cc_start: 0.6854 (t0) cc_final: 0.6430 (p0) REVERT: E 392 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.6896 (tmm-80) REVERT: E 394 LYS cc_start: 0.8673 (mptt) cc_final: 0.8175 (mtpp) REVERT: E 404 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.5855 (mp10) REVERT: E 464 HIS cc_start: 0.5634 (t70) cc_final: 0.5365 (t-170) REVERT: E 480 ILE cc_start: 0.8550 (mt) cc_final: 0.8177 (pt) REVERT: E 497 ARG cc_start: 0.5900 (OUTLIER) cc_final: 0.4333 (ttt-90) REVERT: F 122 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7665 (pt) REVERT: F 129 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8431 (tpt90) REVERT: F 195 ILE cc_start: 0.1241 (OUTLIER) cc_final: 0.1032 (tt) REVERT: F 333 ILE cc_start: 0.8216 (mm) cc_final: 0.7923 (tp) REVERT: F 347 LYS cc_start: 0.4335 (OUTLIER) cc_final: 0.3152 (tppp) REVERT: F 437 PHE cc_start: 0.7163 (OUTLIER) cc_final: 0.6822 (t80) REVERT: F 492 GLN cc_start: 0.5484 (OUTLIER) cc_final: 0.5023 (tp-100) REVERT: F 549 THR cc_start: 0.5164 (m) cc_final: 0.4814 (m) REVERT: F 558 VAL cc_start: 0.7341 (OUTLIER) cc_final: 0.7094 (t) outliers start: 157 outliers final: 83 residues processed: 376 average time/residue: 0.5249 time to fit residues: 229.6654 Evaluate side-chains 334 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 231 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 668 MET 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 B residue 33 VAL Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 128 LEU 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 167 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 164 HIS Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 392 ARG Chi-restraints excluded: chain E residue 404 GLN Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain E residue 498 GLU Chi-restraints excluded: chain E residue 525 ILE Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 129 ARG Chi-restraints excluded: chain F residue 130 LEU 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 193 VAL Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 262 PHE Chi-restraints excluded: chain F residue 329 LYS Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 492 GLN Chi-restraints excluded: chain F residue 499 PHE Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 558 VAL Chi-restraints excluded: chain F residue 588 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: [222, 129, 149, 120, 134, 240, 145, 186, 48, 49, 6] chunk 222 optimal weight: 0.0570 chunk 129 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 240 optimal weight: 0.0770 chunk 145 optimal weight: 1.9990 chunk 186 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.0060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 18 GLN D 105 ASN E 531 GLN F 177 ASN F 265 ASN F 531 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.166306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.134829 restraints weight = 33190.185| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.01 r_work: 0.3547 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22333 Z= 0.140 Angle : 0.634 14.447 30692 Z= 0.307 Chirality : 0.044 0.319 3569 Planarity : 0.004 0.039 3621 Dihedral : 11.513 150.847 3791 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 6.05 % Allowed : 16.79 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.92 (0.16), residues: 2541 helix: 0.44 (0.17), residues: 1014 sheet: -0.72 (0.29), residues: 298 loop : -1.47 (0.17), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 442 TYR 0.018 0.001 TYR F 224 PHE 0.023 0.001 PHE F 262 TRP 0.016 0.001 TRP F 167 HIS 0.007 0.001 HIS F 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (22300) covalent geometry : angle 0.61983 / 0.31 (30666) hydrogen bonds : bond 0.04014 / 2.73 ( 935) hydrogen bonds : angle 4.36177 / 3.17 ( 2553) metal coordination : bond 0.00712 / 0.47 ( 32) metal coordination : angle 4.62172 / 3.29 ( 26) Misc. bond : bond 0.00015 / 0.01 ( 1) *********************** 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 375 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 242 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.7018 (mtp85) cc_final: 0.6586 (mtp180) REVERT: A 31 VAL cc_start: 0.8420 (OUTLIER) cc_final: 0.8150 (m) REVERT: A 74 ARG cc_start: 0.8583 (ptp-170) cc_final: 0.8157 (ptp-170) REVERT: A 138 ASN cc_start: 0.8211 (t0) cc_final: 0.7892 (t0) REVERT: A 408 GLN cc_start: 0.8784 (tt0) cc_final: 0.8565 (tt0) REVERT: A 431 GLU cc_start: 0.7815 (tt0) cc_final: 0.7072 (mm-30) REVERT: A 451 SER cc_start: 0.8503 (m) cc_final: 0.8115 (p) REVERT: A 553 ARG cc_start: 0.8022 (ptp-110) cc_final: 0.7511 (ttm-80) REVERT: A 566 MET cc_start: 0.8432 (mtp) cc_final: 0.8088 (mtm) REVERT: A 666 MET cc_start: 0.8572 (mmt) cc_final: 0.8353 (mmt) REVERT: A 668 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8462 (tpt) REVERT: A 773 GLN cc_start: 0.8291 (mt0) cc_final: 0.8068 (mt0) REVERT: A 807 LYS cc_start: 0.8145 (mtpp) cc_final: 0.7865 (mttm) REVERT: A 811 GLU cc_start: 0.8722 (tt0) cc_final: 0.8396 (tt0) REVERT: B 50 ASP cc_start: 0.6741 (p0) cc_final: 0.6379 (t0) REVERT: B 51 ARG cc_start: 0.6147 (OUTLIER) cc_final: 0.5649 (tpm-80) REVERT: B 55 MET cc_start: 0.2754 (tpp) cc_final: 0.2382 (mpp) REVERT: B 56 GLN cc_start: 0.3697 (OUTLIER) cc_final: 0.3381 (tm-30) REVERT: B 65 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7741 (mp10) REVERT: B 96 ARG cc_start: 0.7149 (mtp-110) cc_final: 0.6629 (mtm-85) REVERT: B 108 ASN cc_start: 0.7337 (m-40) cc_final: 0.6848 (m110) REVERT: B 112 ASP cc_start: 0.7058 (t0) cc_final: 0.6610 (t0) REVERT: B 155 GLU cc_start: 0.7949 (pt0) cc_final: 0.7631 (pt0) REVERT: C 38 ASP cc_start: 0.8378 (m-30) cc_final: 0.8054 (m-30) REVERT: D 43 ASN cc_start: 0.5526 (m-40) cc_final: 0.5060 (t0) REVERT: D 56 GLN cc_start: 0.6228 (OUTLIER) cc_final: 0.5981 (pt0) REVERT: D 69 GLN cc_start: 0.7855 (tt0) cc_final: 0.7057 (tp40) REVERT: D 70 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.7903 (ttm) REVERT: D 87 MET cc_start: 0.8329 (tpp) cc_final: 0.7961 (tpp) REVERT: D 94 MET cc_start: 0.7785 (mtp) cc_final: 0.7541 (mtp) REVERT: D 155 GLU cc_start: 0.7494 (pt0) cc_final: 0.7151 (pt0) REVERT: D 189 LEU cc_start: 0.7582 (mt) cc_final: 0.7079 (mm) REVERT: E 155 ARG cc_start: 0.5873 (mmt90) cc_final: 0.4897 (mmt180) REVERT: E 156 GLU cc_start: 0.4628 (OUTLIER) cc_final: 0.3547 (tp30) REVERT: E 168 GLU cc_start: 0.6651 (OUTLIER) cc_final: 0.6412 (tt0) REVERT: E 173 ARG cc_start: 0.7994 (mtm180) cc_final: 0.7255 (mpt90) REVERT: E 349 ASN cc_start: 0.6836 (t0) cc_final: 0.6453 (p0) REVERT: E 392 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.6805 (tmm-80) REVERT: E 394 LYS cc_start: 0.8676 (mptt) cc_final: 0.8154 (mtpp) REVERT: E 404 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.5610 (mp10) REVERT: E 464 HIS cc_start: 0.5413 (t70) cc_final: 0.4822 (t-90) REVERT: E 480 ILE cc_start: 0.8563 (mt) cc_final: 0.8235 (pt) REVERT: E 497 ARG cc_start: 0.5956 (OUTLIER) cc_final: 0.4390 (ttt-90) REVERT: F 180 TYR cc_start: 0.5300 (m-10) cc_final: 0.4967 (m-80) REVERT: F 333 ILE cc_start: 0.8264 (mm) cc_final: 0.7938 (tp) REVERT: F 347 LYS cc_start: 0.3963 (OUTLIER) cc_final: 0.2822 (tppp) REVERT: F 437 PHE cc_start: 0.7158 (OUTLIER) cc_final: 0.6813 (t80) REVERT: F 464 HIS cc_start: 0.5275 (OUTLIER) cc_final: 0.4946 (m-70) REVERT: F 492 GLN cc_start: 0.5412 (OUTLIER) cc_final: 0.4953 (tp-100) REVERT: F 549 THR cc_start: 0.5116 (m) cc_final: 0.4812 (m) outliers start: 133 outliers final: 78 residues processed: 354 average time/residue: 0.4997 time to fit residues: 207.2739 Evaluate side-chains 309 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 215 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 164 HIS Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 346 PHE Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 392 ARG Chi-restraints excluded: chain E residue 404 GLN Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain E residue 498 GLU Chi-restraints excluded: chain E residue 525 ILE Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 130 LEU 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 188 THR Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 464 HIS Chi-restraints excluded: chain F residue 492 GLN Chi-restraints excluded: chain F residue 499 PHE Chi-restraints excluded: chain F residue 526 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: [13, 72, 239, 121, 246, 193, 101, 4, 157, 76, 8] chunk 13 optimal weight: 0.0770 chunk 72 optimal weight: 3.9990 chunk 239 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 246 optimal weight: 5.9990 chunk 193 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 157 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 65 GLN D 105 ASN D 136 ASN F 177 ASN F 265 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.165766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.134564 restraints weight = 33414.113| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.89 r_work: 0.3547 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 22333 Z= 0.190 Angle : 0.668 14.683 30692 Z= 0.323 Chirality : 0.045 0.323 3569 Planarity : 0.004 0.039 3621 Dihedral : 11.376 163.366 3775 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 6.82 % Allowed : 16.65 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.94 (0.16), residues: 2541 helix: 0.38 (0.17), residues: 1022 sheet: -0.76 (0.29), residues: 295 loop : -1.44 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 57 TYR 0.020 0.002 TYR F 224 PHE 0.028 0.002 PHE F 262 TRP 0.016 0.001 TRP F 167 HIS 0.008 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (22300) covalent geometry : angle 0.65306 / 0.32 (30666) hydrogen bonds : bond 0.04268 / 2.88 ( 935) hydrogen bonds : angle 4.41285 / 3.19 ( 2553) metal coordination : bond 0.01062 / 0.68 ( 32) metal coordination : angle 4.81879 / 3.42 ( 26) Misc. bond : bond 0.00031 / 0.02 ( 1) *********************** 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 374 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 224 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.7225 (mtp85) cc_final: 0.6767 (mtp180) REVERT: A 31 VAL cc_start: 0.8681 (OUTLIER) cc_final: 0.8424 (m) REVERT: A 74 ARG cc_start: 0.8684 (ptp-170) cc_final: 0.8239 (ptp-170) REVERT: A 138 ASN cc_start: 0.8423 (t0) cc_final: 0.8091 (t0) REVERT: A 431 GLU cc_start: 0.7816 (tt0) cc_final: 0.7149 (mm-30) REVERT: A 451 SER cc_start: 0.8818 (m) cc_final: 0.8445 (p) REVERT: A 553 ARG cc_start: 0.8189 (ptp-110) cc_final: 0.7689 (ttm-80) REVERT: A 566 MET cc_start: 0.8791 (mtp) cc_final: 0.8435 (mtm) REVERT: A 668 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8600 (tpt) REVERT: A 773 GLN cc_start: 0.8530 (mt0) cc_final: 0.8237 (mt0) REVERT: A 807 LYS cc_start: 0.8419 (mtpp) cc_final: 0.8143 (mttm) REVERT: A 811 GLU cc_start: 0.8715 (tt0) cc_final: 0.8435 (tt0) REVERT: B 51 ARG cc_start: 0.6262 (OUTLIER) cc_final: 0.5615 (tpm-80) REVERT: B 55 MET cc_start: 0.3115 (tpp) cc_final: 0.2896 (mpp) REVERT: B 56 GLN cc_start: 0.3765 (OUTLIER) cc_final: 0.3558 (tm-30) REVERT: B 65 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7957 (mp10) REVERT: B 96 ARG cc_start: 0.7455 (mtp-110) cc_final: 0.6946 (mtm-85) REVERT: B 108 ASN cc_start: 0.7599 (m-40) cc_final: 0.7092 (m110) REVERT: B 112 ASP cc_start: 0.7176 (t0) cc_final: 0.6777 (t0) REVERT: B 155 GLU cc_start: 0.8120 (pt0) cc_final: 0.7816 (pt0) REVERT: C 38 ASP cc_start: 0.8618 (m-30) cc_final: 0.8264 (m-30) REVERT: D 56 GLN cc_start: 0.6502 (OUTLIER) cc_final: 0.6271 (pt0) REVERT: D 69 GLN cc_start: 0.8063 (tt0) cc_final: 0.7281 (tp40) REVERT: D 70 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8013 (ttm) REVERT: D 87 MET cc_start: 0.8585 (tpp) cc_final: 0.8208 (tpp) REVERT: D 94 MET cc_start: 0.8140 (mtp) cc_final: 0.7936 (mtp) REVERT: D 155 GLU cc_start: 0.7623 (pt0) cc_final: 0.7286 (pt0) REVERT: D 168 GLN cc_start: 0.7732 (mp10) cc_final: 0.6807 (mm110) REVERT: D 189 LEU cc_start: 0.7917 (mt) cc_final: 0.7445 (mm) REVERT: E 155 ARG cc_start: 0.5852 (mmt90) cc_final: 0.4968 (mmt180) REVERT: E 156 GLU cc_start: 0.4759 (OUTLIER) cc_final: 0.3610 (tp30) REVERT: E 168 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.6457 (tt0) REVERT: E 173 ARG cc_start: 0.7954 (mtm180) cc_final: 0.7357 (mpt90) REVERT: E 178 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7747 (ttp80) REVERT: E 349 ASN cc_start: 0.6906 (t0) cc_final: 0.6658 (p0) REVERT: E 394 LYS cc_start: 0.8658 (mptt) cc_final: 0.8164 (mtpp) REVERT: E 404 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.5810 (mp10) REVERT: E 464 HIS cc_start: 0.5437 (t70) cc_final: 0.4823 (t-90) REVERT: E 480 ILE cc_start: 0.8604 (mt) cc_final: 0.8294 (pt) REVERT: E 497 ARG cc_start: 0.6120 (OUTLIER) cc_final: 0.4532 (ttt-90) REVERT: E 531 GLN cc_start: 0.8425 (tp40) cc_final: 0.8001 (tp-100) REVERT: F 177 ASN cc_start: 0.1365 (OUTLIER) cc_final: 0.0626 (p0) REVERT: F 180 TYR cc_start: 0.5564 (m-10) cc_final: 0.5276 (m-80) REVERT: F 333 ILE cc_start: 0.8261 (mm) cc_final: 0.7949 (tp) REVERT: F 347 LYS cc_start: 0.4026 (OUTLIER) cc_final: 0.2843 (tppp) REVERT: F 437 PHE cc_start: 0.7297 (OUTLIER) cc_final: 0.7005 (t80) REVERT: F 464 HIS cc_start: 0.5506 (OUTLIER) cc_final: 0.5169 (m-70) REVERT: F 492 GLN cc_start: 0.5518 (OUTLIER) cc_final: 0.5292 (tp40) REVERT: F 549 THR cc_start: 0.5100 (m) cc_final: 0.4808 (m) REVERT: F 558 VAL cc_start: 0.7575 (OUTLIER) cc_final: 0.7359 (t) outliers start: 150 outliers final: 94 residues processed: 349 average time/residue: 0.5232 time to fit residues: 212.8155 Evaluate side-chains 333 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 221 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 164 HIS Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 225 PHE Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 346 PHE Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 404 GLN Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain E residue 498 GLU Chi-restraints excluded: chain E residue 525 ILE Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 130 LEU 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 188 THR Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 329 LYS Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 464 HIS Chi-restraints excluded: chain F residue 492 GLN Chi-restraints excluded: chain F residue 499 PHE Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 558 VAL Chi-restraints excluded: chain F residue 581 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: [200, 55, 207, 187, 107, 226, 227, 3, 41, 211, 94] chunk 200 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 207 optimal weight: 0.8980 chunk 187 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 226 optimal weight: 0.7980 chunk 227 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 211 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 408 GLN D 65 GLN D 136 ASN F 177 ASN F 531 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.167556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.136334 restraints weight = 33443.260| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.90 r_work: 0.3571 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22333 Z= 0.134 Angle : 0.638 14.289 30692 Z= 0.308 Chirality : 0.044 0.318 3569 Planarity : 0.004 0.038 3621 Dihedral : 11.205 169.397 3775 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 5.78 % Allowed : 17.70 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.17), residues: 2541 helix: 0.51 (0.17), residues: 1016 sheet: -0.71 (0.29), residues: 299 loop : -1.36 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 57 TYR 0.018 0.001 TYR F 224 PHE 0.023 0.001 PHE F 262 TRP 0.023 0.001 TRP F 506 HIS 0.007 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (22300) covalent geometry : angle 0.62343 / 0.31 (30666) hydrogen bonds : bond 0.03931 / 2.68 ( 935) hydrogen bonds : angle 4.32344 / 3.13 ( 2553) metal coordination : bond 0.00655 / 0.44 ( 32) metal coordination : angle 4.72109 / 3.31 ( 26) Misc. bond : bond 0.00045 / 0.02 ( 1) *********************** 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 355 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 228 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: A 18 ARG cc_start: 0.7217 (mtp85) cc_final: 0.6768 (mtp180) REVERT: A 31 VAL cc_start: 0.8677 (OUTLIER) cc_final: 0.8417 (m) REVERT: A 74 ARG cc_start: 0.8685 (ptp-170) cc_final: 0.8287 (ptp-170) REVERT: A 138 ASN cc_start: 0.8430 (t0) cc_final: 0.8133 (t0) REVERT: A 431 GLU cc_start: 0.7828 (tt0) cc_final: 0.7177 (mm-30) REVERT: A 451 SER cc_start: 0.8834 (m) cc_final: 0.8495 (p) REVERT: A 553 ARG cc_start: 0.8198 (ptp-110) cc_final: 0.7707 (ttm-80) REVERT: A 666 MET cc_start: 0.8629 (mmt) cc_final: 0.8416 (mmt) REVERT: A 668 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8568 (tpt) REVERT: A 761 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.7822 (m-30) REVERT: A 773 GLN cc_start: 0.8585 (mt0) cc_final: 0.8300 (mt0) REVERT: A 807 LYS cc_start: 0.8482 (mtpp) cc_final: 0.8169 (mttm) REVERT: A 811 GLU cc_start: 0.8721 (tt0) cc_final: 0.8458 (tt0) REVERT: B 51 ARG cc_start: 0.6236 (OUTLIER) cc_final: 0.5670 (tpm-80) REVERT: B 56 