Starting phenix.real_space_refine on Sun Sep 29 08:42:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7re0_24429/09_2024/7re0_24429.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7re0_24429/09_2024/7re0_24429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7re0_24429/09_2024/7re0_24429.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7re0_24429/09_2024/7re0_24429.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7re0_24429/09_2024/7re0_24429.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7re0_24429/09_2024/7re0_24429.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 1.077 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians Zn 8 6.06 5 Al 2 5.89 5 P 77 5.49 5 Mg 3 5.21 5 S 151 5.16 5 C 13390 2.51 5 N 3653 2.21 5 O 4287 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 21577 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 7470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 927, 7470 Classifications: {'peptide': 927} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 896} Chain: "B" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1408 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'GLN: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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 4550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4550 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'CIS': 1, 'PTRANS': 29, 'TRANS': 559} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "F" Number of atoms: 4550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4550 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'CIS': 2, 'PTRANS': 29, 'TRANS': 558} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "P" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 719 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 15, 'rna3p_pyr': 18} Link IDs: {'rna3p': 33} Chain: "T" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 789 Classifications: {'RNA': 37} Modifications used: {'rna3p_pur': 20, 'rna3p_pyr': 17} Link IDs: {'rna3p': 36} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 1, ' ZN': 2, 'ADP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 35 Unusual residues: {' MG': 1, ' ZN': 3, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "F" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 35 Unusual residues: {' MG': 1, ' ZN': 3, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2454 SG CYS A 301 67.264 45.450 119.235 1.00 66.41 S ATOM 2495 SG CYS A 306 66.670 46.803 122.763 1.00 65.72 S ATOM 2527 SG CYS A 310 68.298 43.392 122.281 1.00 59.62 S ATOM 3935 SG CYS A 487 69.093 60.435 105.395 1.00 66.69 S ATOM 5188 SG CYS A 645 67.891 62.289 108.535 1.00 71.92 S ATOM 5194 SG CYS A 646 67.250 58.546 108.018 1.00 69.89 S ATOM 10896 SG CYS E 5 110.546 65.599 55.107 1.00 81.99 S ATOM 10917 SG CYS E 8 113.550 67.537 55.418 1.00 83.81 S ATOM 11055 SG CYS E 26 110.403 69.419 56.178 1.00 81.91 S ATOM 11076 SG CYS E 29 110.790 68.661 52.763 1.00 82.02 S ATOM 11241 SG CYS E 50 85.966 71.045 62.688 1.00 85.94 S ATOM 11271 SG CYS E 55 83.332 69.827 60.118 1.00 89.95 S ATOM 11404 SG CYS E 72 84.595 73.574 60.136 1.00 82.73 S ATOM 10978 SG CYS E 16 100.009 63.068 52.210 1.00 81.29 S ATOM 10993 SG CYS E 19 101.569 60.239 50.186 1.00 83.44 S ATOM 15446 SG CYS F 5 65.161 64.889 58.228 1.00 74.00 S ATOM 15467 SG CYS F 8 67.970 65.171 55.838 1.00 77.58 S ATOM 15605 SG CYS F 26 67.431 68.139 57.916 1.00 77.71 S ATOM 15626 SG CYS F 29 64.838 67.636 55.596 1.00 79.20 S ATOM 15791 SG CYS F 50 57.936 79.431 79.759 1.00 81.53 S ATOM 15821 SG CYS F 55 54.398 80.847 79.865 1.00 87.91 S ATOM 15954 SG CYS F 72 56.807 82.410 77.540 1.00 77.99 S ATOM 15528 SG CYS F 16 56.279 67.501 63.967 1.00 72.40 S ATOM 15543 SG CYS F 19 54.232 64.466 62.732 1.00 75.25 S Time building chain proxies: 12.48, per 1000 atoms: 0.58 Number of scatterers: 21577 At special positions: 0 Unit cell: (156.22, 150.87, 182.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 8 29.99 S 151 16.00 P 77 15.00 Al 2 13.00 Mg 3 11.99 F 6 9.00 O 4287 8.00 N 3653 7.00 C 13390 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.40 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2000 " pdb="ZN ZN A2000 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 310 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 306 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 301 " pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 487 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 646 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 645 " pdb=" ZN E1000 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 8 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 26 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 5 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 29 " pdb=" ZN E1001 " pdb="ZN ZN E1001 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 50 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 72 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 55 " pdb=" ZN E1002 " pdb="ZN ZN E1002 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E1002 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 19 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 16 " pdb=" ZN F1000 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 26 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 8 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 29 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 5 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" ND1 HIS F 75 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 55 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 72 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 50 " pdb=" ZN F1002 " pdb="ZN ZN F1002 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F1002 " - pdb=" NE2 HIS F 33 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 19 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 16 " Number of angles added : 27 5078 Ramachandran restraints generated. 