GLN cc_start: 0.3767 (OUTLIER) cc_final: 0.3524 (tm-30) REVERT: B 65 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7976 (mp10) REVERT: B 96 ARG cc_start: 0.7329 (mtp-110) cc_final: 0.6830 (mtm-85) REVERT: B 108 ASN cc_start: 0.7629 (m-40) cc_final: 0.7129 (m110) REVERT: B 112 ASP cc_start: 0.7138 (t0) cc_final: 0.6732 (t0) REVERT: B 155 GLU cc_start: 0.8144 (pt0) cc_final: 0.7826 (pt0) REVERT: D 43 ASN cc_start: 0.5862 (m-40) cc_final: 0.5358 (t0) REVERT: D 56 GLN cc_start: 0.6538 (OUTLIER) cc_final: 0.6284 (pt0) REVERT: D 69 GLN cc_start: 0.8089 (tt0) cc_final: 0.7321 (tp40) REVERT: D 70 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8045 (ttm) REVERT: D 87 MET cc_start: 0.8604 (tpp) cc_final: 0.8223 (tpp) REVERT: D 94 MET cc_start: 0.8154 (mtp) cc_final: 0.7950 (mtp) REVERT: D 155 GLU cc_start: 0.7662 (pt0) cc_final: 0.7353 (pt0) REVERT: D 168 GLN cc_start: 0.7793 (mp10) cc_final: 0.6851 (mm110) REVERT: D 189 LEU cc_start: 0.7968 (mt) cc_final: 0.7533 (mm) REVERT: E 155 ARG cc_start: 0.5770 (mmt90) cc_final: 0.5000 (mmt180) REVERT: E 156 GLU cc_start: 0.4629 (OUTLIER) cc_final: 0.3564 (tp30) REVERT: E 168 GLU cc_start: 0.6661 (OUTLIER) cc_final: 0.6442 (tt0) REVERT: E 173 ARG cc_start: 0.7927 (mtm180) cc_final: 0.7370 (mpt90) REVERT: E 178 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7669 (ttp80) REVERT: E 253 TYR cc_start: 0.8367 (m-80) cc_final: 0.8022 (m-10) REVERT: E 349 ASN cc_start: 0.6947 (t0) cc_final: 0.6702 (p0) REVERT: E 392 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.6929 (tmm-80) REVERT: E 394 LYS cc_start: 0.8620 (mptt) cc_final: 0.8180 (mtpp) REVERT: E 404 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.5890 (mp10) REVERT: E 420 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8711 (pm20) REVERT: E 464 HIS cc_start: 0.5462 (t70) cc_final: 0.4703 (t-90) REVERT: E 480 ILE cc_start: 0.8557 (mt) cc_final: 0.8271 (pt) REVERT: E 497 ARG cc_start: 0.6091 (OUTLIER) cc_final: 0.4551 (ttt-90) REVERT: E 531 GLN cc_start: 0.8385 (tp40) cc_final: 0.7954 (tp-100) REVERT: F 122 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7536 (pp) REVERT: F 177 ASN cc_start: 0.0979 (OUTLIER) cc_final: 0.0454 (p0) REVERT: F 180 TYR cc_start: 0.5431 (m-10) cc_final: 0.5179 (m-80) REVERT: F 256 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.7070 (pp) REVERT: F 333 ILE cc_start: 0.8204 (mm) cc_final: 0.7944 (tp) REVERT: F 347 LYS cc_start: 0.3895 (OUTLIER) cc_final: 0.2816 (tppp) REVERT: F 438 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.6618 (pp) REVERT: F 492 GLN cc_start: 0.5380 (OUTLIER) cc_final: 0.5172 (tp40) REVERT: F 546 PHE cc_start: 0.5001 (t80) cc_final: 0.4569 (t80) REVERT: F 549 THR cc_start: 0.5087 (m) cc_final: 0.4796 (m) outliers start: 127 outliers final: 80 residues processed: 332 average time/residue: 0.5362 time to fit residues: 207.0930 Evaluate side-chains 316 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 215 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 164 HIS Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 346 PHE Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 392 ARG Chi-restraints excluded: chain E residue 404 GLN Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 420 GLU Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain E residue 498 GLU Chi-restraints excluded: chain E residue 525 ILE Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 130 LEU 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 188 THR Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 492 GLN Chi-restraints excluded: chain F residue 499 PHE Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 588 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: [156, 97, 75, 113, 230, 71, 6, 7, 104, 122, 257] chunk 156 optimal weight: 7.9990 chunk 97 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 230 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 104 optimal weight: 0.1980 chunk 122 optimal weight: 1.9990 chunk 257 optimal weight: 8.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 408 GLN A 613 HIS D 65 GLN D 136 ASN F 177 ASN F 531 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.167022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.135639 restraints weight = 33521.099| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.96 r_work: 0.3558 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22333 Z= 0.158 Angle : 0.658 14.433 30692 Z= 0.316 Chirality : 0.045 0.319 3569 Planarity : 0.004 0.038 3621 Dihedral : 11.098 175.807 3768 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 5.87 % Allowed : 18.06 % Favored : 76.07 % 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: -0.76 (0.17), residues: 2541 helix: 0.50 (0.17), residues: 1018 sheet: -0.65 (0.29), residues: 291 loop : -1.31 (0.18), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 442 TYR 0.019 0.001 TYR F 224 PHE 0.025 0.002 PHE D 15 TRP 0.021 0.002 TRP F 167 HIS 0.007 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (22300) covalent geometry : angle 0.64401 / 0.32 (30666) hydrogen bonds : bond 0.04023 / 2.73 ( 935) hydrogen bonds : angle 4.31496 / 3.12 ( 2553) metal coordination : bond 0.00820 / 0.53 ( 32) metal coordination : angle 4.75662 / 3.35 ( 26) Misc. bond : bond 0.00249 / 0.13 ( 1) *********************** 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 353 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 224 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.7182 (mtp85) cc_final: 0.6752 (mtp180) REVERT: A 31 VAL cc_start: 0.8627 (OUTLIER) cc_final: 0.8364 (m) REVERT: A 74 ARG cc_start: 0.8678 (ptp-170) cc_final: 0.8262 (ptp-170) REVERT: A 138 ASN cc_start: 0.8408 (t0) cc_final: 0.8083 (t0) REVERT: A 338 VAL cc_start: 0.8318 (p) cc_final: 0.8115 (m) REVERT: A 431 GLU cc_start: 0.7886 (tt0) cc_final: 0.7220 (mm-30) REVERT: A 451 SER cc_start: 0.8772 (m) cc_final: 0.8424 (p) REVERT: A 553 ARG cc_start: 0.8154 (ptp-110) cc_final: 0.7658 (ttm-80) REVERT: A 666 MET cc_start: 0.8623 (mmt) cc_final: 0.8402 (mmt) REVERT: A 668 MET cc_start: 0.9022 (OUTLIER) cc_final: 0.8561 (tpt) REVERT: A 761 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.7867 (m-30) REVERT: A 807 LYS cc_start: 0.8386 (mtpp) cc_final: 0.8072 (mttm) REVERT: A 811 GLU cc_start: 0.8724 (tt0) cc_final: 0.8441 (tt0) REVERT: B 51 ARG cc_start: 0.5925 (OUTLIER) cc_final: 0.5552 (tpm-80) REVERT: B 65 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7918 (mp10) REVERT: B 96 ARG cc_start: 0.7282 (mtp-110) cc_final: 0.6778 (mtm-85) REVERT: B 108 ASN cc_start: 0.7605 (m-40) cc_final: 0.7100 (m110) REVERT: B 112 ASP cc_start: 0.7101 (t0) cc_final: 0.6692 (t0) REVERT: B 155 GLU cc_start: 0.8120 (pt0) cc_final: 0.7796 (pt0) REVERT: D 43 ASN cc_start: 0.5873 (m-40) cc_final: 0.5397 (t0) REVERT: D 56 GLN cc_start: 0.6439 (OUTLIER) cc_final: 0.6119 (pt0) REVERT: D 69 GLN cc_start: 0.8049 (tt0) cc_final: 0.7266 (tp40) REVERT: D 70 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8010 (ttm) REVERT: D 87 MET cc_start: 0.8614 (tpp) cc_final: 0.8237 (tpp) REVERT: D 155 GLU cc_start: 0.7585 (pt0) cc_final: 0.7205 (pt0) REVERT: D 168 GLN cc_start: 0.7728 (mp10) cc_final: 0.6787 (mm110) REVERT: D 189 LEU cc_start: 0.7871 (mt) cc_final: 0.7387 (mm) REVERT: E 156 GLU cc_start: 0.4622 (OUTLIER) cc_final: 0.3517 (tp30) REVERT: E 168 GLU cc_start: 0.6636 (OUTLIER) cc_final: 0.6399 (tt0) REVERT: E 173 ARG cc_start: 0.7951 (mtm180) cc_final: 0.7394 (mpt180) REVERT: E 178 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7668 (ttp80) REVERT: E 253 TYR cc_start: 0.8415 (m-80) cc_final: 0.8084 (m-10) REVERT: E 349 ASN cc_start: 0.7000 (t0) cc_final: 0.6721 (p0) REVERT: E 394 LYS cc_start: 0.8639 (mptt) cc_final: 0.8117 (mtpp) REVERT: E 404 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.5877 (mp10) REVERT: E 464 HIS cc_start: 0.5420 (t70) cc_final: 0.4633 (t-90) REVERT: E 480 ILE cc_start: 0.8650 (mt) cc_final: 0.8337 (pt) REVERT: E 497 ARG cc_start: 0.6085 (OUTLIER) cc_final: 0.4517 (ttt-90) REVERT: E 531 GLN cc_start: 0.8385 (tp40) cc_final: 0.7900 (tp-100) REVERT: F 122 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7617 (pp) REVERT: F 177 ASN cc_start: 0.0931 (OUTLIER) cc_final: 0.0448 (OUTLIER) REVERT: F 180 TYR cc_start: 0.5352 (m-10) cc_final: 0.5093 (m-80) REVERT: F 333 ILE cc_start: 0.8204 (mm) cc_final: 0.7973 (tp) REVERT: F 347 LYS cc_start: 0.3885 (OUTLIER) cc_final: 0.2804 (tppp) REVERT: F 438 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.7015 (pp) REVERT: F 492 GLN cc_start: 0.5455 (OUTLIER) cc_final: 0.5227 (tp40) REVERT: F 543 TYR cc_start: 0.4991 (m-10) cc_final: 0.4248 (m-10) REVERT: F 546 PHE cc_start: 0.5068 (t80) cc_final: 0.4680 (t80) REVERT: F 549 THR cc_start: 0.5178 (m) cc_final: 0.4887 (m) outliers start: 129 outliers final: 85 residues processed: 329 average time/residue: 0.5287 time to fit residues: 201.6436 Evaluate side-chains 324 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 223 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 164 HIS Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 225 PHE Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 346 PHE Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 404 GLN Chi-restraints excluded: chain E residue 420 GLU Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain E residue 498 GLU Chi-restraints excluded: chain E residue 525 ILE Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 581 LEU Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 130 LEU 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 188 THR Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 492 GLN Chi-restraints excluded: chain F residue 499 PHE Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 581 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: [199, 226, 92, 169, 37, 176, 257, 113, 244, 138, 153] chunk 199 optimal weight: 3.9990 chunk 226 optimal weight: 0.6980 chunk 92 optimal weight: 0.0370 chunk 169 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 176 optimal weight: 4.9990 chunk 257 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 244 optimal weight: 0.0060 chunk 138 optimal weight: 0.8980 chunk 153 optimal weight: 8.9990 overall best weight: 0.5274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 408 GLN D 65 GLN D 136 ASN F 177 ASN F 519 ASN F 531 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.169115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.138710 restraints weight = 32889.899| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.84 r_work: 0.3602 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22333 Z= 0.113 Angle : 0.634 14.147 30692 Z= 0.302 Chirality : 0.043 0.312 3569 Planarity : 0.004 0.038 3621 Dihedral : 10.871 175.336 3767 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 5.05 % Allowed : 19.02 % Favored : 75.93 % 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: -0.55 (0.17), residues: 2541 helix: 0.70 (0.17), residues: 1005 sheet: -0.52 (0.30), residues: 273 loop : -1.20 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 178 TYR 0.019 0.001 TYR F 224 PHE 0.018 0.001 PHE F 262 TRP 0.025 0.001 TRP F 167 HIS 0.006 0.001 HIS F 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (22300) covalent geometry : angle 0.61918 / 0.30 (30666) hydrogen bonds : bond 0.03696 / 2.54 ( 935) hydrogen bonds : angle 4.21662 / 3.05 ( 2553) metal coordination : bond 0.00500 / 0.35 ( 32) metal coordination : angle 4.64424 / 3.21 ( 26) Misc. bond : bond 