2539 Oldfield, 0 Emsley, 2539 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4874 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 28 sheets defined 44.9% alpha, 12.8% beta 34 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 7.45 Creating SS restraints... Processing helix chain 'A' and resid 3 through 13 removed outlier: 3.536A pdb=" N PHE A 7 " --> pdb=" O ASP A 3 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 8 " --> pdb=" O ALA A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 91 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 140 through 149 Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 169 through 177 removed outlier: 4.231A pdb=" N ARG A 173 " --> pdb=" O PRO A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 200 Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 234 through 248 Proline residue: A 243 - end of helix removed outlier: 4.022A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 260 removed outlier: 4.421A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS A 256 " --> pdb=" O ALA A 253 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL A 257 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ASP A 258 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP A 260 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.566A pdb=" N CYS A 301 " --> pdb=" O CYS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.804A pdb=" N HIS A 309 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.753A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 377 through 385 removed outlier: 4.740A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 448 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 480 removed outlier: 4.153A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.575A pdb=" N VAL A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.895A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 removed outlier: 3.522A pdb=" N LEU A 527 " --> pdb=" O ASP A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 580 removed outlier: 4.110A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 640 through 642 No H-bonds generated for 'chain 'A' and resid 640 through 642' Processing helix chain 'A' and resid 647 through 662 Processing helix chain 'A' and resid 687 through 710 Processing helix chain 'A' and resid 717 through 733 Processing helix chain 'A' and resid 738 through 753 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.610A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 808 Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 846 through 851 removed outlier: 3.534A pdb=" N LYS A 849 " --> pdb=" O ASP A 846 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP A 851 " --> pdb=" O VAL A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 867 Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 874 through 903 removed outlier: 3.986A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 917 removed outlier: 3.925A pdb=" N ARG A 914 " --> pdb=" O ASN A 911 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TRP A 916 " --> pdb=" O SER A 913 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU A 917 " --> pdb=" O ARG A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 923 Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'B' and resid 9 through 28 removed outlier: 4.186A pdb=" N ALA B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 79 removed outlier: 4.047A pdb=" N ALA B 54 " --> pdb=" O ASP B 50 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N MET B 55 " --> pdb=" O ARG B 51 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLN B 56 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 98 removed outlier: 3.643A pdb=" N LEU B 98 " --> pdb=" O MET B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 109 Processing helix chain 'B' and resid 118 through 125 removed outlier: 4.338A pdb=" N LEU B 122 " --> pdb=" O ASN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 143 removed outlier: 4.083A pdb=" N ASP B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 2 through 20 removed outlier: 3.653A pdb=" N LYS C 7 " --> pdb=" O MET C 3 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N CYS C 8 " --> pdb=" O SER C 4 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL C 11 " --> pdb=" O LYS C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 24 Processing helix chain 'C' and resid 25 through 41 removed outlier: 3.588A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 62 removed outlier: 3.712A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'D' and resid 9 through 29 Processing helix chain 'D' and resid 32 through 82 removed outlier: 3.570A pdb=" N GLN D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 99 removed outlier: 3.634A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 134 through 141 removed outlier: 3.579A pdb=" N ASN D 140 " --> pdb=" O ASN D 136 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR D 141 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 removed outlier: 3.686A pdb=" N ILE D 172 " --> pdb=" O LEU D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 180 Processing helix chain 'E' and resid 26 through 37 removed outlier: 3.824A pdb=" N SER E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 63 Processing helix chain 'E' and resid 93 through 97 removed outlier: 3.885A pdb=" N CYS E 97 " --> pdb=" O LYS E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 112 removed outlier: 3.894A pdb=" N ALA E 108 " --> pdb=" O THR E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 123 removed outlier: 3.507A pdb=" N ILE E 121 " --> pdb=" O ALA E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 145 removed outlier: 3.526A pdb=" N ALA E 135 " --> pdb=" O LYS E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 149 Processing helix chain 'E' and resid 265 through 275 Processing helix chain 'E' and resid 287 through 299 removed outlier: 3.504A pdb=" N ALA E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE E 293 " --> pdb=" O SER E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 325 removed outlier: 3.655A pdb=" N ALA E 316 " --> pdb=" O ALA E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 391 Processing helix chain 'E' and resid 418 through 422 Processing helix chain 'E' and resid 423 through 432 Processing helix chain 'E' and resid 445 through 456 removed outlier: 4.556A pdb=" N ALA E 454 " --> pdb=" O ASP E 450 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL E 456 " --> pdb=" O VAL E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 499 Processing helix chain 'E' and resid 515 through 526 removed outlier: 4.491A pdb=" N SER E 523 " --> pdb=" O ASN E 519 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LYS E 524 " --> pdb=" O ALA E 520 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE E 525 " --> pdb=" O VAL E 521 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 537 removed outlier: 3.563A pdb=" N GLN E 537 " --> pdb=" O VAL E 533 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 533 through 537' Processing helix chain 'E' and resid 557 through 566 Processing helix chain 'E' and resid 580 through 585 removed outlier: 3.713A pdb=" N LEU E 585 " --> pdb=" O LEU E 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 37 removed outlier: 3.641A pdb=" N SER F 36 " --> pdb=" O ASP F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 112 removed outlier: 4.538A pdb=" N ALA F 108 " --> pdb=" O THR F 104 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS F 112 " --> pdb=" O ALA F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 123 removed outlier: 3.596A pdb=" N ILE F 121 " --> pdb=" O ALA F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 146 removed outlier: 3.755A pdb=" N PHE F 133 " --> pdb=" O ARG F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 264 No H-bonds generated for 'chain 'F' and resid 262 through 264' Processing helix chain 'F' and resid 265 through 275 removed outlier: 3.904A pdb=" N GLN F 275 " --> pdb=" O LYS F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 299 removed outlier: 4.047A pdb=" N ILE F 293 " --> pdb=" O SER F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 324 removed outlier: 3.570A pdb=" N VAL F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 363 No H-bonds generated for 'chain 'F' and resid 361 through 363' Processing helix chain 'F' and resid 380 through 390 Processing helix chain 'F' and resid 418 through 422 Processing helix chain 'F' and resid 423 through 432 Processing helix chain 'F' and resid 445 through 456 removed outlier: 3.675A pdb=" N VAL F 456 " --> pdb=" O VAL F 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 499 removed outlier: 3.755A pdb=" N ILE F 493 " --> pdb=" O ASN F 489 " (cutoff:3.500A) Processing helix chain 'F' and resid 515 through 526 removed outlier: 3.515A pdb=" N SER F 523 " --> pdb=" O ASN F 519 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS F 524 " --> pdb=" O ALA F 520 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE F 525 " --> pdb=" O VAL F 521 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU F 526 " --> pdb=" O ALA F 522 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 566 removed outlier: 3.765A pdb=" N THR F 566 " --> pdb=" O ASN F 562 " (cutoff:3.500A) Processing helix chain 'F' and resid 578 through 584 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 5.326A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASP A 60 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ILE A 66 " --> pdb=" O ASP A 60 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N TYR A 69 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LYS A 98 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 33 removed outlier: 6.980A pdb=" N ASP A 29 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ASN A 52 " --> pdb=" O ASP A 29 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 36 through 38 Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 224 removed outlier: 6.416A pdb=" N ILE A 201 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.433A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 9.468A pdb=" N SER A 363 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N PHE A 334 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.433A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.696A pdb=" N LEU A 673 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU A 387 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL B 131 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU A 389 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA9, first strand: chain 'A' and resid 755 through 758 Processing sheet with id=AB1, first strand: chain 'A' and resid 816 through 822 Processing sheet with id=AB2, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.453A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.453A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N VAL D 159 " --> pdb=" O VAL D 167 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 3 through 4 Processing sheet with id=AB5, first strand: chain 'E' and resid 24 through 25 removed outlier: 3.907A pdb=" N LEU E 14 " --> pdb=" O LEU E 25 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 64 through 66 Processing sheet with id=AB7, first strand: chain 'E' and resid 84 through 85 Processing sheet with id=AB8, first strand: chain 'E' and resid 212 through 213 Processing sheet with id=AB9, first strand: chain 'E' and resid 355 through 359 removed outlier: 6.714A pdb=" N ILE E 304 " --> pdb=" O VAL E 356 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N CYS E 358 " --> pdb=" O ILE E 304 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N TYR E 306 " --> pdb=" O CYS E 358 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL E 371 " --> pdb=" O VAL E 397 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ILE E 399 " --> pdb=" O VAL E 371 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N PHE E 373 " --> pdb=" O ILE E 399 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N SER E 278 " --> pdb=" O TYR E 398 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N MET E 436 " --> pdb=" O TYR E 277 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N THR E 279 " --> pdb=" O MET E 436 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 471 through 475 removed outlier: 6.127A pdb=" N PHE E 472 " --> pdb=" O CYS E 574 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N MET E 576 " --> pdb=" O PHE E 472 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N MET E 474 " --> pdb=" O MET E 576 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASP E 542 " --> pdb=" O GLY E 571 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N LEU E 573 " --> pdb=" O ASP E 542 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL E 544 " --> pdb=" O LEU E 573 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ILE E 575 " --> pdb=" O VAL E 544 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE E 546 " --> pdb=" O ILE E 575 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N PHE E 511 " --> pdb=" O GLN E 531 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 481 through 482 Processing sheet with id=AC3, first strand: chain 'F' and resid 3 through 4 Processing sheet with id=AC4, first strand: chain 'F' and resid 64 through 66 Processing sheet with id=AC5, first strand: chain 'F' and resid 84 through 85 Processing sheet with id=AC6, first strand: chain 'F' and resid 152 through 153 Processing sheet with id=AC7, first strand: chain 'F' and resid 