0.00219 / 0.12 ( 1) *********************** 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 341 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 230 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: A 18 ARG cc_start: 0.7250 (mtp85) cc_final: 0.6854 (mtp180) REVERT: A 138 ASN cc_start: 0.8427 (t0) cc_final: 0.8155 (t0) REVERT: A 338 VAL cc_start: 0.8338 (p) cc_final: 0.8114 (m) REVERT: A 431 GLU cc_start: 0.7825 (tt0) cc_final: 0.7203 (mm-30) REVERT: A 451 SER cc_start: 0.8825 (m) cc_final: 0.8515 (p) REVERT: A 553 ARG cc_start: 0.8157 (ptp-110) cc_final: 0.7693 (ttm-80) REVERT: A 668 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8486 (tpt) REVERT: A 761 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7739 (m-30) REVERT: A 807 LYS cc_start: 0.8513 (mtpp) cc_final: 0.8204 (mttm) REVERT: A 811 GLU cc_start: 0.8687 (tt0) cc_final: 0.8472 (tt0) REVERT: A 915 TYR cc_start: 0.9172 (m-80) cc_final: 0.8972 (m-80) REVERT: B 51 ARG cc_start: 0.5841 (OUTLIER) cc_final: 0.5563 (tpm-80) REVERT: B 65 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7812 (mp10) REVERT: B 96 ARG cc_start: 0.7370 (mtp-110) cc_final: 0.6880 (mtm-85) REVERT: B 108 ASN cc_start: 0.7576 (m-40) cc_final: 0.7020 (m110) REVERT: B 112 ASP cc_start: 0.7192 (t0) cc_final: 0.6764 (t0) REVERT: B 155 GLU cc_start: 0.8092 (pt0) cc_final: 0.7784 (pt0) REVERT: D 43 ASN cc_start: 0.6021 (m-40) cc_final: 0.5507 (t0) REVERT: D 69 GLN cc_start: 0.8114 (tt0) cc_final: 0.7340 (tp40) REVERT: D 87 MET cc_start: 0.8648 (tpp) cc_final: 0.8272 (tpp) REVERT: D 155 GLU cc_start: 0.7671 (pt0) cc_final: 0.7332 (pt0) REVERT: D 168 GLN cc_start: 0.7817 (mp10) cc_final: 0.6865 (mm110) REVERT: D 189 LEU cc_start: 0.7977 (mt) cc_final: 0.7542 (mm) REVERT: E 155 ARG cc_start: 0.5611 (mmt90) cc_final: 0.5031 (mmt90) REVERT: E 156 GLU cc_start: 0.4518 (OUTLIER) cc_final: 0.3512 (tp30) REVERT: E 168 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.6343 (tt0) REVERT: E 173 ARG cc_start: 0.7904 (mtm180) cc_final: 0.7385 (mpt90) REVERT: E 178 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7663 (ttp80) REVERT: E 394 LYS cc_start: 0.8604 (mptt) cc_final: 0.8110 (mtpp) REVERT: E 404 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.5793 (mp10) REVERT: E 480 ILE cc_start: 0.8566 (mt) cc_final: 0.8284 (pt) REVERT: E 497 ARG cc_start: 0.5941 (OUTLIER) cc_final: 0.4558 (ttt-90) REVERT: E 531 GLN cc_start: 0.8331 (tp40) cc_final: 0.7932 (tp-100) REVERT: E 562 ASN cc_start: 0.7947 (OUTLIER) cc_final: 0.7682 (t0) REVERT: F 122 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7488 (pp) REVERT: F 177 ASN cc_start: 0.0765 (OUTLIER) cc_final: 0.0215 (OUTLIER) REVERT: F 180 TYR cc_start: 0.5313 (m-10) cc_final: 0.5072 (m-80) REVERT: F 256 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.7027 (pp) REVERT: F 347 LYS cc_start: 0.3476 (OUTLIER) cc_final: 0.2567 (tppp) REVERT: F 438 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7078 (pp) REVERT: F 531 GLN cc_start: 0.6136 (tp40) cc_final: 0.5904 (tp-100) REVERT: F 543 TYR cc_start: 0.4989 (m-10) cc_final: 0.4426 (m-10) REVERT: F 546 PHE cc_start: 0.5090 (t80) cc_final: 0.4701 (t80) REVERT: F 549 THR cc_start: 0.5153 (m) cc_final: 0.4843 (m) REVERT: F 567 ARG cc_start: 0.5797 (mmp-170) cc_final: 0.5430 (mmp80) outliers start: 111 outliers final: 69 residues processed: 319 average time/residue: 0.5144 time to fit residues: 189.8751 Evaluate side-chains 298 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 215 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 164 HIS Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 225 PHE Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 346 PHE Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 404 GLN Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain E residue 498 GLU Chi-restraints excluded: chain E residue 525 ILE Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 130 LEU 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 188 THR Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 499 PHE Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 590 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: [170, 124, 203, 139, 243, 116, 194, 43, 133, 129, 237] chunk 170 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 203 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 133 optimal weight: 0.0170 chunk 129 optimal weight: 0.7980 chunk 237 optimal weight: 3.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 65 GLN D 136 ASN E 349 ASN F 177 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.169277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.138799 restraints weight = 33076.991| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 1.85 r_work: 0.3601 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22333 Z= 0.121 Angle : 0.639 14.100 30692 Z= 0.304 Chirality : 0.044 0.311 3569 Planarity : 0.004 0.039 3621 Dihedral : 10.608 176.682 3757 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.73 % Allowed : 19.56 % Favored : 75.71 % 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: -0.51 (0.17), residues: 2541 helix: 0.70 (0.17), residues: 1013 sheet: -0.58 (0.29), residues: 291 loop : -1.14 (0.18), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 332 TYR 0.022 0.001 TYR E 253 PHE 0.026 0.001 PHE D 15 TRP 0.028 0.001 TRP F 167 HIS 0.006 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (22300) covalent geometry : angle 0.62520 / 0.30 (30666) hydrogen bonds : bond 0.03705 / 2.55 ( 935) hydrogen bonds : angle 4.17221 / 3.03 ( 2553) metal coordination : bond 0.00548 / 0.37 ( 32) metal coordination : angle 4.59254 / 3.19 ( 26) Misc. bond : bond 0.00157 / 0.08 ( 1) *********************** 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 