162 through 163 Processing sheet with id=AC8, first strand: chain 'F' and resid 277 through 280 removed outlier: 6.384A pdb=" N SER F 278 " --> pdb=" O TYR F 398 " (cutoff:3.500A) removed outlier: 9.197A pdb=" N THR F 367 " --> pdb=" O ALA F 393 " (cutoff:3.500A) removed outlier: 9.971A pdb=" N HIS F 395 " --> pdb=" O THR F 367 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ASP F 369 " --> pdb=" O HIS F 395 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N VAL F 397 " --> pdb=" O ASP F 369 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL F 371 " --> pdb=" O VAL F 397 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ILE F 399 " --> pdb=" O VAL F 371 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N PHE F 373 " --> pdb=" O ILE F 399 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ILE F 304 " --> pdb=" O VAL F 356 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N CYS F 358 " --> pdb=" O ILE F 304 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N TYR F 306 " --> pdb=" O CYS F 358 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 440 through 441 Processing sheet with id=AD1, first strand: chain 'F' and resid 510 through 512 863 hydrogen bonds defined for protein. 2382 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 83 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 8.40 Time building geometry restraints manager: 6.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.41: 9075 1.41 - 1.61: 12879 1.61 - 1.81: 222 1.81 - 2.02: 1 2.02 - 2.22: 1 Bond restraints: 22178 Sorted by residual: bond pdb=" C ALA B 74 " pdb=" N ARG B 75 " ideal model delta sigma weight residual 1.332 2.222 -0.889 1.40e-02 5.10e+03 4.04e+03 bond pdb=" C ALA B 53 " pdb=" N ALA B 54 " ideal model delta sigma weight residual 1.332 1.789 -0.457 1.40e-02 5.10e+03 1.06e+03 bond pdb=" C PRO F 234 " pdb=" N LEU F 235 " ideal model delta sigma weight residual 1.329 1.621 -0.292 1.43e-02 4.89e+03 4.17e+02 bond pdb=" F1 AF3 F1005 " pdb="AL AF3 F1005 " ideal model delta sigma weight residual 1.637 1.801 -0.164 2.00e-02 2.50e+03 6.70e+01 bond pdb=" F2 AF3 F1005 " pdb="AL AF3 F1005 " ideal model delta sigma weight residual 1.637 1.801 -0.164 2.00e-02 2.50e+03 6.69e+01 ... (remaining 22173 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.91: 30468 11.91 - 23.82: 9 23.82 - 35.73: 0 35.73 - 47.64: 0 47.64 - 59.55: 1 Bond angle restraints: 30478 Sorted by residual: angle pdb=" O ALA B 53 " pdb=" C ALA B 53 " pdb=" N ALA B 54 " ideal model delta sigma weight residual 122.59 63.04 59.55 1.33e+00 5.65e-01 2.00e+03 angle pdb=" O PRO F 234 " pdb=" C PRO F 234 " pdb=" N LEU F 235 " ideal model delta sigma weight residual 123.10 106.18 16.92 1.20e+00 6.94e-01 1.99e+02 angle pdb=" CA PRO F 234 " pdb=" C PRO F 234 " pdb=" N LEU F 235 " ideal model delta sigma weight residual 115.50 130.25 -14.75 1.27e+00 6.20e-01 1.35e+02 angle pdb=" C PRO F 234 " pdb=" N LEU F 235 " pdb=" CA LEU F 235 " ideal model delta sigma weight residual 122.65 139.75 -17.10 1.49e+00 4.50e-01 1.32e+02 angle pdb=" CA ALA B 53 " pdb=" C ALA B 53 " pdb=" N ALA B 54 " ideal model delta sigma weight residual 116.84 135.68 -18.84 1.71e+00 3.42e-01 1.21e+02 ... (remaining 30473 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.00: 12881 34.00 - 68.01: 446 68.01 - 102.01: 30 102.01 - 136.02: 6 136.02 - 170.02: 3 Dihedral angle restraints: 13366 sinusoidal: 5811 harmonic: 7555 Sorted by residual: dihedral pdb=" CA SER E 80 " pdb=" C SER E 80 " pdb=" N PHE E 81 " pdb=" CA PHE E 81 " ideal model delta harmonic sigma weight residual 180.00 48.83 131.17 0 5.00e+00 4.00e-02 6.88e+02 dihedral pdb=" CA LYS E 189 " pdb=" C LYS E 189 " pdb=" N ASN E 190 " pdb=" CA ASN E 190 " ideal model delta harmonic sigma weight residual 0.00 42.52 -42.52 0 5.00e+00 4.00e-02 7.23e+01 dihedral pdb=" CA ASN F 190 " pdb=" C ASN F 190 " pdb=" N SER F 191 " pdb=" CA SER F 191 " ideal model delta harmonic sigma weight residual 180.00 139.31 40.69 0 5.00e+00 4.00e-02 6.62e+01 ... (remaining 13363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 3008 0.062 - 0.123: 472 0.123 - 0.185: 47 0.185 - 0.247: 6 0.247 - 0.308: 3 Chirality restraints: 3536 Sorted by residual: chirality pdb=" CA TYR F 149 " pdb=" N TYR F 149 " pdb=" C TYR F 149 " pdb=" CB TYR F 149 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA VAL E 2 " pdb=" N VAL E 2 " pdb=" C VAL E 2 " pdb=" CB VAL E 2 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA ASN F 190 " pdb=" N ASN F 190 " pdb=" C ASN F 190 " pdb=" CB ASN F 190 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 3533 not shown) Planarity restraints: 3617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 53 " 0.174 2.00e-02 2.50e+03 2.20e-01 4.83e+02 pdb=" C ALA B 53 " -0.377 2.00e-02 2.50e+03 pdb=" O ALA B 53 " 0.100 2.00e-02 2.50e+03 pdb=" N ALA B 54 " 0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 74 " -0.088 2.00e-02 2.50e+03 1.45e-01 2.10e+02 pdb=" C ALA B 74 " 0.248 2.00e-02 2.50e+03 pdb=" O ALA B 74 " -0.108 2.00e-02 2.50e+03 pdb=" N ARG B 75 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET E 233 " 0.077 5.00e-02 4.00e+02 1.17e-01 2.20e+01 pdb=" N PRO E 234 " -0.203 5.00e-02 4.00e+02 pdb=" CA PRO E 234 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO E 234 " 0.062 5.00e-02 4.00e+02 ... (remaining 3614 not shown) Histogram of nonbonded interaction distances: 1.13 - 1.88: 12 1.88 - 2.64: 413 2.64 - 3.39: 28830 3.39 - 4.15: 53558 4.15 - 4.90: 96158 Nonbonded interactions: 178971 Sorted by model distance: nonbonded pdb=" O ASP E 101 " pdb=" N VAL E 103 " model vdw 1.129 3.120 nonbonded pdb=" CG2 THR E 214 " pdb=" NH1 ARG E 337 " model vdw 1.208 3.540 nonbonded pdb=" O ASP F 204 " pdb=" CE LYS F 524 " model vdw 1.226 3.440 nonbonded pdb=" NZ LYS B 61 " pdb=" OP1 G T 113 " model vdw 1.429 3.120 nonbonded pdb=" O ASP F 101 " pdb=" N VAL F 103 " model vdw 1.432 3.120 ... (remaining 178966 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 7 through 22 or (resid 23 through 25 and (name N or name C \ A or name C or name O or name CB )) or resid 26 through 191)) selection = (chain 'D' and (resid 7 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 35 or (resid 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 38 or (resid 39 and (n \ ame N or name CA or name C or name O or name CB )) or resid 40 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB )) or resid 49 thro \ ugh 191)) } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 3.040 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: 0.020 Extract box with map and model: 0.870 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 56.170 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 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 0.889 22178 Z= 0.617 Angle : 0.882 59.546 30478 Z= 0.544 Chirality : 0.046 0.308 3536 Planarity : 0.007 0.220 3617 Dihedral : 16.126 170.022 8492 Min Nonbonded Distance : 1.129 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.66 % Favored : 93.15 % Rotamer: Outliers : 9.24 % Allowed : 9.11 % Favored : 81.65 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.16), residues: 2539 helix: -0.60 (0.16), residues: 1004 sheet: -1.02 (0.29), residues: 299 loop : -1.71 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 916 HIS 0.012 0.001 HIS F 290 PHE 0.019 0.002 PHE A 102 TYR 0.020 0.002 TYR F 224 ARG 0.005 0.001 ARG F 443 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5078 Ramachandran restraints generated. 