333 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 229 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: A 18 ARG cc_start: 0.7255 (mtp85) cc_final: 0.6860 (mtp180) REVERT: A 138 ASN cc_start: 0.8481 (t0) cc_final: 0.8226 (t0) REVERT: A 338 VAL cc_start: 0.8283 (p) cc_final: 0.8021 (m) REVERT: A 431 GLU cc_start: 0.7817 (tt0) cc_final: 0.7202 (mm-30) REVERT: A 451 SER cc_start: 0.8831 (m) cc_final: 0.8517 (p) REVERT: A 553 ARG cc_start: 0.8159 (ptp-110) cc_final: 0.7716 (ttm-80) REVERT: A 668 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8482 (tpt) REVERT: A 761 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7738 (m-30) REVERT: A 807 LYS cc_start: 0.8516 (mtpp) cc_final: 0.8209 (mttm) REVERT: A 811 GLU cc_start: 0.8702 (tt0) cc_final: 0.8487 (tt0) REVERT: B 51 ARG cc_start: 0.5973 (OUTLIER) cc_final: 0.5739 (mmp80) REVERT: B 60 GLU cc_start: 0.6022 (mp0) cc_final: 0.5817 (mp0) REVERT: B 62 MET cc_start: 0.6938 (mmm) cc_final: 0.6703 (mpm) REVERT: B 65 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7993 (mp10) REVERT: B 96 ARG cc_start: 0.7412 (mtp-110) cc_final: 0.6918 (mtm-85) REVERT: B 108 ASN cc_start: 0.7540 (m-40) cc_final: 0.6994 (m110) REVERT: B 112 ASP cc_start: 0.7133 (t0) cc_final: 0.6737 (t0) REVERT: B 155 GLU cc_start: 0.8080 (pt0) cc_final: 0.7773 (pt0) REVERT: D 43 ASN cc_start: 0.6018 (m-40) cc_final: 0.5507 (t0) REVERT: D 56 GLN cc_start: 0.5929 (OUTLIER) cc_final: 0.4495 (tp40) REVERT: D 69 GLN cc_start: 0.8145 (tt0) cc_final: 0.7352 (tp40) REVERT: D 87 MET cc_start: 0.8714 (tpp) cc_final: 0.8356 (tpp) REVERT: D 155 GLU cc_start: 0.7699 (pt0) cc_final: 0.7362 (pt0) REVERT: D 189 LEU cc_start: 0.7979 (mt) cc_final: 0.7568 (mm) REVERT: E 155 ARG cc_start: 0.5680 (mmt90) cc_final: 0.5200 (mmt90) REVERT: E 156 GLU cc_start: 0.4473 (OUTLIER) cc_final: 0.3482 (tp30) REVERT: E 173 ARG cc_start: 0.7937 (mtm180) cc_final: 0.7376 (mpt90) REVERT: E 192 LYS cc_start: 0.5689 (tppt) cc_final: 0.5256 (ttmm) REVERT: E 394 LYS cc_start: 0.8608 (mptt) cc_final: 0.8115 (mtpp) REVERT: E 404 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.5856 (mp10) REVERT: E 480 ILE cc_start: 0.8553 (mt) cc_final: 0.8285 (pt) REVERT: E 497 ARG cc_start: 0.5980 (OUTLIER) cc_final: 0.4636 (ttt-90) REVERT: E 531 GLN cc_start: 0.8359 (tp40) cc_final: 0.7976 (tp-100) REVERT: E 562 ASN cc_start: 0.7982 (OUTLIER) cc_final: 0.7720 (t0) REVERT: F 177 ASN cc_start: 0.0741 (OUTLIER) cc_final: 0.0223 (p0) REVERT: F 180 TYR cc_start: 0.5342 (m-10) cc_final: 0.5070 (m-80) REVERT: F 233 MET cc_start: 0.7925 (ptp) cc_final: 0.7504 (ppp) REVERT: F 253 TYR cc_start: 0.5892 (m-80) cc_final: 0.5643 (m-10) REVERT: F 256 LEU cc_start: 0.7175 (OUTLIER) cc_final: 0.6967 (pp) REVERT: F 334 ILE cc_start: 0.6112 (OUTLIER) cc_final: 0.5837 (tp) REVERT: F 378 MET cc_start: 0.8864 (mmm) cc_final: 0.8461 (mpp) REVERT: F 438 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7241 (pp) REVERT: F 549 THR cc_start: 0.5250 (m) cc_final: 0.4949 (m) REVERT: F 567 ARG cc_start: 0.5798 (mmp-170) cc_final: 0.5449 (mmp80) outliers start: 104 outliers final: 73 residues processed: 318 average time/residue: 0.5066 time to fit residues: 187.9681 Evaluate side-chains 300 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 214 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 164 HIS Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 225 PHE Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 346 PHE Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 404 GLN Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain E residue 498 GLU Chi-restraints excluded: chain E residue 525 ILE Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 130 LEU 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 188 THR Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 499 PHE Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 590 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: [60, 5, 54, 180, 191, 104, 108, 227, 149, 136, 230] chunk 60 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 180 optimal weight: 0.7980 chunk 191 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 chunk 227 optimal weight: 0.8980 chunk 149 optimal weight: 0.5980 chunk 136 optimal weight: 1.9990 chunk 230 optimal weight: 0.0870 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 773 GLN D 65 GLN D 136 ASN ** E 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.169330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.138877 restraints weight = 32994.963| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 1.85 r_work: 0.3602 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.142 22333 Z= 0.148 Angle : 0.777 59.200 30692 Z= 0.414 Chirality : 0.044 0.311 3569 Planarity : 0.004 0.100 3621 Dihedral : 10.585 176.686 3755 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.05 % Allowed : 20.29 % Favored : 75.66 % Cbeta Deviations : 0.04 % 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: -0.50 (0.17), residues: 2541 helix: 0.68 (0.17), residues: 1014 sheet: -0.49 (0.30), residues: 281 loop : -1.14 (0.18), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG B 57 TYR 0.020 0.001 TYR F 224 PHE 0.018 0.001 PHE D 15 TRP 0.023 0.001 TRP F 167 HIS 0.006 0.001 HIS F 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 (22300) covalent geometry : angle 0.76541 / 0.41 (30666) hydrogen bonds : bond 0.03722 / 2.56 ( 935) hydrogen bonds : angle 4.17467 / 3.03 ( 2553) metal coordination : bond 0.00535 / 0.36 ( 32) metal coordination : angle 4.59053 / 3.19 ( 26) Misc. bond : bond 0.00175 / 0.09 ( 1) ********************** 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 303 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 214 