2539 Oldfield, 0 Emsley, 2539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5078 Ramachandran restraints generated. 2539 Oldfield, 0 Emsley, 2539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 241 time to evaluate : 2.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 VAL cc_start: 0.8228 (t) cc_final: 0.7942 (m) REVERT: A 758 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8815 (tt) REVERT: A 761 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7177 (m-30) REVERT: B 15 PHE cc_start: 0.8373 (t80) cc_final: 0.7768 (t80) REVERT: B 94 MET cc_start: 0.8404 (mtm) cc_final: 0.8190 (mtt) REVERT: D 42 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8288 (tp) REVERT: D 48 GLU cc_start: 0.9093 (tp30) cc_final: 0.8883 (tp30) REVERT: E 204 ASP cc_start: 0.3220 (OUTLIER) cc_final: 0.1975 (t0) REVERT: E 441 CYS cc_start: 0.2933 (OUTLIER) cc_final: 0.2605 (t) REVERT: E 548 GLN cc_start: -0.0621 (OUTLIER) cc_final: -0.0848 (tt0) REVERT: F 210 VAL cc_start: 0.4201 (OUTLIER) cc_final: 0.3574 (m) REVERT: F 258 ILE cc_start: -0.0112 (OUTLIER) cc_final: -0.0494 (tt) REVERT: F 376 ILE cc_start: 0.7459 (OUTLIER) cc_final: 0.7100 (mp) REVERT: F 455 LEU cc_start: 0.6824 (OUTLIER) cc_final: 0.6124 (tp) outliers start: 203 outliers final: 43 residues processed: 426 average time/residue: 0.3245 time to fit residues: 212.6692 Evaluate side-chains 180 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 127 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 525 ILE Chi-restraints excluded: chain E residue 548 GLN Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain F residue 177 ASN Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 262 PHE Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 525 ILE Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain F residue 588 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 218 optimal weight: 5.9990 chunk 196 optimal weight: 5.9990 chunk 108 optimal weight: 0.0270 chunk 67 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 203 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 151 optimal weight: 30.0000 chunk 235 optimal weight: 1.9990 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN B 56 GLN C 19 GLN D 176 ASN ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 GLN F 518 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22178 Z= 0.194 Angle : 0.668 14.642 30478 Z= 0.340 Chirality : 0.043 0.250 3536 Planarity : 0.004 0.045 3617 Dihedral : 14.361 169.634 3999 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.92 % Favored : 95.00 % Rotamer: Outliers : 4.60 % Allowed : 14.12 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.16), residues: 2541 helix: 0.08 (0.16), residues: 1012 sheet: -0.65 (0.31), residues: 264 loop : -1.51 (0.17), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.007 0.001 HIS E 290 PHE 0.022 0.001 PHE B 15 TYR 0.023 0.002 TYR E 299 ARG 0.012 0.001 ARG E 337 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 137 time to evaluate : 2.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 ASP cc_start: 0.7421 (t0) cc_final: 0.7139 (t0) REVERT: A 855 MET cc_start: 0.8231 (mmt) cc_final: 0.8010 (mmt) REVERT: A 924 MET cc_start: 0.9257 (mmm) cc_final: 0.8991 (tpp) REVERT: B 15 PHE cc_start: 0.8388 (t80) cc_final: 0.8074 (t80) REVERT: C 47 GLU cc_start: 0.7559 (tm-30) cc_final: 0.7278 (tm-30) REVERT: D 42 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8447 (tp) REVERT: E 204 ASP cc_start: 0.3323 (OUTLIER) cc_final: 0.1867 (t0) REVERT: F 258 ILE cc_start: 0.0076 (OUTLIER) cc_final: -0.0313 (tt) outliers start: 101 outliers final: 46 residues processed: 233 average time/residue: 0.3176 time to fit residues: 117.2160 Evaluate side-chains 162 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 113 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 525 ILE Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 525 ILE Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 588 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 130 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 195 optimal weight: 9.9990 chunk 160 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 235 optimal weight: 0.0020 chunk 254 optimal weight: 10.0000 chunk 209 optimal weight: 20.0000 chunk 233 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 189 optimal weight: 9.9990 overall best weight: 4.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN A 572 HIS A 791 ASN D 43 ASN D 157 GLN E 492 GLN E 531 GLN ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 554 HIS E 562 ASN ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 22178 Z= 0.464 Angle : 0.752 14.371 30478 Z= 0.387 Chirality : 0.046 0.243 3536 Planarity : 0.005 0.057 3617 Dihedral : 13.881 167.692 3954 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 4.51 % Allowed : 14.89 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.16), residues: 2541 helix: 0.24 (0.16), residues: 1031 sheet: -0.39 (0.32), residues: 258 loop : -1.51 (0.17), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 114 HIS 0.009 0.002 HIS C 36 PHE 0.023 0.002 PHE D 92 TYR 0.022 0.002 TYR A 887 ARG 0.005 0.001 ARG F 579 *********************** 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 221 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 122 time to evaluate : 2.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.8834 (mtp180) REVERT: A 615 MET cc_start: 0.8548 (tmm) cc_final: 0.8341 (tmm) REVERT: A 855 MET cc_start: 0.8322 (mmt) cc_final: 0.8063 (mmp) REVERT: B 51 ARG cc_start: 0.9223 (tpp80) cc_final: 0.9021 (tpp80) REVERT: C 47 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7637 (tm-30) REVERT: C 54 SER cc_start: 0.9346 (m) cc_final: 0.9022 (t) REVERT: C 67 ASP cc_start: 0.7940 (t0) cc_final: 0.7690 (t0) REVERT: E 204 ASP cc_start: 0.3091 (OUTLIER) cc_final: 0.1743 (t0) REVERT: F 258 ILE cc_start: 0.0279 (OUTLIER) cc_final: -0.0090 (tt) outliers start: 99 outliers final: 57 residues processed: 211 average time/residue: 0.3262 time to fit residues: 109.0247 Evaluate side-chains 168 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 108 time to evaluate : 2.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 525 ILE Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 572 ILE Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 525 ILE Chi-restraints excluded: chain F residue 530 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 232 optimal weight: 7.9990 chunk 177 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 26 optimal weight: 0.0770 chunk 112 optimal weight: 0.9980 chunk 158 optimal weight: 0.7980 chunk 236 optimal weight: 0.9990 chunk 250 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 224 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN D 176 ASN ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 492 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22178 Z= 0.168 Angle : 0.593 14.281 30478 Z= 0.301 Chirality : 0.040 0.251 3536 Planarity : 0.003 0.051 3617 Dihedral : 13.532 150.327 3939 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.73 % Allowed : 16.71 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.17), residues: 2541 helix: 0.68 (0.17), residues: 1019 sheet: -0.28 (0.33), residues: 248 loop : -1.30 (0.17), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 916 HIS 0.006 0.001 HIS A 892 PHE 0.015 0.001 PHE D 92 TYR 0.015 0.001 TYR E 277 ARG 0.004 0.000 ARG E 337 *********************** 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 187 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 127 time to evaluate : 2.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.7955 (mmm) cc_final: 0.7660 (mmm) REVERT: A 242 MET cc_start: 0.8576 (mtt) cc_final: 0.8301 (mtt) REVERT: A 336 ASP cc_start: 0.7439 (t0) cc_final: 0.7046 (t0) REVERT: A 615 MET cc_start: 0.8291 (tmm) cc_final: 0.7534 (ttt) REVERT: A 665 GLU cc_start: 0.7143 (pm20) cc_final: 0.6877 (pm20) REVERT: B 65 GLN cc_start: 0.8524 (mm-40) cc_final: 0.8284 (mm-40) REVERT: B 94 MET cc_start: 0.8231 (mtp) cc_final: 0.7858 (mtp) REVERT: C 47 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7544 (tm-30) REVERT: C 54 SER cc_start: 0.9253 (m) cc_final: 0.8932 (t) REVERT: C 67 ASP cc_start: 0.7959 (t0) cc_final: 0.7742 (t0) REVERT: D 67 MET cc_start: 0.5514 (mmt) cc_final: 0.5013 (mmt) REVERT: E 204 ASP cc_start: 0.3041 (OUTLIER) cc_final: 0.1900 (t0) REVERT: F 258 ILE cc_start: 0.0565 (OUTLIER) cc_final: 0.0224 (tt) REVERT: F 272 VAL cc_start: 0.7370 (t) cc_final: 0.7094 (p) outliers start: 60 outliers final: 39 residues processed: 181 average time/residue: 0.3122 time to fit residues: 90.7493 Evaluate side-chains 157 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 116 time to evaluate : 2.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 572 ILE Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 525 ILE Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 588 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 208 optimal weight: 10.0000 chunk 142 optimal weight: 20.0000 chunk 3 optimal weight: 0.0010 chunk 186 optimal weight: 20.0000 chunk 103 optimal weight: 0.8980 chunk 213 optimal weight: 6.9990 chunk 173 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 127 optimal weight: 0.8980 chunk 224 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 464 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22178 Z= 0.231 Angle : 0.607 14.215 30478 Z= 0.306 Chirality : 0.041 0.223 3536 Planarity : 0.004 0.050 3617 Dihedral : 13.366 150.048 3933 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.78 % Allowed : 16.89 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.17), residues: 2541 helix: 0.82 (0.17), residues: 1022 sheet: -0.24 (0.33), residues: 253 loop : -1.25 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.014 0.001 HIS E 164 PHE 0.018 0.001 PHE F 90 TYR 0.015 0.001 TYR E 277 ARG 0.012 0.000 ARG B 51 *********************** 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 184 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 123 time to evaluate : 2.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 615 MET cc_start: 0.8260 (tmm) cc_final: 0.7550 (ttt) REVERT: A 665 GLU cc_start: 0.7202 (pm20) cc_final: 0.6945 (pm20) REVERT: B 15 PHE cc_start: 0.8348 (t80) cc_final: 0.8037 (t80) REVERT: B 94 MET cc_start: 0.8285 (mtp) cc_final: 0.7814 (mtp) REVERT: C 47 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7629 (tm-30) REVERT: C 54 SER cc_start: 0.9267 (m) cc_final: 0.8963 (t) REVERT: C 67 ASP cc_start: 0.7964 (t0) cc_final: 0.7729 (t0) REVERT: D 52 ASP cc_start: 0.8882 (t0) cc_final: 0.8577 (m-30) REVERT: E 204 ASP cc_start: 0.3143 (OUTLIER) cc_final: 0.2003 (t0) REVERT: F 258 ILE cc_start: 0.0867 (OUTLIER) cc_final: 0.0520 (tt) REVERT: F 272 VAL cc_start: 0.7234 (t) cc_final: 0.6995 (p) outliers start: 61 outliers final: 45 residues processed: 175 average time/residue: 0.3189 time to fit residues: 89.8152 Evaluate side-chains 163 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 116 time to evaluate : 2.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 572 ILE Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 177 ASN Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 506 TRP Chi-restraints excluded: chain F residue 507 ARG Chi-restraints excluded: chain F residue 525 ILE Chi-restraints excluded: chain F residue 530 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 84 optimal weight: 2.9990 chunk 225 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 146 optimal weight: 9.9990 chunk 61 optimal weight: 0.9990 chunk 250 optimal weight: 10.0000 chunk 208 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN D 168 GLN ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22178 Z= 0.188 Angle : 0.589 14.126 30478 Z= 0.297 Chirality : 0.040 0.218 3536 Planarity : 0.003 0.046 3617 Dihedral : 13.236 148.595 3927 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.82 % Allowed : 17.40 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.17), residues: 2541 helix: 1.01 (0.17), residues: 1014 sheet: -0.10 (0.33), residues: 249 loop : -1.16 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 916 HIS 0.010 0.001 HIS E 164 PHE 0.016 0.001 PHE F 90 TYR 0.017 0.001 TYR A 903 ARG 0.008 0.000 ARG E 155 *********************** 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 185 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 123 time to evaluate : 2.