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: A 18 ARG cc_start: 0.7258 (mtp85) cc_final: 0.6866 (mtp180) REVERT: A 138 ASN cc_start: 0.8466 (t0) cc_final: 0.8211 (t0) REVERT: A 167 GLU cc_start: 0.8292 (mm-30) cc_final: 0.8045 (mm-30) REVERT: A 338 VAL cc_start: 0.8276 (p) cc_final: 0.8004 (m) REVERT: A 431 GLU cc_start: 0.7823 (tt0) cc_final: 0.7197 (mm-30) REVERT: A 451 SER cc_start: 0.8826 (m) cc_final: 0.8515 (p) REVERT: A 553 ARG cc_start: 0.8152 (ptp-110) cc_final: 0.7707 (ttm-80) REVERT: A 668 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8475 (tpt) REVERT: A 761 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.7739 (m-30) REVERT: A 807 LYS cc_start: 0.8516 (mtpp) cc_final: 0.8212 (mttm) REVERT: A 811 GLU cc_start: 0.8694 (tt0) cc_final: 0.8481 (tt0) REVERT: B 51 ARG cc_start: 0.5993 (OUTLIER) cc_final: 0.5596 (tpm-80) REVERT: B 60 GLU cc_start: 0.6045 (mp0) cc_final: 0.5824 (mp0) REVERT: B 65 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7988 (mp10) REVERT: B 96 ARG cc_start: 0.7414 (mtp-110) cc_final: 0.6917 (mtm-85) REVERT: B 108 ASN cc_start: 0.7541 (m-40) cc_final: 0.6999 (m110) REVERT: B 112 ASP cc_start: 0.7139 (t0) cc_final: 0.6744 (t0) REVERT: B 155 GLU cc_start: 0.8073 (pt0) cc_final: 0.7764 (pt0) REVERT: D 43 ASN cc_start: 0.5910 (m-40) cc_final: 0.5421 (t0) REVERT: D 56 GLN cc_start: 0.5914 (OUTLIER) cc_final: 0.4499 (tp40) REVERT: D 69 GLN cc_start: 0.8141 (tt0) cc_final: 0.7349 (tp40) REVERT: D 87 MET cc_start: 0.8712 (tpp) cc_final: 0.8355 (tpp) REVERT: D 155 GLU cc_start: 0.7703 (pt0) cc_final: 0.7368 (pt0) REVERT: D 189 LEU cc_start: 0.7982 (mt) cc_final: 0.7575 (mm) REVERT: E 155 ARG cc_start: 0.5697 (mmt90) cc_final: 0.5209 (mmt90) REVERT: E 156 GLU cc_start: 0.4472 (OUTLIER) cc_final: 0.3479 (tp30) REVERT: E 173 ARG cc_start: 0.7920 (mtm180) cc_final: 0.7386 (mpt90) REVERT: E 192 LYS cc_start: 0.5682 (tppt) cc_final: 0.5251 (ttmm) REVERT: E 394 LYS cc_start: 0.8612 (mptt) cc_final: 0.8120 (mtpp) REVERT: E 404 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.5852 (mp10) REVERT: E 480 ILE cc_start: 0.8546 (mt) cc_final: 0.8274 (pt) REVERT: E 497 ARG cc_start: 0.5979 (OUTLIER) cc_final: 0.4640 (ttt-90) REVERT: E 531 GLN cc_start: 0.8358 (tp40) cc_final: 0.7972 (tp-100) REVERT: E 562 ASN cc_start: 0.7974 (OUTLIER) cc_final: 0.7713 (t0) REVERT: F 180 TYR cc_start: 0.5294 (m-10) cc_final: 0.5051 (m-80) REVERT: F 233 MET cc_start: 0.7923 (ptp) cc_final: 0.7498 (ppp) REVERT: F 256 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6962 (pp) REVERT: F 334 ILE cc_start: 0.6091 (OUTLIER) cc_final: 0.5819 (tp) REVERT: F 378 MET cc_start: 0.8859 (mmm) cc_final: 0.8460 (mpp) REVERT: F 438 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7327 (pp) REVERT: F 549 THR cc_start: 0.5242 (m) cc_final: 0.4946 (m) REVERT: F 567 ARG cc_start: 0.5768 (mmp-170) cc_final: 0.5442 (mmp80) outliers start: 89 outliers final: 72 residues processed: 292 average time/residue: 0.5267 time to fit residues: 178.6932 Evaluate side-chains 297 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 213 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 152 CYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 739 THR 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 B residue 33 VAL Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 164 HIS Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 225 PHE Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 346 PHE Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 404 GLN Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain E residue 498 GLU Chi-restraints excluded: chain E residue 525 ILE Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 130 LEU 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 193 VAL Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 499 PHE Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 590 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: [149, 174, 139, 98, 51, 140, 203, 91, 55, 5, 239] chunk 149 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 139 optimal weight: 0.0570 chunk 98 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 140 optimal weight: 0.4980 chunk 203 optimal weight: 0.3980 chunk 91 optimal weight: 0.4980 chunk 55 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 239 optimal weight: 2.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 773 GLN D 65 GLN D 136 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.169236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.138796 restraints weight = 32904.098| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.84 r_work: 0.3605 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.142 22333 Z= 0.148 Angle : 0.777 59.200 30692 Z= 0.414 Chirality : 0.044 0.311 3569 Planarity : 0.004 0.100 3621 Dihedral : 10.585 176.686 3755 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.87 % Allowed : 20.47 % Favored : 75.66 % Cbeta Deviations : 0.04 % 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: -0.50 (0.17), residues: 2541 helix: 0.68 (0.17), residues: 1014 sheet: -0.49 (0.30), residues: 281 loop : -1.14 (0.18), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG B 57 TYR 0.020 0.001 TYR F 224 PHE 0.018 0.001 PHE D 15 TRP 0.023 0.001 TRP F 167 HIS 0.006 0.001 HIS F 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 (22300) covalent geometry : angle 0.76541 / 0.41 (30666) hydrogen bonds : bond 0.03722 / 2.56 ( 935) hydrogen bonds : angle 4.17467 / 3.03 ( 2553) metal coordination : bond 0.00535 / 0.36 ( 32) metal coordination : angle 4.59053 / 3.19 ( 26) Misc. bond : bond 0.00175 / 0.09 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8864.60 seconds wall clock time: 151 minutes 22.02 seconds (9082.02 seconds total)