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 TRP cc_start: 0.8590 (OUTLIER) cc_final: 0.7185 (m-90) REVERT: A 615 MET cc_start: 0.8182 (tmm) cc_final: 0.7514 (ttt) REVERT: A 855 MET cc_start: 0.7900 (mmp) cc_final: 0.7606 (mmt) REVERT: B 15 PHE cc_start: 0.8302 (t80) cc_final: 0.7960 (t80) REVERT: B 94 MET cc_start: 0.8190 (mtp) cc_final: 0.7826 (mtp) REVERT: C 34 GLN cc_start: 0.8258 (tp40) cc_final: 0.7824 (tm-30) REVERT: C 38 ASP cc_start: 0.8299 (m-30) cc_final: 0.7766 (m-30) REVERT: C 47 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7578 (tm-30) REVERT: C 54 SER cc_start: 0.9256 (m) cc_final: 0.8960 (t) REVERT: C 67 ASP cc_start: 0.7936 (t0) cc_final: 0.7705 (t0) REVERT: D 48 GLU cc_start: 0.9143 (tp30) cc_final: 0.8842 (tp30) REVERT: E 204 ASP cc_start: 0.3388 (OUTLIER) cc_final: 0.2381 (t0) REVERT: F 258 ILE cc_start: 0.1069 (OUTLIER) cc_final: 0.0709 (tt) REVERT: F 272 VAL cc_start: 0.7243 (t) cc_final: 0.6810 (p) outliers start: 62 outliers final: 46 residues processed: 178 average time/residue: 0.3135 time to fit residues: 89.9758 Evaluate side-chains 168 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 119 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 572 ILE Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 506 TRP Chi-restraints excluded: chain F residue 507 ARG Chi-restraints excluded: chain F residue 525 ILE Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 588 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 241 optimal weight: 9.9990 chunk 28 optimal weight: 0.1980 chunk 142 optimal weight: 0.0060 chunk 182 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 chunk 210 optimal weight: 9.9990 chunk 139 optimal weight: 0.0870 chunk 249 optimal weight: 2.9990 chunk 156 optimal weight: 50.0000 chunk 152 optimal weight: 0.7980 chunk 115 optimal weight: 0.6980 overall best weight: 0.3574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN E 164 HIS ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22178 Z= 0.141 Angle : 0.588 14.053 30478 Z= 0.290 Chirality : 0.039 0.211 3536 Planarity : 0.003 0.045 3617 Dihedral : 13.113 148.699 3926 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.50 % Allowed : 18.21 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.17), residues: 2541 helix: 1.09 (0.17), residues: 1016 sheet: -0.05 (0.33), residues: 249 loop : -1.08 (0.17), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 916 HIS 0.006 0.001 HIS E 164 PHE 0.014 0.001 PHE F 561 TYR 0.030 0.001 TYR A 903 ARG 0.002 0.000 ARG A 726 *********************** 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 186 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 131 time to evaluate : 2.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.7683 (mmm) cc_final: 0.7386 (tpt) REVERT: A 153 ASP cc_start: 0.7106 (p0) cc_final: 0.6784 (p0) REVERT: A 268 TRP cc_start: 0.8548 (OUTLIER) cc_final: 0.7133 (m-90) REVERT: A 365 ARG cc_start: 0.7115 (mmm160) cc_final: 0.6911 (mmm160) REVERT: A 615 MET cc_start: 0.8094 (tmm) cc_final: 0.7630 (ttt) REVERT: A 855 MET cc_start: 0.7861 (mmp) cc_final: 0.7627 (mmt) REVERT: B 15 PHE cc_start: 0.8298 (t80) cc_final: 0.7992 (t80) REVERT: C 34 GLN cc_start: 0.8178 (tp40) cc_final: 0.7724 (tm-30) REVERT: C 47 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7430 (tm-30) REVERT: C 54 SER cc_start: 0.9226 (m) cc_final: 0.8835 (t) REVERT: C 67 ASP cc_start: 0.7931 (t0) cc_final: 0.7703 (t0) REVERT: C 74 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7462 (mp0) REVERT: D 48 GLU cc_start: 0.9151 (tp30) cc_final: 0.7816 (tp30) REVERT: D 52 ASP cc_start: 0.8857 (t0) cc_final: 0.8648 (m-30) REVERT: E 204 ASP cc_start: 0.3697 (OUTLIER) cc_final: 0.2989 (t0) REVERT: F 272 VAL cc_start: 0.6992 (t) cc_final: 0.6752 (p) outliers start: 55 outliers final: 41 residues processed: 182 average time/residue: 0.3057 time to fit residues: 90.0000 Evaluate side-chains 157 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 114 time to evaluate : 2.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 572 ILE Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 506 TRP Chi-restraints excluded: chain F residue 525 ILE Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 588 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 154 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 158 optimal weight: 8.9990 chunk 170 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 196 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN E 349 ASN ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 557 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 22178 Z= 0.402 Angle : 0.689 13.949 30478 Z= 0.347 Chirality : 0.044 0.235 3536 Planarity : 0.004 0.044 3617 Dihedral : 13.105 143.617 3923 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.46 % Allowed : 18.62 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.17), residues: 2541 helix: 0.88 (0.17), residues: 1015 sheet: -0.29 (0.33), residues: 262 loop : -1.14 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 114 HIS 0.008 0.001 HIS A 816 PHE 0.018 0.002 PHE D 92 TYR 0.032 0.002 TYR A 831 ARG 0.005 0.001 ARG E 567 *********************** 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 165 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 111 time to evaluate : 3.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 TRP cc_start: 0.8635 (OUTLIER) cc_final: 0.7207 (m-90) REVERT: A 924 MET cc_start: 0.8823 (tpp) cc_final: 0.8375 (ttm) REVERT: C 34 GLN cc_start: 0.8364 (tp40) cc_final: 0.8060 (tm-30) REVERT: C 47 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7682 (tm-30) REVERT: C 54 SER cc_start: 0.9277 (m) cc_final: 0.8955 (t) REVERT: C 67 ASP cc_start: 0.7927 (t0) cc_final: 0.7583 (t70) REVERT: D 48 GLU cc_start: 0.9129 (tp30) cc_final: 0.8853 (tp30) REVERT: E 204 ASP cc_start: 0.3361 (OUTLIER) cc_final: 0.2828 (t0) outliers start: 54 outliers final: 46 residues processed: 160 average time/residue: 0.3538 time to fit residues: 92.4448 Evaluate side-chains 156 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 108 time to evaluate : 2.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 572 ILE Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 177 ASN Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 506 TRP Chi-restraints excluded: chain F residue 507 ARG Chi-restraints excluded: chain F residue 525 ILE Chi-restraints excluded: chain F residue 588 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 227 optimal weight: 30.0000 chunk 239 optimal weight: 0.0980 chunk 218 optimal weight: 0.7980 chunk 232 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 182 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 210 optimal weight: 40.0000 chunk 220 optimal weight: 5.9990 chunk 231 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 557 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22178 Z= 0.186 Angle : 0.598 13.959 30478 Z= 0.297 Chirality : 0.041 0.464 3536 Planarity : 0.003 0.043 3617 Dihedral : 13.072 142.091 3922 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.91 % Allowed : 19.35 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.17), residues: 2541 helix: 1.08 (0.17), residues: 1008 sheet: -0.36 (0.32), residues: 275 loop : -1.04 (0.18), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 916 HIS 0.006 0.001 HIS F 482 PHE 0.014 0.001 PHE D 92 TYR 0.025 0.001 TYR A 903 ARG 0.007 0.000 ARG A 365 *********************** 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 157 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 115 time to evaluate : 2.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.7712 (mmm) cc_final: 0.7375 (tpt) REVERT: A 268 TRP cc_start: 0.8554 (OUTLIER) cc_final: 0.7086 (m-90) REVERT: A 615 MET cc_start: 0.8035 (tmm) cc_final: 0.7441 (ttt) REVERT: A 924 MET cc_start: 0.8582 (tpp) cc_final: 0.8269 (ttm) REVERT: B 15 PHE cc_start: 0.8404 (t80) cc_final: 0.8031 (t80) REVERT: C 34 GLN cc_start: 0.8155 (tp40) cc_final: 0.7954 (tm-30) REVERT: C 47 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7605 (tm-30) REVERT: C 54 SER cc_start: 0.9197 (m) cc_final: 0.8875 (t) REVERT: C 67 ASP cc_start: 0.7975 (t0) cc_final: 0.7664 (t0) REVERT: D 48 GLU cc_start: 0.9122 (tp30) cc_final: 0.8844 (tp30) REVERT: E 219 LEU cc_start: -0.0900 (OUTLIER) cc_final: -0.1233 (mp) REVERT: F 272 VAL cc_start: 0.7228 (t) cc_final: 0.7019 (p) outliers start: 42 outliers final: 34 residues processed: 155 average time/residue: 0.3101 time to fit residues: 77.8596 Evaluate side-chains 147 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 111 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 572 ILE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 506 TRP Chi-restraints excluded: chain F residue 507 ARG Chi-restraints excluded: chain F residue 525 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 152 optimal weight: 0.0040 chunk 245 optimal weight: 9.9990 chunk 150 optimal weight: 9.9990 chunk 116 optimal weight: 0.7980 chunk 171 optimal weight: 0.0970 chunk 258 optimal weight: 10.0000 chunk 237 optimal weight: 9.9990 chunk 205 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 158 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 557 ASN ** F 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22178 Z= 0.231 Angle : 0.615 13.896 30478 Z= 0.305 Chirality : 0.041 0.351 3536 Planarity : 0.003 0.042 3617 Dihedral : 12.975 143.527 3919 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.91 % Allowed : 19.44 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.17), residues: 2541 helix: 1.10 (0.17), residues: 1012 sheet: -0.37 (0.32), residues: 293 loop : -0.97 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 506 HIS 0.007 0.001 HIS F 482 PHE 0.014 0.001 PHE D 92 TYR 0.018 0.001 TYR A 903 ARG 0.004 0.000 ARG D 96 ********************** 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 154 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 112 time to evaluate : 2.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.7662 (mmm) cc_final: 0.7340 (tpt) REVERT: A 268 TRP cc_start: 0.8574 (OUTLIER) cc_final: 0.7154 (m-90) REVERT: A 615 MET cc_start: 0.8076 (tmm) cc_final: 0.7492 (ttt) REVERT: A 924 MET cc_start: 0.8661 (tpp) cc_final: 0.8305 (ttm) REVERT: C 34 GLN cc_start: 0.8200 (tp40) cc_final: 0.7999 (tm-30) REVERT: C 47 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7686 (tm-30) REVERT: C 54 SER cc_start: 0.9209 (m) cc_final: 0.8902 (t) REVERT: C 67 ASP cc_start: 0.7950 (t0) cc_final: 0.7555 (t70) REVERT: D 48 GLU cc_start: 0.9046 (tp30) cc_final: 0.8772 (tp30) REVERT: E 204 ASP cc_start: 0.3679 (OUTLIER) cc_final: 0.3074 (t0) REVERT: E 219 LEU cc_start: -0.0871 (OUTLIER) cc_final: -0.1207 (mp) outliers start: 42 outliers final: 34 residues processed: 151 average time/residue: 0.3135 time to fit residues: 76.9106 Evaluate side-chains 147 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 110 time to evaluate : 2.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 572 ILE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 506 TRP Chi-restraints excluded: chain F residue 507 ARG Chi-restraints excluded: chain F residue 525 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 163 optimal weight: 6.9990 chunk 218 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 189 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 205 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 211 optimal weight: 7.9990 chunk 26 optimal weight: 0.0270 chunk 37 optimal weight: 0.6980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 557 ASN ** F 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.088133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.057681 restraints weight = 89672.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.059627 restraints weight = 38468.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.060839 restraints weight = 22391.175| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22178 Z= 0.155 Angle : 0.595 13.876 30478 Z= 0.292 Chirality : 0.040 0.369 3536 Planarity : 0.003 0.042 3617 Dihedral : 12.966 149.806 3919 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.05 % Allowed : 19.03 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.17), residues: 2541 helix: 1.16 (0.17), residues: 1008 sheet: -0.38 (0.32), residues: 288 loop : -0.94 (0.18), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 916 HIS 0.007 0.001 HIS F 482 PHE 0.014 0.001 PHE B 15 TYR 0.015 0.001 TYR A 903 ARG 0.004 0.000 ARG A 365 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3836.70 seconds wall clock time: 70 minutes 18.43 seconds (4218.43 seconds total)